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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-treetime">Debian Med / python-treetime</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-treetime/-/commit/28bc86c786c8bd2d64186d1097fa8230d8bdc986">28bc86c7</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-01-09T16:15:26+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.8.1</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4c23f3e77a0ef00cf8da63e8e50eef5197724f75">
changelog.md
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<li class="file-stats">
<a href="#716e6f6c16580800d13452615e2c01668aacc288">
treetime/__init__.py
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<a href="#82a08428349f48dbbab4c8ccac6320f52b4c7a7b">
treetime/seq_utils.py
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<li class="file-stats">
<a href="#a2e471fd9fc09543e8fd92727442680e1b76576b">
treetime/treeanc.py
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<h4>Changes:</h4>
<li id="4c23f3e77a0ef00cf8da63e8e50eef5197724f75">
<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/28bc86c786c8bd2d64186d1097fa8230d8bdc986#4c23f3e77a0ef00cf8da63e8e50eef5197724f75"><strong>changelog.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># 0.8.1 -- bug fixe amino acid profile map.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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1
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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">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #999;"># 0.8.0 -- drop python 2.7 support, bug fixes.</span></span>
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2
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gh" style="color: #999;"># 0.7.6 -- catch of distributions are too short for calculating confidence intervals.</span></span>
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<li id="716e6f6c16580800d13452615e2c01668aacc288">
<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/28bc86c786c8bd2d64186d1097fa8230d8bdc986#716e6f6c16580800d13452615e2c01668aacc288"><strong>treetime/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span><span class="p">,</span> <span class="n" style="color: #333;">division</span><span class="p">,</span> <span class="n" style="color: #333;">absolute_import</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.8.<span class="idiff left right">0</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.8.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TreeTimeError</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">"""TreeTimeError class"""</span></span>
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<li id="82a08428349f48dbbab4c8ccac6320f52b4c7a7b">
<a href="https://salsa.debian.org/med-team/python-treetime/-/commit/28bc86c786c8bd2d64186d1097fa8230d8bdc986#82a08428349f48dbbab4c8ccac6320f52b4c7a7b"><strong>treetime/seq_utils.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="83" style="width: 35px; color: rgba(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">@@ -83,7 +83,7 @@ profile_maps = {</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="s" style="color: #d14;">'V'</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float'</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">#Valine Val</span></span>
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84
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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="s" style="color: #d14;">'W'</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float'</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">#Tryptophan Trp</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"> <span class="s" style="color: #d14;">'Y'</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float'</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">#Tyrosine Tyr</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">'*'</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;"><span class="idiff left">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float'</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">#stop</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">'*'</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float'</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">#stop</span></span>
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87
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">'-'</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float'</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">#gap</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">'X'</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float'</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">#not specified/any</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">'B'</span><span class="p">:</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'float'</span><span class="p">),</span> <span class="c1" style="color: #998; font-style: italic;">#Asparagine/Aspartic Acid Asx</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1611" style="width: 35px; color: rgba(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">@@ -1611,8 +1611,10 @@ class TreeAnc(object):</td>
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1611
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<pre style="margin: 0;"> <span id="LC1611" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1612
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1612
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<pre style="margin: 0;"> <span id="LC1612" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">reconstructed</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">aln</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC1613" class="line" lang="python"> <span class="n" style="color: #333;">tmp_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">aln</span><span class="p">[</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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1614
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<pre style="margin: 0;">-<span id="LC1614" class="line" lang="python"> <span class="k" style="font-weight: 600;">el<span class="idiff left right">s</span>e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC1614" class="line" lang="python"> <span class="k" style="font-weight: 600;">el<span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">node</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">cseq</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">is</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">Non</span>e</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="python"> <span class="n" style="color: #333;">tmp_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">compressed_to_full_sequence</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">cseq</span><span class="p">,</span> <span class="n" style="color: #333;">as_string</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1616" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC1617" class="line" lang="python"> <span class="n" style="color: #333;">tmp_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gtr</span><span class="p">.</span><span class="n" style="color: #333;">ambiguous</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">'N'</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">compressed_length</span><span class="p">)</span></span>
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1616
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1618
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<pre style="margin: 0;"> <span id="LC1618" class="line" lang="python"></span>
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1617
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1619
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<pre style="margin: 0;"> <span id="LC1619" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">as_string</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">tmp_seq</span><span class="p">)</span></span>
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1620
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<pre style="margin: 0;"> <span id="LC1620" class="line" lang="python"></span>
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