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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/graphlan">Debian Med / graphlan</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/graphlan/commit/44895364fd96a332c00fa3d738cd901177b510e7">44895364</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-26T11:35:01Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.3</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/graphlan/commit/acbfc83923a0a66be5c956fcf67eba49fcf99712">acbfc839</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-26T11:35:27Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.1.3'

Update to upstream version '1.1.3'

with Debian dir 01a232141bbd9e03b83ce4a03757be53b9f08a6d</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/graphlan/commit/70db3e12d84c45e4b2dab027f8bde1170fcaa16f">70db3e12</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-26T11:35:27Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/graphlan/commit/e629be31512481a8535d3eae75d9e06f51d07a33">e629be31</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-26T11:35:27Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/graphlan/commit/de48d5d658dd4c1035d05f3a139fdfdd93501edb">de48d5d6</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-26T11:35:32Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/graphlan/commit/42e4c86477333a8cb741dd094a3ded5054bdcccd">42e4c864</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-26T11:35:32Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/graphlan/commit/ed2e94feb06db5c7f53f23234ce6d7613aae58ad">ed2e94fe</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-26T11:46:26Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>13 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#b650a02deb9f16531aec1c8085f25f4f1e9942de">

.hg_archival.txt

</a>

</li>

<li class="file-stats">

<a href="#39764dc6adbe1c6e740db8636ab21a5f44f41f59">

.hgignore

</a>

</li>

<li class="file-stats">

<a href="#36f0da65aead1a17f79e4de21fce381f2886958e">

.hgsubstate

</a>

</li>

<li class="file-stats">

<a href="#fc1a47a75cc8dc593b20b5e840173df634b008a1">

.hgtags

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

debian/compat

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#0c06e5d549e6bb337922fc653e55c3220d739d1c">

examples/guide/annot_3.txt

</a>

</li>

<li class="file-stats">

<a href="#77ef8d9cd746f18d9c67720e63fb881c0aaa664c">

examples/metaref_fams/mr1.a.txt

</a>

</li>

<li class="file-stats">

<a href="#62ead152fe794d7c4c3b366afde0b84f9c83cc7c">

graphlan.py

</a>

</li>

<li class="file-stats">

<a href="#880688220cf20790e2dd9b60987646049f73423c">

graphlan_annotate.py

</a>

</li>

<li class="file-stats">

<a href="#d6b50778acd9c1c785126c13272a0f81d1baa7b9">

src/graphlan_lib.py

</a>

</li>

<li class="file-stats">

<a href="#a83b13e720a39a8cb2334f0070f73f907a09eb06">

src/pyphlan.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="b650a02deb9f16531aec1c8085f25f4f1e9942de">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#b650a02deb9f16531aec1c8085f25f4f1e9942de"><strong>.hg_archival.txt</strong></a>

<hr>

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1

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1

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">repo: 0fdb21ec3cf53e710d679fbd7768f91510570ae7</span>

</pre>

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2

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">node: <span class="idiff left right">edea23ce7c21765cbd9ff601e1f91614241eae81</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="3" 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="2" 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">

2

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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="LC2" class="line" lang="plaintext">node: <span class="idiff left right">c1fa530b9bcac13bbccacf8bfafd500536d17b7c</span></span>

</pre>

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<td class="diff-line-num old_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="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="plaintext">branch: default</span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="4" 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">

4

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<td class="diff-line-num new_line old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">tag: 1.1</span></pre>

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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="plaintext">tag: 1.1<span class="idiff left right">.3</span></span></pre>

</td>

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<br>

</li>

<li id="39764dc6adbe1c6e740db8636ab21a5f44f41f59">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#39764dc6adbe1c6e740db8636ab21a5f44f41f59"><strong>.hgignore</strong></a>

<hr>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,4 +3,10 @@ syntax: glob</td>

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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="plaintext">*.pyc</span>

</pre>

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<td class="diff-line-num old_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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4

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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="LC4" class="line" lang="plaintext">*.DS_Store</span>

</pre>

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5

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5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">*.log</span>

</pre>

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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="LC6" class="line" lang="plaintext">examples/ade_pcopri</span>

</pre>

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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="LC7" class="line" lang="plaintext">examples/neisseriaceae/</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" 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">

8

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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="LC8" class="line" lang="plaintext">examples/caritro_fig6/</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

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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="LC9" class="line" lang="plaintext">examples/andrew_crc_cutc/</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">examples/nic_erectale/</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" 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">

11

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">examples/rand/</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_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

</td>

<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">examples/test/</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="36f0da65aead1a17f79e4de21fce381f2886958e">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#36f0da65aead1a17f79e4de21fce381f2886958e"><strong>.hgsubstate</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1" 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">

1

</td>

<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">b2e0ba66718673ea28cb217c8e5dcd8e578fd033</span> export2graphlan</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">c168a100f37e23e2c110849a8d91fac8da49f5bd</span> export2graphlan</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

</td>

<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="plaintext">eae40ebc0030c7179baed999c74de412ba696598 pyphlan</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="fc1a47a75cc8dc593b20b5e840173df634b008a1">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#fc1a47a75cc8dc593b20b5e840173df634b008a1"><strong>.hgtags</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,3 +5,6 @@ ba9c6f680022333b5b1bf0652748ab2db29e888a 0.9</td>

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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="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

</td>

<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="plaintext">eaa3d2e05d74912da0f013bbfbb199764b180f05 0.9.5</span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="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="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="plaintext">64570f7d4ae33f46ddd360101c13555396a0cab1 0.9.6</span>

</pre>

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<td class="diff-line-num old_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="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="plaintext">7d483b7d34ccadb30f5c56f82b7aab19a820d1d6 1.0</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="8" 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="8" 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">

8

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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="LC8" class="line" lang="plaintext">edea23ce7c21765cbd9ff601e1f91614241eae81 1.1</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" 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">

9

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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="LC9" class="line" lang="plaintext">17f32c8d85849d397884564680c145e5b8d28923 1.1.1</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" 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">

10

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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="LC10" class="line" lang="plaintext">3820c323e3c68d3d9e02bae2aefbc7d179df80bf 1.1.2</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" 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">

1

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">graphlan (1.1.3-1) unstable; urgency=medium</span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="3" 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">

3

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * debhelper 11</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Point Vcs fields to salsa.debian.org</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  * Standards-Version: 4.2.1</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1" 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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" 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">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Wed, 26 Sep 2018 13:35:33 +0200</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>

</pre>

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1

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">graphlan (1.1-3) unstable; urgency=medium</span>

</pre>

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2

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11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_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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12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">  * Moved packaging from SVN to Git</span>

</pre>

</td>

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<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" 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="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>

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<td class="diff-line-num old_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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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="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>

</pre>

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<td class="diff-line-num old_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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<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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>

</pre>

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5

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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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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>

</pre>

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6

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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>),</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>

</pre>

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<td class="diff-line-num old_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="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="plaintext">               python-all,</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">               dh-python</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="9" 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">

9

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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1</span>.1</span>

</pre>

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10

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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/graphlan.git</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="11" 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">

11

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<td class="diff-line-num new_line old" data-linenumber="9" 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="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/graphlan.git</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="12" 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="9" 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">

9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2</span>.1</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/graphlan</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/graphlan.git</span>

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Homepage: https://bitbucket.org/nsegata/graphlan/wiki/Home</span>

</pre>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Package: graphlan</span>

</pre>

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</li>

<li id="0c06e5d549e6bb337922fc653e55c3220d739d1c">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#0c06e5d549e6bb337922fc653e55c3220d739d1c"><strong>examples/guide/annot_3.txt</strong></a>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="418" style="width: 35px; color: rgba(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">@@ -418,7 +418,7 @@ Staphylococcaceae.Staphylococcus.Swarneri  ring_height     5       2.39465498028</td>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="plaintext">Bacillaceae.Bacillus.Bsubtilis      clade_marker_label      65</span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="plaintext">Staphylococcaceae.Staphylococcus.Saureus    clade_marker_label      17</span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="plaintext">Bacillaceae.Bacillus.Banthracis     clade_marker_label      x<span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext">Bacillaceae.Bacillus.Banthracis     clade_marker_label      x</span>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="plaintext">Bacillaceae.Bacillus.Banthracis     clade_marker_font_color w</span>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="plaintext">Bacillaceae.Bacillus.Banthracis     clade_marker_edge_color b</span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="plaintext">Bacillaceae.Lysinibacillus.Lfusiformis      clade_marker_label      156</span>

</pre>

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<br>

</li>

<li id="77ef8d9cd746f18d9c67720e63fb881c0aaa664c">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#77ef8d9cd746f18d9c67720e63fb881c0aaa664c"><strong>examples/metaref_fams/mr1.a.txt</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(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="15" style="width: 35px; color: rgba(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">@@ -15,9 +15,9 @@ c2   clade_marker_color      #0000FF</td>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">c2   clade_marker_size       35</span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">c3   clade_marker_color      #00FF00</span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">c3   clade_marker_size       35</span>

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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC18" class="line" lang="plaintext">#class2      annotation_background_color     #0000FF<span class="idiff left right">  </span></span>

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">#class2      annotation_background_color     #0000FF</span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">#class2      class_label     Clades in which X is a core gene</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="20" 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="LC20" class="line" lang="plaintext">clade_marker_size    10<span class="idiff left right">       </span></span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">clade_marker_size    10</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">branch_thickness     0.5</span>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(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="LC22" class="line" lang="plaintext">Bacill.Bacillale     class   c3</span>

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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="plaintext">Bacill.Bacillale.Staphylococcaceae.Gemella   class   c1</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(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="48" style="width: 35px; color: rgba(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">@@ -48,7 +48,7 @@ Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium</td>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(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="LC48" class="line" lang="plaintext">#Bacill.Bacillale    class   class2</span>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(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="LC49" class="line" lang="plaintext">Bacill.Bacillale     annotation      Y</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(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="LC50" class="line" lang="plaintext">Bacill.Bacillale.Staphylococcaceae   annotation      Y1</span>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="51" 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="LC51" class="line" lang="plaintext">Bacill.Bacillale.Thermoactinomycetaceae      annotation      Y2<span class="idiff left right">       </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Bacill.Bacillale.Thermoactinomycetaceae      annotation      Y2</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(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="LC52" class="line" lang="plaintext">Bacill.Bacillale.unclassified        annotation      Y3</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(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="LC53" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae        class   c2</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(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="LC54" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Aerococcus     class   c2</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="69" style="width: 35px; color: rgba(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="69" style="width: 35px; color: rgba(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">@@ -69,8 +69,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified ring_shape      1       v</td>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Eremococcus    ring_shape      1       v</span>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="plaintext">Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium     ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="plaintext">Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia   ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="72" 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="LC72" class="line" lang="plaintext">Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus       ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="72" 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="LC73" class="line" lang="plaintext">Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus ring_shape      1       v</span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia        ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(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="LC73" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(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="LC74" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus       ring_shape      1       v</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" style="width: 35px; color: rgba(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="76" style="width: 35px; color: rgba(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">@@ -78,7 +76,7 @@ Clostridia.Clostridiales.Incertae_Sedis_XI.Peptoniphilus     ring_shape      1       v</td>

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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(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="LC76" class="line" lang="plaintext">Clostridi.Clostridiales.Ruminococcaceae.Papillibacter        ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="77" style="width: 35px; color: rgba(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="LC77" class="line" lang="plaintext">Clostridi.Clostridiale.Veillonellaceae.Selenomonas   ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(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="LC78" class="line" lang="plaintext">Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium      ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" 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="LC81" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Aerococcus     ring_shape      1       v<span class="idiff left right">        </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="82" 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="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Aerococcus     ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(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="LC80" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Eremococcus    ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(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="LC81" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.unclassified   ring_shape      1       v</span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="82" style="width: 35px; color: rgba(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="LC82" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Abiotrophia    ring_shape      1       v</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" style="width: 35px; color: rgba(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="94" style="width: 35px; color: rgba(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">@@ -96,8 +94,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified ring_width      1       0.6</td>

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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Eremococcus    ring_width      1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="95" style="width: 35px; color: rgba(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="LC95" class="line" lang="plaintext">Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium     ring_width      1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(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="LC96" class="line" lang="plaintext">Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia   ring_width      1       0.6</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" 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="LC99" class="line" lang="plaintext">Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus       ring_width      1       0.6</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="97" 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="LC100" class="line" lang="plaintext">Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus        ring_width      1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(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="LC97" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia        ring_width      1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(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="LC98" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola ring_width      1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(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="LC99" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus       ring_width      1       0.6</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(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="101" style="width: 35px; color: rgba(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">@@ -105,7 +101,7 @@ Clostridia.Clostridiales.Incertae_Sedis_XI.Peptoniphilus   ring_width      1       0.6</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(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="LC101" class="line" lang="plaintext">Clostridi.Clostridiales.Ruminococcaceae.Papillibacter       ring_width      1       0.6</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(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="LC102" class="line" lang="plaintext">Clostridi.Clostridiale.Veillonellaceae.Selenomonas  ring_width      1       0.6</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(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="LC103" class="line" lang="plaintext">Clostridia.Thermoanaerobacterales.Thermoanaerobacteraceae.Thermoanaerobacterium     ring_width      1       0.6</span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Aerococcus    ring_width      1       0.6<span class="idiff left right">      </span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC104" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Aerococcus    ring_width      1       0.6</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(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="LC105" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Eremococcus   ring_width      1       0.6</span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(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="LC106" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.unclassified  ring_width      1       0.6</span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(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="LC107" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Abiotrophia   ring_width      1       0.6</span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" style="width: 35px; color: rgba(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="119" style="width: 35px; color: rgba(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">@@ -123,8 +119,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified       ring_height     1       0.6</td>

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<td class="diff-line-num old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(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="LC119" class="line" lang="plaintext">Bacilli.Lactobacillales.Aerococcaceae.Eremococcus   ring_height     1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(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="LC120" class="line" lang="plaintext">Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium    ring_height     1       0.6</span>

</pre>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(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="LC121" class="line" lang="plaintext">Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia  ring_height     1       0.6</span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC126" class="line" lang="plaintext">Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus      ring_height     1       0.6</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC127" class="line" lang="plaintext">Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus        ring_height     1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="122" style="width: 35px; color: rgba(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="LC122" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia       ring_height     1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="123" style="width: 35px; color: rgba(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="LC123" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola        ring_height     1       0.6</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(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="LC124" class="line" lang="plaintext">Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus      ring_height     1       0.6</span>

</pre>

</td>

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</table>

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<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#62ead152fe794d7c4c3b366afde0b84f9c83cc7c"><strong>graphlan.py</strong></a>

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(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="LC2" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#------------------------------------------------------------------------------</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># NAME: graphlan.py</span></span>

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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC5" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># DESCRIPTION:  GraPhlAn is a python program for creating images of circular<span class="idiff left right"> </span></span></span>

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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC6" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#               cladogram starting from a tree given in PhyloXML format. The<span class="idiff left right"> </span></span></span>

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<td class="diff-line-num old old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC7" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#               PhyloXML input tree can be formatted and annotated using the<span class="idiff left right"> </span></span></span>

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<td class="diff-line-num new old_line" data-linenumber="8" 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="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># DESCRIPTION:  GraPhlAn is a python program for creating images of circular</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="8" 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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#               cladogram starting from a tree given in PhyloXML format. The</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="8" 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="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#               PhyloXML input tree can be formatted and annotated using the</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#               graphlan_annotate.py script.</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(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="LC10" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;"># Author:   Nicola Segata</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(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="14" style="width: 35px; color: rgba(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">@@ -14,10 +14,16 @@</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#------------------------------------------------------------------------------</span></span>

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(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="LC15" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(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="LC16" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Nicola Segata (nsegata@hsph.harvard.edu)'</span></span>

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC17" 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;">'<span class="idiff left right">0.9.7</span>'</span></span>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="17" 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="LC18" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">21 July 2014</span>'</span></span>

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<td class="diff-line-num new old_line" data-linenumber="19" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC17" 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;">'<span class="idiff left right">1.1.3</span>'</span></span>

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<td class="diff-line-num new old_line" data-linenumber="19" 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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">5 June 2018</span>'</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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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="LC20" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" 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="21" 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">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" 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">

22

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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="LC22" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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">

23

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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="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"GraPhlAn requires Python 2, your current Python version is {}.{}.{}"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">                    <span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="21" 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="26" 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">

26

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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="LC26" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(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="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">argv</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(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="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">src.graphlan_lib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CircTree</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">CTree</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="34" style="width: 35px; color: rgba(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="40" style="width: 35px; color: rgba(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">@@ -34,7 +40,7 @@ def read_params(args):</td>

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<td class="diff-line-num old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(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="LC40" class="line" lang="python">        <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"the output image, the format is guessed from the extension "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(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="LC41" class="line" lang="python">               <span class="s" style="color: #d14;">"unless --format is given. Available file formats are: png, "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(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="LC42" class="line" lang="python">               <span class="s" style="color: #d14;">"pdf, ps, eps, svg"</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="python">    <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--format'</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'png'</span><span class="p">,</span><span class="s" style="color: #d14;">'pdf'</span><span class="p">,</span><span class="s" style="color: #d14;">'ps'</span><span class="p">,</span><span class="s" style="color: #d14;">'eps'</span><span class="p">,</span><span class="s" style="color: #d14;">'svg'</span><span class="p">],</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="38" 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="43" 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">

43

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">    <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--format'</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'png'</span><span class="p">,</span><span class="s" style="color: #d14;">'pdf'</span><span class="p">,</span><span class="s" style="color: #d14;">'ps'</span><span class="p">,</span><span class="s" style="color: #d14;">'eps'</span><span class="p">,</span><span class="s" style="color: #d14;">'svg'</span><span class="p">],</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python">        <span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'output_image_format'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(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="LC45" class="line" lang="python">        <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"set the format of the output image (default none meaning that "</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(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="LC46" class="line" lang="python">               <span class="s" style="color: #d14;">"the format is guessed from the output file extension)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(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">@@ -53,7 +59,9 @@ def read_params(args):</td>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python">    <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--external_legends'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="python">        <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"specify whether the two external legends should be put in separate file or keep them "</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">               <span class="s" style="color: #d14;">"along with the image (default behavior)"</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="62" 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="LC56" class="line" lang="python">    <span class="n" style="color: #333;">arg</span><span class="p">(</span> <span class="s" style="color: #d14;">'-v'</span><span class="p">,</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'version'</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GraPhlAn version "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">__version__</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;">__date__</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">")"</span><span class="p">,</span> </span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" 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="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">    <span class="n" style="color: #333;">arg</span><span class="p">(</span><span class="s" style="color: #d14;">'--avoid_reordering'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_false'</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="57" 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="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">        <span class="n" style="color: #333;">help</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"specify whether the tree will be reorder or not (default the tree will be reordered)"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="57" 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="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">    <span class="n" style="color: #333;">arg</span><span class="p">(</span> <span class="s" style="color: #d14;">'-v'</span><span class="p">,</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'version'</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GraPhlAn version "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">__version__</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;">__date__</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="LC65" class="line" lang="python">        <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Prints the current GraPhlAn version and exit"</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">vars</span><span class="p">(</span><span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="62" style="width: 35px; color: rgba(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="70" style="width: 35px; color: rgba(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">@@ -62,9 +70,10 @@ if __name__ == "__main__":</td>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_params</span><span class="p">(</span> <span class="n" style="color: #333;">argv</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python">    <span class="n" style="color: #333;">ctree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CTree</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">'intree'</span><span class="p">],</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">'warnings'</span><span class="p">]</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python">    <span class="n" style="color: #333;">ctree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">positions</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;">'positions'</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python">    <span class="n" style="color: #333;">ctree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">draw</span><span class="p">(</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">'outimg'</span><span class="p">],</span> </span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python">                <span class="n" style="color: #333;">out_format</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;">'format'</span><span class="p">],</span> </span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python">                <span class="n" style="color: #333;">out_dpi</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;">'dpi'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python">                <span class="n" style="color: #333;">out_size</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;">'size'</span><span class="p">],</span></span>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python">                <span class="n" style="color: #333;">out_pad</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;">'pad'</span><span class="p">],</span></span>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python">                <span class="n" style="color: #333;">external_legends</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;">'external_legends'</span><span class="p">])</span></span></pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">    <span class="n" style="color: #333;">ctree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">draw</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="s" style="color: #d14;">'outimg'</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">               <span class="n" style="color: #333;">out_format</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;">'format'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">               <span class="n" style="color: #333;">out_dpi</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;">'dpi'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">               <span class="n" style="color: #333;">out_size</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;">'size'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">               <span class="n" style="color: #333;">out_pad</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;">'pad'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">               <span class="n" style="color: #333;">external_legends</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;">'external_legends'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">               <span class="n" style="color: #333;">reorder_tree</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;">'avoid_reordering'</span><span class="p">])</span></span></pre>

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<br>

</li>

<li id="880688220cf20790e2dd9b60987646049f73423c">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#880688220cf20790e2dd9b60987646049f73423c"><strong>graphlan_annotate.py</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,10 +11,16 @@</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="c" style="color: #998; font-style: italic;">#------------------------------------------------------------------------------</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Nicola Segata (nsegata@hsph.harvard.edu)'</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="14" 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">

14

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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC14" 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;">'<span class="idiff left right">0.9</span>'</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">22 August 2012</span>'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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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="LC14" 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;">'<span class="idiff left right">1.1.3</span>'</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="15" 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">

15

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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="LC15" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'<span class="idiff left right">5 June 2018</span>'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

</td>

<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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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="LC16" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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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="LC17" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="18" 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="18" 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">

18

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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="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="19" 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">

19

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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="LC19" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="20" 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">

20

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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="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="21" 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">

21

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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="LC21" class="line" lang="python">    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"GraPhlAn requires Python 2, your current Python version is {}.{}.{}"</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="22" 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">

22

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">                    <span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="23" 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">

23

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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="LC23" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

24

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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="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">argv</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

25

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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="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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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="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">src.graphlan_lib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CircTree</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">CTree</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="d6b50778acd9c1c785126c13272a0f81d1baa7b9">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#d6b50778acd9c1c785126c13272a0f81d1baa7b9"><strong>src/graphlan_lib.py</strong></a>

<hr>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="1" 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">

1

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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="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="2" 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">

2

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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="LC2" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="3" 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">

3

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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="LC3" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="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">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python">    <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"GraPhlAn requires Python 2, your current Python version is {}.{}.{}"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python">                    <span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1" 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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC6" class="line" lang="python"></span>

</pre>

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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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Phylo</span></span>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Phylo</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PhyloXML</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(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="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio.Phylo</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PhyloXMLIO</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(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="23" style="width: 35px; color: rgba(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">@@ -17,87 +23,79 @@ import matplotlib.patches as mpatches</td>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(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="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">matplotlib.lines</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">lines</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">matplotlib</span></span>

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(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="LC25" class="line" lang="python"><span class="n" style="color: #333;">matplotlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">use</span><span class="p">(</span><span class="s" style="color: #d14;">'Agg'</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="20" 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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="n" style="color: #333;">matplotlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rcParams</span><span class="p">[</span><span class="s" style="color: #d14;">'svg.fonttype'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'none'</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pylab</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(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="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pyphlan</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PpaTree</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC24" class="line" lang="python"><span class="n" style="color: #333;">clade_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_size'</span><span class="p">,</span>               <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">20.0</span>        <span class="p">),</span></span>

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC25" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_color'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'#FFFFFF'</span>   <span class="p">),</span></span>

</pre>

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26

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC26" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_edge_width'</span><span class="p">,</span>         <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">0.5</span>         <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_shape'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'o'</span>         <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC28" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_edge_color'</span><span class="p">,</span>         <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'#000000'</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC29" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_label'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">''</span>          <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" 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">

30

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC30" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_font_size'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'7'</span>         <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="31" 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">

31

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC31" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_font_color'</span><span class="p">,</span>         <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'k'</span>         <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="32" 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">

32

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC32" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'class_label'</span><span class="p">,</span>                     <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">""</span>          <span class="p">),</span>  <span class="c" style="color: #998; font-style: italic;"># to rem</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" 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">

33

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC33" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_font_size'</span><span class="p">,</span>            <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>    <span class="mi" style="color: #099;">7</span>           <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" 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">

34

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC34" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_font_stretch'</span><span class="p">,</span>         <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>    <span class="mi" style="color: #099;">0</span>           <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" 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">

35

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC35" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_color'</span><span class="p">,</span>     <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'#FF0000'</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" 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">

36

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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC36" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_edge_color'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'#FF0000'</span>   <span class="p">),</span>  <span class="c" style="color: #998; font-style: italic;"># not implemented yet</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="37" 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">

37

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC37" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation'</span><span class="p">,</span>                      <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">''</span>          <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" 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">

38

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_rotation'</span><span class="p">,</span>             <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>    <span class="mi" style="color: #099;">0</span>           <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" 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">

39

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC39" class="line" lang="python">             <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="31" 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">

31

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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="LC31" class="line" lang="python"><span class="n" style="color: #333;">clade_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_size'</span><span class="p">,</span>                <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">20.0</span>      <span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

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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="LC32" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_color'</span><span class="p">,</span>               <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'#FFFFFF'</span> <span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="33" 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">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_edge_width'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.5</span>       <span class="p">),</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="34" 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">

34

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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="LC34" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_shape'</span><span class="p">,</span>               <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'o'</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" 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">

35

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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="LC35" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_edge_color'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'#000000'</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="36" 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">

36

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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="LC36" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_label'</span><span class="p">,</span>               <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">''</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" 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">

37

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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="LC37" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_font_size'</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'7'</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="38" 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">

38

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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="LC38" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'clade_marker_font_color'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'k'</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="39" 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">

39

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'class_label'</span><span class="p">,</span>                      <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">""</span>        <span class="p">),</span>  <span class="c" style="color: #998; font-style: italic;"># to rem</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="40" 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">

40

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_font_size'</span><span class="p">,</span>             <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">7</span>         <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="41" 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">

41

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_font_stretch'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">0</span>         <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" 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="42" 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">

42

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_color'</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'#FF0000'</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="43" 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">

43

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_edge_color'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'#FF0000'</span> <span class="p">),</span>  <span class="c" style="color: #998; font-style: italic;"># not implemented yet</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="44" 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">

44

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation'</span><span class="p">,</span>                       <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">''</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="45" 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">

45

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">               <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_rotation'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">0</span>         <span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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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="LC46" class="line" lang="python"><span class="n" style="color: #333;">clade_attr_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</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;">d</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</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;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade_attr</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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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="LC47" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" 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">

42

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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"><span class="n" style="color: #333;">ext_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'ring_color'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'#000000'</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" 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">

43

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC43" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_width'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>   <span class="mf" style="color: #099;">1.0</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" 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">

44

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC44" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_height'</span><span class="p">,</span>                       <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>   <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" 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">

45

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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC45" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_alpha'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>   <span class="mf" style="color: #099;">1.0</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" 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">

46

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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC46" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_shape'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>     <span class="s" style="color: #d14;">"R"</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC47" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_label'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>     <span class="bp" style="color: #999;">None</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC48" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_label_font_size'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>     <span class="mi" style="color: #099;">11</span>         <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC49" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_label_color'</span><span class="p">,</span>                  <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>     <span class="s" style="color: #d14;">'k'</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" 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">

50

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC50" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_edge_width'</span><span class="p">,</span>                   <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>   <span class="mf" style="color: #099;">0.1</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC51" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_edge_color'</span><span class="p">,</span>                   <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>     <span class="bp" style="color: #999;">None</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC52" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_internal_separator_thickness'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>   <span class="mf" style="color: #099;">0.0</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC53" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_separator_color'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>     <span class="s" style="color: #d14;">'k'</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC54" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_external_separator_thickness'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>   <span class="mf" style="color: #099;">0.0</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" 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="LC55" class="line" lang="python">           <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" 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="48" 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">

48

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">ext_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'ring_color'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'#000000'</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" 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="49" 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">

49

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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="LC49" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_width'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" 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="50" 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">

50

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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="LC50" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_height'</span><span class="p">,</span>                       <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span>      <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" 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="51" 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">

51

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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="LC51" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_alpha'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_shape'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">"R"</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" 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="53" 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">

53

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_label'</span><span class="p">,</span>                        <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="bp" style="color: #999;">None</span>      <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" 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="54" 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">

54

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_label_font_size'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">11</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" 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="55" 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">

55

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_label_color'</span><span class="p">,</span>                  <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'k'</span>       <span class="p">),</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="56" 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">

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_edge_width'</span><span class="p">,</span>                   <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.1</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_edge_color'</span><span class="p">,</span>                   <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="bp" style="color: #999;">None</span>      <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_internal_separator_thickness'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_separator_color'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'k'</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'ring_external_separator_thickness'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span>       <span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(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="LC61" class="line" lang="python"><span class="n" style="color: #333;">ext_attr_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</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;">d</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</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;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ext_attr</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(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="LC62" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="63" 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="LC58" class="line" lang="python"><span class="n" style="color: #333;">int_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="63" 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="LC59" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'internal_label'</span><span class="p">,</span>                    <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>     <span class="bp" style="color: #999;">None</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="63" 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="LC60" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'internal_label_font_size'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>     <span class="mi" style="color: #099;">8</span>          <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="63" 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="LC61" class="line" lang="python">           <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" 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="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="n" style="color: #333;">int_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'internal_label'</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" 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="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">             <span class="p">(</span> <span class="s" style="color: #d14;">'internal_label_font_size'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="mi" style="color: #099;">8</span>    <span class="p">)</span> <span class="p">)</span></span>

</pre>

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62

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"><span class="n" style="color: #333;">int_attr_d</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</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;">d</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</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;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">int_attr</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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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="LC66" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC64" class="line" lang="python"><span class="n" style="color: #333;">structural_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'ignore_branch_len'</span><span class="p">,</span>              <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>    <span class="mi" style="color: #099;">0</span>       <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" 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">

65

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC65" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'total_plotted_degrees'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">360.0</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC66" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'start_rotation'</span><span class="p">,</span>                 <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">180.0</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC67" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'clade_separation'</span><span class="p">,</span>               <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">0.0</span>     <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC68" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'branch_bracket_width'</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">0.25</span>    <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="69" 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="LC69" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'branch_bracket_depth'</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">1.0</span>     <span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python">                  <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC71" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="n" style="color: #333;">global_graphical_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_width'</span><span class="p">,</span>       <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">0.1</span>    <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC73" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_alpha'</span><span class="p">,</span>       <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">0.2</span>    <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC74" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_separation'</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">0.02</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC75" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_offset'</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">0.02</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC76" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'class_legend_font_size'</span><span class="p">,</span>            <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>    <span class="mi" style="color: #099;">7</span>      <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="77" 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="LC77" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'title'</span><span class="p">,</span>                             <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">""</span>     <span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'title_font_size'</span><span class="p">,</span>                   <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>    <span class="mi" style="color: #099;">15</span>     <span class="p">),</span></span>

</pre>

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79

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'class_legend_marker_size'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">1.0</span>    <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" 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">

80

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_legend_font_size'</span><span class="p">,</span>       <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>    <span class="mi" style="color: #099;">7</span>      <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" 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">

81

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'internal_labels_rotation'</span><span class="p">,</span>          <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>   <span class="bp" style="color: #999;">None</span>  <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="82" 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">

82

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python">                        <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" 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">

83

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"><span class="n" style="color: #333;">branch_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'branch_thickness'</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="mf" style="color: #099;">0.75</span>        <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" 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">

85

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC85" class="line" lang="python">                <span class="p">(</span> <span class="s" style="color: #d14;">'branch_color'</span><span class="p">,</span>               <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>    <span class="s" style="color: #d14;">'#000000'</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" 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">

86

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC86" class="line" lang="python">                <span class="p">(</span> <span class="s" style="color: #d14;">'branch_color_from_ancestor'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>    <span class="mi" style="color: #099;">1</span>           <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" 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">

87

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC87" class="line" lang="python">              <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC88" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" 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="67" 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">

67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="n" style="color: #333;">structural_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'ignore_branch_len'</span><span class="p">,</span>     <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">0</span>     <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" 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="68" 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">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'total_plotted_degrees'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">360.0</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" 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="69" 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">

69

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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'start_rotation'</span><span class="p">,</span>        <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">180.0</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="70" 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">

70

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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="LC70" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'clade_separation'</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="71" 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">

71

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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="LC71" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'branch_bracket_width'</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.25</span>  <span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="89" 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="72" 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">

72

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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="LC72" class="line" lang="python">                    <span class="p">(</span> <span class="s" style="color: #d14;">'branch_bracket_depth'</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span>   <span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" 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="73" 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">

73

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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="LC73" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="74" 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">

74

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="n" style="color: #333;">global_graphical_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_width'</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.1</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="75" 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">

75

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_alpha'</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.2</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="76" 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">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_separation'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.02</span>  <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="77" 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">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_background_offset'</span><span class="p">,</span>     <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.02</span>  <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" 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">

78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'class_legend_font_size'</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">7</span>     <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="79" 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">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'title'</span><span class="p">,</span>                            <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">""</span>    <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" 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="80" 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">

80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'title_font_size'</span><span class="p">,</span>                  <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">15</span>    <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="81" 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">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'class_legend_marker_size'</span><span class="p">,</span>         <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">1.0</span>   <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" 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">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'annotation_legend_font_size'</span><span class="p">,</span>      <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">7</span>     <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="83" 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">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">                          <span class="p">(</span> <span class="s" style="color: #d14;">'internal_labels_rotation'</span><span class="p">,</span>         <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span>  <span class="bp" style="color: #999;">None</span> <span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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">

85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"><span class="n" style="color: #333;">branch_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="p">(</span> <span class="s" style="color: #d14;">'branch_thickness'</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="mf" style="color: #099;">0.75</span>      <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" 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">

86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">                <span class="p">(</span> <span class="s" style="color: #d14;">'branch_color'</span><span class="p">,</span>               <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span>   <span class="s" style="color: #d14;">'#000000'</span> <span class="p">),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="87" 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">

87

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python">                <span class="p">(</span> <span class="s" style="color: #d14;">'branch_color_from_ancestor'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span>   <span class="mi" style="color: #099;">1</span>         <span class="p">)</span> <span class="p">)</span></span>

</pre>

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89

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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(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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89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"><span class="n" style="color: #333;">leg_sep</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'_._._'</span></span>

</pre>

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91

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"><span class="n" style="color: #333;">leg_attr</span> <span class="idiff left">   </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'annotation_background_color'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">        </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">    </span><span class="s" style="color: #d14;"><span class="idiff">"w"</span></span><span class="idiff right">       </span>  <span class="p">),</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" 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">

92

</td>

<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC92" class="line" lang="python">             <span class="idiff left">   </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'annotation_background_edge_color'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">   </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">    </span><span class="s" style="color: #d14;"><span class="idiff">"k"</span></span><span class="idiff right">       </span>  <span class="p">),</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="93" 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">

93

</td>

<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC93" class="line" lang="python">             <span class="idiff left">   </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'clade_marker_color'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">                 </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">    </span><span class="s" style="color: #d14;"><span class="idiff">"w"</span></span><span class="idiff right">       </span>  <span class="p">),</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="94" 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">

94

</td>

<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC94" class="line" lang="python">             <span class="idiff left">   </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'clade_marker_edge_width'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">            </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">  </span><span class="mf" style="color: #099;"><span class="idiff">0.5</span></span><span class="idiff right">       </span>  <span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="95" 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">

95

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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC95" class="line" lang="python">             <span class="idiff left">   </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'clade_marker_size'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">                  </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">  </span><span class="mf" style="color: #099;"><span class="idiff">20.0</span></span><span class="idiff right">       </span> <span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="96" 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">

96

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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC96" class="line" lang="python">             <span class="idiff left">   </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'keys'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">                               </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">    </span><span class="s" style="color: #d14;"><span class="idiff">"?"</span></span><span class="idiff right">        </span> <span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="97" 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">

97

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<td class="diff-line-num new_line old" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC97" class="line" lang="python">              <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="90" 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">

90

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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="LC90" class="line" lang="python"><span class="n" style="color: #333;">leg_attr</span> <span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'annotation_background_color'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">      </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">   </span><span class="s" style="color: #d14;"><span class="idiff right">"w"</span></span>  <span class="p">),</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="91" 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">

91

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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="LC91" class="line" lang="python">             <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'annotation_background_edge_color'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">   </span><span class="s" style="color: #d14;"><span class="idiff right">"k"</span></span>  <span class="p">),</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="92" 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">

92

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC92" class="line" lang="python">             <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'clade_marker_color'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">               </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">   </span><span class="s" style="color: #d14;"><span class="idiff right">"w"</span></span>  <span class="p">),</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="93" 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">

93

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC93" class="line" lang="python">             <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'clade_marker_edge_width'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">          </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.5</span></span>  <span class="p">),</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="94" 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">

94

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC94" class="line" lang="python">             <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'clade_marker_size'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">                </span><span class="nb" style="color: #0086b3;"><span class="idiff">float</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">20.0</span></span> <span class="p">),</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="95" 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">

95

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC95" class="line" lang="python">             <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'clade_marker_shape'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">               </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">   </span><span class="s" style="color: #d14;"><span class="idiff right">'o'</span></span> <span class="p">),</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="96" 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">

96

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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="LC96" class="line" lang="python">             <span class="p"><span class="idiff left">(</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'keys'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">                             </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff">   </span><span class="s" style="color: #d14;"><span class="idiff">"?"</span></span><span class="idiff">  </span><span class="p"><span class="idiff right">)</span></span> <span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

98

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"><span class="n" style="color: #333;">lev_sep</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span></span>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="n" style="color: #333;">legal_options</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">clade_attr</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ext_attr</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">int_attr</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">structural_attr</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">global_graphical_attr</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">branch_attr</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">leg_attr</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">|</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="s" style="color: #d14;">'class'</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">random_keys</span><span class="p">(</span><span class="n" style="color: #333;">used_keys</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -115,8 +113,8 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">annotate</span><span class="p">(</span>   <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">inp_file</span><span class="p">,</span> <span class="n" style="color: #333;">out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">                    <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">term_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()])</span></span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python">        <span class="n" style="color: #333;">nterm_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_nonterminals</span><span class="p">()])</span></span>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python">        <span class="n" style="color: #333;">term_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python">        <span class="n" style="color: #333;">nterm_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_nonterminals</span><span class="p">()</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">t</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python">        <span class="n" style="color: #333;">clade_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">term_names</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">nterm_names</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">        <span class="n" style="color: #333;">props</span><span class="p">,</span> <span class="n" style="color: #333;">gprops</span><span class="p">,</span> <span class="n" style="color: #333;">classes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ddict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">),</span> <span class="p">{},</span> <span class="n" style="color: #333;">ddict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" style="width: 35px; color: rgba(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="145" style="width: 35px; color: rgba(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">@@ -147,8 +145,14 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_tmp_levs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">lines</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'#'</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">):</span> <span class="c" style="color: #998; font-style: italic;"># skip empty lines</span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">            <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">ll</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="LC152" class="line" lang="python">                <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Unrecognized annotation "{}", maybe spaces '</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python">                                 <span class="s" style="color: #d14;">'instead of tabs?</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python">                <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">                <span class="n" style="color: #333;">legal</span><span class="p">(</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="p">)</span> <span class="c" style="color: #998; font-style: italic;">#  in legal_options, "%s is not a valid option" % line[1]</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">                <span class="n" style="color: #333;">gprops</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" style="width: 35px; color: rgba(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="163" style="width: 35px; color: rgba(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">@@ -159,7 +163,12 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(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="LC163" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">clade</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ext_attr_d</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="160" style="width: 35px; color: rgba(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="LC164" class="line" lang="python">                    <span class="n" style="color: #333;">prop</span><span class="p">,</span><span class="n" style="color: #333;">lev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span><span class="n" style="color: #333;">prop</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">                    <span class="n" style="color: #333;">legal</span><span class="p">(</span> <span class="n" style="color: #333;">prop</span> <span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="166" 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="LC162" class="line" lang="python">                    <span class="n" style="color: #333;">ilev</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">lev</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python">                    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="163" 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="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python">                        <span class="n" style="color: #333;">ilev</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">lev</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python">                    <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python">                        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python">                        <span class="n" style="color: #333;">asdasdasd</span></span>

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<td class="diff-line-num new old_line" data-linenumber="163" 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="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prop</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gprops</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="173" style="width: 35px; color: rgba(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="LC173" class="line" lang="python">                        <span class="n" style="color: #333;">gprops</span><span class="p">[</span><span class="n" style="color: #333;">prop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ilev</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gprops</span><span class="p">[</span><span class="n" style="color: #333;">prop</span><span class="p">]:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(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="212" style="width: 35px; color: rgba(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">@@ -203,9 +212,21 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC212" 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="LC213" class="line" lang="python">                        <span class="n" style="color: #333;">gprops</span><span class="p">[</span><span class="n" style="color: #333;">prop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">ilev</span><span class="p">:</span><span class="n" style="color: #333;">val</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">lev_sep</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade_names</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python">                    <span class="n" style="color: #333;">ilev</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">lev</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python">                    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num new old_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">

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python">                        <span class="n" style="color: #333;">ilev</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">lev</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python">                    <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python">                        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python">                        <span class="n" style="color: #333;">asdasdasd</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_tmp_levs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span> <span class="n" style="color: #333;">ilev</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prop</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">props</span><span class="p">[</span><span class="n" style="color: #333;">clade</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python">                        <span class="c" style="color: #998; font-style: italic;"># print "clade", clade</span></span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python">                        <span class="c" style="color: #998; font-style: italic;"># print "prop", prop</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python">                        <span class="c" style="color: #998; font-style: italic;"># print "props[clade]", props[clade]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python">                        <span class="c" style="color: #998; font-style: italic;"># print "val", val</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python">                        <span class="c" style="color: #998; font-style: italic;"># print "ilev", ilev</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python">                        <span class="c" style="color: #998; font-style: italic;"># print</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python">                        <span class="n" style="color: #333;">props</span><span class="p">[</span><span class="n" style="color: #333;">clade</span><span class="p">][</span><span class="n" style="color: #333;">prop</span><span class="p">][</span><span class="n" style="color: #333;">ilev</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">val</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC231" 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="LC232" class="line" lang="python">                        <span class="n" style="color: #333;">props</span><span class="p">[</span><span class="n" style="color: #333;">clade</span><span class="p">][</span><span class="n" style="color: #333;">prop</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">ilev</span><span class="p">:</span><span class="n" style="color: #333;">val</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">@@ -214,12 +235,11 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ilev</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gprops</span><span class="p">[</span><span class="n" style="color: #333;">prop</span><span class="p">]:</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python">                        <span class="n" style="color: #333;">gprops</span><span class="p">[</span><span class="n" style="color: #333;">prop</span><span class="p">][</span><span class="n" style="color: #333;">ilev</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ext_attr_d</span><span class="p">[</span><span class="n" style="color: #333;">prop</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC237" 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="LC217" class="line" lang="python">                    <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">ll</span></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python">                    <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">lev_sep</span><span class="p">)[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python">                    <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">clade_names</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python">                    <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">line</span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python">                    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">"Classes not implemented for external "</span></span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python">                                       <span class="s" style="color: #d14;">"annotations</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="LC238" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print ll</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print clade.split(lev_sep)[-1]</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print clade_names</span></span>

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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print line</span></span>

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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python">                    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="s" style="color: #d14;">"Classes not implemented for external annotations</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="LC243" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="249" style="width: 35px; color: rgba(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="269" style="width: 35px; color: rgba(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">@@ -249,7 +269,13 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python">                        <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'annotation'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python">                            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python">                                <span class="n" style="color: #333;">kkk</span><span class="p">,</span><span class="n" style="color: #333;">vvv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python">                                <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<td class="diff-line-num new old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python">                                    <span class="n" style="color: #333;">kkk</span><span class="p">,</span><span class="n" style="color: #333;">vvv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python">                                <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python">                                    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python">                                    <span class="n" style="color: #333;">asdasdasd</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">                                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kkk</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="LC280" class="line" lang="python">                                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fn</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python">                                        <span class="n" style="color: #333;">kkk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rkeys_gen</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="258" style="width: 35px; color: rgba(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="284" style="width: 35px; color: rgba(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">@@ -258,7 +284,7 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python">                                    <span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kkk</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python">                                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">vvv</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="LC286" class="line" lang="python">                                    <span class="n" style="color: #333;">vvv</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python">                                <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kkk</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;">vvv</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python">                                <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kkk</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":<span class="idiff left right"> </span>"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">vvv</span></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python">                            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">v</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="LC289" class="line" lang="python">                                <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python">                        <span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span>  <span class="n" style="color: #333;">Prop</span><span class="p">(</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'A:1'</span><span class="p">,</span> <span class="n" style="color: #333;">id_ref</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">k</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="333" style="width: 35px; color: rgba(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="359" style="width: 35px; color: rgba(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">@@ -333,6 +359,8 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># visual separation between subtrees.</span></span>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># This is executed if the user sets clade_separatio > 0.0</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ord_leaves</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">compute_tot_add</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_terminal</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ord_leaves</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span> <span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="349" style="width: 35px; color: rgba(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="377" style="width: 35px; color: rgba(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">@@ -349,8 +377,8 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python">                <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">t</span></span>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python">        <span class="n" style="color: #333;">coffset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">rpi2</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total_plotted_degrees</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span></span>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python">        <span class="n" style="color: #333;">circ_step</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total_plotted_degrees</span><span class="o" style="font-weight: 600;"><span class="idiff left">*</span></span><span class="p"><span class="idiff">(</span></span><span class="mf" style="color: #099;"><span class="idiff">1.0</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">-</span></span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clade_separation</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_n_terminals</span></span>

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">circ_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coffset</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="n" style="color: #333;"><span class="idiff">circ_step</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span></span>

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python">        <span class="n" style="color: #333;">circ_step</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total_plotted_degrees</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="mf" style="color: #099;"><span class="idiff">1.0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clade_separation</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_n_terminals</span></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">circ_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">coffset</span><span class="idiff left"> </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">circ_step</span></span></span>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_last_leaf</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span></span>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_varf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">circ_step</span></span>

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<td class="diff-line-num new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="359" style="width: 35px; color: rgba(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="387" style="width: 35px; color: rgba(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">@@ -359,6 +387,7 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_levs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;">#self._ext_max_height = {}</span></span>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_clade_data_rec</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ignore_branch_len</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python">                <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="464" style="width: 35px; color: rgba(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="493" style="width: 35px; color: rgba(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">@@ -464,6 +493,7 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="464" style="width: 35px; color: rgba(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="LC493" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_levs</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">default</span></span>

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_all_ext_attr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ext_attr</span><span class="p">]</span></span>

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<td class="diff-line-num new_line" data-linenumber="495" style="width: 35px; color: rgba(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="LC495" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rec_set_exts</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span> <span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="498" style="width: 35px; color: rgba(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="LC498" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="s" style="color: #d14;">"ext"</span> <span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="499" style="width: 35px; color: rgba(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="LC499" class="line" lang="python">                <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ext</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="570" style="width: 35px; color: rgba(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="600" style="width: 35px; color: rgba(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">@@ -570,7 +600,6 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="570" style="width: 35px; color: rgba(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="LC600" class="line" lang="python">        <span class="n" style="color: #333;">gprops</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id_ref</span><span class="p">,</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC601" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">properties</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"ext__"</span><span class="p">)</span> <span class="p">])</span></span>

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<td class="diff-line-num new_line" data-linenumber="602" style="width: 35px; color: rgba(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="LC602" class="line" lang="python"></span>

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<td class="diff-line-num new_line old" data-linenumber="603" 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="LC573" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python">        <span class="n" style="color: #333;">eggrops</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'__'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'__'</span><span class="p">)[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python">                        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">properties</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"ext__"</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python">        <span class="n" style="color: #333;">iggrops</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'__'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">id_ref</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'__'</span><span class="p">)[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="622" style="width: 35px; color: rgba(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="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -622,7 +651,6 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">attr</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ring_height'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="623" style="width: 35px; color: rgba(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="LC652" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_max_height</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">lev</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mf" style="color: #099;">0.0</span> <span class="k" style="font-weight: 600;">else</span> <span class="mf" style="color: #099;">0.0</span></span>

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<td class="diff-line-num old_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="653" style="width: 35px; color: rgba(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="LC653" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="654" 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="LC625" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC654" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_n_terminals</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_terminals</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

627

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<td class="diff-line-num new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

655

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># with few leaves, the total rotation is lowered (unless the user set it)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="628" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_n_terminals</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">16</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'total_plotted_degrees'</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gprops</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -630,6 +658,7 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

630

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658

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total_plotted_degrees</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total_plotted_degrees</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rpi</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">180.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="659" style="width: 35px; color: rgba(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="LC659" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rpi</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">180.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

660

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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="633" style="width: 35px; color: rgba(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="LC662" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_branches</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="634" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="663" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_branches_rec</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">fcol</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="664" style="width: 35px; color: rgba(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="LC664" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</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">@@ -674,82 +703,146 @@ class CircTree(PpaTree):</td>

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<pre style="margin: 0;"> <span id="LC703" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python">        <span class="n" style="color: #333;">set_branches_rec</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_color</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="677" 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="706" 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">

706

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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="707" style="width: 35px; color: rgba(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="LC707" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_wings</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>

</pre>

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678

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<td class="diff-line-num new_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="679" 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="709" 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">

709

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<pre style="margin: 0;">+<span id="LC709" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;"># print "not self._wing_levs", not self._wing_levs</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="679" 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="710" 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">

710

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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="LC710" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_tot_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="c" style="color: #998; font-style: italic;"># self._max_depth</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

712

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_tot_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

713

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="682" 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="714" 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">

714

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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="LC714" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

682

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<td class="diff-line-num new_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC715" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ignore_branch_len</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="683" 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="716" 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">

716

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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="LC716" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;"># print "self.ignore_branch_len", self.ignore_branch_len</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="683" 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="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

717

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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="LC717" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="683" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

683

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<td class="diff-line-num new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

718

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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="LC718" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="684" 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">

684

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<td class="diff-line-num new_line old" data-linenumber="719" 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="LC684" class="line" lang="python">            <span class="n" style="color: #333;">nlevs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span> <span class="p">)</span></span>

</pre>

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685

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<td class="diff-line-num new_line old" data-linenumber="719" 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="LC685" class="line" lang="python">            <span class="n" style="color: #333;">minl</span><span class="p">,</span> <span class="n" style="color: #333;">maxl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="p">),</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="p">)</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="719" 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">

719

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<pre style="margin: 0;">+<span id="LC719" class="line" lang="python">            <span class="n" style="color: #333;">nlevs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="720" 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">

720

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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python">            <span class="n" style="color: #333;">minl</span><span class="p">,</span> <span class="n" style="color: #333;">maxl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="p">)</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="721" 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">

721

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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="LC721" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="722" 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">

722

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<pre style="margin: 0;">+<span id="LC722" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;"># print "nlevs", nlevs</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="723" 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">

723

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<pre style="margin: 0;">+<span id="LC723" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;"># print "minl", minl</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="724" 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">

724

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<pre style="margin: 0;">+<span id="LC724" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;"># print "maxl", maxl</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

725

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<pre style="margin: 0;">+<span id="LC725" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="686" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

686

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<td class="diff-line-num new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python">        <span class="n" style="color: #333;">lthetas</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="687" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

687

</td>

<td class="diff-line-num new_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

727

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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python">        <span class="n" style="color: #333;">rad_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_background_separation</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="688" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

688

</td>

<td class="diff-line-num new_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

</td>

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<pre style="margin: 0;"> <span id="LC728" class="line" lang="python">        <span class="n" style="color: #333;">lev_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_background_width</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

689

</td>

<td class="diff-line-num new_line" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

729

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC729" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="730" 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">

730

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC730" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># print "lthetas", lthetas</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="731" 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">

731

</td>

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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># print "rad_offset", rad_offset</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="732" 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">

732

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<pre style="margin: 0;">+<span id="LC732" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># print "lev_width", lev_width</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="733" 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">

733

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC733" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

690

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<td class="diff-line-num new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC734" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_wings_rec</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span> <span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="691" 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">

691

</td>

<td class="diff-line-num new_line old" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC691" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">clade</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'annotation'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</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="nb" style="color: #0086b3;"><span class="idiff">hasattr</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="s" style="color: #d14;">'annotation_background_color'</span><span class="p">):</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

735

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC735" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">clade</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'annotation'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</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="nb" style="color: #0086b3;"><span class="idiff">hasattr</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="s" style="color: #d14;">'annotation_background_color'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

692

</td>

<td class="diff-line-num new_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC736" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warnings</span><span class="p">:</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="693" 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">

693

</td>

<td class="diff-line-num new_line old" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC693" class="line" lang="python">                    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: label "</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="694" 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">

694

</td>

<td class="diff-line-num new_line old" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC694" class="line" lang="python">                                     <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> has "</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="695" 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">

695

</td>

<td class="diff-line-num new_line old" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC695" class="line" lang="python">                                     <span class="s" style="color: #d14;">"a default gray background because no color is found for "</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="696" 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">

696

</td>

<td class="diff-line-num new_line old" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC696" class="line" lang="python">                                     <span class="s" style="color: #d14;">"the corresponding </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">annotation</span><span class="se" style="color: #d14;">\"\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="697" 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">

697

</td>

<td class="diff-line-num new_line old" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC697" class="line" lang="python">                <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_background_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mf" style="color: #099;">0.3</span><span class="p">,</span><span class="mf" style="color: #099;">0.3</span><span class="p">,</span><span class="mf" style="color: #099;">0.3</span><span class="p">]</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="698" 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">

698

</td>

<td class="diff-line-num new_line old" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC698" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="s" style="color: #d14;">'annotation_background_color'</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="737" 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">

737

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC737" class="line" lang="python">                    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'Warning: label "{}" has a default gray background because no color is found for the corresponding "annotation"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="738" 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">

738

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC738" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="739" 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">

739

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC739" class="line" lang="python">                <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_background_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">,</span> <span class="mf" style="color: #099;">0.3</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="740" 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">

740

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC740" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

741

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC741" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="s" style="color: #d14;">'annotation_background_color'</span><span class="p">):</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

699

</td>

<td class="diff-line-num new_line" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC742" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_terminal</span><span class="p">():</span> <span class="c" style="color: #998; font-style: italic;"># same as non-terminal ??</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="743" 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">

743

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC743" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.theta", clade.theta</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="744" 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">

744

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<pre style="margin: 0;">+<span id="LC744" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print ''</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="745" 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">

745

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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="LC745" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.pc", clade.pc</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="746" 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">

746

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC746" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.nc", clade.nc</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="747" 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">

747

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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="LC747" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print ''</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="748" 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">

748

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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="LC748" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.pc.theta", clade.pc.theta</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="749" 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">

749

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC749" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.nc.theta", clade.nc.theta</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="750" 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">

750

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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="LC750" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

700

</td>

<td class="diff-line-num new_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

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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="LC751" class="line" lang="python">                    <span class="n" style="color: #333;">cpc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

701

</td>

<td class="diff-line-num new_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC752" class="line" lang="python">                    <span class="n" style="color: #333;">cnc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="753" 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">

753

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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="LC753" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

702

</td>

<td class="diff-line-num new_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

754

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC754" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cpc</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

</td>

<td class="diff-line-num new_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

755

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC755" class="line" lang="python">                        <span class="n" style="color: #333;">cpc</span> <span class="o" style="font-weight: 600;">-=</span> <span class="n" style="color: #333;">rpi2</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="756" 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">

756

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC756" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

</td>

<td class="diff-line-num new_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC757" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cnc</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

</td>

<td class="diff-line-num new_line" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

758

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC758" class="line" lang="python">                        <span class="n" style="color: #333;">cnc</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rpi2</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="706" 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">

706

</td>

<td class="diff-line-num new_line old" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC706" class="line" lang="python">                    <span class="n" style="color: #333;">lsm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cpc</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="707" 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">

707

</td>

<td class="diff-line-num new_line old" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC707" class="line" lang="python">                    <span class="n" style="color: #333;">lgr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cnc</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

</td>

<td class="diff-line-num new_line" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

759

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC759" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="760" 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">

760

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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="LC760" class="line" lang="python">                    <span class="n" style="color: #333;">lsm</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cpc</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="761" 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">

761

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<pre style="margin: 0;">+<span id="LC761" class="line" lang="python">                    <span class="n" style="color: #333;">lgr</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cnc</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

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<td class="diff-line-num new_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

762

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<pre style="margin: 0;"> <span id="LC762" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="710" 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">

710

</td>

<td class="diff-line-num new_line old" data-linenumber="763" 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="LC710" class="line" lang="python">                    <span class="n" style="color: #333;">f</span><span class="p">,</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="711" 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">

711

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<td class="diff-line-num new_line old" data-linenumber="763" 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="LC711" class="line" lang="python">                    <span class="n" style="color: #333;">cpc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">),</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">),</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="712" 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">

712

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<td class="diff-line-num new_line old" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC712" class="line" lang="python">                    <span class="n" style="color: #333;">f</span><span class="p">,</span><span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="713" 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">

713

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<td class="diff-line-num new_line old" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC713" class="line" lang="python">                    <span class="n" style="color: #333;">cnc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">),</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">),</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="763" 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">

763

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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="LC763" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.fc.pc", clade.fc.pc</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="764" 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">

764

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC764" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.lc.nc", clade.lc.nc</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="765" 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">

765

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC765" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print ''</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="766" 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">

766

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC766" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.fc.theta", clade.fc.theta</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="767" 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">

767

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC767" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.lc.theta", clade.lc.theta</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="768" 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">

768

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<pre style="margin: 0;">+<span id="LC768" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print ''</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="769" 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">

769

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<pre style="margin: 0;">+<span id="LC769" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.fc.pc.theta", clade.fc.pc.theta</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="770" 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">

770

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<pre style="margin: 0;">+<span id="LC770" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.fc.nc.theta", clade.fc.nc.theta</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="771" 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">

771

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<pre style="margin: 0;">+<span id="LC771" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print ''</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="772" 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">

772

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<pre style="margin: 0;">+<span id="LC772" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.lc.pc.theta", clade.lc.pc.theta</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="773" 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">

773

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<pre style="margin: 0;">+<span id="LC773" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "clade.lc.nc.theta", clade.lc.nc.theta</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="774" 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">

774

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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="LC774" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="775" 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">

775

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<pre style="margin: 0;">+<span id="LC775" class="line" lang="python">                    <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC776" class="line" lang="python">                    <span class="n" style="color: #333;">cpc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="777" 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">

777

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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="LC777" class="line" lang="python">                    <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">t</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="714" 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="778" 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">

778

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<pre style="margin: 0;">+<span id="LC778" class="line" lang="python">                    <span class="n" style="color: #333;">cnc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">t</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<td class="diff-line-num new_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

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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="LC779" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

715

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<td class="diff-line-num new_line" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

780

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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="LC780" class="line" lang="python">                    <span class="n" style="color: #333;">lsm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cpc</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<td class="diff-line-num new_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

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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="LC781" class="line" lang="python">                    <span class="n" style="color: #333;">lgr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cnc</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

717

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<td class="diff-line-num new_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

782

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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="LC782" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

718

</td>

<td class="diff-line-num new_line old" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC718" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_thetas</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">lsm</span> <span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="783" 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">

783

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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="LC783" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># print ''</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="784" 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">

784

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC784" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># print "cpc", cpc</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="785" 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">

785

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC785" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># print "cnc", cnc</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="786" 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">

786

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC786" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># print "lsm", lsm</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="787" 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">

787

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC787" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># print "lgr", lgr</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="788" 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">

788

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC788" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="789" 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">

789

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC789" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_thetas</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">lsm</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="790" 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">

790

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC790" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

719

</td>

<td class="diff-line-num new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

791

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC791" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ignore_branch_len</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="720" 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">

720

</td>

<td class="diff-line-num new_line old" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC720" class="line" lang="python">                    <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lev_width</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_depths</span><span class="p">[</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">]))</span> <span class="idiff left right"> </span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">r</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="792" 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">

792

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC792" class="line" lang="python">                    <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lev_width</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_depths</span><span class="p">[</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">]))</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">r</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

721

</td>

<td class="diff-line-num new_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

793

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC793" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

</td>

<td class="diff-line-num new_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

794

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC794" class="line" lang="python">                    <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">r</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lev_width</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

723

</td>

<td class="diff-line-num new_line old" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC723" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_radii</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rad_offset</span> <span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

724

</td>

<td class="diff-line-num new_line old" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC724" class="line" lang="python">                <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span> <span class="n" style="color: #333;">lgr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lsm</span><span class="p">)</span></span>

</pre>

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725

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<td class="diff-line-num new_line old" data-linenumber="795" 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="LC725" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_widths</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">width</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="726" 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">

726

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<td class="diff-line-num new_line old" data-linenumber="795" 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="LC726" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_bottoms</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">r</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="727" 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">

727

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<td class="diff-line-num new_line old" data-linenumber="795" 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="LC727" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_colors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_background_color</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="795" 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">

795

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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="LC795" class="line" lang="python"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="796" 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">

796

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<pre style="margin: 0;">+<span id="LC796" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># print "rad", rad</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="797" 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">

797

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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="LC797" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="798" 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">

798

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<pre style="margin: 0;">+<span id="LC798" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_radii</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rad_offset</span><span class="p">)</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="799" 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">

799

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<pre style="margin: 0;">+<span id="LC799" class="line" lang="python">                <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">lgr</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lsm</span><span class="p">)</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="800" 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">

800

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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="LC800" class="line" lang="python"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="801" 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">

801

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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="LC801" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># print "width", width</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="802" 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">

802

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<pre style="margin: 0;">+<span id="LC802" class="line" lang="python"></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="803" 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">

803

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<pre style="margin: 0;">+<span id="LC803" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_widths</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">)</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="804" 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">

804

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<pre style="margin: 0;">+<span id="LC804" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_bottoms</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">r</span><span class="p">)</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="805" 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">

805

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<pre style="margin: 0;">+<span id="LC805" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_colors</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_background_color</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="806" 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">

806

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<pre style="margin: 0;">+<span id="LC806" class="line" lang="python"></span>

</pre>

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728

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<td class="diff-line-num new_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

807

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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="LC807" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rad_offset</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_tot_offset</span><span class="p">:</span></span>

</pre>

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729

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<td class="diff-line-num new_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

808

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC808" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_tot_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rad_offset</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

730

</td>

<td class="diff-line-num new_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

809

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC809" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_tot_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_tot_offset</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

731

</td>

<td class="diff-line-num new_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

810

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC810" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="811" 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">

811

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC811" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print ''</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="812" 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">

812

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC812" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "self._wing_tot_offset", self._wing_tot_offset</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="813" 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">

813

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC813" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "self._tot_offset", self._tot_offset</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="814" 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">

814

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC814" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

732

</td>

<td class="diff-line-num new_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

815

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC815" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="s" style="color: #d14;">'annotation'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

733

</td>

<td class="diff-line-num new_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC816" class="line" lang="python">                    <span class="n" style="color: #333;">lab</span><span class="p">,</span> <span class="n" style="color: #333;">ext_key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="817" 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">

817

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC817" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

</td>

<td class="diff-line-num new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC818" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lab</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

</td>

<td class="diff-line-num new_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC819" class="line" lang="python">                        <span class="n" style="color: #333;">ext_key</span><span class="p">,</span> <span class="n" style="color: #333;">lab</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lab</span><span class="p">,</span> <span class="n" style="color: #333;">lab</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="736" 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">

736

</td>

<td class="diff-line-num new_line old" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC736" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_label</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">lab</span> <span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="820" 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">

820

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC820" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="821" 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">

821

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC821" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_label</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">lab</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="822" 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">

822

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC822" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

</td>

<td class="diff-line-num new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

823

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC823" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ext_key</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

</td>

<td class="diff-line-num new_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

824

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC824" class="line" lang="python">                        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">ext_key</span> <span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="825" 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">

825

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC825" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

</td>

<td class="diff-line-num new_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

826

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC826" class="line" lang="python">                    <span class="n" style="color: #333;">avgtheta</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">lgr</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lsm</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.5</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

</td>

<td class="diff-line-num new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

827

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC827" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_label_theta</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">avgtheta</span> <span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="diff-line-num new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

828

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC828" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="742" 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">

742

</td>

<td class="diff-line-num new_line old" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC742" class="line" lang="python">                    <span class="n" style="color: #333;">rot90</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="idiff left right"> </span><span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="s" style="color: #d14;">'annotation_rotation'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_rotation</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="829" 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">

829

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC829" class="line" lang="python">                    <span class="n" style="color: #333;">rot90</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="s" style="color: #d14;">'annotation_rotation'</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_rotation</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

<td class="diff-line-num new_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

830

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC830" class="line" lang="python">                    <span class="n" style="color: #333;">fract</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.05</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rot90</span> <span class="k" style="font-weight: 600;">else</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="831" 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">

831

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC831" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

744

</td>

<td class="diff-line-num new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC832" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ignore_branch_len</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

</td>

<td class="diff-line-num new_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC833" class="line" lang="python">                        <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lev_width</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_levs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">index</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_depths</span><span class="p">[</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">]))</span>  <span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lev_width</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fract</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

</td>

<td class="diff-line-num new_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

834

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC834" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

747

</td>

<td class="diff-line-num new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC835" class="line" lang="python">                        <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">lev_width</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">fract</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

</td>

<td class="diff-line-num new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC836" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="837" 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">

837

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC837" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "rad", rad</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="838" 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">

838

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC838" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

<td class="diff-line-num new_line" data-linenumber="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

839

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC839" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_label_r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">rad</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">rad_offset</span> <span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

</td>

<td class="diff-line-num new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

840

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC840" class="line" lang="python">                    <span class="n" style="color: #333;">rot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">avgtheta</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">180.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rpi</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">90.0</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rpi</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">theta</span><span class="o" style="font-weight: 600;">%</span><span class="n" style="color: #333;">rpi2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">rpi2</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">avgtheta</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">180.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">rpi</span> <span class="o" style="font-weight: 600;">-</span> <span class="mf" style="color: #099;">90.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

751

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<td class="diff-line-num new_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

841

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<pre style="margin: 0;"> <span id="LC841" class="line" lang="python">                    <span class="n" style="color: #333;">rot</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rot</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">360.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">%</span> <span class="mf" style="color: #099;">360.0</span> <span class="o" style="font-weight: 600;">+</span> <span class="mf" style="color: #099;">1e-10</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

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<td class="diff-line-num new_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

842

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<pre style="margin: 0;"> <span id="LC842" class="line" lang="python">                    <span class="n" style="color: #333;">rot</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">rot</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rot90</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">rot</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="843" 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">

843

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<pre style="margin: 0;">+<span id="LC843" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC844" class="line" lang="python">                    <span class="c" style="color: #998; font-style: italic;"># print "rot", rot</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="753" 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="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC845" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

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<td class="diff-line-num new_line" data-linenumber="846" style="width: 35px; color: rgba(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="LC846" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_label_rot</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">rot</span> <span class="p">)</span></span>

</pre>

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754

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<td class="diff-line-num new_line" data-linenumber="847" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

847

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<pre style="margin: 0;"> <span id="LC847" class="line" lang="python">                    <span class="n" style="color: #333;">lfs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_font_size</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="p">,</span><span class="s" style="color: #d14;">"annotation_font_size"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_annotation_font_size</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

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<pre style="margin: 0;"> <span id="LC848" class="line" lang="python">                    <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_annotation_font_size</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">lfs</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="761" style="width: 35px; color: rgba(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="854" style="width: 35px; color: rgba(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">@@ -761,6 +854,7 @@ class CircTree(PpaTree):</td>

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761

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<td class="diff-line-num new_line" data-linenumber="854" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

854

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<pre style="margin: 0;"> <span id="LC854" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

762

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855

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<pre style="margin: 0;"> <span id="LC855" class="line" lang="python">        <span class="n" style="color: #333;">set_wings_rec</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

763

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<td class="diff-line-num new_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

856

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<pre style="margin: 0;"> <span id="LC856" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="764" 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="857" 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">

857

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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="858" style="width: 35px; color: rgba(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="LC858" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">disambiguate_names</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="859" style="width: 35px; color: rgba(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="LC859" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">disambiguate_names_rec</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">cnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span> <span class="p">):</span></span>

</pre>

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766

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<td class="diff-line-num new_line" data-linenumber="860" style="width: 35px; color: rgba(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="LC860" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="p">,</span><span class="s" style="color: #d14;">'name'</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -771,34 +865,41 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num new_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="866" style="width: 35px; color: rgba(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="LC866" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="867" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

867

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<pre style="margin: 0;"> <span id="LC867" class="line" lang="python">                <span class="n" style="color: #333;">disambiguate_names_rec</span><span class="p">(</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">cnames</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="774" 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="868" 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">

868

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<pre style="margin: 0;">+<span id="LC868" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="869" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python">        <span class="n" style="color: #333;">disambiguate_names_rec</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span> <span class="p">)</span></span>

</pre>

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775

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<td class="diff-line-num new_line" data-linenumber="870" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

870

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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="871" style="width: 35px; color: rgba(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="LC871" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="872" style="width: 35px; color: rgba(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="LC872" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_legend</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="873" style="width: 35px; color: rgba(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="LC873" class="line" lang="python">        <span class="n" style="color: #333;">ax1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">subplot</span><span class="p">(</span><span class="mi" style="color: #099;">111</span><span class="p">,</span> <span class="n" style="color: #333;">visible</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="779" 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="874" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC874" class="line" lang="python">        <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_keys"</span><span class="p">)</span></span>

</pre>

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779

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<td class="diff-line-num new_line" data-linenumber="875" style="width: 35px; color: rgba(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="LC875" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="876" 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="LC780" class="line" lang="python">        <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_keys"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="781" 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">

781

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<td class="diff-line-num new_line old" data-linenumber="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC781" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="876" 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="LC782" class="line" lang="python">        <span class="n" style="color: #333;">clade_marker_color</span>        <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_clade_marker_color"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="783" 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="876" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC876" class="line" lang="python">        <span class="n" style="color: #333;">clade_marker_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_clade_marker_color"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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<td class="diff-line-num new_line" data-linenumber="877" style="width: 35px; color: rgba(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="LC877" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">clade_marker_color</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="878" style="width: 35px; color: rgba(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="LC878" class="line" lang="python">            <span class="n" style="color: #333;">clade_marker_color</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_clade_marker_color</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="785" 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">

785

</td>

<td class="diff-line-num new_line old" data-linenumber="879" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC785" class="line" lang="python">        <span class="n" style="color: #333;">clade_marker_size</span>              <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_clade_marker_size"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="879" 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">

879

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC879" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="880" 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">

880

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC880" class="line" lang="python">        <span class="n" style="color: #333;">clade_marker_size</span>  <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_clade_marker_size"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

786

</td>

<td class="diff-line-num new_line" data-linenumber="881" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

881

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC881" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">clade_marker_size</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

787

</td>

<td class="diff-line-num new_line" data-linenumber="882" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

882

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC882" class="line" lang="python">            <span class="n" style="color: #333;">clade_marker_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_clade_marker_size</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="788" 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">

788

</td>

<td class="diff-line-num new_line old" data-linenumber="883" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC788" class="line" lang="python">        <span class="n" style="color: #333;">clade_marker_edge_width</span>   <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_clade_marker_edge_width"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="883" 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">

883

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC883" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="884" 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">

884

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC884" class="line" lang="python">        <span class="n" style="color: #333;">clade_marker_edge_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_clade_marker_edge_width"</span><span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

</td>

<td class="diff-line-num new_line" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC885" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">clade_marker_edge_width</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

790

</td>

<td class="diff-line-num new_line" data-linenumber="886" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

886

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC886" class="line" lang="python">            <span class="n" style="color: #333;">clade_marker_edge_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_clade_marker_edge_width</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

791

</td>

<td class="diff-line-num new_line" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC887" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="888" 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">

888

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC888" class="line" lang="python">        <span class="n" style="color: #333;">clade_marker_shape</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="s" style="color: #d14;">"leg_clade_marker_shape"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="889" 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">

889

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC889" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">clade_marker_shape</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="890" 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">

890

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC890" class="line" lang="python">            <span class="n" style="color: #333;">clade_marker_shape</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_clade_marker_shape</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">keys</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="891" 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">

891

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC891" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

</td>

<td class="diff-line-num new_line" data-linenumber="892" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

892

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC892" class="line" lang="python">        <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

793

</td>

<td class="diff-line-num new_line old" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC793" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">lw</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">clade_marker_size</span><span class="p">,</span><span class="n" style="color: #333;">clade_marker_color</span><span class="p">,</span><span class="n" style="color: #333;">clade_marker_edge_width</span><span class="p">):</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="794" 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">

794

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<td class="diff-line-num new_line old" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC794" class="line" lang="python">            <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ax1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">scatter</span><span class="p">(</span>   <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="795" 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">

795

</td>

<td class="diff-line-num new_line old" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC795" class="line" lang="python">                                <span class="n" style="color: #333;">linewidths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lw</span> <span class="p">)</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="893" 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">

893

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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="LC893" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">lw</span><span class="p">,</span><span class="n" style="color: #333;">m</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">clade_marker_size</span><span class="p">,</span> <span class="n" style="color: #333;">clade_marker_color</span><span class="p">,</span> <span class="n" style="color: #333;">clade_marker_edge_width</span><span class="p">,</span> <span class="n" style="color: #333;">clade_marker_shape</span><span class="p">):</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="894" 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">

894

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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="LC894" class="line" lang="python">            <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ax1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">scatter</span><span class="p">(</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">linewidths</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">lw</span><span class="p">,</span> <span class="n" style="color: #333;">marker</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">m</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

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<td class="diff-line-num new_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

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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="LC895" class="line" lang="python">            <span class="n" style="color: #333;">ll</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="896" 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">

896

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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="LC896" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

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<td class="diff-line-num new_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

897

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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="LC897" class="line" lang="python">        <span class="n" style="color: #333;">ax1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_xlim</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

</td>

<td class="diff-line-num new_line" data-linenumber="898" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

898

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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="LC898" class="line" lang="python">        <span class="n" style="color: #333;">ax1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_ylim</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

<td class="diff-line-num new_line" data-linenumber="899" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

899

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC899" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

800

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<td class="diff-line-num new_line" data-linenumber="900" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

900

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC900" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ll</span> <span class="p">,</span> <span class="n" style="color: #333;">keys</span><span class="p">,</span> <span class="s" style="color: #d14;">'upper right'</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

801

</td>

<td class="diff-line-num new_line" data-linenumber="901" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

901

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC901" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="902" 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">

902

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC902" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

802

</td>

<td class="diff-line-num new_line" data-linenumber="903" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

903

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC903" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_init_attr</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

803

</td>

<td class="diff-line-num new_line" data-linenumber="904" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

904

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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="LC904" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_depths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span><span class="n" style="color: #333;">dist</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">dist</span> <span class="ow" style="font-weight: 600;">in</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

804

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<td class="diff-line-num new_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

905

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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="LC905" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">depths</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ignore_branch_len</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()])</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="834" style="width: 35px; color: rgba(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="935" style="width: 35px; color: rgba(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">@@ -834,17 +935,13 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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</td>

<td class="diff-line-num new_line" data-linenumber="935" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

935

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<pre style="margin: 0;"> <span id="LC935" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_patches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

<td class="diff-line-num new_line" data-linenumber="936" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

936

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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="LC936" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

<td class="diff-line-num new_line" data-linenumber="937" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

937

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC937" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="837" 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">

837

</td>

<td class="diff-line-num new_line old" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC837" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">draw</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out_img</span><span class="p">,</span> <span class="n" style="color: #333;">out_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">out_dpi</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">72</span><span class="p">,</span> <span class="n" style="color: #333;">out_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">7.0</span><span class="p">,</span> <span class="n" style="color: #333;">out_pad</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.5</span><span class="p">,</span> <span class="n" style="color: #333;">external_legends</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

838

</td>

<td class="diff-line-num new_line" data-linenumber="938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

938

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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="LC938" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="839" 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">

839

</td>

<td class="diff-line-num new_line old" data-linenumber="939" 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="LC839" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reorder_tree</span><span class="p">()</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="939" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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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="LC939" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">draw</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">out_img</span><span class="p">,</span> <span class="n" style="color: #333;">out_format</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">out_dpi</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">72</span><span class="p">,</span> <span class="n" style="color: #333;">out_size</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">7.0</span><span class="p">,</span> <span class="n" style="color: #333;">out_pad</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">,</span> <span class="n" style="color: #333;">external_legends</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">reorder_tree</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">):</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="940" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

940

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC940" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reorder_tree</span><span class="p">(</span><span class="n" style="color: #333;">reorder_tree</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

840

</td>

<td class="diff-line-num new_line" data-linenumber="941" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

941

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC941" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;">#self.tree.ladderize()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

841

</td>

<td class="diff-line-num new_line old" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC841" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

842

</td>

<td class="diff-line-num new_line" data-linenumber="942" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

942

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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="LC942" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_set_attr</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

843

</td>

<td class="diff-line-num new_line old" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC843" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

844

</td>

<td class="diff-line-num new_line" data-linenumber="943" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

943

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC943" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">disambiguate_names</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

845

</td>

<td class="diff-line-num new_line old" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC845" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

846

</td>

<td class="diff-line-num new_line" data-linenumber="944" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

944

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC944" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_init_attr</span><span class="p">()</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="847" 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">

847

</td>

<td class="diff-line-num new_line old" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC847" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="848" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

848

</td>

<td class="diff-line-num new_line" data-linenumber="945" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

945

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC945" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_clade_data</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="849" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

849

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<td class="diff-line-num new_line" data-linenumber="946" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

946

</td>

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<pre style="margin: 0;"> <span id="LC946" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_branches</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="850" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

850

</td>

<td class="diff-line-num new_line" data-linenumber="947" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

947

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC947" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_wings</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="859" style="width: 35px; color: rgba(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="956" style="width: 35px; color: rgba(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">@@ -859,7 +956,6 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="859" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

859

</td>

<td class="diff-line-num new_line" data-linenumber="956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

956

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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="LC956" class="line" lang="python">        <span class="n" style="color: #333;">xticks</span><span class="p">([])</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="860" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

860

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<td class="diff-line-num new_line" data-linenumber="957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

957

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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="LC957" class="line" lang="python">        <span class="n" style="color: #333;">yticks</span><span class="p">([])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="861" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

861

</td>

<td class="diff-line-num new_line" data-linenumber="958" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

958

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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="LC958" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="862" 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">

862

</td>

<td class="diff-line-num new_line old" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC862" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="863" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

863

</td>

<td class="diff-line-num new_line" data-linenumber="959" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

959

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC959" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_r</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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="864" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

864

</td>

<td class="diff-line-num new_line" data-linenumber="960" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

960

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC960" class="line" lang="python">            <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">scatter</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_t</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_r</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="865" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

865

</td>

<td class="diff-line-num new_line" data-linenumber="961" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

961

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC961" class="line" lang="python">                        <span class="n" style="color: #333;">marker</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_clade_marker_shape</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="889" style="width: 35px; color: rgba(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="985" style="width: 35px; color: rgba(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">@@ -889,19 +985,13 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="889" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

889

</td>

<td class="diff-line-num new_line" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

985

</td>

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<pre style="margin: 0;"> <span id="LC985" class="line" lang="python">                                            <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_br_colors</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="890" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

890

</td>

<td class="diff-line-num new_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC986" class="line" lang="python">                                            <span class="n" style="color: #333;">linewidth</span><span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_thickness</span> <span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="891" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

891

</td>

<td class="diff-line-num new_line" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

987

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC987" class="line" lang="python"></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="892" 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">

892

</td>

<td class="diff-line-num new_line old" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC892" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="893" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

893

</td>

<td class="diff-line-num new_line" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

988

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC988" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_thetas</span> <span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="894" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

894

</td>

<td class="diff-line-num new_line" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

989

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC989" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_thetas</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="895" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

895

</td>

<td class="diff-line-num new_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

990

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC990" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_radii</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="896" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

896

</td>

<td class="diff-line-num new_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

991

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<pre style="margin: 0;"> <span id="LC991" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_widths</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

897

</td>

<td class="diff-line-num new_line" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

992

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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="LC992" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_bottoms</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="898" 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">

898

</td>

<td class="diff-line-num new_line old" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC898" class="line" lang="python">        <span class="n" style="color: #333;">wbar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bar</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_thetas</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_radii</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="899" 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">

899

</td>

<td class="diff-line-num new_line old" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC899" class="line" lang="python">                       <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_widths</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="900" 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">

900

</td>

<td class="diff-line-num new_line old" data-linenumber="993" 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="LC900" class="line" lang="python">                       <span class="n" style="color: #333;">bottom</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_bottoms</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="901" 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">

901

</td>

<td class="diff-line-num new_line old" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC901" class="line" lang="python">                       <span class="n" style="color: #333;">alpha</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_background_alpha</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="902" 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">

902

</td>

<td class="diff-line-num new_line old" data-linenumber="993" 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="LC902" class="line" lang="python">                       <span class="n" style="color: #333;">color</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_colors</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="903" 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">

903

</td>

<td class="diff-line-num new_line old" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC903" class="line" lang="python">                       <span class="n" style="color: #333;">edgecolor</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_colors</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="904" 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">

904

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<td class="diff-line-num new_line old" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC904" class="line" lang="python">                       <span class="p">)</span></span>

</pre>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="993" 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">

993

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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="LC993" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="994" 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">

994

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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="LC994" class="line" lang="python">        <span class="n" style="color: #333;">wbar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">bar</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_thetas</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_radii</span><span class="p">,</span> <span class="n" style="color: #333;">width</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_widths</span><span class="p">,</span> <span class="n" style="color: #333;">bottom</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_bottoms</span><span class="p">,</span> <span class="n" style="color: #333;">alpha</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_background_alpha</span><span class="p">,</span> <span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_colors</span><span class="p">,</span> <span class="n" style="color: #333;">edgecolor</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_wing_colors</span><span class="p">,</span> <span class="n" style="color: #333;">align</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'edge'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="905" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

905

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<td class="diff-line-num new_line" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

995

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC995" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="906" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

906

</td>

<td class="diff-line-num new_line" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

996

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC996" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lev</span><span class="p">,</span><span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">int_levs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="907" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

907

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<td class="diff-line-num new_line" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

997

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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC997" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'internal_label'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">d</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1060" style="width: 35px; color: rgba(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">@@ -970,6 +1060,10 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

970

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<td class="diff-line-num new_line" data-linenumber="1060" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1060

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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="LC1060" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span><span class="p">,</span><span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ext_levs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

971

</td>

<td class="diff-line-num new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1061

</td>

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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'ring_internal_separator_thickness'</span><span class="p">,</span><span class="s" style="color: #d14;">'ring_external_separator_thickness'</span><span class="p">]:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

972

</td>

<td class="diff-line-num new_line" data-linenumber="1062" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1062

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1062" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="n" style="color: #333;">p</span><span class="p">])</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1063" 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">

1063

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1063" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_bottoms</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">():</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1064" 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">

1064

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1064" class="line" lang="python">                        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'[e] External ring #'</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">),</span> <span class="s" style="color: #d14;">'defined, but not used. Please check your annotations file'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1065" 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">

1065

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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="LC1065" class="line" lang="python">                        <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1066" 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">

1066

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1066" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

973

</td>

<td class="diff-line-num new_line" data-linenumber="1067" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1067

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1067" class="line" lang="python">                    <span class="n" style="color: #333;">bot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_bottoms</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

974

</td>

<td class="diff-line-num new_line" data-linenumber="1068" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1068

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1068" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ring_external_separator_thickness'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

975

</td>

<td class="diff-line-num new_line" data-linenumber="1069" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1069

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1069" class="line" lang="python">                        <span class="n" style="color: #333;">bot</span> <span class="o" style="font-weight: 600;">+=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_max_height</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_max_height</span> <span class="k" style="font-weight: 600;">else</span> <span class="mf" style="color: #099;">0.1</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="981" style="width: 35px; color: rgba(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="1075" style="width: 35px; color: rgba(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">@@ -981,12 +1075,12 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

981

</td>

<td class="diff-line-num new_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1075

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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="LC1075" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'ring_label'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">v</span><span class="p">[</span><span class="s" style="color: #d14;">'ring_label'</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

982

</td>

<td class="diff-line-num new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1076

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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="LC1076" class="line" lang="python">                <span class="n" style="color: #333;">bot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_bottoms</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

983

</td>

<td class="diff-line-num new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1077

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1077" class="line" lang="python">                <span class="n" style="color: #333;">bot1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_bottoms</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_bottoms</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_bottoms</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="984" 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">

984

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<td class="diff-line-num new_line old" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC984" class="line" lang="python">                            <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_max_height</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_max_height</span> <span class="k" style="font-weight: 600;">else</span> <span class="mf" style="color: #099;">0.1</span><span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="985" 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">

985

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<td class="diff-line-num new_line old" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC985" class="line" lang="python">                <span class="n" style="color: #333;">off</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">rpi2</span><span class="o" style="font-weight: 600;">-</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total_plotted_degrees</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1078" 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">

1078

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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="LC1078" class="line" lang="python">                                 <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_max_height</span><span class="p">[</span><span class="n" style="color: #333;">l</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.1</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_max_height</span> <span class="k" style="font-weight: 600;">else</span> <span class="mf" style="color: #099;">0.1</span><span class="p">)</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1079" 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">

1079

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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="LC1079" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1080" 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">

1080

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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="LC1080" class="line" lang="python">                <span class="n" style="color: #333;">off</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="n" style="color: #333;">rpi2</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total_plotted_degrees</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

986

</td>

<td class="diff-line-num new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1081

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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="LC1081" class="line" lang="python">                <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">bot</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">bot1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">0.5</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="987" 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">

987

</td>

<td class="diff-line-num new_line old" data-linenumber="1082" 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="LC987" class="line" lang="python">                <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">90</span> <span class="k" style="font-weight: 600;">if</span> <span class="mf" style="color: #099;">0.5</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rpi</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.5</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rpi</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">90</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="988" 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">

988

</td>

<td class="diff-line-num new_line old" data-linenumber="1082" 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="LC988" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;">#rot = (self.start_rotation*360.0/rpi2 + s + off*360.0/rpi2 )%360.0</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="989" 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">

989

</td>

<td class="diff-line-num new_line old" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC989" class="line" lang="python">                <span class="n" style="color: #333;">rot</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">360.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">rpi2</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span> <span class="p">)</span><span class="o" style="font-weight: 600;">%</span><span class="mf" style="color: #099;">360.0</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1082" 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">

1082

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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="LC1082" class="line" lang="python">                <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">180.0</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">rpi</span> <span class="k" style="font-weight: 600;">else</span> <span class="mf" style="color: #099;">0.0</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1083" 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">

1083

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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="LC1083" class="line" lang="python">                <span class="n" style="color: #333;">rot</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span><span class="o" style="font-weight: 600;">*</span><span class="mf" style="color: #099;">360.0</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">rpi2</span><span class="p">)</span><span class="o" style="font-weight: 600;">%</span><span class="mf" style="color: #099;">180.0</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">90</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

990

</td>

<td class="diff-line-num new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1084

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1084" class="line" lang="python">                <span class="n" style="color: #333;">fs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">[</span><span class="s" style="color: #d14;">'ring_label_font_size'</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

991

</td>

<td class="diff-line-num new_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1085

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1085" class="line" lang="python">                <span class="n" style="color: #333;">lcol</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">[</span><span class="s" style="color: #d14;">'ring_label_color'</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

992

</td>

<td class="diff-line-num new_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1086

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1086" class="line" lang="python">                <span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">text</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_rotation</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">[</span><span class="s" style="color: #d14;">'ring_label'</span><span class="p">],</span> <span class="n" style="color: #333;">rotation</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rot</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1004" style="width: 35px; color: rgba(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="1098" style="width: 35px; color: rgba(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">@@ -1004,31 +1098,19 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="1004" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1004

</td>

<td class="diff-line-num new_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1098

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1098" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;">#ax.text( 0, 1, t )</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1005

</td>

<td class="diff-line-num new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1099

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1099" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1006

</td>

<td class="diff-line-num new_line" data-linenumber="1100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1100

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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="LC1100" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1007" 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">

1007

</td>

<td class="diff-line-num new_line old" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1007" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#a = ax.legend( bbox_to_anchor=(.0, 1), loc = 'upper left', shadow=False, frameon = False,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1008" 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">

1008

</td>

<td class="diff-line-num new_line old" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1008" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#           scatterpoints = 1, borderpad = 0, handlelength = 0,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1009" 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">

1009

</td>

<td class="diff-line-num new_line old" data-linenumber="1101" 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="LC1009" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#           handletextpad = 0, markerscale = 0.0, ncol = 1,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1010" 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">

1010

</td>

<td class="diff-line-num new_line old" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1010" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#           labelspacing = 0.05,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1011" 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">

1011

</td>

<td class="diff-line-num new_line old" data-linenumber="1101" 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="LC1011" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#           prop = {'size':self.annotation_legend_font_size}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1012" 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">

1012

</td>

<td class="diff-line-num new_line old" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1012" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#        )</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1013" 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">

1013

</td>

<td class="diff-line-num new_line old" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1013" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1014" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1014

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<td class="diff-line-num new_line" data-linenumber="1101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1101

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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">external_legends</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1015" 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">

1015

</td>

<td class="diff-line-num new_line old" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1015" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1016" 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">

1016

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<td class="diff-line-num new_line old" data-linenumber="1102" 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="LC1016" class="line" lang="python">                    <span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1017" 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">

1017

</td>

<td class="diff-line-num new_line old" data-linenumber="1102" 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="LC1017" class="line" lang="python">                    <span class="n" style="color: #333;">charsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_legend_font_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.0138889</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1018" 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">

1018

</td>

<td class="diff-line-num new_line old" data-linenumber="1102" 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="LC1018" class="line" lang="python">                    <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">charsize</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">10.</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">10.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1019" 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">

1019

</td>

<td class="diff-line-num new_line old" data-linenumber="1102" 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="LC1019" class="line" lang="python">                    <span class="n" style="color: #333;">height</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_tot_offset</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">charsize</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">10.</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">10.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1020" 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">

1020

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<td class="diff-line-num new_line old" data-linenumber="1102" 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="LC1020" class="line" lang="python">                    <span class="n" style="color: #333;">fig_annot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">figure</span><span class="p">(</span><span class="n" style="color: #333;">figsize</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">height</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1021" 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">

1021

</td>

<td class="diff-line-num new_line old" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1021" class="line" lang="python">                    <span class="n" style="color: #333;">ax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fig_annot</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_subplot</span><span class="p">(</span><span class="mi" style="color: #099;">111</span><span class="p">,</span> <span class="n" style="color: #333;">frame_on</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">xticks</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">yticks</span><span class="o" style="font-weight: 600;">=</span><span class="p">[])</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1022" 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">

1022

</td>

<td class="diff-line-num new_line old" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1022" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1023" 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">

1023

</td>

<td class="diff-line-num new_line old" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1023" class="line" lang="python">                    <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'[W] External annotation not created, no annotated labels!'</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1102" 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">

1102

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1102" class="line" lang="python">                <span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">]</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1103" 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">

1103

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1103" class="line" lang="python">                <span class="n" style="color: #333;">charsize</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_legend_font_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.0138889</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1104" 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">

1104

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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="LC1104" class="line" lang="python">                <span class="n" style="color: #333;">width</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">charsize</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">10.</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">10.</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1105" 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">

1105

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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="LC1105" class="line" lang="python">                <span class="n" style="color: #333;">height</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_tot_offset</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">charsize</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">10.</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">10.</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1106" 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">

1106

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1106" class="line" lang="python">                <span class="n" style="color: #333;">fig_annot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">figure</span><span class="p">(</span><span class="n" style="color: #333;">figsize</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">height</span><span class="p">))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1107" 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">

1107

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1107" class="line" lang="python">                <span class="n" style="color: #333;">ax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fig_annot</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_subplot</span><span class="p">(</span><span class="mi" style="color: #099;">111</span><span class="p">,</span> <span class="n" style="color: #333;">frame_on</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">xticks</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">yticks</span><span class="o" style="font-weight: 600;">=</span><span class="p">[])</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1024

</td>

<td class="diff-line-num new_line" data-linenumber="1108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1108

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1108" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1025

</td>

<td class="diff-line-num new_line" data-linenumber="1109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1109

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1109" class="line" lang="python">            <span class="n" style="color: #333;">ll</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">ax</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">scatter</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1026" 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">

1026

</td>

<td class="diff-line-num new_line old" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1026" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1027" 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">

1027

</td>

<td class="diff-line-num new_line old" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1027" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1028" 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">

1028

</td>

<td class="diff-line-num new_line old" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1028" class="line" lang="python">                <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">figlegend</span><span class="p">(</span><span class="n" style="color: #333;">ll</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">),</span> <span class="s" style="color: #d14;">'upper left'</span><span class="p">,</span> <span class="n" style="color: #333;">frameon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1029" 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">

1029

</td>

<td class="diff-line-num new_line old" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1029" class="line" lang="python">                    <span class="n" style="color: #333;">shadow</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">scatterpoints</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">handlelength</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;">markerscale</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1030" 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">

1030

</td>

<td class="diff-line-num new_line old" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1030" class="line" lang="python">                    <span class="n" style="color: #333;">handletextpad</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">labelspacing</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1031" 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">

1031

</td>

<td class="diff-line-num new_line old" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1031" class="line" lang="python">                    <span class="n" style="color: #333;">prop</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'size'</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_legend_font_size</span><span class="p">})</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1110" 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">

1110

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1110" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">figlegend</span><span class="p">(</span><span class="n" style="color: #333;">ll</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">),</span> <span class="s" style="color: #d14;">'upper left'</span><span class="p">,</span> <span class="n" style="color: #333;">frameon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1111" 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">

1111

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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="LC1111" class="line" lang="python">                <span class="n" style="color: #333;">shadow</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">scatterpoints</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">handlelength</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;">markerscale</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.0</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1112" 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">

1112

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1112" class="line" lang="python">                <span class="n" style="color: #333;">handletextpad</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">labelspacing</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1113" 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">

1113

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1113" class="line" lang="python">                <span class="n" style="color: #333;">prop</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'size'</span><span class="p">:</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">annotation_legend_font_size</span><span class="p">})</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1032

</td>

<td class="diff-line-num new_line" data-linenumber="1114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1114

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1114" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1033

</td>

<td class="diff-line-num new_line" data-linenumber="1115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1115

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1115" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">external_legends</span><span class="p">:</span> <span class="c" style="color: #998; font-style: italic;"># add '_annot' to the filename</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1034

</td>

<td class="diff-line-num new_line" data-linenumber="1116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1116

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1116" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">out_format</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1036" style="width: 35px; color: rgba(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="1118" style="width: 35px; color: rgba(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">@@ -1036,10 +1118,11 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="1036" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1036

</td>

<td class="diff-line-num new_line" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1118

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1118" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1037

</td>

<td class="diff-line-num new_line" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1119

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1119" class="line" lang="python">                    <span class="n" style="color: #333;">img_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_img</span><span class="p">[:</span><span class="n" style="color: #333;">out_img</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"_annot"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">out_img</span><span class="p">[</span><span class="n" style="color: #333;">out_img</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rfind</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">):]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1038" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1038

</td>

<td class="diff-line-num new_line" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1120

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1120" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1039" 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">

1039

</td>

<td class="diff-line-num new_line old" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1039" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ext_key</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1040" 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">

1040

</td>

<td class="diff-line-num new_line old" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1040" class="line" lang="python">                    <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">savefig</span><span class="p">(</span><span class="n" style="color: #333;">img_name</span><span class="p">,</span> <span class="n" style="color: #333;">dpi</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_dpi</span><span class="p">,</span> <span class="n" style="color: #333;">bbox_inches</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'tight'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1041" 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">

1041

</td>

<td class="diff-line-num new_line old" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1041" class="line" lang="python">                        <span class="n" style="color: #333;">bbox_extra_artists</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">handles</span><span class="p">,</span> <span class="n" style="color: #333;">pad_inches</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_pad</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_format</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1042" 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">

1042

</td>

<td class="diff-line-num new_line old" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1042" class="line" lang="python">                    <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1121" 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">

1121

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1121" class="line" lang="python">                <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">savefig</span><span class="p">(</span><span class="n" style="color: #333;">img_name</span><span class="p">,</span> <span class="n" style="color: #333;">dpi</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_dpi</span><span class="p">,</span> <span class="n" style="color: #333;">bbox_inches</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'tight'</span><span class="p">,</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1122" 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">

1122

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1122" class="line" lang="python">                    <span class="n" style="color: #333;">bbox_extra_artists</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">handles</span><span class="p">,</span> <span class="n" style="color: #333;">pad_inches</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_pad</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_format</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1123" 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">

1123

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1123" class="line" lang="python">                <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1124" 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">

1124

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1124" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># else:</span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1125" 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">

1125

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1125" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;">#     print '[w] External annotation not created, no annotated labels!'</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1043" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1043

</td>

<td class="diff-line-num new_line" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1126

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1126" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1044" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1044

</td>

<td class="diff-line-num new_line" data-linenumber="1127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1127

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1127" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">external_legends</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1045

</td>

<td class="diff-line-num new_line" data-linenumber="1128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1128

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1128" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">labels</span><span class="p">:</span> <span class="c" style="color: #998; font-style: italic;"># need to check if there are annotated labels!</span></span>

</pre>

</td>

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<tr class="line_holder match" id="" style="line-height: 1.6;">

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1048" style="width: 35px; color: rgba(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="1131" style="width: 35px; color: rgba(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">@@ -1048,7 +1131,7 @@ class CircTree(PpaTree):</td>

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<td class="diff-line-num old_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1048

</td>

<td class="diff-line-num new_line" data-linenumber="1131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1131

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1131" class="line" lang="python">                <span class="n" style="color: #333;">height</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_tot_offset</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">labels</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">charsize</span> <span class="o" style="font-weight: 600;">*</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">class_legend_marker_size</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">10.</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">10.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1049

</td>

<td class="diff-line-num new_line" data-linenumber="1132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1132

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1132" class="line" lang="python">                <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">figure</span><span class="p">(</span><span class="n" style="color: #333;">figsize</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">height</span><span class="p">))</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1050

</td>

<td class="diff-line-num new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1133

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1133" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1051" 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">

1051

</td>

<td class="diff-line-num new_line old" data-linenumber="1134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC1051" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;"><span class="idiff right">'[W] External legend not created, no annotated labels!'</span></span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1134" 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">

1134

</td>

<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1134" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'[w] External legend not created, no annotated labels!'</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1052

</td>

<td class="diff-line-num new_line" data-linenumber="1135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1135

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1135" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="1136" style="width: 35px; color: rgba(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="LC1136" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">labels</span><span class="p">:</span></span>

</pre>

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1054

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<td class="diff-line-num new_line" data-linenumber="1137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1137

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<pre style="margin: 0;"> <span id="LC1137" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">figlegend</span><span class="p">(</span><span class="n" style="color: #333;">handles</span><span class="p">,</span> <span class="n" style="color: #333;">labels</span><span class="p">,</span> <span class="n" style="color: #333;">loc</span><span class="p">,</span> <span class="n" style="color: #333;">labelspacing</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span> <span class="n" style="color: #333;">frameon</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1073" style="width: 35px; color: rgba(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="1156" style="width: 35px; color: rgba(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">@@ -1073,7 +1156,6 @@ class CircTree(PpaTree):</td>

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1073

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<td class="diff-line-num new_line" data-linenumber="1156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1156

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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="python">                <span class="n" style="color: #333;">pad_inches</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_pad</span><span class="p">,</span> <span class="n" style="color: #333;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_format</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1074

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<td class="diff-line-num new_line" data-linenumber="1157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1157

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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;"># edgecolor=fc</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1075

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<td class="diff-line-num new_line" data-linenumber="1158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1158

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<pre style="margin: 0;"> <span id="LC1158" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1076" 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">

1076

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<td class="diff-line-num new_line old" data-linenumber="1159" 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="LC1076" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1077" style="width: 35px; color: rgba(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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1159

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<pre style="margin: 0;"> <span id="LC1159" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1160

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<pre style="margin: 0;"> <span id="LC1160" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="1161" style="width: 35px; color: rgba(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="LC1161" class="line" lang="python">            <span class="n" style="color: #333;">plt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">show</span><span class="p">()</span></span></pre>

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<br>

</li>

<li id="a83b13e720a39a8cb2334f0070f73f907a09eb06">

<a href="https://salsa.debian.org/med-team/graphlan/compare/7e3e813f69b7af460ed049567354f1b68ce143a0...ed2e94feb06db5c7f53f23234ce6d7613aae58ad#a83b13e720a39a8cb2334f0070f73f907a09eb06"><strong>src/pyphlan.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(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="9" style="width: 35px; color: rgba(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">@@ -9,7 +9,7 @@ from Bio.Phylo.BaseTree import Clade as BClade</td>

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9

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9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">string</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">numpy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">pi</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">rpi</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="python"><span class="n" style="color: #333;">rpi2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">2.0</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">rpi</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="12" 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="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">array</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">arr</span></span>

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(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="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">colls</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="115" style="width: 35px; color: rgba(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="115" style="width: 35px; color: rgba(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">@@ -115,7 +115,7 @@ def reroot_mid_fat_edge( tree, node ):</td>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">clades2terms</span><span class="p">(</span> <span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">startswith</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">    <span class="n" style="color: #333;">c2t</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">clades2terms_rec</span><span class="p">(</span> <span class="n" style="color: #333;">c</span> <span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">startswith</span><span class="p">:</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">startswith</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span> <span class="n" style="color: #333;">startswith</span> <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">                <span class="n" style="color: #333;">c2t</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(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="127" style="width: 35px; color: rgba(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">@@ -127,11 +127,11 @@ def clades2terms( tree, startswith = None ):</td>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dist_matrix</span><span class="p">(</span> <span class="n" style="color: #333;">tree</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">    <span class="n" style="color: #333;">terminals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">())</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python">    <span class="n" style="color: #333;">term_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">terminals</span><span class="p">]</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python">    <span class="n" style="color: #333;">term_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">terminals</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># can be made faster with recursion</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_nonterminals</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">        <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> <span class="p">[</span><span class="n" style="color: #333;">nn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()]</span>  <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python">    <span class="n" style="color: #333;">dists</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">n</span><span class="p">,</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="n" style="color: #333;">nn</span><span class="p">,</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">term_names</span><span class="p">]))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">term_names</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dist_matrix_rec</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span> <span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" style="width: 35px; color: rgba(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="160" style="width: 35px; color: rgba(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">@@ -160,18 +160,21 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__load_tree_txt__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">        <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Phylo</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BaseTree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Tree</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python">            <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python">            <span class="n" style="color: #333;">rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"><span class="idiff left right">      </span></span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python">        <span class="n" style="color: #333;">clades</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">lev_sep</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rows</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python">        <span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BTree</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python">        <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BClade</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"><span class="idiff left right">       </span></span>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_clade_rec</span><span class="p">(</span> <span class="n" style="color: #333;">father</span><span class="p">,</span> <span class="n" style="color: #333;">txt_tree</span> <span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python">            <span class="n" style="color: #333;">fl</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">txt_tree</span><span class="p">])</span></span>

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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python">            <span class="n" style="color: #333;">fl</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">t</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">txt_tree</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fl</span><span class="p">:</span> <span class="k" style="font-weight: 600;">continue</span></span>

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="n" style="color: #333;">fl</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python">            <span class="n" style="color: #333;">father</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fl</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python">                <span class="n" style="color: #333;">nclade</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BClade</span><span class="p">(</span> <span class="n" style="color: #333;">branch_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -184,7 +187,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python">        <span class="n" style="color: #333;">add_clade_rec</span><span class="p">(</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">clades</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ignore_branch_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">as_phyloxml</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__read_tree__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ff</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'phyloxml'</span><span class="p">,</span><span class="s" style="color: #d14;">'newick'</span><span class="p">,</span><span class="s" style="color: #d14;">'nexus'</span><span class="p">,</span><span class="s" style="color: #d14;">"txt"</span><span class="p">]:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="199" style="width: 35px; color: rgba(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="202" style="width: 35px; color: rgba(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">@@ -199,25 +202,25 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python">                <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: No tree file found: "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fn</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="LC202" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC208" 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="LC209" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">as_phyloxml</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: unrecognized input format "</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">fn</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>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="211" 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="LC208" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="214" style="width: 35px; color: rgba(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="LC214" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">warnings</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warnings</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">warnings</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="216" style="width: 35px; color: rgba(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="LC216" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(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="LC217" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="218" 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="LC215" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="216" 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="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(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="LC219" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC217" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__read_tree__</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="218" 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="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__read_tree__</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_full_paths</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line old" 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">

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="221" 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="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">

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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">core_test</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">ok</span><span class="p">,</span> <span class="n" style="color: #333;">tot</span><span class="p">,</span> <span class="n" style="color: #333;">pr</span> <span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="245" style="width: 35px; color: rgba(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">@@ -242,7 +245,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python">        <span class="n" style="color: #333;">add</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">subclade</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"?"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python">                <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">intersection</span> <span class="c" style="color: #998; font-style: italic;"># targs<span class="idiff left right">  </span></span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python">                <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">intersection</span> <span class="c" style="color: #998; font-style: italic;"># targs</span></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python">                <span class="n" style="color: #333;">add</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">add</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">len_intersection</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">add</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python">            <span class="n" style="color: #333;">len_intersection</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">add</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">1.99</span><span class="p">))</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="259" style="width: 35px; color: rgba(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="262" style="width: 35px; color: rgba(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">@@ -259,10 +262,10 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">targs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python">                    <span class="n" style="color: #333;">nsubclades_absent</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="265" 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="LC262" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">            <span class="n" style="color: #333;">sc_intersection</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">targs</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python">            <span class="n" style="color: #333;">sc_len_intersection</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sc_intersection</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"><span class="idiff left right">           </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python">            <span class="n" style="color: #333;">sc_add</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sc_subclade</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"?"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sc_subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(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="274" style="width: 35px; color: rgba(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">@@ -271,7 +274,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">add</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sc_len_intersection</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">sc_add</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python">                <span class="n" style="color: #333;">sc_len_intersection</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">sc_add</span><span class="o" style="font-weight: 600;">/</span><span class="mf" style="color: #099;">1.99</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python">            <span class="n" style="color: #333;">subcore</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">core_test</span><span class="p">(</span> <span class="n" style="color: #333;">sc_len_intersection</span><span class="p">,</span> <span class="n" style="color: #333;">subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nterminals</span><span class="p">,</span> <span class="n" style="color: #333;">er</span> <span class="p">)</span><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python">            <span class="n" style="color: #333;">subcore</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">core_test</span><span class="p">(</span> <span class="n" style="color: #333;">sc_len_intersection</span><span class="p">,</span> <span class="n" style="color: #333;">subclade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nterminals</span><span class="p">,</span> <span class="n" style="color: #333;">er</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subcore</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.05</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">core</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nsubclades</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nsubclades</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">nsubclades_absent</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="295" style="width: 35px; color: rgba(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="298" style="width: 35px; color: rgba(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">@@ -295,7 +298,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python">                                <span class="mf" style="color: #099;">1.0</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">skip_qm</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">"?"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python">                <span class="n" style="color: #333;">cimg</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cimg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">terminals</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="320" style="width: 35px; color: rgba(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="323" style="width: 35px; color: rgba(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">@@ -320,7 +323,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_full_paths</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_add_full_paths_</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">path</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python">            <span class="n" style="color: #333;">lpath</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">([</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[])</span></span>

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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python">            <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"."</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="n" style="color: #333;">lpath</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="330" style="width: 35px; color: rgba(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="333" style="width: 35px; color: rgba(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">@@ -330,7 +333,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_cores</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">cl_taxa_file</span><span class="p">,</span> <span class="n" style="color: #333;">min_core_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.95</span><span class="p">,</span> <span class="n" style="color: #333;">subtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">skip_qm</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subtree</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">subtree</span><span class="p">(</span> <span class="s" style="color: #d14;">'name'</span><span class="p">,</span> <span class="n" style="color: #333;">subtree</span> <span class="p">)</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">subtree</span><span class="p">(</span> <span class="s" style="color: #d14;">'name'</span><span class="p">,</span> <span class="n" style="color: #333;">subtree</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ctc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python">        <span class="n" style="color: #333;">imgids2terminals</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">():</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="343" style="width: 35px; color: rgba(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="346" style="width: 35px; color: rgba(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">@@ -343,7 +346,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python">            <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> <span class="p">[</span><span class="n" style="color: #333;">nn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgid</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()]</span>  <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python">            <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nterminals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_full_paths</span><span class="p">()</span> <span class="c" style="color: #998; font-style: italic;"># unnecessary<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_full_paths</span><span class="p">()</span> <span class="c" style="color: #998; font-style: italic;"># unnecessary</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python">        <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">vec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">cl_taxa_file</span><span class="p">)):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" style="width: 35px; color: rgba(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="360" style="width: 35px; color: rgba(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">@@ -357,7 +360,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python">                <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="n" style="color: #333;">sid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_find_core</span><span class="p">(</span> <span class="n" style="color: #333;">tgts</span><span class="p">,</span> <span class="n" style="color: #333;">er</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">error_rate</span><span class="p">,</span> <span class="n" style="color: #333;">root_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subtree</span><span class="p">,</span> <span class="n" style="color: #333;">skip_qm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">skip_qm</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python">                <span class="c" style="color: #998; font-style: italic;">#print sid #, ret[sid]</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span></span>

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"><span class="idiff left right">   </span></span>

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">markerness</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">coreness</span><span class="p">,</span> <span class="n" style="color: #333;">uniqueness</span><span class="p">,</span> <span class="n" style="color: #333;">cn_min</span><span class="p">,</span> <span class="n" style="color: #333;">cn_max</span><span class="p">,</span> <span class="n" style="color: #333;">cn_avg</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">coreness</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">uniqueness</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">cn_max</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">cn_min</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">cn_avg</span></span>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"></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">@@ -376,9 +379,9 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python">            <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> <span class="p">[</span><span class="n" style="color: #333;">nn</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgid</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()]</span>  <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">            <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nterminals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_full_paths</span><span class="p">()</span> <span class="c" style="color: #998; font-style: italic;"># unnecessary<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python">        <span class="n" style="color: #333;">cus</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ll</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ll</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_full_paths</span><span class="p">()</span> <span class="c" style="color: #998; font-style: italic;"># unnecessary</span></span>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python">        <span class="n" style="color: #333;">cus</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ll</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ll</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">l</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span></span>

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<td class="diff-line-num new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python">                        <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">cu_file</span><span class="p">))])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python">        <span class="n" style="color: #333;">cinfo</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">([(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]),[</span><span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">vv</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">vv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">:</span><span class="mi" style="color: #099;">6</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">vv</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">vv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">:]])</span></span>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python">                        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">core_file</span><span class="p">))])</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -390,7 +393,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python">            <span class="n" style="color: #333;">lca</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lca</span><span class="p">(</span> <span class="n" style="color: #333;">cus</span><span class="p">[</span><span class="n" style="color: #333;">sid</span><span class="p">],</span> <span class="n" style="color: #333;">ids2clades</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lca</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_terminal</span><span class="p">():</span></span>

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<td class="diff-line-num new_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python">                <span class="n" style="color: #333;">tin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">lca</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgid</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="python">                <span class="n" style="color: #333;">tout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tgts_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tin</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python">                <span class="n" style="color: #333;">tout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tgts_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">tin</span></span>

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<td class="diff-line-num new_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python">                <span class="n" style="color: #333;">tout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tgts_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lca</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python">                <span class="n" style="color: #333;">tin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lca</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">imgids</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tgts_l</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -403,15 +406,15 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python">            <span class="n" style="color: #333;">gtax</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ci</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python">            <span class="n" style="color: #333;">cobs</span><span class="p">,</span> <span class="n" style="color: #333;">ctot</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ci</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">ci</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python">            <span class="n" style="color: #333;">markerness</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">markerness</span><span class="p">(</span> <span class="n" style="color: #333;">coreness</span><span class="p">,</span> <span class="n" style="color: #333;">uniqueness</span><span class="p">,</span> <span class="n" style="color: #333;">cn_min</span><span class="p">,</span> <span class="n" style="color: #333;">cp_max</span><span class="p">,</span> <span class="n" style="color: #333;">cn_avg</span> <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python">            <span class="n" style="color: #333;">res_lin</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span> <span class="n" style="color: #333;">gtax</span><span class="p">,</span> <span class="n" style="color: #333;">markerness</span><span class="p">,</span> <span class="n" style="color: #333;">coreness</span><span class="p">,</span> <span class="n" style="color: #333;">uniqueness</span><span class="p">,</span> <span class="n" style="color: #333;">cobs</span><span class="p">,</span> <span class="n" style="color: #333;">ctot</span><span class="p">,</span> <span class="n" style="color: #333;">cn_min</span><span class="p">,</span> <span class="n" style="color: #333;">cp_max</span><span class="p">,</span> <span class="n" style="color: #333;">cn_avg</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python">                        <span class="n" style="color: #333;">ltin</span><span class="p">,</span> <span class="n" style="color: #333;">ltout</span><span class="p">,</span> <span class="s" style="color: #d14;">"|"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tin</span><span class="p">]),</span> <span class="s" style="color: #d14;">"|"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tout</span><span class="p">])</span> <span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python">            <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="n" style="color: #333;">sid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">res_lin</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python">            <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="n" style="color: #333;">sid</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">res_lin</span></span>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span></span>

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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"><span class="idiff left right">       </span></span>

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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">select_markers</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">marker_file</span><span class="p">,</span> <span class="n" style="color: #333;">markerness_th</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">,</span> <span class="n" style="color: #333;">max_markers</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">200</span> <span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python">        <span class="n" style="color: #333;">cl2markers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">colls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">list</span> <span class="p">)</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python">        <span class="n" style="color: #333;">cl2markers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">colls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span> <span class="nb" style="color: #0086b3;">list</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span> <span class="n" style="color: #333;">marker_file</span> <span class="p">)):</span></span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python">            <span class="n" style="color: #333;">gid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python">            <span class="n" style="color: #333;">markerness</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">])</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="433" style="width: 35px; color: rgba(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="436" style="width: 35px; color: rgba(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">@@ -433,7 +436,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python">                <span class="n" style="color: #333;">_get_c2t_</span><span class="p">(</span> <span class="n" style="color: #333;">c</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python">        <span class="n" style="color: #333;">_get_c2t_</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="439" 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="LC436" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tc2t</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tc2t</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="440" style="width: 35px; color: rgba(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="LC440" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ltcs</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">terminals</span><span class="p">,</span> <span class="n" style="color: #333;">tc2t</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">terminals2clades</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">lca_precomputed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="442" style="width: 35px; color: rgba(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="LC442" class="line" lang="python">        <span class="n" style="color: #333;">set_terminals</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span> <span class="n" style="color: #333;">terminals</span> <span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="444" style="width: 35px; color: rgba(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="447" style="width: 35px; color: rgba(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">@@ -444,7 +447,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python">            <span class="n" style="color: #333;">terms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tc2t</span><span class="p">[</span><span class="n" style="color: #333;">clade</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">tc2t</span> <span class="k" style="font-weight: 600;">else</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">cc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cc</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">terms</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">cur_max</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">terms</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">set_terminals</span><span class="p">:</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">terms</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">set_terminals</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="451" style="width: 35px; color: rgba(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="LC451" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">terms</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python">            <span class="n" style="color: #333;">rets</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="453" style="width: 35px; color: rgba(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="LC453" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="456" style="width: 35px; color: rgba(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="459" style="width: 35px; color: rgba(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">@@ -456,7 +459,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rets</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="460" style="width: 35px; color: rgba(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="LC460" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">rets</span><span class="p">,</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">cur_max</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC461" 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="LC459" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="bp" style="color: #999;">None</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span><span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="463" style="width: 35px; color: rgba(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="LC463" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_ltcs_rec_</span><span class="p">(</span> <span class="n" style="color: #333;">lca</span><span class="p">,</span> <span class="n" style="color: #333;">cur_max</span> <span class="o" style="font-weight: 600;">=</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>

</pre>

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<td class="diff-line-num new_line" data-linenumber="464" style="width: 35px; color: rgba(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="LC464" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="465" style="width: 35px; color: rgba(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="LC465" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">lca</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">terminals</span><span class="p">,</span> <span class="n" style="color: #333;">terminals2clades</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="476" style="width: 35px; color: rgba(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="479" style="width: 35px; color: rgba(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">@@ -476,7 +479,7 @@ class PpaTree:</td>

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<td class="diff-line-num new_line" data-linenumber="479" style="width: 35px; color: rgba(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="LC479" class="line" lang="python">        <span class="n" style="color: #333;">lca</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">common_ancestor</span><span class="p">(</span> <span class="n" style="color: #333;">clade_targets</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="480" style="width: 35px; color: rgba(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="LC480" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">lca</span></span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC479" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">lcca</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">t2c</span> <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python">        <span class="n" style="color: #333;">node_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_path</span><span class="p">(</span><span class="n" style="color: #333;">t</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">node_path</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">node_path</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="520" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="523" style="width: 35px; color: rgba(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">@@ -520,7 +523,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python">            <span class="n" style="color: #333;">outs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">out_terms</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python">                <span class="n" style="color: #333;">diam</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">ltcs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">depths</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">())[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">:])</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python">                <span class="n" style="color: #333;">outs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">":"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distance</span><span class="p">(</span><span class="n" style="color: #333;">ltcs</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">diam</span> <span class="p">)])</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new new_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python">                <span class="n" style="color: #333;">outs</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">":"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">distance</span><span class="p">(</span><span class="n" style="color: #333;">ltcs</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">diam</span> <span class="p">)])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="527" style="width: 35px; color: rgba(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="LC527" class="line" lang="python">                             <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">t</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">out_terms</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python">            <span class="n" style="color: #333;">res</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">outs</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="526" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="529" style="width: 35px; color: rgba(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="LC529" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">res</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="528" style="width: 35px; color: rgba(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="531" style="width: 35px; color: rgba(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">@@ -528,7 +531,7 @@ class PpaTree:</td>

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531

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">tax_resolution</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">terminals</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

529

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<td class="diff-line-num new_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

532

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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="LC532" class="line" lang="python">        <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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530

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<td class="diff-line-num new_line" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

533

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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="LC533" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="531" 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">

531

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<td class="diff-line-num new_line old" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC531" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="534" 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">

534

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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="LC534" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

532

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<td class="diff-line-num new_line" data-linenumber="535" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

535

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">prune</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">strategy</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'lca'</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">newname</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="p">):</span></span>

</pre>

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533

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<td class="diff-line-num new_line" data-linenumber="536" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

536

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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python">        <span class="n" style="color: #333;">prune</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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534

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<td class="diff-line-num new_line" data-linenumber="537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

537

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strategy</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'root_name'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="557" style="width: 35px; color: rgba(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="560" style="width: 35px; color: rgba(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">@@ -557,7 +560,7 @@ class PpaTree:</td>

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557

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<td class="diff-line-num new_line" data-linenumber="560" style="width: 35px; color: rgba(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="LC560" class="line" lang="python">            <span class="n" style="color: #333;">toprune</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_path</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="558" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

558

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<td class="diff-line-num new_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python">            <span class="n" style="color: #333;">fat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node_path</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python">            <span class="n" style="color: #333;">fat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">cc</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">cc</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fat</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cc</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">toprune</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="560" 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">

560

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<td class="diff-line-num new_line old" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC560" class="line" lang="python">            <span class="n" style="color: #333;">prune</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="563" 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">

563

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python">            <span class="n" style="color: #333;">prune</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<td class="diff-line-num new_line" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

564

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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<td class="diff-line-num new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

565

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span> <span class="n" style="color: #333;">strategy</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" not supported yet."</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

566

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</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>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -620,8 +623,8 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reroot</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">strategy</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'lca'</span><span class="p">,</span> <span class="n" style="color: #333;">tf</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strategy</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span> <span class="s" style="color: #d14;">'lca'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ltcs'</span> <span class="p">]:</span></span>

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<pre style="margin: 0;">-<span id="LC623" class="line" lang="python">            <span class="n" style="color: #333;">targets</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_targets</span><span class="p">(</span> <span class="n" style="color: #333;">tf</span> <span class="p">)</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">-<span id="LC624" class="line" lang="python"><span class="idiff left right">          </span></span>

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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python">            <span class="n" style="color: #333;">targets</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_targets</span><span class="p">(</span> <span class="n" style="color: #333;">tf</span> <span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python">            <span class="n" style="color: #333;">lca</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lca</span><span class="p">(</span> <span class="n" style="color: #333;">targets</span> <span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">strategy</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'lca'</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ltcs</span><span class="p">(</span> <span class="n" style="color: #333;">targets</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python">            <span class="n" style="color: #333;">reroot_mid_fat_edge</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">lca</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="641" style="width: 35px; color: rgba(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="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -641,46 +644,55 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#self.tree.reroot_at_midpoint(update_splits=True)</span></span>

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<pre style="margin: 0;"> <span id="LC645" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">strategy</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'longest_edge'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python">            <span class="n" style="color: #333;">nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_nonterminals</span><span class="p">())</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">())</span></span>

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<pre style="margin: 0;">-<span id="LC644" class="line" lang="python">            <span class="n" style="color: #333;">longest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span> <span class="n" style="color: #333;">nodes</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_length</span> <span class="p">)</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC647" class="line" lang="python">            <span class="n" style="color: #333;">longest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span> <span class="n" style="color: #333;">nodes</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_length</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python">            <span class="n" style="color: #333;">reroot_mid_fat_edge</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">longest</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC649" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#longest_edge = max( self.ntree.get_edge_set(),</span></span>

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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#                    key=lambda x:x.length)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#self.tree.reroot_at_edge(longest_edge, update_splits=True)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="652" style="width: 35px; color: rgba(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="LC652" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">strategy</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'longest_internal_edge'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="653" style="width: 35px; color: rgba(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="LC653" class="line" lang="python">            <span class="n" style="color: #333;">nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_nonterminals</span><span class="p">())</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC651" class="line" lang="python">            <span class="n" style="color: #333;">longest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span> <span class="n" style="color: #333;">nodes</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_length</span> <span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC654" class="line" lang="python">            <span class="n" style="color: #333;">longest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span> <span class="n" style="color: #333;">nodes</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_length</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC655" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">longest</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python">                <span class="n" style="color: #333;">reroot_mid_fat_edge</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">longest</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="657" style="width: 35px; color: rgba(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="LC657" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#longest = get_lensorted_int_edges( self.tree )</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="658" style="width: 35px; color: rgba(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="LC658" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#self.tree.reroot_at_edge( list(longest)[-1], update_splits=True )</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="659" style="width: 35px; color: rgba(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="LC659" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">strategy</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'longest_internal_edge_n'</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python">            <span class="n" style="color: #333;">nodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_nonterminals</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="661" 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="LC658" class="line" lang="python">            <span class="n" style="color: #333;">longest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span> <span class="n" style="color: #333;">nodes</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_length</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">-<span id="LC659" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">())</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">n</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python">            <span class="n" style="color: #333;">longest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span> <span class="n" style="color: #333;">nodes</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">branch_length</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC662" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">())</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">n</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span></span>

</pre>

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660

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663

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python">            <span class="n" style="color: #333;">reroot_mid_fat_edge</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">longest</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="664" style="width: 35px; color: rgba(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="LC664" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#longest = get_lensorted_int_edges( self.tree, n )</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="665" style="width: 35px; color: rgba(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="LC665" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#self.tree.reroot_at_edge( list(longest)[-1], update_splits=True )</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="666" style="width: 35px; color: rgba(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="LC666" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="668" 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="LC665" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reorder_tree</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span> <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reorder_tree</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">reorder_tree</span></span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="669" style="width: 35px; color: rgba(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="LC669" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ord_terms</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="670" 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="LC667" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reorder_tree_rec</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="668" 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="670" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="668" 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="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reorder_tree_rec</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span> <span class="n" style="color: #333;">reorder_tree</span> <span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

673

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_terminal</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="674" style="width: 35px; color: rgba(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="LC674" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ord_terms</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="n" style="color: #333;">clade</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC675" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">clade</span><span class="p">,</span><span class="n" style="color: #333;">clade</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC671" class="line" lang="python">            <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()),</span> <span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reorder_tree</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python">                <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_terminals</span><span class="p">()),</span> <span class="n" style="color: #333;">reverse</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC680" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC673" class="line" lang="python">                <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reorder_tree_rec</span><span class="p">(</span> <span class="n" style="color: #333;">c</span> <span class="p">)</span> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC674" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="p">,</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC681" class="line" lang="python">                <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="p">,</span><span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reorder_tree_rec</span><span class="p">(</span> <span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">reorder_tree</span> <span class="p">)</span></span>

</pre>

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682

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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"></span>

</pre>

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683

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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fc</span><span class="p">,</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lc</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="684" style="width: 35px; color: rgba(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="LC684" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;">#clade.fc, clade.lc = clade.clades[0], clade.clades[-1]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC676" class="line" lang="python">        </span>

</pre>

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677

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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python">        <span class="n" style="color: #333;">reorder_tree_rec</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span> <span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC685" class="line" lang="python"></span>

</pre>

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686

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python">        <span class="n" style="color: #333;">reorder_tree_rec</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">reorder_tree</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC688" class="line" lang="python">        <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c" style="color: #998; font-style: italic;"># self._ord_terms[-1]</span></span>

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<td class="diff-line-num new new_line" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_ord_terms</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC691" class="line" lang="python">            <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last</span></span>

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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">last</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python">                <span class="n" style="color: #333;">last</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span></span>

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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python">            <span class="n" style="color: #333;">last</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c</span></span>

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<pre style="margin: 0;">+<span id="LC695" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python">        <span class="n" style="color: #333;">c</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;">#self._ord_terms[-1].nc = None # self._ord_terms[0]</span></span>

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<pre style="margin: 0;"> <span id="LC698" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="696" style="width: 35px; color: rgba(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="708" style="width: 35px; color: rgba(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">@@ -696,7 +708,7 @@ class PpaTree:</td>

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python">                <span class="n" style="color: #333;">leaves</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rec_subtree_leaves</span><span class="p">(</span> <span class="n" style="color: #333;">c</span> <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python">            <span class="n" style="color: #333;">leaves</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">l</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">l</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">leaves</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">l</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python">            <span class="n" style="color: #333;">subtrees</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="n" style="color: #333;">leaves</span><span class="p">)</span>  <span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="711" 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="LC699" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">leaves</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC711" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">leaves</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="713" style="width: 35px; color: rgba(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="LC713" class="line" lang="python">        <span class="n" style="color: #333;">rec_subtree_leaves</span><span class="p">(</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span> <span class="p">)</span></span>

</pre>

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702

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<td class="diff-line-num new_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">subtrees</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="713" style="width: 35px; color: rgba(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="725" style="width: 35px; color: rgba(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">@@ -713,14 +725,14 @@ class PpaTree:</td>

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<td class="diff-line-num new_line" data-linenumber="725" style="width: 35px; color: rgba(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="LC725" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">nam</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python">                    <span class="n" style="color: #333;">lnam</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">nam</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="728" 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="LC716" class="line" lang="python">                    <span class="n" style="color: #333;">lnam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC728" class="line" lang="python">                    <span class="n" style="color: #333;">lnam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="729" style="width: 35px; color: rgba(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="LC729" class="line" lang="python">                <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="730" style="width: 35px; color: rgba(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="LC730" class="line" lang="python">                    <span class="n" style="color: #333;">lnam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nam</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

731

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<pre style="margin: 0;"> <span id="LC731" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="732" 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="LC720" class="line" lang="python">                    <span class="n" style="color: #333;">lnam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lev_sep</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="p">[</span><span class="n" style="color: #333;">nam</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span><span class="p">]</span> <span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

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721

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<td class="diff-line-num new_line old" data-linenumber="732" 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="LC721" class="line" lang="python">                <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="n" style="color: #333;">lnam</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lnam</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[]</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="722" 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="732" 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">

732

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<pre style="margin: 0;">+<span id="LC732" class="line" lang="python">                    <span class="n" style="color: #333;">lnam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lev_sep</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span> <span class="p">[</span><span class="n" style="color: #333;">nam</span><span class="p">,</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span><span class="p">]</span> <span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="722" 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="733" 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">

733

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<pre style="margin: 0;">+<span id="LC733" class="line" lang="python">                <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="n" style="color: #333;">lnam</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lnam</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[]</span></span>

</pre>

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722

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<td class="diff-line-num new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

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<pre style="margin: 0;"> <span id="LC734" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">clade</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">clades</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

723

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<td class="diff-line-num new_line old" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC723" class="line" lang="python">                    <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rec_name</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">lnam</span><span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

735

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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python">                    <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">rec_name</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span><span class="n" style="color: #333;">lnam</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

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<td class="diff-line-num new_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

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<pre style="margin: 0;"> <span id="LC736" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

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<td class="diff-line-num new_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

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<pre style="margin: 0;"> <span id="LC737" class="line" lang="python">            <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">rec_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

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<td class="diff-line-num new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

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<pre style="margin: 0;"> <span id="LC738" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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