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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/gfapy">Debian Med / gfapy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gfapy/-/commit/d6805080f3fc41ca93ecd5bcee5f40378d6012f7">d6805080</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2022-01-21T11:24:18+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.2+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gfapy/-/commit/4cf6c96d6c1d8ec5f302e1381506b95baba393d5">4cf6c96d</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2022-01-21T11:24:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.2.2+dfsg'
Update to upstream version '1.2.2+dfsg'
with Debian dir de047bab247683bfbfb41200aba5e83e69787671</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/gfapy/-/commit/f7f120aab1cd22f9256abb3b2acf206de1bb1feb">f7f120aa</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2022-01-21T11:24:48+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release
</pre>
</li>
</ul>
<h4>23 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#3251d7a8143ce2e789f0468513df8f285f842c3a">
CHANGES.txt
</a>
</li>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#df0576cbb783bc50b36e1efa3cbe0564a26c8295">
doc/conf.py
</a>
</li>
<li class="file-stats">
<a href="#bb19636c3d6967a1bdb42cdb1ec11a7167e8368e">
doc/tutorial/errors.rst
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<li class="file-stats">
<a href="#28b6a19acf1222e9f125898ae2881b0dd3004edd">
doc/tutorial/positional_fields.rst
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<li class="file-stats">
<a href="#db666852fce3c7bad6780e97b0d6b347f38541f5">
doc/tutorial/references.rst
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</li>
<li class="file-stats">
<a href="#1056ac3c43d31e282aaf394ca990a029ade39b93">
gfapy/graph_operations/topology.py
</a>
</li>
<li class="file-stats">
<a href="#d7b8f908654cbd38f33e00432962a8fb4e8d7dc9">
gfapy/line/edge/containment/containment.py
</a>
</li>
<li class="file-stats">
<a href="#ecce0442b981de5c3681aca7a47636641632d5b3">
gfapy/line/edge/containment/to_gfa2.py
</a>
</li>
<li class="file-stats">
<a href="#2934d2af9b19847ff0ec6ae53ebb0dcc67d09861">
gfapy/line/edge/gfa1/other.py
</a>
</li>
<li class="file-stats">
<a href="#5e7a1e5e1ef94bbafdf895c184671cf0d6a2061a">
gfapy/line/edge/gfa1/references.py
</a>
</li>
<li class="file-stats">
<a href="#a20c1c647aa709501847045c2ff07bfdee36326c">
gfapy/line/edge/gfa1/to_gfa2.py
</a>
</li>
<li class="file-stats">
<a href="#f10de5babd1799ced6f8b3f72100833185743303">
gfapy/line/edge/gfa2/to_gfa1.py
</a>
</li>
<li class="file-stats">
<a href="#a9dd602a4c3a3926ff3c2e80f0422075b07f8d38">
gfapy/line/edge/link/complement.py
</a>
</li>
<li class="file-stats">
<a href="#13d5296d08774e9a3659494d70d55431b7a5215a">
gfapy/line/edge/link/link.py
</a>
</li>
<li class="file-stats">
<a href="#2fb007b2bce9366794a352497520f2db86c8a94a">
gfapy/line/edge/link/to_gfa2.py
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
<li class="file-stats">
<a href="#b0e9b69c9ced5fca48aa2636c2276801544a248a">
tests/test_api_lines_finders.py
</a>
</li>
<li class="file-stats">
<a href="#cbae2fdca3d0bf0f5ca7ed531135d2c21eeefdc0">
tests/test_api_positionals.py
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</li>
<li class="file-stats">
<a href="#5648c6866c1dc931b050f2bf66db7b3c3924a6cc">
tests/test_unit_line_connection.py
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</li>
<li class="file-stats">
<a href="#f60e208a18c78673b90ea164b418d06519381af9">
tests/test_unit_line_dynamic_fields.py
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</li>
<li class="file-stats">
<a href="#cc934b6791576910b4db64fb3e751f2aaa4cf4a7">
tests/test_unit_line_equivalence.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="3251d7a8143ce2e789f0468513df8f285f842c3a">
<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#3251d7a8143ce2e789f0468513df8f285f842c3a"><strong>CHANGES.txt</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">== 1.2.2 ==</span>
</pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="new_line diff-line-num new" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">- remove to/from aliases for GFA1 containment/link fields</span>
</pre>
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<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> since `to` potentially clashes with a tag name</span>
</pre>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
</pre>
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1
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<td class="new_line diff-line-num" 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">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">== 1.2.1 ==</span>
</pre>
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2
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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
</pre>
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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">- fixed an issue with linear path merging (issue 21)</span>
</pre>
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<br>
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<li id="561b88e19de321ca62c7590bbb350765fb110905">
<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Gfapy</span>
</pre>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">~~~~~</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">|travis| |readthedocs| |latesttag| |license|<span class="idiff left right"> |requiresio|</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">|travis| |readthedocs| |latesttag| |license|</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">|bioconda| |pypi| |debian| |ubuntu|</span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gfapy (1.2.2+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org> Fri, 21 Jan 2022 11:24:22 +0100</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">gfapy (1.2.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream release.</span>
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<li id="df0576cbb783bc50b36e1efa3cbe0564a26c8295">
<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/conf.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,7 +66,7 @@ master_doc = 'index'</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Gfapy'</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2017--202<span class="idiff left right">1</span>, Giorgio Gonnella and others (see CONTRIBUTORS)'</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2017--202<span class="idiff left right">2</span>, Giorgio Gonnella and others (see CONTRIBUTORS)'</span></span>
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<pre style="margin: 0;"> <span id="LC70" 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;">'Giorgio Gonnella and others (see CONTRIBUTORS)'</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</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">@@ -76,7 +76,7 @@ author = 'Giorgio Gonnella and others (see CONTRIBUTORS)'</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The short X.Y version.</span></span>
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<pre style="margin: 0;"> <span id="LC77" 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;">'1.2'</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full version, including alpha/beta/rc tags.</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.2.<span class="idiff left right">1</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'1.2.<span class="idiff left right">2</span>'</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The language for content autogenerated by Sphinx. Refer to documentation</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for a list of supported languages.</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#bb19636c3d6967a1bdb42cdb1ec11a7167e8368e"><strong>doc/tutorial/errors.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +29,7 @@ all library errors.</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">| `InconsistencyError` | Pieces of information collide | length of sequence and LN tag |</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">| | with each other | do not match |</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">+-----------------------+-------------------------------+---------------------------------+</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">| `RuntimeError` | The user tried to do | editing from<span class="idiff left">/to</span> field in <span class="idiff right"> </span>|</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">| `RuntimeError` | The user tried to do | editing from<span class="idiff left right">_segment</span> field in |</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">| | something which is not | connected links |</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">| | allowed | |</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">+-----------------------+-------------------------------+---------------------------------+</span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#28b6a19acf1222e9f125898ae2881b0dd3004edd"><strong>doc/tutorial/positional_fields.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,8 @@ Field names</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">The field names are derived from the specification. Lower case versions</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">of the field names are used and spaces are substituted with underscores.</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">In some cases, the field names were changed, as they represent keywords</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">in common programming languages (``from``, ``send``).</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">in common programming languages or clash with potential tag names</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">(``from``, ``to``, ``send``).</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">The following tables shows the field names used in Gfapy, for each kind</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">of line. Headers have no positional fields. Comments and custom records</span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#db666852fce3c7bad6780e97b0d6b347f38541f5"><strong>doc/tutorial/references.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -60,9 +60,9 @@ GFA1</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">+---------------+-------------------+---------------------------+</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">| Record type | Fields | Type of reference |</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">+===============+===================+===========================+</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">| Link | from<span class="idiff left">, to </span> | Segment <span class="idiff right"> </span>|</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">| Link | from<span class="idiff left right">_segment, to_segment</span> | Segment |</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">+---------------+-------------------+---------------------------+</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">| Containment | from<span class="idiff left">, to </span> | Segment <span class="idiff right"> </span>|</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">| Containment | from<span class="idiff left right">_segment, to_segment</span> | Segment |</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">+---------------+-------------------+---------------------------+</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext">| Path | segment\_names, | [OrientedLine(Segment)] |</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext">+---------------+-------------------+---------------------------+</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -361,7 +361,8 @@ Renaming an element</td>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="plaintext">The name field of a line (e.g. segment ``name``/``sid``) is not a</span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="plaintext">reference and thus can be edited also in connected lines. When the name</span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="plaintext">of the line is changed, no manual editing of references (e.g. from/to</span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">of the line is changed, no manual editing of references (e.g.</span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">``from_segment``/``to_segment``</span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="plaintext">fields in links) is necessary, as all lines which refer to the line will</span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="plaintext">still refer to the same instance. The references to the instance in the</span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="plaintext">Gfa lines collections will be automatically updated. Also, the new name</span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#1056ac3c43d31e282aaf394ca990a029ade39b93"><strong>gfapy/graph_operations/topology.py</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -16,16 +16,16 @@ class Topology:</td>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">is_circular</span><span class="p">():</span></span>
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18
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" 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;">link</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from"</span><span class="p">).</span><span class="n" style="color: #333;">dovetails_of_end</span><span class="p">(</span>\</span>
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<pre style="margin: 0;">+<span id="LC19" 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;">link</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">).</span><span class="n" style="color: #333;">dovetails_of_end</span><span class="p">(</span>\</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">invert</span><span class="p">(</span><span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">from_end</span><span class="p">.</span><span class="n" style="color: #333;">end_type</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">-<span id="LC22" 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;">link</span><span class="p">.</span><span class="n" style="color: #333;">to</span><span class="p">.</span><span class="n" style="color: #333;">dovetails_of_end</span><span class="p">(</span><span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">invert</span><span class="p">(</span><span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">to_end</span><span class="p">.</span><span class="n" style="color: #333;">end_type</span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC22" 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;">link</span><span class="p">.</span><span class="n" style="color: #333;">to<span class="idiff left right">_segment</span></span><span class="p">.</span><span class="n" style="color: #333;">dovetails_of_end</span><span class="p">(</span><span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">invert</span><span class="p">(</span><span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">to_end</span><span class="p">.</span><span class="n" style="color: #333;">end_type</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">et</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"from"</span><span class="p">,</span> <span class="s" style="color: #d14;">"to"</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="n" style="color: #333;">et</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>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">visited</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="LC28" class="line" lang="python"> <span class="n" style="color: #333;">segend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">et</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"from"</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">to</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">segend</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from<span class="idiff left">_segment</span>"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">et</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"from"</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">to<span class="idiff right">_segment</span></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">visited</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">segend</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">visited</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">link</span><span class="p">.</span><span class="n" style="color: #333;">other_end</span><span class="p">(</span><span class="n" style="color: #333;">segend</span><span class="p">).</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">__traverse_component</span><span class="p">(</span><span class="n" style="color: #333;">segend</span><span class="p">,</span> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="n" style="color: #333;">et</span><span class="p">],</span> <span class="n" style="color: #333;">visited</span><span class="p">)</span></span>
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<li id="d7b8f908654cbd38f33e00432962a8fb4e8d7dc9">
<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#d7b8f908654cbd38f33e00432962a8fb4e8d7dc9"><strong>gfapy/line/edge/containment/containment.py</strong></a>
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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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,9 +17,8 @@ class Containment(Containment_ToGFA2, Pos, Canonical, Other,</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> Note:</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> from_segment and to_segment are used instead of from/to</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> as from is not a valid method name in Python. However, when not</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> used as method name (e.g. as argument of get()), from and to can</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> be used, as an alias has been defined.</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> as from is not a valid method name in Python and "to" alone</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> potentially clashes with the tag namespace.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> Note:</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> The from segment is considered the container, the to segment the contained</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">@@ -31,8 +30,6 @@ class Containment(Containment_ToGFA2, Pos, Canonical, Other,</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"to_orient"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pos"</span><span class="p">,</span> <span class="s" style="color: #d14;">"overlap"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">FIELD_ALIAS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"container"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"from_segment"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"contained"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"to_segment"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">"from"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"from_segment"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"to"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"to_segment"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">"container_orient"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"from_orient"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">"contained_orient"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"to_orient"</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">PREDEFINED_TAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"MQ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"NM"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">]</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#ecce0442b981de5c3681aca7a47636641632d5b3"><strong>gfapy/line/edge/containment/to_gfa2.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,7 @@ class ToGFA2:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_overlap</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">rpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overlap</span><span class="p">.</span><span class="n" style="color: #333;">length_on_reference</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lastpos_of</span><span class="p">(</span><span class="s" style="color: #d14;">"from"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">rpos</span> <span class="o" style="font-weight: 600;">==</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lastpos_of</span><span class="p">(</span><span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">rpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">LastPos</span><span class="p">(</span><span class="n" style="color: #333;">rpos</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">rpos</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC27" 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">@@ -30,4 +30,4 @@ class ToGFA2:</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="s" style="color: #d14;"> GFA2 positions of the alignment on the **to** segment</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lastpos_of</span><span class="p">(</span><span class="s" style="color: #d14;">"to"</span><span class="p">)]</span></span></pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lastpos_of</span><span class="p">(</span><span class="s" style="color: #d14;">"to<span class="idiff left right">_segment</span>"</span><span class="p">)]</span></span></pre>
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<li id="2934d2af9b19847ff0ec6ae53ebb0dcc67d09861">
<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#2934d2af9b19847ff0ec6ae53ebb0dcc67d09861"><strong>gfapy/line/edge/gfa1/other.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,7 +52,7 @@ class Other:</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">segment_name</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;">segment</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">segment_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_segment</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to<span class="idiff left right">_segment</span></span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">segment_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to_segment</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_segment</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">tolerant</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#5e7a1e5e1ef94bbafdf895c184671cf0d6a2061a"><strong>gfapy/line/edge/gfa1/references.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ import gfapy</td>
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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="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">References</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_initialize_references</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="LC5" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"from<span class="idiff left">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"to</span>"</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">"from<span class="idiff left">_segment"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"to_segment</span>"</span><span class="p">]:</span></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gfa</span><span class="p">.</span><span class="n" style="color: #333;">segment</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</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="LC8" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gfa</span><span class="p">.</span><span class="n" style="color: #333;">_segments_first_order</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">@@ -12,13 +12,14 @@ class References:</td>
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<pre style="margin: 0;"> <span id="LC12" 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;">"gfa1"</span><span class="p">,</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">virtual</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="LC14" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">connect</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gfa</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_set_existing_field</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="s" style="color: #d14;"><span class="idiff right">"_segment"</span></span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">set_reference</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="LC15" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_set_existing_field</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">set_reference</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="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">record_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"L"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">et</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_end</span><span class="p">.</span><span class="n" style="color: #333;">end_type</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"from"</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to_end</span><span class="p">.</span><span class="n" style="color: #333;">end_type</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">et</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_end</span><span class="p">.</span><span class="n" style="color: #333;">end_type</span> \</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"from_segment"</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to_end</span><span class="p">.</span><span class="n" style="color: #333;">end_type</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"dovetails_{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">et</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC20" 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="LC20" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left">"edges_to_contained"</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"from"</span></span><span class="p"><span class="idiff right">)</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"edges_to_containers"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">"edges_to_contained"</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">d</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"from_segment"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span>\</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="idiff left right"> </span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"edges_to_containers"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">_add_reference</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_import_field_references</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">previous</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#a20c1c647aa709501847045c2ff07bfdee36326c"><strong>gfapy/line/edge/gfa1/to_gfa2.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -83,7 +83,7 @@ class ToGFA2:</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">length</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">length</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="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">"Length of segment {} unknown"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">"Length of segment {} unknown"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to<span class="idiff left right">_segment</span></span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">LastPos</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_overlap</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#f10de5babd1799ced6f8b3f72100833185743303"><strong>gfapy/line/edge/gfa2/to_gfa1.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,7 +96,8 @@ class ToGFA1:</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">from_orient</span><span class="p">.</span><span class="n" style="color: #333;">setter</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_orient</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;">"""Set the orientation of the field which will be returned by calling from</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="s" style="color: #d14;">"""Set the orientation of the field which will be returned by calling</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> from_segment</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"><span class="s" style="color: #d14;"> value (str): one of ["+", "-"]</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">@@ -119,7 +120,7 @@ class ToGFA1:</td>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">to_segment</span><span class="p">.</span><span class="n" style="color: #333;">setter</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_segment</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">"""Set the field which will be returned by calling ``to``.</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">"""Set the field which will be returned by calling ``to<span class="idiff left right">_segment</span>``.</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> value (str or gfapy.line.segment.GFA2)</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">@@ -142,7 +143,8 @@ class ToGFA1:</td>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">to_orient</span><span class="p">.</span><span class="n" style="color: #333;">setter</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">to_orient</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"""Set the orientation of the field which will be returned by calling ``to``.</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">"""Set the orientation of the field which will be returned by calling</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;"> ``to_segment``.</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> Parameters:</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> value (str): one of ["+", "-"]</span></span>
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<li id="a9dd602a4c3a3926ff3c2e80f0422075b07f8d38">
<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#a9dd602a4c3a3926ff3c2e80f0422075b07f8d38"><strong>gfapy/line/edge/link/complement.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,7 @@ class Complement:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> gfapy.line.edge.Link: The inverted link.</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">l</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">clone</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">from_segment</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">from_segment</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to<span class="idiff left right">_segment</span></span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">from_orient</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">invert</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to_orient</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">to_segment</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_segment</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">to_orient</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">invert</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_orient</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#13d5296d08774e9a3659494d70d55431b7a5215a"><strong>gfapy/line/edge/link/link.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,16 +19,14 @@ class Link(Link_ToGFA2, GFA1_ToGFA2, Link_References, Equivalence, Complement, \</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> Note:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> from_segment and to_segment are used instead of from/to</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> as from is not a valid method name in Python. However, when not</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> used as method name (e.g. as argument of get()), from and to can</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> be used, as an alias has been defined.</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> as from is not a valid method name in Python and "to" alone</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> potentially clashes with the tag namespace.</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">RECORD_TYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"L"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">POSFIELDS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"from_segment"</span><span class="p">,</span> <span class="s" style="color: #d14;">"from_orient"</span><span class="p">,</span> <span class="s" style="color: #d14;">"to_segment"</span><span class="p">,</span> <span class="s" style="color: #d14;">"to_orient"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">"overlap"</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">PREDEFINED_TAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"MQ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"NM"</span><span class="p">,</span> <span class="s" style="color: #d14;">"RC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"FC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"KC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ID"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">FIELD_ALIAS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"from"</span><span class="p">:</span> <span class="s" style="color: #d14;">"from_segment"</span><span class="p">,</span> <span class="s" style="color: #d14;">"to"</span><span class="p">:</span> <span class="s" style="color: #d14;">"to_segment"</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">DATATYPE</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">"from_segment"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"segment_name_gfa1"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">"from_orient"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"orientation"</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#2fb007b2bce9366794a352497520f2db86c8a94a"><strong>gfapy/line/edge/link/to_gfa2.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ class ToGFA2:</td>
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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="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_coords</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="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">"""GFA2 positions of the alignment on the from segment.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"> <span class="s" style="color: #d14;">"""GFA2 positions of the alignment on the <span class="idiff left">**</span>from<span class="idiff right">**</span> segment.</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;"> Returns</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;"> -------</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">@@ -20,7 +20,7 @@ class ToGFA2:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_check_overlap</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_orient</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="LC23" class="line" lang="python"> <span class="n" style="color: #333;">from_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lastpos_of</span><span class="p">(</span><span class="s" style="color: #d14;">"from"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">from_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lastpos_of</span><span class="p">(</span><span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">from_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overlap</span><span class="p">.</span><span class="n" style="color: #333;">length_on_reference</span><span class="p">(),</span> <span class="n" style="color: #333;">from_l</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC25" 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="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overlap</span><span class="p">.</span><span class="n" style="color: #333;">length_on_reference</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">@@ -32,5 +32,5 @@ class ToGFA2:</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">to_orient</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="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overlap</span><span class="p">.</span><span class="n" style="color: #333;">length_on_query</span><span class="p">()]</span></span>
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<pre style="margin: 0;"> <span id="LC34" 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="LC35" class="line" lang="python"> <span class="n" style="color: #333;">to_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lastpos_of</span><span class="p">(</span><span class="s" style="color: #d14;">"to"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">to_l</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_lastpos_of</span><span class="p">(</span><span class="s" style="color: #d14;">"to<span class="idiff left right">_segment</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">to_l</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">overlap</span><span class="p">.</span><span class="n" style="color: #333;">length_on_query</span><span class="p">(),</span> <span class="n" style="color: #333;">to_l</span><span class="p">]</span></span></pre>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ if not sys.version_info[0] == 3:</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"Sorry, only Python 3 is supported"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'gfapy'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC12" 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;">'1.2.<span class="idiff left right">1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC12" 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;">'1.2.<span class="idiff left right">2</span>'</span><span class="p">,</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Library for handling data in the GFA1 and GFA2 formats'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">readme</span><span class="p">(),</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/ggonnella/gfapy'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#b0e9b69c9ced5fca48aa2636c2276801544a248a"><strong>tests/test_api_lines_finders.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="112" style="width: 35px; color: rgba(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">@@ -112,20 +112,22 @@ class TestAPILinesFinders(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="s" style="color: #d14;">"name"</span><span class="p">:</span><span class="s" style="color: #d14;">"1"</span><span class="p">}))</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># search links</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">:</span><span class="mi" style="color: #099;">5</span><span class="p">],</span> <span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"record_type"</span><span class="p">:</span><span class="s" style="color: #d14;">"L"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"from"</span><span class="p">:</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">:</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"from_orient"</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="LC117" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># search containments</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</span><span class="p">[</span><span class="mi" style="color: #099;">6</span><span class="p">:</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> <span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"record_type"</span><span class="p">:</span><span class="s" style="color: #d14;">"C"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"from"</span><span class="p">:</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">:</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">"pos"</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="LC121" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># search paths</span></span>
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">:</span><span class="mi" style="color: #099;">8</span><span class="p">],</span> <span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"record_type"</span><span class="p">:</span><span class="s" style="color: #d14;">"P"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="s" style="color: #d14;">"segment_names"</span><span class="p">:</span><span class="s" style="color: #d14;">"1+,2+"</span><span class="p">}))</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># no record type specified</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"name"</span><span class="p">:</span><span class="s" style="color: #d14;">"1"</span><span class="p">}))</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">:</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> <span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"from"</span><span class="p">:</span><span class="s" style="color: #d14;">"1"</span><span class="p">}))</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">:</span><span class="mi" style="color: #099;">7</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"from_segment"</span><span class="p">:</span><span class="s" style="color: #d14;">"1"</span><span class="p">}))</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># reference as value</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">:</span><span class="mi" style="color: #099;">7</span><span class="p">],</span> <span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"from"</span><span class="p">:</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</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="LC129" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">:</span><span class="mi" style="color: #099;">7</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;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"from_segment"</span><span class="p">:</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1</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="LC131" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># placeholder is equal to any value</span></span>
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130
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">l_gfa1_a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">3</span><span class="p">]),</span></span>
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131
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">TestAPILinesFinders</span><span class="p">.</span><span class="n" style="color: #333;">gfa1</span><span class="p">.</span><span class="n" style="color: #333;">select</span><span class="p">({</span><span class="s" style="color: #d14;">"sequence"</span><span class="p">:</span><span class="s" style="color: #d14;">"ACC"</span><span class="p">})]))</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#cbae2fdca3d0bf0f5ca7ed531135d2c21eeefdc0"><strong>tests/test_api_positionals.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="86" style="width: 35px; color: rgba(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">@@ -86,7 +86,6 @@ class TestAPIPositionals(unittest.TestCase):</td>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="s" style="color: #d14;">"S1"</span><span class="p">:{</span><span class="s" style="color: #d14;">"name"</span><span class="p">:</span><span class="s" style="color: #d14;">"sid"</span><span class="p">},</span> <span class="s" style="color: #d14;">"P"</span><span class="p">:{</span><span class="s" style="color: #d14;">"path_name"</span><span class="p">:</span><span class="s" style="color: #d14;">"name"</span><span class="p">},</span></span>
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87
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"S2"</span><span class="p">:{</span><span class="s" style="color: #d14;">"sid"</span><span class="p">:</span><span class="s" style="color: #d14;">"name"</span><span class="p">},</span> <span class="s" style="color: #d14;">"E"</span><span class="p">:{</span><span class="s" style="color: #d14;">"eid"</span><span class="p">:</span><span class="s" style="color: #d14;">"name"</span><span class="p">},</span> <span class="s" style="color: #d14;">"G"</span><span class="p">:{</span><span class="s" style="color: #d14;">"gid"</span><span class="p">:</span><span class="s" style="color: #d14;">"name"</span><span class="p">},</span></span>
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88
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="s" style="color: #d14;">"U"</span><span class="p">:{</span><span class="s" style="color: #d14;">"pid"</span><span class="p">:</span><span class="s" style="color: #d14;">"name"</span><span class="p">},</span> <span class="s" style="color: #d14;">"O"</span><span class="p">:{</span><span class="s" style="color: #d14;">"pid"</span><span class="p">:</span><span class="s" style="color: #d14;">"name"</span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">"L"</span><span class="p">:{</span><span class="s" style="color: #d14;">"from_segment"</span><span class="p">:</span> <span class="s" style="color: #d14;">"from"</span><span class="p">,</span> <span class="s" style="color: #d14;">"to_segment"</span><span class="p">:</span> <span class="s" style="color: #d14;">"to"</span><span class="p">},</span></span>
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90
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">"C"</span><span class="p">:{</span><span class="s" style="color: #d14;">"from_segment"</span><span class="p">:</span><span class="s" style="color: #d14;">"container"</span><span class="p">,</span> <span class="s" style="color: #d14;">"from_orient"</span><span class="p">:</span><span class="s" style="color: #d14;">"container_orient"</span><span class="p">,</span></span>
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91
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">"to_segment"</span><span class="p">:</span><span class="s" style="color: #d14;">"contained"</span><span class="p">,</span> <span class="s" style="color: #d14;">"to_orient"</span><span class="p">:</span><span class="s" style="color: #d14;">"contained_orient"</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#5648c6866c1dc931b050f2bf66db7b3c3924a6cc"><strong>tests/test_unit_line_connection.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,10 +62,10 @@ class TestUnitLineConnection(unittest.TestCase):</td>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">g</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">Gfa</span><span class="p">()</span></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">g</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">g</span><span class="p">.</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>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">s1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">s1</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;">l</span><span class="p">.</span><span class="n" style="color: #333;">disconnect</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">s1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from"</span><span class="p">))</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">s1</span><span class="p">)</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">))</span></span>
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69
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_disconnect_disconnects_depent_lines</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">s1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">Line</span><span class="p">(</span><span class="s" style="color: #d14;">"S</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">1</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">ACCAT"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#f60e208a18c78673b90ea164b418d06519381af9"><strong>tests/test_unit_line_dynamic_fields.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,8 +8,8 @@ class TestUnitLineDynamicFields(unittest.TestCase):</td>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># record_type</span></span>
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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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="s" style="color: #d14;">"record_type"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># reqfields</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="s" style="color: #d14;">"from"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIsInstance</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">.</span><span class="n" style="color: #333;">__getattribute__</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="s" style="color: #d14;">"from"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertIsInstance</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">.</span><span class="n" style="color: #333;">__getattribute__</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="s" style="color: #d14;">"from<span class="idiff left right">_segment</span>"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">gfapy</span><span class="p">.</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">common</span><span class="p">.</span><span class="n" style="color: #333;">dynamic_fields</span><span class="p">.</span><span class="n" style="color: #333;">DynamicField</span><span class="p">)</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># predefined tags</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="s" style="color: #d14;">"KC"</span><span class="p">))</span></span>
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<a href="https://salsa.debian.org/med-team/gfapy/-/compare/e4735e65d3ebdc0840bc14fdd63b1a2991e99ba4...f7f120aab1cd22f9256abb3b2acf206de1bb1feb#cc934b6791576910b4db64fb3e751f2aaa4cf4a7"><strong>tests/test_unit_line_equivalence.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -94,7 +94,8 @@ class TestUnitLineEquivalence(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">_has_eql_fields</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">clone</span><span class="p">()))</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># positional field difference</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_has_eql_fields</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">l_from</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_has_eql_fields</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">l_from</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"from"</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">.</span><span class="n" style="color: #333;">_has_eql_fields</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">l_from</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"from_segment"</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># positional field difference: name alias</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">_has_eql_fields</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">e_name</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">_has_eql_fields</span><span class="p">(</span><span class="n" style="color: #333;">TestUnitLineEquivalence</span><span class="p">.</span><span class="n" style="color: #333;">e_name</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"eid"</span><span class="p">]))</span></span>
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