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<h3>
Diane Trout pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/htseq">Debian Med / htseq</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5">c1d63d39</a></strong>
<div>
<span>by Diane Trout</span>
<i>at 2020-03-03T21:27:49-08:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.3</pre>
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<h4>12 changed files:</h4>
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<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
</a>
</li>
<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#b33892fbddeffc3368077b4904ad0b3d562a7312">
VERSION
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<li class="file-stats">
<a href="#e860acebd843648e033662eac1a1d0620e7dc6d7">
python2/HTSeq/_version.py
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<li class="file-stats">
<a href="#48d1d1c7549dfe506a0f860bd23b62c026693628">
python2/HTSeq/scripts/count.py
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<li class="file-stats">
<a href="#32f4d600d961590aec144e88b0b5d57f65c70a2a">
python2/src/StepVector.py
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<li class="file-stats">
<a href="#5f8bf900fa412d21d637ab1c77a631a00551279d">
python3/HTSeq/__init__.py
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<li class="file-stats">
<a href="#6ef6a1ad5db69d445d8356610d7f345cb83afe6a">
python3/HTSeq/_version.py
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<li class="file-stats">
<a href="#e5673f04e9098a0bf1f4da138b373b347616dfe0">
python3/HTSeq/scripts/count.py
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<li class="file-stats">
<a href="#a8dcb9b2f363c919df57f4b82171ac5afa3861eb">
python3/src/HTSeq/_HTSeq.pyx
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<li class="file-stats">
<a href="#8738b4507555e0fff7576c4c11dc20077120c658">
python3/src/StepVector.i
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 2.1</span>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: HTSeq</span>
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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 0.11.<span class="idiff left right">2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.11.<span class="idiff left right">3</span></span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://github.com/simon-anders/htseq</span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Simon Anders</span>
</pre>
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<br>
</li>
<li id="561b88e19de321ca62c7590bbb350765fb110905">
<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,7 @@ Requirements</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">To use ``HTSeq`` you will need:</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">- ``Python 2.7``\ or ``Python >= 3.<span class="idiff left right">4`` (tested up to 3.6</span>)</span>
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<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">- ``Python 2.7``\ or ``Python >= 3.<span class="idiff left right">5`` (tested up to 3.8</span>)</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">- ``numpy``</span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">- ``pysam >= 0.9.0``</span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<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 @@ To run the ``htseq-qa`` script, you will also need:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">To **build** the package from source, you will **also** need:</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">- ``Cython``</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">- ``Cython<span class="idiff left right"> >=0.29.5</span>``</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">- ``SWIG >=3.0.8``</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">The latter packages are not required if you have already built ``HTSeq``</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">@@ -125,3 +125,8 @@ http://htseq.readthedocs.io</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext"> :target: https://travis-ci.org/simon-anders/htseq</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext">.. |Documentation Status| image:: https://camo.githubusercontent.com/d3d354c898588bb4b62f559a3a30fa6b6364dfc3/68747470733a2f2f72656164746865646f63732e6f72672f70726f6a656374732f68747365712f62616467652f3f76657273696f6e3d6d6173746572</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"> :target: http://htseq.readthedocs.io</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">Authors</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">~~~~~~~~~~~~~</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">Simon Anders and Wolfgang Huber are the original authors. Since 2016, ``HTSeq`` is maintained by Fabio Zanini (http://fabilab.org).</span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#b33892fbddeffc3368077b4904ad0b3d562a7312"><strong>VERSION</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">0.11.<span class="idiff left right">2</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">0.11.<span class="idiff left right">3</span></span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#e860acebd843648e033662eac1a1d0620e7dc6d7"><strong>python2/HTSeq/_version.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.11.2"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.11.3"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#48d1d1c7549dfe506a0f860bd23b62c026693628"><strong>python2/HTSeq/scripts/count.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -44,10 +44,19 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optional_fields</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="s" style="color: #d14;">'XF'</span><span class="p">,</span> <span class="n" style="color: #333;">assignment</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">samoutfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sam_line</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"sam"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">SAM_or_BAM_Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SAM_Reader</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">samname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SAM'</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">samtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bam"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">SAM_or_BAM_Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BAM_Reader</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">samname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'BAM'</span></span>
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<pre style="margin: 0;">+<span id="LC53" 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="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown input format </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s specified."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">samtype</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samouts</span> <span class="o" style="font-weight: 600;">!=</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;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">samouts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sam_filenames</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">'Select the same number of <span class="idiff left right">SAM input and output files'</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">'Select the same number of <span class="idiff left">{:} input and output files'</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">samname</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Try to open samout files early in case any of them has issues</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">samout</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samouts</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">samout</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -105,13 +114,6 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"Warning: No features of type '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' found.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">feature_type</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"sam"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">SAM_or_BAM_Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SAM_Reader</span></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">samtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bam"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">SAM_or_BAM_Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BAM_Reader</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" 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="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown input format </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s specified."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">samtype</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">counts_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">empty_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">ambiguous_all</span> <span class="o" style="font-weight: 600;">=</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">@@ -143,7 +145,8 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">read_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when reading beginning of SAM/BAM file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when reading beginning of {:} file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">samname</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</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">@@ -197,8 +200,8 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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197
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">write_to_samout</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="s" style="color: #d14;">"__too_low_aQual"</span><span class="p">,</span> <span class="n" style="color: #333;">samoutfile</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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199
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stranded</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"reverse"</span><span class="p">:</span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">iv_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ref_iv</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">co</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">==</span></span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left">"M"</span></span><span class="idiff right"> </span><span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">iv_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ref_iv</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">co</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">com</span></span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC205" 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="LC206" class="line" lang="python"> <span class="n" style="color: #333;">iv_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">invert_strand</span><span class="p">(</span><span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ref_iv</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">co</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">co</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">type</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">com</span> <span class="ow" style="font-weight: 600;">and</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">@@ -305,14 +308,14 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when processing <span class="idiff left right">SAM</span> input (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s):</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">read_seq_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_line_number_string</span></span><span class="p"><span class="idiff right">(</span>))</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when processing </span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span> input (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s):</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">samname</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">read_seq_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_line_number_string</span></span><span class="p"><span class="idiff right">()</span>))</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC315" 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;">quiet</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d <span class="idiff left right">SAM</span> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"alignments "</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"alignment pairs"</span><span class="p">))</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d </span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">samname</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"alignments "</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"alignment pairs"</span><span class="p">))</span></span>
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316
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samoutfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</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">@@ -351,7 +354,8 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"> <span class="s" style="color: #d14;">"the number of reads mapping to it. See "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="s" style="color: #d14;">"http://htseq.readthedocs.io/en/master/count.html for details."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">epilog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Written by Simon Anders (sanders@fs.tum.de), "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="s" style="color: #d14;">"European Molecular Biology Laboratory (EMBL). (c) 2010. "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="s" style="color: #d14;">"European Molecular Biology Laboratory (EMBL) and Fabio Zanini "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="s" style="color: #d14;">"(fabio.zanini@stanford.edu), Stanford University. (c) 2010-2019. "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="s" style="color: #d14;">"Released under the terms of the GNU General Public License v3. "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"> <span class="s" style="color: #d14;">"Part of the 'HTSeq' framework, version </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__version__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC361" 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">@@ -362,12 +366,12 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"> <span class="s" style="color: #d14;">"featuresfilename"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Path to the file containing the features"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Path to the <span class="idiff left right">GTF </span>file containing the features"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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368
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--format"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"samtype"</span><span class="p">,</span></span>
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369
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"sam"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bam"</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"sam"</span><span class="p">,</span></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">t</span>ype of <alignment_file> data, either 'sam' or 'bam' (default: sam)"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">T</span>ype of <alignment_file> data, either 'sam' or 'bam' (default: sam)"</span><span class="p">)</span></span>
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371
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375
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"></span>
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"> <span class="s" style="color: #d14;">"-r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--order"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"order"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -387,38 +391,43 @@ def main():</td>
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--stranded"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"stranded"</span><span class="p">,</span></span>
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"yes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"no"</span><span class="p">,</span> <span class="s" style="color: #d14;">"reverse"</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"yes"</span><span class="p">,</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">w</span>hether the data is from a strand-specific assay. Specify 'yes', "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">W</span>hether the data is from a strand-specific assay. Specify 'yes', "</span> <span class="o" style="font-weight: 600;">+</span></span>
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"> <span class="s" style="color: #d14;">"'no', or 'reverse' (default: yes). "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="s" style="color: #d14;">"'reverse' means 'yes' with reversed strand interpretation"</span><span class="p">)</span></span>
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"></span>
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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395
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399
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--minaqual"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"minaqual"</span><span class="p">,</span></span>
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396
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"skip all reads with alignment quality lower than the given "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="s" style="color: #d14;">"minimum value (default: 10)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Skip all reads with MAPQ alignment quality lower than the given "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="s" style="color: #d14;">"minimum value (default: 10). MAPQ is the 5th column of a SAM/BAM "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="s" style="color: #d14;">"file and its usage depends on the software used to map the reads."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python"> <span class="s" style="color: #d14;">"-t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--type"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"featuretype"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"exon"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"feature type (3rd column in GFF file) to be used, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"exon"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Feature type (3rd column in GTF file) to be used, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="s" style="color: #d14;">"all features of other type are ignored (default, suitable for Ensembl "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="s" style="color: #d14;">"GTF files: exon)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--idattr"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"idattr"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gene_id"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GFF attribute to be used as feature ID (default, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gene_id"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GTF attribute to be used as feature ID (default, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="s" style="color: #d14;">"suitable for Ensembl GTF files: gene_id)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="s" style="color: #d14;">"--additional-attr"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'append'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Additional feature attributes (default: none, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Additional feature attributes (default: none, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="s" style="color: #d14;">"suitable for Ensembl GTF files: gene_name). Use multiple times "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"> <span class="s" style="color: #d14;">"for each different attribute"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--mode"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"mode"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"union"</span><span class="p">,</span> <span class="s" style="color: #d14;">"intersection-strict"</span><span class="p">,</span> <span class="s" style="color: #d14;">"intersection-nonempty"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"union"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"mode to handle reads overlapping more than one feature "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"union"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Mode to handle reads overlapping more than one feature "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"> <span class="s" style="color: #d14;">"(choices: union, intersection-strict, intersection-nonempty; default: union)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</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">@@ -440,16 +449,25 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--samout"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"samouts"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'append'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"write out all SAM alignment records into "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Write out all SAM alignment records into "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"> <span class="s" style="color: #d14;">"SAM files (one per input file needed), annotating each line "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"> <span class="s" style="color: #d14;">"with its feature assignment (as an optional field with tag 'XF')"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--quiet"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"quiet"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC449" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"suppress progress report"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># and warnings" )</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Suppress progress report"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># and warnings" )</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"> <span class="s" style="color: #d14;">"--version"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show software version and exit'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__version__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">showwarning</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">my_showwarning</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">count_reads_in_features</span><span class="p">(</span></span>
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<li id="32f4d600d961590aec144e88b0b5d57f65c70a2a">
<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#32f4d600d961590aec144e88b0b5d57f65c70a2a"><strong>python2/src/StepVector.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This file was automatically generated by SWIG (http://www.swig.org).</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Version <span class="idiff left right">3.0.12</span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Version <span class="idiff left right">4.0.1</span></span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Do not make changes to this file unless you know what you are doing--modify</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># the SWIG interface file instead.</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sys</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">version_info</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">_swig_python_version_info</span></span>
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8
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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="n" style="color: #333;">_swig_python_version_info</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">7</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="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">swig_import_helper</span><span class="p">():</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">importlib</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">pkg</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__name__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rpartition</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">mname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">((</span><span class="n" style="color: #333;">pkg</span><span class="p">,</span> <span class="s" style="color: #d14;">'_StepVector'</span><span class="p">))</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</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="k" style="font-weight: 600;">try</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">importlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="n" style="color: #333;">mname</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">importlib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'_StepVector'</span><span class="p">)</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">swig_import_helper</span><span class="p">()</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">swig_import_helper</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">_swig_python_version_info</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">swig_import_helper</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os.path</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dirname</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">imp</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">fp</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">pathname</span><span class="p">,</span> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">imp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find_module</span><span class="p">(</span><span class="s" style="color: #d14;">'_StepVector'</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</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;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">_StepVector</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">_mod</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">imp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_module</span><span class="p">(</span><span class="s" style="color: #d14;">'_StepVector'</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">pathname</span><span class="p">,</span> <span class="n" style="color: #333;">description</span><span class="p">)</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>
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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="n" style="color: #333;">fp</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</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;">return</span> <span class="n" style="color: #333;">_mod</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">swig_import_helper</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;">del</span> <span class="n" style="color: #333;">swig_import_helper</span></span>
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8
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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="n" style="color: #333;">_swig_python_version_info</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">):</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">(</span><span class="s" style="color: #d14;">"Python 2.7 or later required"</span><span class="p">)</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Import the low-level C/C++ module</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__package__</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"."</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">__name__</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="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">_StepVector</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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38
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">_StepVector</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">_swig_python_version_info</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">_swig_property</span> <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="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">NameError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span> <span class="c1" style="color: #998; font-style: italic;"># Python < 2.2 doesn't have 'property'.</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">builtins</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">__builtin__</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">__builtin__</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_swig_setattr_nondynamic</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">class_type</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">static</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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;">"thisown"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</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="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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;">"this"</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;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'SwigPyObject'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</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>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">class_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__swig_setmethods__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">method</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="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">static</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"> <span class="nb" style="color: #0086b3;">object</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__setattr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC22" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_swig_repr</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="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">strthis</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"proxy of "</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__repr__</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;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</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;">strthis</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s; </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s >"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__module__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="n" style="color: #333;">strthis</span><span class="p">,)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_swig_setattr_nondynamic_instance_variable</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_instance_attr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"thisown"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</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="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"this"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">),</span> <span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC38" 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="LC65" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__dict__</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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<pre style="margin: 0;">-<span id="LC66" 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="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">(</span><span class="s" style="color: #d14;">"You cannot add attributes to </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">(</span><span class="s" style="color: #d14;">"You cannot add instance attributes to </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">set_instance_attr</span></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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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;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">class_type</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_swig_setattr_nondynamic</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">class_type</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</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="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_swig_setattr_nondynamic_class_variable</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_class_attr</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">(</span><span class="s" style="color: #d14;">"You cannot add class attributes to </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">cls</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">set_class_attr</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">class_type</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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;">"thisown"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">method</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">class_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__swig_getmethods__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">method</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">method</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="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">(</span><span class="s" style="color: #d14;">"'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' object has no attribute '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">class_type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_swig_add_metaclass</span><span class="p">(</span><span class="n" style="color: #333;">metaclass</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">"""Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">wrapper</span><span class="p">(</span><span class="n" style="color: #333;">cls</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="n" style="color: #333;">metaclass</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__bases__</span><span class="p">,</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__dict__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">wrapper</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_swig_repr</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="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">strthis</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"proxy of "</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__repr__</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">strthis</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"<</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s; </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s >"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__module__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="n" style="color: #333;">strthis</span><span class="p">,)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_SwigNonDynamicMeta</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="s" style="color: #d14;">"""Meta class to enforce nondynamic attributes (no new attributes) for a class"""</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_setattr_nondynamic_class_variable</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__setattr__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">_object</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">object</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">_newclass</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_object</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">_newclass</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Pair_int_float</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_Pair_int_float</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC101" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_Pair_int_float</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="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Pair_int_float</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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103
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"first"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_first_set</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"first"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_first_get</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_first_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_first_set</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"second"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_second_set</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"second"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_second_get</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_second_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_second_set</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="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_first_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_first_set</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="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_second_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_second_set</span><span class="p">)</span></span>
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112
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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113
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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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__Pair_int_float</span><span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__Pair_int_float</span><span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">))</span></span>
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119
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__Pair_int_float</span></span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">__del__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"><span class="n" style="color: #333;">_Pair_int_float_swigregister</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_swigregister</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"><span class="n" style="color: #333;">_Pair_int_float_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_Pair_int_float</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_Iterator_float</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_Iterator_float</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC127" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_Iterator_float</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="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Register _Pair_int_float in _StepVector:</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_float_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_Pair_int_float</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_Iterator_float</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_Iterator_float</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">)</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_float_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_Iterator_float</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">next</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="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_float_next</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -141,85 +87,58 @@ class _StepVector_Iterator_float(_object):</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</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="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_float___iter__</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="LC89" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__StepVector_Iterator_float</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">__del__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_Iterator_float_swigregister</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_float_swigregister</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_Iterator_float_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_Iterator_float</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_float</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_float</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC151" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_float</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="LC90" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Register _StepVector_Iterator_float in _StepVector:</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_float_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_Iterator_float</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_float</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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153
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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154
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>
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155
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98
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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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_float</span><span class="p">()</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_float</span><span class="p">())</span></span>
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161
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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164
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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167
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"></span>
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168
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_all_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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169
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_get_all_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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170
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">):</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">):</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">)</span></span>
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173
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>
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174
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">num_values</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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175
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_num_values</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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176
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__StepVector_float</span></span>
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">__del__</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span></span>
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"><span class="n" style="color: #333;"><span class="idiff left">_StepVector_float_swigregister</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_StepVector</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_StepVector_float_swigregister</span></span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_float_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_float</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"></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;"><span class="idiff left right"># Register _StepVector_float in _StepVector:</span></span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_StepVector</span>_float_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_float</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"><span class="n" style="color: #333;">cvar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_float</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_min_index</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_float</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_float_max_index</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Pair_int_int</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_Pair_int_int</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC187" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_Pair_int_int</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="LC123" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Pair_int_int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"first"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_first_set</span></span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"first"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_first_get</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_first_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_first_set</span><span class="p">)</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"second"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_second_set</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"second"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_second_get</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_second_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_second_set</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_first_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_first_set</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;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_second_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_second_set</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__Pair_int_int</span><span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">)</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__Pair_int_int</span><span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">))</span></span>
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205
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__Pair_int_int</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">__del__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"><span class="n" style="color: #333;">_Pair_int_int_swigregister</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_swigregister</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"><span class="n" style="color: #333;">_Pair_int_int_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_Pair_int_int</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_Iterator_int</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_Iterator_int</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC213" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_Iterator_int</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="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Register _Pair_int_int in _StepVector:</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_int_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_Pair_int_int</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_Iterator_int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_Iterator_int</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_int_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_Iterator_int</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">next</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="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_int_next</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -227,84 +146,57 @@ class _StepVector_Iterator_int(_object):</td>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</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="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_int___iter__</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="LC148" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__StepVector_Iterator_int</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">__del__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_Iterator_int_swigregister</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_int_swigregister</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_Iterator_int_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_Iterator_int</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_int</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_int</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC237" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_int</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="LC149" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Register _StepVector_Iterator_int in _StepVector:</span></span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_int_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_Iterator_int</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_int</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_int</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC162" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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253
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_all_values_pystyle</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="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_get_all_values_pystyle</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="LC168" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">)</span></span>
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259
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"></span>
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">num_values</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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261
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_num_values</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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262
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__StepVector_int</span></span>
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">__del__</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"><span class="n" style="color: #333;"><span class="idiff left">_StepVector_int_swigregister</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_StepVector</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_StepVector_int_swigregister</span></span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_int_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_int</span><span class="p">)</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># Register _StepVector_int in _StepVector:</span></span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_StepVector</span>_int_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_int</span><span class="p">)</span></span>
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266
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_int</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_min_index</span></span>
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267
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_int</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_int_max_index</span></span>
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268
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Pair_int_bool</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_Pair_int_bool</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC272" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_Pair_int_bool</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="LC181" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Pair_int_bool</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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274
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"first"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_first_set</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"first"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_first_get</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_first_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_first_set</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"second"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_second_set</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"second"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_second_get</span></span>
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_second_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_second_set</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_first_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_first_set</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_second_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_second_set</span><span class="p">)</span></span>
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"></span>
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284
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__Pair_int_bool</span><span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__Pair_int_bool</span><span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__Pair_int_bool</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">__del__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"><span class="n" style="color: #333;">_Pair_int_bool_swigregister</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_swigregister</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"><span class="n" style="color: #333;">_Pair_int_bool_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_Pair_int_bool</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_Iterator_bool</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_Iterator_bool</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC298" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_Iterator_bool</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="LC190" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Register _Pair_int_bool in _StepVector:</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_bool_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_Pair_int_bool</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_Iterator_bool</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"></span>
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302
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">):</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_Iterator_bool</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">)</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_bool_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_Iterator_bool</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">))</span></span>
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">next</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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310
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_bool_next</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -312,84 +204,57 @@ class _StepVector_Iterator_bool(_object):</td>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</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="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_bool___iter__</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="LC206" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__StepVector_Iterator_bool</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">__del__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_Iterator_bool_swigregister</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_bool_swigregister</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_Iterator_bool_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_Iterator_bool</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_bool</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_bool</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC322" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_bool</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="LC207" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Register _StepVector_Iterator_bool in _StepVector:</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_bool_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_Iterator_bool</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_bool</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_bool</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_bool</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC220" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC223" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_all_values_pystyle</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="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_get_all_values_pystyle</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="LC226" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">num_values</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="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_num_values</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="LC232" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__StepVector_bool</span></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">__del__</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"><span class="n" style="color: #333;"><span class="idiff left">_StepVector_bool_swigregister</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_StepVector</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_StepVector_bool_swigregister</span></span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_bool_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_bool</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># Register _StepVector_bool in _StepVector:</span></span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_StepVector</span>_bool_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_bool</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_bool</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_min_index</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_bool</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_bool_max_index</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Pair_int_obj</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_Pair_int_obj</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC357" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_Pair_int_obj</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="LC239" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_Pair_int_obj</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"first"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_first_set</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"first"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_first_get</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_first_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_first_set</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"second"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_second_set</span></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span><span class="p">[</span><span class="s" style="color: #d14;">"second"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_second_get</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">_newclass</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_second_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_second_set</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_first_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_first_set</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_second_get</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_second_set</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__Pair_int_obj</span><span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">)</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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372
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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373
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__Pair_int_obj</span><span class="p">(</span><span class="n" style="color: #333;">first_</span><span class="p">,</span> <span class="n" style="color: #333;">second_</span><span class="p">))</span></span>
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375
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__Pair_int_obj</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">__del__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"><span class="n" style="color: #333;">_Pair_int_obj_swigregister</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_swigregister</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"><span class="n" style="color: #333;">_Pair_int_obj_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_Pair_int_obj</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_Iterator_obj</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_Iterator_obj</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC383" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_Iterator_obj</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="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Register _Pair_int_obj in _StepVector:</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_Pair_int_obj_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_Pair_int_obj</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_Iterator_obj</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_Iterator_obj</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_obj_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_Iterator_obj</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">last_</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">next</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="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_obj_next</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -397,42 +262,35 @@ class _StepVector_Iterator_obj(_object):</td>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</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="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_obj___iter__</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="LC264" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__StepVector_Iterator_obj</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">__del__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_Iterator_obj_swigregister</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_obj_swigregister</span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_Iterator_obj_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_Iterator_obj</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_obj</span><span class="p">(</span><span class="n" style="color: #333;">_object</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">__swig_setmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">__setattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_setattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_obj</span><span class="p">,</span> <span class="n" style="color: #333;">name</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="LC407" class="line" lang="python"> <span class="n" style="color: #333;">__swig_getmethods__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">__getattr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">:</span> <span class="n" style="color: #333;">_swig_getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector_obj</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="LC265" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Register _StepVector_Iterator_obj in _StepVector:</span></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_Iterator_obj_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_Iterator_obj</span><span class="p">)</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">_StepVector_obj</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">thisown</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">property</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">own</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">doc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"The membership flag"</span><span class="p">)</span></span>
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409
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">__repr__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_swig_repr</span></span>
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410
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"></span>
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411
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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412
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_obj</span><span class="p">()</span></span>
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413
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">this</span><span class="p">)</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">__builtin__</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">:</span></span>
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416
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">this</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">this</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_swiginit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">new__StepVector_obj</span><span class="p">())</span></span>
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417
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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419
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_set_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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420
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>
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422
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</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="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_add_value</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">,</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_all_values_pystyle</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="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_get_all_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span></span>
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426
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">):</span></span>
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428
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">arg2</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_get_values_pystyle</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_from</span></span><span class="p">)</span></span>
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429
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">num_values</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="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_num_values</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="LC290" class="line" lang="python"> <span class="n" style="color: #333;">__swig_destroy__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delete__StepVector_obj</span></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">__del__</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">lambda</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="python"><span class="n" style="color: #333;"><span class="idiff left">_StepVector_obj_swigregister</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_StepVector</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_StepVector_obj_swigregister</span></span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_obj_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_obj</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right"># Register _StepVector_obj in _StepVector:</span></span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"><span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_StepVector</span>_obj_swigregister</span><span class="p">(</span><span class="n" style="color: #333;">_StepVector_obj</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_min_index</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"><span class="n" style="color: #333;">_StepVector_obj</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cvar</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_StepVector_obj_max_index</span></span>
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<pre style="margin: 0;"> <span id="LC296" 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">@@ -692,6 +550,5 @@ def _StepVector_unpickle( length, typecode, start ):</td>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">StepVector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">create</span><span class="p">(</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">typecode</span><span class="p">,</span> <span class="n" style="color: #333;">start</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This file is compatible with both classic and new-style classes.</span></span>
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<li id="5f8bf900fa412d21d637ab1c77a631a00551279d">
<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#5f8bf900fa412d21d637ab1c77a631a00551279d"><strong>python3/HTSeq/__init__.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">@@ -402,11 +402,28 @@ class FastqReader(FileOrSequence):</td>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__iter__</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="LC404" class="line" lang="python"> <span class="n" style="color: #333;">fin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileOrSequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__iter__</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="LC405" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">id1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">id2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">fin</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">il</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">id1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">id2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fin</span><span class="p">:</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">il</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">id1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">il</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">il</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">il</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">il</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">id2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python"> <span class="n" style="color: #333;">il</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">il</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python"></span>
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410
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427
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qual</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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411
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">id1</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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412
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warn</span><span class="p">(</span></span>
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<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#6ef6a1ad5db69d445d8356610d7f345cb83afe6a"><strong>python3/HTSeq/_version.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.11.2"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.11.3"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#e5673f04e9098a0bf1f4da138b373b347616dfe0"><strong>python3/HTSeq/scripts/count.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">@@ -44,9 +44,19 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optional_fields</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="s" style="color: #d14;">'XF'</span><span class="p">,</span> <span class="n" style="color: #333;">assignment</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">samoutfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_sam_line</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"sam"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">SAM_or_BAM_Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SAM_Reader</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">samname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SAM'</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">samtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bam"</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">SAM_or_BAM_Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BAM_Reader</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">samname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'BAM'</span></span>
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<pre style="margin: 0;">+<span id="LC53" 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="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown input format </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s specified."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">samtype</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samouts</span> <span class="o" style="font-weight: 600;">!=</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;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">samouts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sam_filenames</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'Select the same number of SAM input and output files'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="s" style="color: #d14;">'Select the same number of {:} input and output files'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">samname</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Try to open samout files early in case any of them has issues</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">samout</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samouts</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">samout</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</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">@@ -73,12 +83,14 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">feature_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attr</span><span class="p">[</span><span class="n" style="color: #333;">id_attribute</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;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Feature </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s does not contain a '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' attribute"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">id_attribute</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="s" style="color: #d14;">"Feature </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s does not contain a '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' attribute"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">id_attribute</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stranded</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"no"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strand</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="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Feature </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s at </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s does not have strand information but you are "</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="s" style="color: #d14;">"running htseq-count in stranded mode. Use '--stranded=no'."</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="s" style="color: #d14;">"Feature </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s at </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s does not have strand information but you are "</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">"running htseq-count in stranded mode. Use '--stranded=no'."</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">features</span><span class="p">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iv</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">feature_id</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attr</span><span class="p">[</span><span class="n" style="color: #333;">id_attribute</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">attributes</span><span class="p">[</span><span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">attr</span><span class="p">[</span><span class="n" style="color: #333;">id_attribute</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</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">@@ -102,13 +114,6 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"Warning: No features of type '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s' found.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">feature_type</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"sam"</span><span class="p">:</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">SAM_or_BAM_Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SAM_Reader</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">samtype</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bam"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">SAM_or_BAM_Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BAM_Reader</span></span>
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<pre style="margin: 0;">-<span id="LC109" 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="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Unknown input format </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s specified."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">samtype</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="n" style="color: #333;">counts_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">empty_all</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">ambiguous_all</span> <span class="o" style="font-weight: 600;">=</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">@@ -140,7 +145,8 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">read_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when reading beginning of SAM/BAM file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when reading beginning of {:} file.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">samname</span><span class="p">))</span></span>
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></span>
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146
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; color: rgba(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="176" style="width: 35px; color: rgba(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">@@ -170,8 +176,8 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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170
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">r</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read_seq</span><span class="p">:</span></span>
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171
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">100000</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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172
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d <span class="idiff left right">SAM</span> alignment record</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"s"</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">" pairs"</span><span class="p">))</span></span>
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<td class="diff-line-num new old_line" data-linenumber="175" style="width: 35px; color: rgba(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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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d </span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span> alignment record</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">samname</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"s"</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">" pairs"</span><span class="p">))</span></span>
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175
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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176
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"></span>
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177
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -189,7 +195,10 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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189
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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190
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<td class="diff-line-num new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">optional_field</span><span class="p">(</span><span class="s" style="color: #d14;">"NH"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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191
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">nonunique</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">write_to_samout</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">,</span> <span class="s" style="color: #d14;">"__alignment_not_unique"</span><span class="p">,</span> <span class="n" style="color: #333;">samoutfile</span><span class="p">)</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">write_to_samout</span><span class="p">(</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">r</span><span class="p">,</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"> <span class="s" style="color: #d14;">"__alignment_not_unique"</span><span class="p">,</span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">samoutfile</span><span class="p">)</span></span>
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193
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multimapped_mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'none'</span><span class="p">:</span></span>
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194
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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195
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</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">@@ -307,14 +316,14 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"></span>
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308
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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309
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when processing <span class="idiff left right">SAM</span> input (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s):</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">read_seq_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_line_number_string</span></span><span class="p"><span class="idiff right">(</span>))</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="s" style="color: #d14;">"Error occured when processing </span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span> input (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s):</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">samname</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">read_seq_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">get_line_number_string</span></span><span class="p"><span class="idiff right">()</span>))</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC323" 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;">quiet</span><span class="p">:</span></span>
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315
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d <span class="idiff left right">SAM</span> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">"alignments "</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"alignment pairs"</span><span class="p">))</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d </span><span class="si" style="color: #d14;"><span class="idiff left">%</span></span><span class="s" style="color: #d14;"><span class="idiff right">s</span> </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s processed.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span></span>
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<td class="diff-line-num new new_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">samname</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"alignments "</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pe_mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"alignment pairs"</span><span class="p">))</span></span>
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318
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samoutfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</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">@@ -339,7 +348,8 @@ def count_reads_in_features(sam_filenames, gff_filename,</td>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">"__alignment_not_unique"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">pad</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">nonunique_all</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">my_showwarning</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">category</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">lineno</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">my_showwarning</span><span class="p">(</span><span class="n" style="color: #333;">message</span><span class="p">,</span> <span class="n" style="color: #333;">category</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">lineno</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">line</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">message</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC355" 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">@@ -352,7 +362,8 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"> <span class="s" style="color: #d14;">"the number of reads mapping to it. See "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"> <span class="s" style="color: #d14;">"http://htseq.readthedocs.io/en/master/count.html for details."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">epilog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Written by Simon Anders (sanders@fs.tum.de), "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="s" style="color: #d14;">"European Molecular Biology Laboratory (EMBL). (c) 2010. "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="s" style="color: #d14;">"European Molecular Biology Laboratory (EMBL) and Fabio Zanini "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="s" style="color: #d14;">"(fabio.zanini@stanford.edu), Stanford University. (c) 2010-2019. "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="s" style="color: #d14;">"Released under the terms of the GNU General Public License v3. "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"> <span class="s" style="color: #d14;">"Part of the 'HTSeq' framework, version </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__version__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC369" 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">@@ -363,12 +374,12 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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376
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="s" style="color: #d14;">"featuresfilename"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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366
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Path to the file containing the features"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Path to the <span class="idiff left right">GTF </span>file containing the features"</span><span class="p">)</span></span>
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"></span>
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--format"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"samtype"</span><span class="p">,</span></span>
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370
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"sam"</span><span class="p">,</span> <span class="s" style="color: #d14;">"bam"</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"sam"</span><span class="p">,</span></span>
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371
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">t</span>ype of <alignment_file> data, either 'sam' or 'bam' (default: sam)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">T</span>ype of <alignment_file> data, either 'sam' or 'bam' (default: sam)"</span><span class="p">)</span></span>
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"> <span class="s" style="color: #d14;">"-r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--order"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"order"</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -388,38 +399,43 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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389
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"> <span class="s" style="color: #d14;">"-s"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--stranded"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"stranded"</span><span class="p">,</span></span>
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390
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"yes"</span><span class="p">,</span> <span class="s" style="color: #d14;">"no"</span><span class="p">,</span> <span class="s" style="color: #d14;">"reverse"</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"yes"</span><span class="p">,</span></span>
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391
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<td class="diff-line-num new_line old" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">w</span>hether the data is from a strand-specific assay. Specify 'yes', "</span> <span class="o" style="font-weight: 600;">+</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"<span class="idiff left right">W</span>hether the data is from a strand-specific assay. Specify 'yes', "</span> <span class="o" style="font-weight: 600;">+</span></span>
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392
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403
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="s" style="color: #d14;">"'no', or 'reverse' (default: yes). "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"> <span class="s" style="color: #d14;">"'reverse' means 'yes' with reversed strand interpretation"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python"> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--minaqual"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"minaqual"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"skip all reads with alignment quality lower than the given "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"> <span class="s" style="color: #d14;">"minimum value (default: 10)"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Skip all reads with MAPQ alignment quality lower than the given "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="s" style="color: #d14;">"minimum value (default: 10). MAPQ is the 5th column of a SAM/BAM "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"> <span class="s" style="color: #d14;">"file and its usage depends on the software used to map the reads."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="s" style="color: #d14;">"-t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--type"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"featuretype"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"exon"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"feature type (3rd column in GFF file) to be used, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"exon"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Feature type (3rd column in GTF file) to be used, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"> <span class="s" style="color: #d14;">"all features of other type are ignored (default, suitable for Ensembl "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"> <span class="s" style="color: #d14;">"GTF files: exon)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--idattr"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"idattr"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gene_id"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GFF attribute to be used as feature ID (default, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"gene_id"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"GTF attribute to be used as feature ID (default, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"> <span class="s" style="color: #d14;">"suitable for Ensembl GTF files: gene_id)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="s" style="color: #d14;">"--additional-attr"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'append'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Additional feature attributes (default: none, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Additional feature attributes (default: none, "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"> <span class="s" style="color: #d14;">"suitable for Ensembl GTF files: gene_name). Use multiple times "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"> <span class="s" style="color: #d14;">"for each different attribute"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python"> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--mode"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"mode"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"union"</span><span class="p">,</span> <span class="s" style="color: #d14;">"intersection-strict"</span><span class="p">,</span> <span class="s" style="color: #d14;">"intersection-nonempty"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"union"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"mode to handle reads overlapping more than one feature "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"union"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Mode to handle reads overlapping more than one feature "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"> <span class="s" style="color: #d14;">"(choices: union, intersection-strict, intersection-nonempty; default: union)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</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">@@ -441,16 +457,25 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--samout"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"samouts"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'append'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"write out all SAM alignment records into "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="p">[],</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Write out all SAM alignment records into "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"> <span class="s" style="color: #d14;">"SAM files (one per input file needed), annotating each line "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"> <span class="s" style="color: #d14;">"with its feature assignment (as an optional field with tag 'XF')"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="s" style="color: #d14;">"-q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--quiet"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"quiet"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC450" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"suppress progress report"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># and warnings" )</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Suppress progress report"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># and warnings" )</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="s" style="color: #d14;">"--version"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show software version and exit'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pa</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">HTSeq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__version__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"> <span class="n" style="color: #333;">warnings</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">showwarning</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">my_showwarning</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">count_reads_in_features</span><span class="p">(</span></span>
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<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#a8dcb9b2f363c919df57f4b82171ac5afa3861eb"><strong>python3/src/HTSeq/_HTSeq.pyx</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">@@ -1326,8 +1326,9 @@ cdef class SAM_Alignment(AlignmentWithSequenceReversal):</td>
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cython"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceWithQualities</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="cython"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_sequence</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(),</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qname</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC1328" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC1329" class="line" lang="cython"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceWithQualities</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_sequence</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC1330" class="line" lang="cython"> <span class="p">),</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qname</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(),</span> <span class="s" style="color: #d14;">"noquals"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="cython"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceWithQualities</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="cython"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_sequence</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(),</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qname</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(),</span></span>
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="cython"> <span class="s" style="color: #d14;">"noquals"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1332" class="line" lang="cython"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">SAM_Alignment</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1333" class="line" lang="cython"> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">build_cigar_list</span><span class="p">([(</span><span class="kt" style="color: #458; font-weight: 600;">cigar_operation_codes</span><span class="p">[</span><span class="n" style="color: #333;">code</span><span class="p">],</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC1334" class="line" lang="cython"> <span class="n" style="color: #333;">code</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</span><span class="p">],</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</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">@@ -1368,10 +1369,15 @@ cdef class SAM_Alignment(AlignmentWithSequenceReversal):</td>
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<pre style="margin: 0;"> <span id="LC1369" class="line" lang="cython"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reference_end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">)</span></span>
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1369
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1370
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<pre style="margin: 0;"> <span id="LC1370" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1370
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1371
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<pre style="margin: 0;"> <span id="LC1371" class="line" lang="cython"> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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1371
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<pre style="margin: 0;">-<span id="LC1371" class="line" lang="cython"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceWithQualities</span><span class="p">(</span></span>
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1372
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<pre style="margin: 0;">-<span id="LC1372" class="line" lang="cython"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_sequence</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(),</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_name</span><span class="p">,</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="s" style="color: #d14;">'noquals'</span><span class="p">)</span></span>
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1373
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<pre style="margin: 0;">-<span id="LC1373" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_qualities</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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1374
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<pre style="margin: 0;">-<span id="LC1374" class="line" lang="cython"> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">numpy</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">array</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_qualities</span><span class="p">)</span></span>
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1372
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<pre style="margin: 0;">+<span id="LC1372" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">b</span><span class="s" style="color: #d14;">"*"</span><span class="p">:</span></span>
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1373
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<pre style="margin: 0;">+<span id="LC1373" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#sys.stderr.write(</span></span>
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1374
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<pre style="margin: 0;">+<span id="LC1374" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># 'query_sequence type: '+str(type(read.query_sequence))+', quality type: '+str(type(read.qual)))</span></span>
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1375
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<pre style="margin: 0;">+<span id="LC1375" class="line" lang="cython"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceWithQualities</span><span class="p">(</span></span>
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1376
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<pre style="margin: 0;">+<span id="LC1376" class="line" lang="cython"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_sequence</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(),</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qname</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">())</span></span>
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1377
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<pre style="margin: 0;">+<span id="LC1377" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1378
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<pre style="margin: 0;">+<span id="LC1378" class="line" lang="cython"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">SequenceWithQualities</span><span class="p">(</span></span>
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1379
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<pre style="margin: 0;">+<span id="LC1379" class="line" lang="cython"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_sequence</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(),</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">query_name</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">(),</span></span>
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1380
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<pre style="margin: 0;">+<span id="LC1380" class="line" lang="cython"> <span class="s" style="color: #d14;">'noquals'</span><span class="p">)</span></span>
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1375
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1381
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<pre style="margin: 0;"> <span id="LC1381" class="line" lang="cython"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">SAM_Alignment</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">iv</span><span class="p">)</span></span>
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1376
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1382
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<pre style="margin: 0;"> <span id="LC1382" class="line" lang="cython"> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">build_cigar_list</span><span class="p">([(</span><span class="kt" style="color: #458; font-weight: 600;">cigar_operation_codes</span><span class="p">[</span><span class="n" style="color: #333;">code</span><span class="p">],</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span></span>
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1377
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1383
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<pre style="margin: 0;"> <span id="LC1383" class="line" lang="cython"> <span class="n" style="color: #333;">code</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigartuples</span><span class="p">],</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reference_start</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">iv</span> <span class="o" style="font-weight: 600;">!=</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[]</span></span>
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<a href="https://salsa.debian.org/med-team/htseq/-/commit/c1d63d3906aec70f2b59f7ae457c9885348447e5#8738b4507555e0fff7576c4c11dc20077120c658"><strong>python3/src/StepVector.i</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">@@ -285,7 +285,7 @@ class StepVector( object ):</td>
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="openedge"><span class="s" style="color: #d14;"> If you use a slice, i.e., 'sv[i:j]', you get a view on the StepVector,</span></span>
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286
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="openedge"><span class="s" style="color: #d14;"> i.e., the same data, but changed boundaries.</span></span>
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287
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="openedge"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">if</span> <span class="nv" style="color: #008080;">isinstance</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">index</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">slice</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">if</span> <span class="nv" style="color: #008080;">isinstance</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">index</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">slice</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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289
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">if</span> <span class="nb" style="color: #0086b3;">index</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">step</span> <span class="nb" style="color: #0086b3;">is</span> <span class="nb" style="color: #0086b3;">not</span> <span class="nb" style="color: #0086b3;">None</span> <span class="nb" style="color: #0086b3;">and</span> <span class="nb" style="color: #0086b3;">index</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">step</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span></span>
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290
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="openedge"> <span class="nv" style="color: #008080;">raise</span> <span class="nv" style="color: #008080;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"Striding slices (i.e., step != 1) are not supported"</span></span>
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291
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">if</span> <span class="nb" style="color: #0086b3;">index</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">start</span> <span class="nb" style="color: #0086b3;">is</span> <span class="nb" style="color: #0086b3;">None</span><span class="o" style="font-weight: 600;">:</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">@@ -307,48 +307,48 @@ class StepVector( object ):</td>
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="openedge"> <span class="nv" style="color: #008080;">res</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">stop</span></span>
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nv" style="color: #008080;">res</span></span>
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">else</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">_swigobj</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">get_values_pystyle</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">index</span></span><span class="idiff right"> </span><span class="p">)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">second</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">_swigobj</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">get_values_pystyle</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">index</span></span><span class="p">)</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">second</span></span>
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="openedge"> </span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__iter__</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__iter__</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">self</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="openedge"> <span class="s" style="color: #d14;">"""When asked to provide an iterator, a StepVector will yield all its</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="openedge"><span class="s" style="color: #d14;"> value, repeating each value according to the length of the step.</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="openedge"><span class="s" style="color: #d14;"> Hence, calling, e.g., 'list( sv )' will transform the StepVector 'sv'</span></span>
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316
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="openedge"><span class="s" style="color: #d14;"> into an ordinary list.</span></span>
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317
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="openedge"><span class="s" style="color: #d14;"> """</span></span>
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318
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">for</span> <span class="nb" style="color: #0086b3;">start</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">stop</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">value</span> <span class="nb" style="color: #0086b3;">in</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">get_steps</span><span class="p">()</span><span class="o" style="font-weight: 600;">:</span></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">for</span> <span class="nv" style="color: #008080;">i</span> <span class="nb" style="color: #0086b3;">in</span> <span class="nv" style="color: #008080;"><span class="idiff left">xrange</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">for</span> <span class="nv" style="color: #008080;">i</span> <span class="nb" style="color: #0086b3;">in</span> <span class="nv" style="color: #008080;"><span class="idiff left">range</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">stop</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="openedge"> <span class="nv" style="color: #008080;">yield</span> <span class="nb" style="color: #0086b3;">value</span></span>
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321
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="openedge"> </span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__repr__</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__repr__</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">self</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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323
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">if</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">sys</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">maxint</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span></span>
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="openedge"> <span class="nv" style="color: #008080;">start_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-inf"</span></span>
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325
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<td class="diff-line-num new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">else</span><span class="o" style="font-weight: 600;">:</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="openedge"> <span class="nv" style="color: #008080;">start_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">str</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="openedge"> <span class="nv" style="color: #008080;">start_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">start</span></span><span class="p">)</span></span>
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327
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">if</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">stop</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: #008080;">sys</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">maxint</span><span class="o" style="font-weight: 600;">:</span></span>
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328
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="openedge"> <span class="nv" style="color: #008080;">stop_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"inf"</span></span>
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329
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<td class="diff-line-num new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">else</span><span class="o" style="font-weight: 600;">:</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="openedge"> <span class="nv" style="color: #008080;">stop_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">str</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="openedge"> <span class="nv" style="color: #008080;">stop_s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">stop</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="s" style="color: #d14;">"<%s object, type '%s', index range %s:%s, %d step(s)>"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">__class__</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">__name__</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">typecode</span><span class="p">(),</span> <span class="nv" style="color: #008080;">start_s</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="openedge"> <span class="nv" style="color: #008080;">stop_s</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">num_steps</span><span class="p">()</span><span class="idiff left right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="openedge"> <span class="nv" style="color: #008080;">stop_s</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">num_steps</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="openedge"> </span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">typecode</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">typecode</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">self</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="openedge"> <span class="s" style="color: #d14;">"Returns the typecode."</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">_typecode</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="openedge"> </span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__len__</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__len__</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">self</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="openedge"> <span class="s" style="color: #d14;">"""The length of a StepVector is defined by its index range, not by</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="openedge"><span class="s" style="color: #d14;"> the number of steps.</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="openedge"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">stop</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">start</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="openedge"> </span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">num_steps</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">num_steps</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">self</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="openedge"> <span class="s" style="color: #d14;">"""Returns the number of steps, i.e., the number of triples that get_steps</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="openedge"><span class="s" style="color: #d14;"> returns.</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="openedge"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">_swigobj</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">num_values</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="openedge"> </span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__eq__</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">other</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__eq__</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">other</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="openedge"> <span class="s" style="color: #d14;">"""StepVectors can be compared for equality. This is conceptually done</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="openedge"><span class="s" style="color: #d14;"> element for element, but, for performance, taking steps in one go.</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="openedge"><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">@@ -374,29 +374,29 @@ class StepVector( object ):</td>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="openedge"> <span class="nv" style="color: #008080;">othrstart</span><span class="p">,</span> <span class="nv" style="color: #008080;">othrstop</span><span class="p">,</span> <span class="nv" style="color: #008080;">othrval</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">othrsteps</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">next</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="kc" style="font-weight: 600;">True</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="openedge"> </span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__neq__</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">other</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nb" style="color: #0086b3;">not</span> <span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">other</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__neq__</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">other</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nb" style="color: #0086b3;">not</span> <span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">other</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="openedge"> </span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__reduce__</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__reduce__</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">self</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">if</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">__class__</span> <span class="nb" style="color: #0086b3;">is</span> <span class="nb" style="color: #0086b3;">not</span> <span class="nv" style="color: #008080;">StepVector</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="openedge"> <span class="nv" style="color: #008080;">raise</span> <span class="nv" style="color: #008080;">NotImplemented</span><span class="p">,</span> <span class="s" style="color: #d14;">"Attempting to pickle a subclass of StepVector without redefined __reduce__."</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="p">(</span> </span>
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384
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="openedge"> <span class="nv" style="color: #008080;">_StepVector_unpickle</span><span class="p">,</span> </span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="openedge"> <span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">_typecode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="idiff right"> </span><span class="p">),</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="openedge"> <span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">_typecode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">start</span></span><span class="p">),</span></span>
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386
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">None</span><span class="p">,</span></span>
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387
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387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">None</span><span class="p">,</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="openedge"> <span class="p">(</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">slice</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="idiff"> </span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">val</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">val</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">get_steps</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="openedge"> <span class="p">(<span class="idiff left">(</span></span><span class="nv" style="color: #008080;"><span class="idiff">slice</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">val</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">val</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">get_steps</span></span><span class="p"><span class="idiff right">())</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="openedge"> </span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__iadd__</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">value</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">_swigobj</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">add_value</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">stop-1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">value</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">__iadd__</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">value</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">_swigobj</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">add_value</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">stop-1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">value</span></span><span class="p">)</span></span>
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nb" style="color: #0086b3;">self</span></span>
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393
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393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="openedge"> </span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">func</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">None</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">def</span> <span class="nb" style="color: #0086b3;">apply</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">func</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">None</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="openedge"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">#</span> <span class="nv" style="color: #008080;">TODO</span><span class="o" style="font-weight: 600;">:</span> <span class="nb" style="color: #0086b3;">check</span><span class="o" style="font-weight: 600;">!</span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">for</span> <span class="nv" style="color: #008080;">stepstart</span><span class="p">,</span> <span class="nv" style="color: #008080;">stepstop</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">value</span> <span class="nb" style="color: #0086b3;">in</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">get_steps</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">stop</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">self</span><span class="p">[</span><span class="idiff left"> </span><span class="nv" style="color: #008080;"><span class="idiff">stepstart</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">stepstop</span></span><span class="idiff"> </span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">func</span></span><span class="p"><span class="idiff">(</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">value</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">for</span> <span class="nv" style="color: #008080;">stepstart</span><span class="p">,</span> <span class="nv" style="color: #008080;">stepstop</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">value</span> <span class="nb" style="color: #0086b3;">in</span> <span class="nb" style="color: #0086b3;">self</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nv" style="color: #008080;">get_steps</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">start</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">stop</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">self</span><span class="p">[</span><span class="nv" style="color: #008080;"><span class="idiff left">stepstart</span></span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="nv" style="color: #008080;"><span class="idiff">stepstop</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">func</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">value</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="openedge"> </span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="openedge"><span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">_StepVector_unpickle</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">typecode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="idiff right"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nv" style="color: #008080;">StepVector</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">create</span><span class="p">(</span><span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">typecode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">start</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="openedge"><span class="nb" style="color: #0086b3;">def</span> <span class="nv" style="color: #008080;">_StepVector_unpickle</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">typecode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">start</span></span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="openedge"> <span class="nb" style="color: #0086b3;">return</span> <span class="nv" style="color: #008080;">StepVector</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="nb" style="color: #0086b3;">create</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff">typecode</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">start</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="openedge"> </span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="openedge"><span class="o" style="font-weight: 600;">%</span><span class="nv" style="color: #008080;">}</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,9 +5,9 @@ import os</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">distutils.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">INFO</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">logINFO</span></span>
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6
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6
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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="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></span><span class="p">)):</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span></span><span class="p">)):</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error in setup script for HTSeq:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"HTSeq support Python 2.7 or 3.<span class="idiff left right">4</span>+."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"HTSeq support Python 2.7 or 3.<span class="idiff left right">5</span>+."</span><span class="p">)</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Manage python2/3 compatibility with symlinks</span></span>
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