obitools/obitools
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
Files
79dbbb8a6be6252d5e4cf68daa9d04bee790c0d0
obitools/html/obitools-pysrc.html
Eric Coissac 30e149a9ff
2009-06-18 12:06:39 +00:00

1016 lines
184 KiB
HTML
Raw Blame History

<?xml version="1.0" encoding="ascii"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>obitools</title>
<link rel="stylesheet" href="epydoc.css" type="text/css" />
<script type="text/javascript" src="epydoc.js"></script>
</head>
<body bgcolor="white" text="black" link="blue" vlink="#204080"
alink="#204080">
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Home link -->
<th bgcolor="#70b0f0" class="navbar-select"
>&nbsp;&nbsp;&nbsp;Home&nbsp;&nbsp;&nbsp;</th>
<!-- Tree link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Index link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Help link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table width="100%" cellpadding="0" cellspacing="0">
<tr valign="top">
<td width="100%">
<span class="breadcrumbs">
Package&nbsp;obitools
</span>
</td>
<td>
<table cellpadding="0" cellspacing="0">
<!-- hide/show private -->
<tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink"
onclick="toggle_private();">hide&nbsp;private</a>]</span></td></tr>
<tr><td align="right"><span class="options"
>[<a href="frames.html" target="_top">frames</a
>]&nbsp;|&nbsp;<a href="obitools-pysrc.html"
target="_top">no&nbsp;frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="obitools-module.html">Package obitools</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">'''</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">logging</tt> <tt class="py-keyword">import</tt> <tt class="py-name">debug</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">weakref</tt> <tt class="py-keyword">import</tt> <tt class="py-name">ref</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package obitools.utils=obitools.utils-module.html"><a title="obitools.utils" class="py-name" href="#" onclick="return doclink('link-1', 'utils', 'link-1');">utils</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module obitools.utils.iterator=obitools.utils.iterator-module.html"><a title="obitools.utils.iterator" class="py-name" href="#" onclick="return doclink('link-2', 'iterator', 'link-2');">iterator</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Function obitools.utils.iterator.uniqueChain()=obitools.utils.iterator-module.html#uniqueChain"><a title="obitools.utils.iterator.uniqueChain" class="py-name" href="#" onclick="return doclink('link-3', 'uniqueChain', 'link-3');">uniqueChain</a></tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">functools</tt> <tt class="py-keyword">import</tt> <tt class="py-name">partial</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-keyword">except</tt><tt class="py-op">:</tt> </tt>
<a name="partial"></a><div id="partial-def"><a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> <tt class="py-comment"># Add for compatibility purpose with Python &lt; 2.5</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"> <tt class="py-comment">#</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <a class="py-toggle" href="#" id="partial-toggle" onclick="return toggle('partial');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools-module.html#partial">partial</a><tt class="py-op">(</tt><tt class="py-param">func</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt><tt class="py-param">args</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">keywords</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="partial-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="partial-expanded"><a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">newfunc</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-param">fargs</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">fkeywords</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-name">newkeywords</tt> <tt class="py-op">=</tt> <tt class="py-name">keywords</tt><tt class="py-op">.</tt><tt class="py-name">copy</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-name">newkeywords</tt><tt class="py-op">.</tt><tt class="py-name">update</tt><tt class="py-op">(</tt><tt class="py-name">fkeywords</tt><tt class="py-op">)</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">func</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">args</tt> <tt class="py-op">+</tt> <tt class="py-name">fargs</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-name">newkeywords</tt><tt class="py-op">)</tt> </tt>
</div><a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-name">newfunc</tt><tt class="py-op">.</tt><tt class="py-name">func</tt> <tt class="py-op">=</tt> <tt class="py-name">func</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-name">newfunc</tt><tt class="py-op">.</tt><tt class="py-name">args</tt> <tt class="py-op">=</tt> <tt class="py-name">args</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> <tt class="py-name">newfunc</tt><tt class="py-op">.</tt><tt class="py-name">keywords</tt> <tt class="py-op">=</tt> <tt class="py-name">keywords</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">newfunc</tt> </tt>
</div><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-4', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Package obitools.sequenceencoder=obitools.sequenceencoder-module.html"><a title="obitools.sequenceencoder" class="py-name" href="#" onclick="return doclink('link-5', 'sequenceencoder', 'link-5');">sequenceencoder</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Class obitools.sequenceencoder.DNAComplementEncoder=obitools.sequenceencoder.DNAComplementEncoder-class.html"><a title="obitools.sequenceencoder.DNAComplementEncoder" class="py-name" href="#" onclick="return doclink('link-6', 'DNAComplementEncoder', 'link-6');">DNAComplementEncoder</a></tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="obitools
obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-7', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name" targets="Package obitools.location=obitools.location-module.html"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-8', 'location', 'link-8');">location</a></tt> <tt class="py-keyword">import</tt> <tt id="link-9" class="py-name" targets="Class obitools.location.Location=obitools.location.Location-class.html"><a title="obitools.location.Location" class="py-name" href="#" onclick="return doclink('link-9', 'Location', 'link-9');">Location</a></tt> </tt>
<a name="WrapperSetIterator"></a><div id="WrapperSetIterator-def"><a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <a class="py-toggle" href="#" id="WrapperSetIterator-toggle" onclick="return toggle('WrapperSetIterator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.WrapperSetIterator-class.html">WrapperSetIterator</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrapperSetIterator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="WrapperSetIterator-expanded"><a name="WrapperSetIterator.__init__"></a><div id="WrapperSetIterator.__init__-def"><a name="L32"></a><tt class="py-lineno"> 32</tt> <a class="py-toggle" href="#" id="WrapperSetIterator.__init__-toggle" onclick="return toggle('WrapperSetIterator.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrapperSetIterator-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">s</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrapperSetIterator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrapperSetIterator.__init__-expanded"><a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_i</tt> <tt class="py-op">=</tt> <tt id="link-10" class="py-name" targets="Class obitools.SVGdraw.set=obitools.SVGdraw.set-class.html"><a title="obitools.SVGdraw.set" class="py-name" href="#" onclick="return doclink('link-10', 'set', 'link-10');">set</a></tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method obitools.BioSequence.__iter__()=obitools.BioSequence-class.html#__iter__,Method obitools.DNAComplementSequence.__iter__()=obitools.DNAComplementSequence-class.html#__iter__,Method obitools.SubSequence.__iter__()=obitools.SubSequence-class.html#__iter__,Method obitools.WrapperSet.__iter__()=obitools.WrapperSet-class.html#__iter__,Method obitools.WrapperSetIterator.__iter__()=obitools.WrapperSetIterator-class.html#__iter__,Method obitools.align.homopolymere.HomoNucBioSeq.__iter__()=obitools.align.homopolymere.HomoNucBioSeq-class.html#__iter__,Method obitools.cns.quality.QualitySequence.__iter__()=obitools.cns.quality.QualitySequence-class.html#__iter__,Method obitools.ecopcr.sequence.EcoPCRDBSequenceIterator.__iter__()=obitools.ecopcr.sequence.EcoPCRDBSequenceIterator-class.html#__iter__,Method obitools.format.ontology.go_obo.OBOFile.__iter__()=obitools.format.ontology.go_obo.OBOFile-class.html#__iter__,Method obitools.graph.Graph.__iter__()=obitools.graph.Graph-class.html#__iter__,Method obitools.graph.Node.__iter__()=obitools.graph.Node-class.html#__iter__,Method obitools.gzip.GzipFile.__iter__()=obitools.gzip.GzipFile-class.html#__iter__,Method obitools.parallel.TaskPool.__iter__()=obitools.parallel.TaskPool-class.html#__iter__,Method obitools.parallel.jobqueue.JobIterator.__iter__()=obitools.parallel.jobqueue.JobIterator-class.html#__iter__,Method obitools.seqdb.genbank.graph.Graph.__iter__()=obitools.seqdb.genbank.graph.Graph-class.html#__iter__,Method obitools.seqdb.genbank.graph.Node.__iter__()=obitools.seqdb.genbank.graph.Node-class.html#__iter__,Method obitools.table.Table.__iter__()=obitools.table.Table-class.html#__iter__,Method obitools.table.TableIteratorAsDict.__iter__()=obitools.table.TableIteratorAsDict-class.html#__iter__,Method obitools.table.TableRow.__iter__()=obitools.table.TableRow-class.html#__iter__,Method obitools.table.iTableIterator.__iter__()=obitools.table.iTableIterator-class.html#__iter__,Method obitools.tagmatcher.parser.TagMatcherIterator.__iter__()=obitools.tagmatcher.parser.TagMatcherIterator-class.html#__iter__,Method obitools.utils.ColumnFile.__iter__()=obitools.utils.ColumnFile-class.html#__iter__,Method obitools.zipfile.ZipExtFile.__iter__()=obitools.zipfile.ZipExtFile-class.html#__iter__"><a title="obitools.BioSequence.__iter__
obitools.DNAComplementSequence.__iter__
obitools.SubSequence.__iter__
obitools.WrapperSet.__iter__
obitools.WrapperSetIterator.__iter__
obitools.align.homopolymere.HomoNucBioSeq.__iter__
obitools.cns.quality.QualitySequence.__iter__
obitools.ecopcr.sequence.EcoPCRDBSequenceIterator.__iter__
obitools.format.ontology.go_obo.OBOFile.__iter__
obitools.graph.Graph.__iter__
obitools.graph.Node.__iter__
obitools.gzip.GzipFile.__iter__
obitools.parallel.TaskPool.__iter__
obitools.parallel.jobqueue.JobIterator.__iter__
obitools.seqdb.genbank.graph.Graph.__iter__
obitools.seqdb.genbank.graph.Node.__iter__
obitools.table.Table.__iter__
obitools.table.TableIteratorAsDict.__iter__
obitools.table.TableRow.__iter__
obitools.table.iTableIterator.__iter__
obitools.tagmatcher.parser.TagMatcherIterator.__iter__
obitools.utils.ColumnFile.__iter__
obitools.zipfile.ZipExtFile.__iter__" class="py-name" href="#" onclick="return doclink('link-11', '__iter__', 'link-11');">__iter__</a></tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
</div><a name="WrapperSetIterator.next"></a><div id="WrapperSetIterator.next-def"><a name="L34"></a><tt class="py-lineno"> 34</tt> <a class="py-toggle" href="#" id="WrapperSetIterator.next-toggle" onclick="return toggle('WrapperSetIterator.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrapperSetIterator-class.html#next">next</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrapperSetIterator.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrapperSetIterator.next-expanded"><a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_i</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method obitools.WrapperSetIterator.next()=obitools.WrapperSetIterator-class.html#next,Method obitools.blast.BlastResultIterator.next()=obitools.blast.BlastResultIterator-class.html#next,Method obitools.ecopcr.EcoPCRFile.next()=obitools.ecopcr.EcoPCRFile-class.html#next,Method obitools.ecotag.parser.EcoTagAbstractIterator.next()=obitools.ecotag.parser.EcoTagAbstractIterator-class.html#next,Method obitools.ecotag.parser.EcoTagFileIterator.next()=obitools.ecotag.parser.EcoTagFileIterator-class.html#next,Method obitools.format.ontology.go_obo.OBOFile.next()=obitools.format.ontology.go_obo.OBOFile-class.html#next,Method obitools.goa.parser.GoAFileIterator.next()=obitools.goa.parser.GoAFileIterator-class.html#next,Method obitools.gzip.GzipFile.next()=obitools.gzip.GzipFile-class.html#next,Method obitools.parallel.jobqueue.JobIterator.next()=obitools.parallel.jobqueue.JobIterator-class.html#next,Method obitools.solexa.SolexaFile.next()=obitools.solexa.SolexaFile-class.html#next,Method obitools.table.ProjectionIterator.next()=obitools.table.ProjectionIterator-class.html#next,Method obitools.table.SelectionIterator.next()=obitools.table.SelectionIterator-class.html#next,Method obitools.table.TableIterator.next()=obitools.table.TableIterator-class.html#next,Method obitools.table.TableIteratorAsDict.next()=obitools.table.TableIteratorAsDict-class.html#next,Method obitools.table.UnionIterator.next()=obitools.table.UnionIterator-class.html#next,Method obitools.table.iTableIterator.next()=obitools.table.iTableIterator-class.html#next,Method obitools.tagmatcher.parser.TagMatcherIterator.next()=obitools.tagmatcher.parser.TagMatcherIterator-class.html#next,Method obitools.utils.ColumnFile.next()=obitools.utils.ColumnFile-class.html#next,Method obitools.zipfile.ZipExtFile.next()=obitools.zipfile.ZipExtFile-class.html#next"><a title="obitools.WrapperSetIterator.next
obitools.blast.BlastResultIterator.next
obitools.ecopcr.EcoPCRFile.next
obitools.ecotag.parser.EcoTagAbstractIterator.next
obitools.ecotag.parser.EcoTagFileIterator.next
obitools.format.ontology.go_obo.OBOFile.next
obitools.goa.parser.GoAFileIterator.next
obitools.gzip.GzipFile.next
obitools.parallel.jobqueue.JobIterator.next
obitools.solexa.SolexaFile.next
obitools.table.ProjectionIterator.next
obitools.table.SelectionIterator.next
obitools.table.TableIterator.next
obitools.table.TableIteratorAsDict.next
obitools.table.UnionIterator.next
obitools.table.iTableIterator.next
obitools.tagmatcher.parser.TagMatcherIterator.next
obitools.utils.ColumnFile.next
obitools.zipfile.ZipExtFile.next" class="py-name" href="#" onclick="return doclink('link-12', 'next', 'link-12');">next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="WrapperSetIterator.__iter__"></a><div id="WrapperSetIterator.__iter__-def"><a name="L36"></a><tt class="py-lineno"> 36</tt> <a class="py-toggle" href="#" id="WrapperSetIterator.__iter__-toggle" onclick="return toggle('WrapperSetIterator.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrapperSetIterator-class.html#__iter__">__iter__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrapperSetIterator.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrapperSetIterator.__iter__-expanded"><a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
</div></div><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> </tt>
<a name="WrapperSet"></a><div id="WrapperSet-def"><a name="L39"></a><tt class="py-lineno"> 39</tt> <a class="py-toggle" href="#" id="WrapperSet-toggle" onclick="return toggle('WrapperSet');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.WrapperSet-class.html">WrapperSet</a><tt class="py-op">(</tt><tt class="py-base-class">set</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrapperSet-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="WrapperSet-expanded"><a name="WrapperSet.__iter__"></a><div id="WrapperSet.__iter__-def"><a name="L40"></a><tt class="py-lineno"> 40</tt> <a class="py-toggle" href="#" id="WrapperSet.__iter__-toggle" onclick="return toggle('WrapperSet.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrapperSet-class.html#__iter__">__iter__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrapperSet.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrapperSet.__iter__-expanded"><a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-13" class="py-name" targets="Class obitools.WrapperSetIterator=obitools.WrapperSetIterator-class.html"><a title="obitools.WrapperSetIterator" class="py-name" href="#" onclick="return doclink('link-13', 'WrapperSetIterator', 'link-13');">WrapperSetIterator</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"> </tt>
<a name="BioSequence"></a><div id="BioSequence-def"><a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <a class="py-toggle" href="#" id="BioSequence-toggle" onclick="return toggle('BioSequence');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.BioSequence-class.html">BioSequence</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BioSequence-expanded"><a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> BioSequence class is the base class for biological</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> sequence representation.</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> It provides storage of :</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> - the sequence itself, </tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> - an identifier,</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> - a definition an manage </tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"> - a set of complementary information on a key / value principle.</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"> BioSequence is an abstract class and must be instanciated</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> from its subclasses</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> </tt>
<a name="BioSequence.__init__"></a><div id="BioSequence.__init__-def"><a name="L60"></a><tt class="py-lineno"> 60</tt> <a class="py-toggle" href="#" id="BioSequence.__init__-toggle" onclick="return toggle('BioSequence.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">,</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt><tt class="py-param">definition</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-param">info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.__init__-expanded"><a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> BioSequence constructor.</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> @param id: sequence identifier</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> @type id: str</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> @param seq: the sequence</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> @type seq: str</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"> @param definition: sequence definition (optional)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> @type definition: str</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> @param info: extra named parameters can be add to associate complementary</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> data to the sequence</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt><tt class="py-op">=</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-14" class="py-name" targets="Variable obitools.sequenceencoder.DNAComplementEncoder._info=obitools.sequenceencoder.DNAComplementEncoder-class.html#_info"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-14', '_info', 'link-14');">_info</a></tt> <tt class="py-op">=</tt> <tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable obitools.BioSequence.definition=obitools.BioSequence-class.html#definition,Variable obitools.WrappedBioSequence.definition=obitools.WrappedBioSequence-class.html#definition,Variable obitools.cns.quality.QualitySequence.definition=obitools.cns.quality.QualitySequence-class.html#definition,Variable obitools.obo.parser.OBOTerm.definition=obitools.obo.parser.OBOTerm-class.html#definition"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-15', 'definition', 'link-15');">definition</a></tt><tt class="py-op">=</tt><tt id="link-16" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-16', 'definition', 'link-15');">definition</a></tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Variable obitools.BioSequence.id=obitools.BioSequence-class.html#id,Variable obitools.DNAComplementSequence.id=obitools.DNAComplementSequence-class.html#id,Variable obitools.WrappedBioSequence.id=obitools.WrappedBioSequence-class.html#id,Variable obitools.cns.quality.QualitySequence.id=obitools.cns.quality.QualitySequence-class.html#id,Variable obitools.obo.parser.OBOTerm.id=obitools.obo.parser.OBOTerm-class.html#id"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-17', 'id', 'link-17');">id</a></tt><tt class="py-op">=</tt><tt id="link-18" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-18', 'id', 'link-17');">id</a></tt> </tt>
</div><a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> </tt>
<a name="BioSequence.getDefinition"></a><div id="BioSequence.getDefinition-def"><a name="L83"></a><tt class="py-lineno"> 83</tt> <a class="py-toggle" href="#" id="BioSequence.getDefinition-toggle" onclick="return toggle('BioSequence.getDefinition');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#getDefinition">getDefinition</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.getDefinition-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.getDefinition-expanded"><a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> Sequence definition getter</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> @return: the sequence definition</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: str</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_definition</tt> </tt>
</div><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> </tt>
<a name="BioSequence.setDefinition"></a><div id="BioSequence.setDefinition-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="BioSequence.setDefinition-toggle" onclick="return toggle('BioSequence.setDefinition');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#setDefinition">setDefinition</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.setDefinition-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.setDefinition-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_definition</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name" targets="Static Method obitools.ecotag.parser.EcoTagFileIterator.value()=obitools.ecotag.parser.EcoTagFileIterator-class.html#value"><a title="obitools.ecotag.parser.EcoTagFileIterator.value" class="py-name" href="#" onclick="return doclink('link-19', 'value', 'link-19');">value</a></tt> </tt>
</div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="BioSequence.getId"></a><div id="BioSequence.getId-def"><a name="L96"></a><tt class="py-lineno"> 96</tt> <a class="py-toggle" href="#" id="BioSequence.getId-toggle" onclick="return toggle('BioSequence.getId');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#getId">getId</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.getId-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.getId-expanded"><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_id</tt> </tt>
</div><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="BioSequence.setId"></a><div id="BioSequence.setId-def"><a name="L99"></a><tt class="py-lineno"> 99</tt> <a class="py-toggle" href="#" id="BioSequence.setId-toggle" onclick="return toggle('BioSequence.setId');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#setId">setId</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.setId-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.setId-expanded"><a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_id</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="obitools.ecotag.parser.EcoTagFileIterator.value" class="py-name" href="#" onclick="return doclink('link-20', 'value', 'link-19');">value</a></tt> </tt>
</div><a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> </tt>
<a name="BioSequence.getStr"></a><div id="BioSequence.getStr-def"><a name="L102"></a><tt class="py-lineno">102</tt> <a class="py-toggle" href="#" id="BioSequence.getStr-toggle" onclick="return toggle('BioSequence.getStr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#getStr">getStr</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.getStr-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.getStr-expanded"><a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> Return the sequence as a string</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> @return: the string representation of the sequence</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: str</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_seq</tt> </tt>
</div><a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> </tt>
<a name="BioSequence.getSymbolAt"></a><div id="BioSequence.getSymbolAt-def"><a name="L111"></a><tt class="py-lineno">111</tt> <a class="py-toggle" href="#" id="BioSequence.getSymbolAt-toggle" onclick="return toggle('BioSequence.getSymbolAt');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#getSymbolAt">getSymbolAt</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.getSymbolAt-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.getSymbolAt-expanded"><a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> Return the symbole at position in the sequence</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> @param position: the desired position. Position start from 0</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> if position is &lt; 0 then they are considered</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> to reference the end of the sequence.</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"> @type position: C{int}</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> @return: a one letter string</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"> @rtype: C{str}</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">[</tt><tt class="py-name">position</tt><tt class="py-op">]</tt> </tt>
</div><a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
<a name="BioSequence.getSubSeq"></a><div id="BioSequence.getSubSeq-def"><a name="L125"></a><tt class="py-lineno">125</tt> <a class="py-toggle" href="#" id="BioSequence.getSubSeq-toggle" onclick="return toggle('BioSequence.getSubSeq');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#getSubSeq">getSubSeq</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">location</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.getSubSeq-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.getSubSeq-expanded"><a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-21', 'location', 'link-8');">location</a></tt><tt class="py-op">,</tt><tt id="link-22" class="py-name"><a title="obitools.location.Location" class="py-name" href="#" onclick="return doclink('link-22', 'Location', 'link-9');">Location</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">key</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method obitools.location.Location.extractSequence()=obitools.location.Location-class.html#extractSequence,Method obitools.location.feature.Feature.extractSequence()=obitools.location.feature.Feature-class.html#extractSequence"><a title="obitools.location.Location.extractSequence
obitools.location.feature.Feature.extractSequence" class="py-name" href="#" onclick="return doclink('link-23', 'extractSequence', 'link-23');">extractSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-24', 'location', 'link-8');">location</a></tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-25" class="py-name" targets="Method obitools.BioSequence.getSymbolAt()=obitools.BioSequence-class.html#getSymbolAt,Method obitools.DNAComplementSequence.getSymbolAt()=obitools.DNAComplementSequence-class.html#getSymbolAt,Method obitools.WrappedBioSequence.getSymbolAt()=obitools.WrappedBioSequence-class.html#getSymbolAt"><a title="obitools.BioSequence.getSymbolAt
obitools.DNAComplementSequence.getSymbolAt
obitools.WrappedBioSequence.getSymbolAt" class="py-name" href="#" onclick="return doclink('link-25', 'getSymbolAt', 'link-25');">getSymbolAt</a></tt><tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-26', 'location', 'link-8');">location</a></tt><tt class="py-op">)</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-27', 'location', 'link-8');">location</a></tt><tt class="py-op">,</tt> <tt class="py-name">slice</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-28" class="py-name" targets="Class obitools.SubSequence=obitools.SubSequence-class.html"><a title="obitools.SubSequence" class="py-name" href="#" onclick="return doclink('link-28', 'SubSequence', 'link-28');">SubSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt id="link-29" class="py-name"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-29', 'location', 'link-8');">location</a></tt><tt class="py-op">)</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt><tt class="py-string">'key must be a C{Location}, an integer or a slice'</tt> </tt>
</div><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> </tt>
<a name="BioSequence.extractTaxon"></a><div id="BioSequence.extractTaxon-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="BioSequence.extractTaxon-toggle" onclick="return toggle('BioSequence.extractTaxon');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#extractTaxon">extractTaxon</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.extractTaxon-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.extractTaxon-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="BioSequence.__str__"></a><div id="BioSequence.__str__-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="BioSequence.__str__-toggle" onclick="return toggle('BioSequence.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.__str__-expanded"><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method obitools.BioSequence.getStr()=obitools.BioSequence-class.html#getStr,Method obitools.DNAComplementSequence.getStr()=obitools.DNAComplementSequence-class.html#getStr,Method obitools.SubSequence.getStr()=obitools.SubSequence-class.html#getStr,Method obitools.WrappedBioSequence.getStr()=obitools.WrappedBioSequence-class.html#getStr,Method obitools.align.homopolymere.HomoNucBioSeq.getStr()=obitools.align.homopolymere.HomoNucBioSeq-class.html#getStr"><a title="obitools.BioSequence.getStr
obitools.DNAComplementSequence.getStr
obitools.SubSequence.getStr
obitools.WrappedBioSequence.getStr
obitools.align.homopolymere.HomoNucBioSeq.getStr" class="py-name" href="#" onclick="return doclink('link-30', 'getStr', 'link-30');">getStr</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> </tt>
<a name="BioSequence.__getitem__"></a><div id="BioSequence.__getitem__-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="BioSequence.__getitem__-toggle" onclick="return toggle('BioSequence.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.__getitem__-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-31', '_info', 'link-14');">_info</a></tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name" targets="Method obitools.BioSequence.getSubSeq()=obitools.BioSequence-class.html#getSubSeq"><a title="obitools.BioSequence.getSubSeq" class="py-name" href="#" onclick="return doclink('link-32', 'getSubSeq', 'link-32');">getSubSeq</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt> </tt>
</div><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="BioSequence.__setitem__"></a><div id="BioSequence.__setitem__-def"><a name="L147"></a><tt class="py-lineno">147</tt> <a class="py-toggle" href="#" id="BioSequence.__setitem__-toggle" onclick="return toggle('BioSequence.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">,</tt><tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.__setitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.__setitem__-expanded"><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-33', '_info', 'link-14');">_info</a></tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-34" class="py-name"><a title="obitools.ecotag.parser.EcoTagFileIterator.value" class="py-name" href="#" onclick="return doclink('link-34', 'value', 'link-19');">value</a></tt> </tt>
</div><a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> </tt>
<a name="BioSequence.__delitem__"></a><div id="BioSequence.__delitem__-def"><a name="L150"></a><tt class="py-lineno">150</tt> <a class="py-toggle" href="#" id="BioSequence.__delitem__-toggle" onclick="return toggle('BioSequence.__delitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#__delitem__">__delitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.__delitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.__delitem__-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-35', '_info', 'link-14');">_info</a></tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">TypeError</tt><tt class="py-op">,</tt><tt class="py-name">key</tt> </tt>
</div><a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> </tt>
<a name="BioSequence.__iter__"></a><div id="BioSequence.__iter__-def"><a name="L156"></a><tt class="py-lineno">156</tt> <a class="py-toggle" href="#" id="BioSequence.__iter__-toggle" onclick="return toggle('BioSequence.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#__iter__">__iter__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.__iter__-expanded"><a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-docstring">'''</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> Iterate through the sequence symbols</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"> '''</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">iter</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="BioSequence.__len__"></a><div id="BioSequence.__len__-def"><a name="L162"></a><tt class="py-lineno">162</tt> <a class="py-toggle" href="#" id="BioSequence.__len__-toggle" onclick="return toggle('BioSequence.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.__len__-expanded"><a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> </tt>
<a name="BioSequence.__contains__"></a><div id="BioSequence.__contains__-def"><a name="L165"></a><tt class="py-lineno">165</tt> <a class="py-toggle" href="#" id="BioSequence.__contains__-toggle" onclick="return toggle('BioSequence.__contains__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#__contains__">__contains__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.__contains__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.__contains__-expanded"><a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-36', '_info', 'link-14');">_info</a></tt> </tt>
</div><a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt>
<a name="BioSequence.iteritems"></a><div id="BioSequence.iteritems-def"><a name="L168"></a><tt class="py-lineno">168</tt> <a class="py-toggle" href="#" id="BioSequence.iteritems-toggle" onclick="return toggle('BioSequence.iteritems');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#iteritems">iteritems</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.iteritems-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.iteritems-expanded"><a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-37', '_info', 'link-14');">_info</a></tt><tt class="py-op">.</tt><tt id="link-38" class="py-name" targets="Method obitools.BioSequence.iteritems()=obitools.BioSequence-class.html#iteritems,Method obitools.WrappedBioSequence.iteritems()=obitools.WrappedBioSequence-class.html#iteritems"><a title="obitools.BioSequence.iteritems
obitools.WrappedBioSequence.iteritems" class="py-name" href="#" onclick="return doclink('link-38', 'iteritems', 'link-38');">iteritems</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> </tt>
<a name="BioSequence.items"></a><div id="BioSequence.items-def"><a name="L171"></a><tt class="py-lineno">171</tt> <a class="py-toggle" href="#" id="BioSequence.items-toggle" onclick="return toggle('BioSequence.items');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#items">items</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.items-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.items-expanded"><a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name"><a title="obitools.BioSequence.iteritems
obitools.WrappedBioSequence.iteritems" class="py-name" href="#" onclick="return doclink('link-39', 'iteritems', 'link-38');">iteritems</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> </tt>
<a name="BioSequence.iterkeys"></a><div id="BioSequence.iterkeys-def"><a name="L174"></a><tt class="py-lineno">174</tt> <a class="py-toggle" href="#" id="BioSequence.iterkeys-toggle" onclick="return toggle('BioSequence.iterkeys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#iterkeys">iterkeys</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.iterkeys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.iterkeys-expanded"><a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-40', '_info', 'link-14');">_info</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Method obitools.BioSequence.iterkeys()=obitools.BioSequence-class.html#iterkeys,Method obitools.WrappedBioSequence.iterkeys()=obitools.WrappedBioSequence-class.html#iterkeys"><a title="obitools.BioSequence.iterkeys
obitools.WrappedBioSequence.iterkeys" class="py-name" href="#" onclick="return doclink('link-41', 'iterkeys', 'link-41');">iterkeys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> </tt>
<a name="BioSequence.keys"></a><div id="BioSequence.keys-def"><a name="L177"></a><tt class="py-lineno">177</tt> <a class="py-toggle" href="#" id="BioSequence.keys-toggle" onclick="return toggle('BioSequence.keys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#keys">keys</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.keys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.keys-expanded"><a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name"><a title="obitools.BioSequence.iterkeys
obitools.WrappedBioSequence.iterkeys" class="py-name" href="#" onclick="return doclink('link-42', 'iterkeys', 'link-41');">iterkeys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> </tt>
<a name="BioSequence.getTags"></a><div id="BioSequence.getTags-def"><a name="L180"></a><tt class="py-lineno">180</tt> <a class="py-toggle" href="#" id="BioSequence.getTags-toggle" onclick="return toggle('BioSequence.getTags');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#getTags">getTags</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.getTags-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.getTags-expanded"><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-43', '_info', 'link-14');">_info</a></tt> </tt>
</div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="BioSequence.getRoot"></a><div id="BioSequence.getRoot-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="BioSequence.getRoot-toggle" onclick="return toggle('BioSequence.getRoot');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#getRoot">getRoot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.getRoot-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.getRoot-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt> </tt>
</div><a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> </tt>
<a name="BioSequence.getWrappers"></a><div id="BioSequence.getWrappers-def"><a name="L186"></a><tt class="py-lineno">186</tt> <a class="py-toggle" href="#" id="BioSequence.getWrappers-toggle" onclick="return toggle('BioSequence.getWrappers');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#getWrappers">getWrappers</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.getWrappers-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.getWrappers-expanded"><a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-string">'_wrappers'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_wrappers</tt><tt class="py-op">=</tt><tt id="link-44" class="py-name" targets="Class obitools.WrapperSet=obitools.WrapperSet-class.html"><a title="obitools.WrapperSet" class="py-name" href="#" onclick="return doclink('link-44', 'WrapperSet', 'link-44');">WrapperSet</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_wrappers</tt> </tt>
</div><a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> </tt>
<a name="BioSequence.register"></a><div id="BioSequence.register-def"><a name="L191"></a><tt class="py-lineno">191</tt> <a class="py-toggle" href="#" id="BioSequence.register-toggle" onclick="return toggle('BioSequence.register');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#register">register</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">wrapper</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence.register-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence.register-expanded"><a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Variable obitools.BioSequence.wrappers=obitools.BioSequence-class.html#wrappers"><a title="obitools.BioSequence.wrappers" class="py-name" href="#" onclick="return doclink('link-45', 'wrappers', 'link-45');">wrappers</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method obitools.carto.SubLevel.add()=obitools.carto.SubLevel-class.html#add,Method obitools.svg.Scene.add()=obitools.svg.Scene-class.html#add"><a title="obitools.carto.SubLevel.add
obitools.svg.Scene.add" class="py-name" href="#" onclick="return doclink('link-46', 'add', 'link-46');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">ref</tt><tt class="py-op">(</tt><tt class="py-name">wrapper</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method obitools.BioSequence._unregister()=obitools.BioSequence-class.html#_unregister"><a title="obitools.BioSequence._unregister" class="py-name" href="#" onclick="return doclink('link-47', '_unregister', 'link-47');">_unregister</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> </tt>
<a name="BioSequence._unregister"></a><div id="BioSequence._unregister-def"><a name="L194"></a><tt class="py-lineno">194</tt> <a class="py-toggle" href="#" id="BioSequence._unregister-toggle" onclick="return toggle('BioSequence._unregister');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.BioSequence-class.html#_unregister">_unregister</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">ref</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BioSequence._unregister-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="BioSequence._unregister-expanded"><a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="obitools.BioSequence.wrappers" class="py-name" href="#" onclick="return doclink('link-48', 'wrappers', 'link-45');">wrappers</a></tt><tt class="py-op">.</tt><tt class="py-name">remove</tt><tt class="py-op">(</tt><tt class="py-name">ref</tt><tt class="py-op">)</tt> </tt>
</div><a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt id="link-49" class="py-name"><a title="obitools.BioSequence.wrappers" class="py-name" href="#" onclick="return doclink('link-49', 'wrappers', 'link-45');">wrappers</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-50" class="py-name" targets="Method obitools.BioSequence.getWrappers()=obitools.BioSequence-class.html#getWrappers"><a title="obitools.BioSequence.getWrappers" class="py-name" href="#" onclick="return doclink('link-50', 'getWrappers', 'link-50');">getWrappers</a></tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-string">''</tt><tt class="py-op">)</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt id="link-51" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-51', 'definition', 'link-15');">definition</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-52" class="py-name" targets="Method obitools.BioSequence.getDefinition()=obitools.BioSequence-class.html#getDefinition,Method obitools.WrappedBioSequence.getDefinition()=obitools.WrappedBioSequence-class.html#getDefinition,Method obitools.cns.quality.QualitySequence.getDefinition()=obitools.cns.quality.QualitySequence-class.html#getDefinition"><a title="obitools.BioSequence.getDefinition
obitools.WrappedBioSequence.getDefinition
obitools.cns.quality.QualitySequence.getDefinition" class="py-name" href="#" onclick="return doclink('link-52', 'getDefinition', 'link-52');">getDefinition</a></tt><tt class="py-op">,</tt> <tt id="link-53" class="py-name" targets="Method obitools.BioSequence.setDefinition()=obitools.BioSequence-class.html#setDefinition,Method obitools.cns.quality.QualitySequence.setDefinition()=obitools.cns.quality.QualitySequence-class.html#setDefinition"><a title="obitools.BioSequence.setDefinition
obitools.cns.quality.QualitySequence.setDefinition" class="py-name" href="#" onclick="return doclink('link-53', 'setDefinition', 'link-53');">setDefinition</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"Sequence Definition"</tt><tt class="py-op">)</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt id="link-54" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-54', 'id', 'link-17');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-55" class="py-name" targets="Method obitools.BioSequence.getId()=obitools.BioSequence-class.html#getId,Method obitools.DNAComplementSequence.getId()=obitools.DNAComplementSequence-class.html#getId,Method obitools.WrappedBioSequence.getId()=obitools.WrappedBioSequence-class.html#getId,Method obitools.cns.quality.QualitySequence.getId()=obitools.cns.quality.QualitySequence-class.html#getId"><a title="obitools.BioSequence.getId
obitools.DNAComplementSequence.getId
obitools.WrappedBioSequence.getId
obitools.cns.quality.QualitySequence.getId" class="py-name" href="#" onclick="return doclink('link-55', 'getId', 'link-55');">getId</a></tt><tt class="py-op">,</tt> <tt id="link-56" class="py-name" targets="Method obitools.BioSequence.setId()=obitools.BioSequence-class.html#setId,Method obitools.cns.quality.QualitySequence.setId()=obitools.cns.quality.QualitySequence-class.html#setId"><a title="obitools.BioSequence.setId
obitools.cns.quality.QualitySequence.setId" class="py-name" href="#" onclick="return doclink('link-56', 'setId', 'link-56');">setId</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">'Sequence identifier'</tt><tt class="py-op">)</tt> </tt>
</div><a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> </tt>
<a name="NucSequence"></a><div id="NucSequence-def"><a name="L203"></a><tt class="py-lineno">203</tt> <a class="py-toggle" href="#" id="NucSequence-toggle" onclick="return toggle('NucSequence');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.NucSequence-class.html">NucSequence</a><tt class="py-op">(</tt><tt class="py-base-class">BioSequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NucSequence-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="NucSequence-expanded"><a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> </tt>
<a name="NucSequence.complement"></a><div id="NucSequence.complement-def"><a name="L205"></a><tt class="py-lineno">205</tt> <a class="py-toggle" href="#" id="NucSequence.complement-toggle" onclick="return toggle('NucSequence.complement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.NucSequence-class.html#complement">complement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NucSequence.complement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NucSequence.complement-expanded"><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-57" class="py-name" targets="Class obitools.DNAComplementSequence=obitools.DNAComplementSequence-class.html"><a title="obitools.DNAComplementSequence" class="py-name" href="#" onclick="return doclink('link-57', 'DNAComplementSequence', 'link-57');">DNAComplementSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
</div><a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> </tt>
<a name="NucSequence.isNucleotide"></a><div id="NucSequence.isNucleotide-def"><a name="L208"></a><tt class="py-lineno">208</tt> <a class="py-toggle" href="#" id="NucSequence.isNucleotide-toggle" onclick="return toggle('NucSequence.isNucleotide');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.NucSequence-class.html#isNucleotide">isNucleotide</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="NucSequence.isNucleotide-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="NucSequence.isNucleotide-expanded"><a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-58" class="py-name" targets="Variable obitools.SVGdraw.True=obitools.SVGdraw-module.html#True"><a title="obitools.SVGdraw.True" class="py-name" href="#" onclick="return doclink('link-58', 'True', 'link-58');">True</a></tt> </tt>
</div></div><a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> </tt>
<a name="AASequence"></a><div id="AASequence-def"><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <a class="py-toggle" href="#" id="AASequence-toggle" onclick="return toggle('AASequence');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.AASequence-class.html">AASequence</a><tt class="py-op">(</tt><tt class="py-base-class">BioSequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AASequence-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="AASequence-expanded"><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> </tt>
<a name="AASequence.isNucleotide"></a><div id="AASequence.isNucleotide-def"><a name="L214"></a><tt class="py-lineno">214</tt> <a class="py-toggle" href="#" id="AASequence.isNucleotide-toggle" onclick="return toggle('AASequence.isNucleotide');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.AASequence-class.html#isNucleotide">isNucleotide</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="AASequence.isNucleotide-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="AASequence.isNucleotide-expanded"><a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-59" class="py-name" targets="Variable obitools.SVGdraw.False=obitools.SVGdraw-module.html#False"><a title="obitools.SVGdraw.False" class="py-name" href="#" onclick="return doclink('link-59', 'False', 'link-59');">False</a></tt> </tt>
</div></div><a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence"></a><div id="WrappedBioSequence-def"><a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <a class="py-toggle" href="#" id="WrappedBioSequence-toggle" onclick="return toggle('WrappedBioSequence');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html">WrappedBioSequence</a><tt class="py-op">(</tt><tt class="py-base-class">BioSequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="WrappedBioSequence-expanded"><a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.__init__"></a><div id="WrappedBioSequence.__init__-def"><a name="L220"></a><tt class="py-lineno">220</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.__init__-toggle" onclick="return toggle('WrappedBioSequence.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">reference</tt><tt class="py-op">,</tt><tt class="py-param">id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">definition</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-param">info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.__init__-expanded"><a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_wrapped</tt> <tt class="py-op">=</tt> <tt class="py-name">reference</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">reference</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name" targets="Method obitools.BioSequence.register()=obitools.BioSequence-class.html#register,Method obitools.parallel.TaskPool.register()=obitools.parallel.TaskPool-class.html#register"><a title="obitools.BioSequence.register
obitools.parallel.TaskPool.register" class="py-name" href="#" onclick="return doclink('link-60', 'register', 'link-60');">register</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_id</tt><tt class="py-op">=</tt><tt id="link-61" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-61', 'id', 'link-17');">id</a></tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-62', 'definition', 'link-15');">definition</a></tt><tt class="py-op">=</tt><tt id="link-63" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-63', 'definition', 'link-15');">definition</a></tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-64', '_info', 'link-14');">_info</a></tt><tt class="py-op">=</tt><tt class="py-name">info</tt> </tt>
</div><a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.getWrapped"></a><div id="WrappedBioSequence.getWrapped-def"><a name="L227"></a><tt class="py-lineno">227</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.getWrapped-toggle" onclick="return toggle('WrappedBioSequence.getWrapped');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#getWrapped">getWrapped</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.getWrapped-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.getWrapped-expanded"><a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_wrapped</tt> </tt>
</div><a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.getDefinition"></a><div id="WrappedBioSequence.getDefinition-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.getDefinition-toggle" onclick="return toggle('WrappedBioSequence.getDefinition');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#getDefinition">getDefinition</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.getDefinition-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.getDefinition-expanded"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_definition</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-string">"%s Wrapped"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name" targets="Variable obitools.WrappedBioSequence.wrapped=obitools.WrappedBioSequence-class.html#wrapped"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-65', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-66', 'definition', 'link-15');">definition</a></tt><tt class="py-op">)</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">d</tt> </tt>
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.getId"></a><div id="WrappedBioSequence.getId-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.getId-toggle" onclick="return toggle('WrappedBioSequence.getId');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#getId">getId</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.getId-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.getId-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_id</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-string">"%s_WBS"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-67', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-68" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-68', 'id', 'link-17');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">d</tt> </tt>
</div><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.isNucleotide"></a><div id="WrappedBioSequence.isNucleotide-def"><a name="L238"></a><tt class="py-lineno">238</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.isNucleotide-toggle" onclick="return toggle('WrappedBioSequence.isNucleotide');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#isNucleotide">isNucleotide</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.isNucleotide-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.isNucleotide-expanded"><a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-69" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-69', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-70" class="py-name" targets="Method obitools.AASequence.isNucleotide()=obitools.AASequence-class.html#isNucleotide,Method obitools.NucSequence.isNucleotide()=obitools.NucSequence-class.html#isNucleotide,Method obitools.WrappedBioSequence.isNucleotide()=obitools.WrappedBioSequence-class.html#isNucleotide"><a title="obitools.AASequence.isNucleotide
obitools.NucSequence.isNucleotide
obitools.WrappedBioSequence.isNucleotide" class="py-name" href="#" onclick="return doclink('link-70', 'isNucleotide', 'link-70');">isNucleotide</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.iterkeys"></a><div id="WrappedBioSequence.iterkeys-def"><a name="L242"></a><tt class="py-lineno">242</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.iterkeys-toggle" onclick="return toggle('WrappedBioSequence.iterkeys');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#iterkeys">iterkeys</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.iterkeys-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.iterkeys-expanded"><a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-71" class="py-name"><a title="obitools.utils.iterator.uniqueChain" class="py-name" href="#" onclick="return doclink('link-71', 'uniqueChain', 'link-3');">uniqueChain</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-72', '_info', 'link-14');">_info</a></tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="obitools.BioSequence.iterkeys
obitools.WrappedBioSequence.iterkeys" class="py-name" href="#" onclick="return doclink('link-73', 'iterkeys', 'link-41');">iterkeys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-74" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-74', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="obitools.BioSequence.iterkeys
obitools.WrappedBioSequence.iterkeys" class="py-name" href="#" onclick="return doclink('link-75', 'iterkeys', 'link-41');">iterkeys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.iteritems"></a><div id="WrappedBioSequence.iteritems-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.iteritems-toggle" onclick="return toggle('WrappedBioSequence.iteritems');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#iteritems">iteritems</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.iteritems-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.iteritems-expanded"><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name"><a title="obitools.BioSequence.iterkeys
obitools.WrappedBioSequence.iterkeys" class="py-name" href="#" onclick="return doclink('link-76', 'iterkeys', 'link-41');">iterkeys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-keyword">yield</tt> <tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">,</tt><tt class="py-name">self</tt><tt class="py-op">[</tt><tt class="py-name">x</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.__getitem__"></a><div id="WrappedBioSequence.__getitem__-def"><a name="L250"></a><tt class="py-lineno">250</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.__getitem__-toggle" onclick="return toggle('WrappedBioSequence.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.__getitem__-expanded"><a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">debug</tt><tt class="py-op">(</tt><tt class="py-string">"coucou from WrappedBioSequence.__getitem__"</tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">str</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-77" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-77', '_info', 'link-14');">_info</a></tt><tt class="py-op">:</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-78" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-78', '_info', 'link-14');">_info</a></tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-79" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-79', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-80" class="py-name"><a title="obitools.BioSequence.getSubSeq" class="py-name" href="#" onclick="return doclink('link-80', 'getSubSeq', 'link-32');">getSubSeq</a></tt><tt class="py-op">(</tt><tt class="py-name">key</tt><tt class="py-op">)</tt> </tt>
</div><a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.getSymbolAt"></a><div id="WrappedBioSequence.getSymbolAt-def"><a name="L260"></a><tt class="py-lineno">260</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.getSymbolAt-toggle" onclick="return toggle('WrappedBioSequence.getSymbolAt');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#getSymbolAt">getSymbolAt</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.getSymbolAt-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.getSymbolAt-expanded"><a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-81" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-81', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-82" class="py-name"><a title="obitools.BioSequence.getSymbolAt
obitools.DNAComplementSequence.getSymbolAt
obitools.WrappedBioSequence.getSymbolAt" class="py-name" href="#" onclick="return doclink('link-82', 'getSymbolAt', 'link-25');">getSymbolAt</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name" targets="Method obitools.WrappedBioSequence.posInWrapped()=obitools.WrappedBioSequence-class.html#posInWrapped"><a title="obitools.WrappedBioSequence.posInWrapped" class="py-name" href="#" onclick="return doclink('link-83', 'posInWrapped', 'link-83');">posInWrapped</a></tt><tt class="py-op">(</tt><tt class="py-name">position</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.posInWrapped"></a><div id="WrappedBioSequence.posInWrapped-def"><a name="L263"></a><tt class="py-lineno">263</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.posInWrapped-toggle" onclick="return toggle('WrappedBioSequence.posInWrapped');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#posInWrapped">posInWrapped</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">,</tt><tt class="py-param">reference</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.posInWrapped-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.posInWrapped-expanded"><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">reference</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt class="py-name">reference</tt> <tt class="py-keyword">is</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-84', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">:</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name" targets="Method obitools.DNAComplementSequence._posInWrapped()=obitools.DNAComplementSequence-class.html#_posInWrapped,Method obitools.SubSequence._posInWrapped()=obitools.SubSequence-class.html#_posInWrapped,Method obitools.WrappedBioSequence._posInWrapped()=obitools.WrappedBioSequence-class.html#_posInWrapped,Method obitools.align.homopolymere.HomoNucBioSeq._posInWrapped()=obitools.align.homopolymere.HomoNucBioSeq-class.html#_posInWrapped"><a title="obitools.DNAComplementSequence._posInWrapped
obitools.SubSequence._posInWrapped
obitools.WrappedBioSequence._posInWrapped
obitools.align.homopolymere.HomoNucBioSeq._posInWrapped" class="py-name" href="#" onclick="return doclink('link-85', '_posInWrapped', 'link-85');">_posInWrapped</a></tt><tt class="py-op">(</tt><tt class="py-name">position</tt><tt class="py-op">)</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-86', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-87" class="py-name"><a title="obitools.WrappedBioSequence.posInWrapped" class="py-name" href="#" onclick="return doclink('link-87', 'posInWrapped', 'link-83');">posInWrapped</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="obitools.DNAComplementSequence._posInWrapped
obitools.SubSequence._posInWrapped
obitools.WrappedBioSequence._posInWrapped
obitools.align.homopolymere.HomoNucBioSeq._posInWrapped" class="py-name" href="#" onclick="return doclink('link-88', '_posInWrapped', 'link-85');">_posInWrapped</a></tt><tt class="py-op">(</tt><tt class="py-name">position</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-name">reference</tt><tt class="py-op">)</tt> </tt>
</div><a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.getStr"></a><div id="WrappedBioSequence.getStr-def"><a name="L270"></a><tt class="py-lineno">270</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.getStr-toggle" onclick="return toggle('WrappedBioSequence.getStr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#getStr">getStr</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.getStr-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.getStr-expanded"><a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-89" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-89', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence.getRoot"></a><div id="WrappedBioSequence.getRoot-def"><a name="L273"></a><tt class="py-lineno">273</tt> <a class="py-toggle" href="#" id="WrappedBioSequence.getRoot-toggle" onclick="return toggle('WrappedBioSequence.getRoot');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#getRoot">getRoot</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence.getRoot-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence.getRoot-expanded"><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-90', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-91" class="py-name" targets="Method obitools.BioSequence.getRoot()=obitools.BioSequence-class.html#getRoot,Method obitools.WrappedBioSequence.getRoot()=obitools.WrappedBioSequence-class.html#getRoot,Method obitools.tree.Tree.getRoot()=obitools.tree.Tree-class.html#getRoot"><a title="obitools.BioSequence.getRoot
obitools.WrappedBioSequence.getRoot
obitools.tree.Tree.getRoot" class="py-name" href="#" onclick="return doclink('link-91', 'getRoot', 'link-91');">getRoot</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="WrappedBioSequence._posInWrapped"></a><div id="WrappedBioSequence._posInWrapped-def"><a name="L276"></a><tt class="py-lineno">276</tt> <a class="py-toggle" href="#" id="WrappedBioSequence._posInWrapped-toggle" onclick="return toggle('WrappedBioSequence._posInWrapped');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.WrappedBioSequence-class.html#_posInWrapped">_posInWrapped</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="WrappedBioSequence._posInWrapped-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="WrappedBioSequence._posInWrapped-expanded"><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">position</tt> </tt>
</div><a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt id="link-92" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-92', 'definition', 'link-15');">definition</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-93" class="py-name"><a title="obitools.BioSequence.getDefinition
obitools.WrappedBioSequence.getDefinition
obitools.cns.quality.QualitySequence.getDefinition" class="py-name" href="#" onclick="return doclink('link-93', 'getDefinition', 'link-52');">getDefinition</a></tt><tt class="py-op">,</tt><tt id="link-94" class="py-name" targets="Class obitools.BioSequence=obitools.BioSequence-class.html"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-94', 'BioSequence', 'link-94');">BioSequence</a></tt><tt class="py-op">.</tt><tt id="link-95" class="py-name"><a title="obitools.BioSequence.setDefinition
obitools.cns.quality.QualitySequence.setDefinition" class="py-name" href="#" onclick="return doclink('link-95', 'setDefinition', 'link-53');">setDefinition</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"Sequence Definition"</tt><tt class="py-op">)</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt id="link-96" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-96', 'id', 'link-17');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-97" class="py-name"><a title="obitools.BioSequence.getId
obitools.DNAComplementSequence.getId
obitools.WrappedBioSequence.getId
obitools.cns.quality.QualitySequence.getId" class="py-name" href="#" onclick="return doclink('link-97', 'getId', 'link-55');">getId</a></tt><tt class="py-op">,</tt><tt id="link-98" class="py-name"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-98', 'BioSequence', 'link-94');">BioSequence</a></tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="obitools.BioSequence.setId
obitools.cns.quality.QualitySequence.setId" class="py-name" href="#" onclick="return doclink('link-99', 'setId', 'link-56');">setId</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"Sequence Identifier"</tt><tt class="py-op">)</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt id="link-100" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-100', 'wrapped', 'link-65');">wrapped</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-101" class="py-name" targets="Method obitools.WrappedBioSequence.getWrapped()=obitools.WrappedBioSequence-class.html#getWrapped"><a title="obitools.WrappedBioSequence.getWrapped" class="py-name" href="#" onclick="return doclink('link-101', 'getWrapped', 'link-101');">getWrapped</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"Wrapped's Docstring"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> </tt>
<a name="SubSequence"></a><div id="SubSequence-def"><a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <a class="py-toggle" href="#" id="SubSequence-toggle" onclick="return toggle('SubSequence');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.SubSequence-class.html">SubSequence</a><tt class="py-op">(</tt><tt class="py-base-class">WrappedBioSequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubSequence-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SubSequence-expanded"><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-decorator">@</tt><tt class="py-decorator">staticmethod</tt> </tt>
<a name="SubSequence._sign"></a><div id="SubSequence._sign-def"><a name="L289"></a><tt class="py-lineno">289</tt> <a class="py-toggle" href="#" id="SubSequence._sign-toggle" onclick="return toggle('SubSequence._sign');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.SubSequence-class.html#_sign">_sign</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubSequence._sign-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubSequence._sign-expanded"><a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">x</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">x</tt> <tt class="py-op">&lt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> </tt>
<a name="SubSequence.__init__"></a><div id="SubSequence.__init__-def"><a name="L296"></a><tt class="py-lineno">296</tt> <a class="py-toggle" href="#" id="SubSequence.__init__-toggle" onclick="return toggle('SubSequence.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.SubSequence-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">reference</tt><tt class="py-op">,</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-param">location</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-param">start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">stop</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-param">id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">definition</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-param">info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubSequence.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubSequence.__init__-expanded"><a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt id="link-102" class="py-name" targets="Class obitools.WrappedBioSequence=obitools.WrappedBioSequence-class.html"><a title="obitools.WrappedBioSequence" class="py-name" href="#" onclick="return doclink('link-102', 'WrappedBioSequence', 'link-102');">WrappedBioSequence</a></tt><tt class="py-op">.</tt><tt id="link-103" class="py-name" targets="Method obitools.BioSequence.__init__()=obitools.BioSequence-class.html#__init__,Method obitools.DNAComplementSequence.__init__()=obitools.DNAComplementSequence-class.html#__init__,Method obitools.SVGdraw.SVGelement.__init__()=obitools.SVGdraw.SVGelement-class.html#__init__,Method obitools.SVGdraw.animate.__init__()=obitools.SVGdraw.animate-class.html#__init__,Method obitools.SVGdraw.animateColor.__init__()=obitools.SVGdraw.animateColor-class.html#__init__,Method obitools.SVGdraw.animateMotion.__init__()=obitools.SVGdraw.animateMotion-class.html#__init__,Method obitools.SVGdraw.animateTransform.__init__()=obitools.SVGdraw.animateTransform-class.html#__init__,Method obitools.SVGdraw.circle.__init__()=obitools.SVGdraw.circle-class.html#__init__,Method obitools.SVGdraw.cursor.__init__()=obitools.SVGdraw.cursor-class.html#__init__,Method obitools.SVGdraw.defs.__init__()=obitools.SVGdraw.defs-class.html#__init__,Method obitools.SVGdraw.description.__init__()=obitools.SVGdraw.description-class.html#__init__,Method obitools.SVGdraw.drawing.__init__()=obitools.SVGdraw.drawing-class.html#__init__,Method obitools.SVGdraw.ellipse.__init__()=obitools.SVGdraw.ellipse-class.html#__init__,Method obitools.SVGdraw.group.__init__()=obitools.SVGdraw.group-class.html#__init__,Method obitools.SVGdraw.image.__init__()=obitools.SVGdraw.image-class.html#__init__,Method obitools.SVGdraw.line.__init__()=obitools.SVGdraw.line-class.html#__init__,Method obitools.SVGdraw.lineargradient.__init__()=obitools.SVGdraw.lineargradient-class.html#__init__,Method obitools.SVGdraw.link.__init__()=obitools.SVGdraw.link-class.html#__init__,Method obitools.SVGdraw.marker.__init__()=obitools.SVGdraw.marker-class.html#__init__,Method obitools.SVGdraw.path.__init__()=obitools.SVGdraw.path-class.html#__init__,Method obitools.SVGdraw.pathdata.__init__()=obitools.SVGdraw.pathdata-class.html#__init__,Method obitools.SVGdraw.pattern.__init__()=obitools.SVGdraw.pattern-class.html#__init__,Method obitools.SVGdraw.point.__init__()=obitools.SVGdraw.point-class.html#__init__,Method obitools.SVGdraw.polygon.__init__()=obitools.SVGdraw.polygon-class.html#__init__,Method obitools.SVGdraw.polyline.__init__()=obitools.SVGdraw.polyline-class.html#__init__,Method obitools.SVGdraw.radialgradient.__init__()=obitools.SVGdraw.radialgradient-class.html#__init__,Method obitools.SVGdraw.rect.__init__()=obitools.SVGdraw.rect-class.html#__init__,Method obitools.SVGdraw.script.__init__()=obitools.SVGdraw.script-class.html#__init__,Method obitools.SVGdraw.set.__init__()=obitools.SVGdraw.set-class.html#__init__,Method obitools.SVGdraw.spannedtext.__init__()=obitools.SVGdraw.spannedtext-class.html#__init__,Method obitools.SVGdraw.stop.__init__()=obitools.SVGdraw.stop-class.html#__init__,Method obitools.SVGdraw.style.__init__()=obitools.SVGdraw.style-class.html#__init__,Method obitools.SVGdraw.svg.__init__()=obitools.SVGdraw.svg-class.html#__init__,Method obitools.SVGdraw.switch.__init__()=obitools.SVGdraw.switch-class.html#__init__,Method obitools.SVGdraw.symbol.__init__()=obitools.SVGdraw.symbol-class.html#__init__,Method obitools.SVGdraw.text.__init__()=obitools.SVGdraw.text-class.html#__init__,Method obitools.SVGdraw.textpath.__init__()=obitools.SVGdraw.textpath-class.html#__init__,Method obitools.SVGdraw.title.__init__()=obitools.SVGdraw.title-class.html#__init__,Method obitools.SVGdraw.tref.__init__()=obitools.SVGdraw.tref-class.html#__init__,Method obitools.SVGdraw.tspan.__init__()=obitools.SVGdraw.tspan-class.html#__init__,Method obitools.SVGdraw.use.__init__()=obitools.SVGdraw.use-class.html#__init__,Method obitools.SVGdraw.view.__init__()=obitools.SVGdraw.view-class.html#__init__,Method obitools.SubSequence.__init__()=obitools.SubSequence-class.html#__init__,Method obitools.WrappedBioSequence.__init__()=obitools.WrappedBioSequence-class.html#__init__,Method obitools.WrapperSetIterator.__init__()=obitools.WrapperSetIterator-class.html#__init__,Method obitools.align.homopolymere.HomoNucBioSeq.__init__()=obitools.align.homopolymere.HomoNucBioSeq-class.html#__init__,Method obitools.align.ssearch.SsearchParser.__init__()=obitools.align.ssearch.SsearchParser-class.html#__init__,Method obitools.blast.Blast.__init__()=obitools.blast.Blast-class.html#__init__,Method obitools.blast.BlastCovMinFilter.__init__()=obitools.blast.BlastCovMinFilter-class.html#__init__,Method obitools.blast.BlastResultIterator.__init__()=obitools.blast.BlastResultIterator-class.html#__init__,Method obitools.blast.NetBlast.__init__()=obitools.blast.NetBlast-class.html#__init__,Method obitools.carto.Level.__init__()=obitools.carto.Level-class.html#__init__,Method obitools.carto.Map.__init__()=obitools.carto.Map-class.html#__init__,Method obitools.carto.MultiPartFeature.__init__()=obitools.carto.MultiPartFeature-class.html#__init__,Method obitools.carto.SimpleFeature.__init__()=obitools.carto.SimpleFeature-class.html#__init__,Method obitools.carto.SubLevel.__init__()=obitools.carto.SubLevel-class.html#__init__,Method obitools.carto.TagFeature.__init__()=obitools.carto.TagFeature-class.html#__init__,Method obitools.cns.quality.QualitySequence.__init__()=obitools.cns.quality.QualitySequence-class.html#__init__,Method obitools.distances.DistanceMatrix.__init__()=obitools.distances.DistanceMatrix-class.html#__init__,Method obitools.ecopcr.EcoPCRFile.__init__()=obitools.ecopcr.EcoPCRFile-class.html#__init__,Method obitools.ecopcr.annotation.EcoPCRDBAnnotationWriter.__init__()=obitools.ecopcr.annotation.EcoPCRDBAnnotationWriter-class.html#__init__,Method obitools.ecopcr.sequence.EcoPCRDBSequenceIterator.__init__()=obitools.ecopcr.sequence.EcoPCRDBSequenceIterator-class.html#__init__,Method obitools.ecopcr.sequence.EcoPCRDBSequenceWriter.__init__()=obitools.ecopcr.sequence.EcoPCRDBSequenceWriter-class.html#__init__,Method obitools.ecopcr.taxonomy.EcoTaxonomyDB.__init__()=obitools.ecopcr.taxonomy.EcoTaxonomyDB-class.html#__init__,Method obitools.ecopcr.taxonomy.Taxonomy.__init__()=obitools.ecopcr.taxonomy.Taxonomy-class.html#__init__,Method obitools.ecopcr.taxonomy.TaxonomyDump.__init__()=obitools.ecopcr.taxonomy.TaxonomyDump-class.html#__init__,Method obitools.ecotag.parser.EcoTagAbstractIterator.__init__()=obitools.ecotag.parser.EcoTagAbstractIterator-class.html#__init__,Method obitools.ecotag.parser.EcoTagFileIterator.__init__()=obitools.ecotag.parser.EcoTagFileIterator-class.html#__init__,Method obitools.eutils.EFetch.__init__()=obitools.eutils.EFetch-class.html#__init__,Method obitools.eutils.EUtils.__init__()=obitools.eutils.EUtils-class.html#__init__,Method obitools.fast.Fast.__init__()=obitools.fast.Fast-class.html#__init__,Method obitools.format.genericparser.GenericParser.__init__()=obitools.format.genericparser.GenericParser-class.html#__init__,Method obitools.format.ontology.go_obo.Entry.__init__()=obitools.format.ontology.go_obo.Entry-class.html#__init__,Method obitools.format.ontology.go_obo.Header.__init__()=obitools.format.ontology.go_obo.Header-class.html#__init__,Method obitools.format.ontology.go_obo.OBOFile.__init__()=obitools.format.ontology.go_obo.OBOFile-class.html#__init__,Method obitools.format.ontology.go_obo.RelatedTerm.__init__()=obitools.format.ontology.go_obo.RelatedTerm-class.html#__init__,Method obitools.format.ontology.go_obo.Term.__init__()=obitools.format.ontology.go_obo.Term-class.html#__init__,Method obitools.format.ontology.go_obo.Xref.__init__()=obitools.format.ontology.go_obo.Xref-class.html#__init__,Method obitools.genbank.ncbi.Genbank.__init__()=obitools.genbank.ncbi.Genbank-class.html#__init__,Method obitools.goa.parser.GoAFileIterator.__init__()=obitools.goa.parser.GoAFileIterator-class.html#__init__,Method obitools.graph.DiGraph.__init__()=obitools.graph.DiGraph-class.html#__init__,Method obitools.graph.Edge.__init__()=obitools.graph.Edge-class.html#__init__,Method obitools.graph.Graph.__init__()=obitools.graph.Graph-class.html#__init__,Method obitools.graph.Indexer.__init__()=obitools.graph.Indexer-class.html#__init__,Method obitools.graph.Node.__init__()=obitools.graph.Node-class.html#__init__,Method obitools.graph.UndirectedGraph.__init__()=obitools.graph.UndirectedGraph-class.html#__init__,Method obitools.graph.dag.DAG.__init__()=obitools.graph.dag.DAG-class.html#__init__,Method obitools.gzip.GzipFile.__init__()=obitools.gzip.GzipFile-class.html#__init__,Method obitools.location.ComplementLocation.__init__()=obitools.location.ComplementLocation-class.html#__init__,Method obitools.location.CompositeLocation.__init__()=obitools.location.CompositeLocation-class.html#__init__,Method obitools.location.PointLocation.__init__()=obitools.location.PointLocation-class.html#__init__,Method obitools.location.SimpleLocation.__init__()=obitools.location.SimpleLocation-class.html#__init__,Method obitools.location.feature.Feature.__init__()=obitools.location.feature.Feature-class.html#__init__,Method obitools.nucdb.genbank.ncbi.Genbank.__init__()=obitools.nucdb.genbank.ncbi.Genbank-class.html#__init__,Method obitools.obischemas.kb.Connection.__init__()=obitools.obischemas.kb.Connection-class.html#__init__,Method obitools.obischemas.kb.Cursor.__init__()=obitools.obischemas.kb.Cursor-class.html#__init__,Method obitools.obischemas.kb.extern.Connection.__init__()=obitools.obischemas.kb.extern.Connection-class.html#__init__,Method obitools.obischemas.kb.extern.Cursor.__init__()=obitools.obischemas.kb.extern.Cursor-class.html#__init__,Method obitools.obo.go.parser.GOTerm.__init__()=obitools.obo.go.parser.GOTerm-class.html#__init__,Method obitools.obo.parser.DefValue.__init__()=obitools.obo.parser.DefValue-class.html#__init__,Method obitools.obo.parser.NameValue.__init__()=obitools.obo.parser.NameValue-class.html#__init__,Method obitools.obo.parser.NamespaceValue.__init__()=obitools.obo.parser.NamespaceValue-class.html#__init__,Method obitools.obo.parser.OBOEntry.__init__()=obitools.obo.parser.OBOEntry-class.html#__init__,Method obitools.obo.parser.OBOTerm.__init__()=obitools.obo.parser.OBOTerm-class.html#__init__,Method obitools.obo.parser.RelationshipValue.__init__()=obitools.obo.parser.RelationshipValue-class.html#__init__,Method obitools.obo.parser.RemarkValue.__init__()=obitools.obo.parser.RemarkValue-class.html#__init__,Method obitools.obo.parser.SynonymValue.__init__()=obitools.obo.parser.SynonymValue-class.html#__init__,Method obitools.obo.parser.TaggedValue.__init__()=obitools.obo.parser.TaggedValue-class.html#__init__,Method obitools.obo.parser.TrailingModifier.__init__()=obitools.obo.parser.TrailingModifier-class.html#__init__,Method obitools.obo.parser.Xref.__init__()=obitools.obo.parser.Xref-class.html#__init__,Method obitools.obo.parser.XrefValue.__init__()=obitools.obo.parser.XrefValue-class.html#__init__,Method obitools.parallel.Task.__init__()=obitools.parallel.Task-class.html#__init__,Method obitools.parallel.TaskPool.__init__()=obitools.parallel.TaskPool-class.html#__init__,Method obitools.parallel.jobqueue.Job.__init__()=obitools.parallel.jobqueue.Job-class.html#__init__,Method obitools.parallel.jobqueue.JobIterator.__init__()=obitools.parallel.jobqueue.JobIterator-class.html#__init__,Method obitools.parallel.jobqueue.JobPool.__init__()=obitools.parallel.jobqueue.JobPool-class.html#__init__,Method obitools.phylogeny.PhylogenicTree.__init__()=obitools.phylogeny.PhylogenicTree-class.html#__init__,Method obitools.seqdb.AnnotatedAASequence.__init__()=obitools.seqdb.AnnotatedAASequence-class.html#__init__,Method obitools.seqdb.AnnotatedNucSequence.__init__()=obitools.seqdb.AnnotatedNucSequence-class.html#__init__,Method obitools.seqdb.AnnotatedSequence.__init__()=obitools.seqdb.AnnotatedSequence-class.html#__init__,Method obitools.seqdb.genbank.GpepSequence.__init__()=obitools.seqdb.genbank.GpepSequence-class.html#__init__,Method obitools.seqdb.genbank.graph.DiGraph.__init__()=obitools.seqdb.genbank.graph.DiGraph-class.html#__init__,Method obitools.seqdb.genbank.graph.Edge.__init__()=obitools.seqdb.genbank.graph.Edge-class.html#__init__,Method obitools.seqdb.genbank.graph.Graph.__init__()=obitools.seqdb.genbank.graph.Graph-class.html#__init__,Method obitools.seqdb.genbank.graph.Indexer.__init__()=obitools.seqdb.genbank.graph.Indexer-class.html#__init__,Method obitools.seqdb.genbank.graph.Node.__init__()=obitools.seqdb.genbank.graph.Node-class.html#__init__,Method obitools.seqdb.genbank.graph.UndirectedGraph.__init__()=obitools.seqdb.genbank.graph.UndirectedGraph-class.html#__init__,Method obitools.seqdb.genbank.graph.dag.DAG.__init__()=obitools.seqdb.genbank.graph.dag.DAG-class.html#__init__,Method obitools.seqdb.genbank.ncbi.NCBIAccession.__init__()=obitools.seqdb.genbank.ncbi.NCBIAccession-class.html#__init__,Method obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__()=obitools.seqdb.genbank.ncbi.NCBIGenbank-class.html#__init__,Method obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__()=obitools.seqdb.genbank.ncbi.NCBIGenpep-class.html#__init__,Method obitools.sequenceencoder.SeqFragmentEncoder.__init__()=obitools.sequenceencoder.SeqFragmentEncoder-class.html#__init__,Method obitools.solexa.SolexaFile.__init__()=obitools.solexa.SolexaFile-class.html#__init__,Method obitools.solexa.SolexaSequence.__init__()=obitools.solexa.SolexaSequence-class.html#__init__,Method obitools.statistics.noncentralhypergeo.Interval.__init__()=obitools.statistics.noncentralhypergeo.Interval-class.html#__init__,Method obitools.statistics.noncentralhypergeo.Product.__init__()=obitools.statistics.noncentralhypergeo.Product-class.html#__init__,Method obitools.svg.Circle.__init__()=obitools.svg.Circle-class.html#__init__,Method obitools.svg.Line.__init__()=obitools.svg.Line-class.html#__init__,Method obitools.svg.Rectangle.__init__()=obitools.svg.Rectangle-class.html#__init__,Method obitools.svg.Scene.__init__()=obitools.svg.Scene-class.html#__init__,Method obitools.svg.Text.__init__()=obitools.svg.Text-class.html#__init__,Method obitools.table.ProjectionIterator.__init__()=obitools.table.ProjectionIterator-class.html#__init__,Method obitools.table.SelectionIterator.__init__()=obitools.table.SelectionIterator-class.html#__init__,Method obitools.table.Table.__init__()=obitools.table.Table-class.html#__init__,Method obitools.table.TableIterator.__init__()=obitools.table.TableIterator-class.html#__init__,Method obitools.table.TableIteratorAsDict.__init__()=obitools.table.TableIteratorAsDict-class.html#__init__,Method obitools.table.TableRow.__init__()=obitools.table.TableRow-class.html#__init__,Method obitools.table.UnionIterator.__init__()=obitools.table.UnionIterator-class.html#__init__,Method obitools.table._Row.__init__()=obitools.table._Row-class.html#__init__,Method obitools.tagmatcher.TagMatcherSequence.__init__()=obitools.tagmatcher.TagMatcherSequence-class.html#__init__,Method obitools.tagmatcher.parser.TagMatcherIterator.__init__()=obitools.tagmatcher.parser.TagMatcherIterator-class.html#__init__,Method obitools.tree.TreeNode.__init__()=obitools.tree.TreeNode-class.html#__init__,Method obitools.utils.CachedDB.__init__()=obitools.utils.CachedDB-class.html#__init__,Method obitools.utils.ColumnFile.__init__()=obitools.utils.ColumnFile-class.html#__init__,Method obitools.zipfile.ZipExtFile.__init__()=obitools.zipfile.ZipExtFile-class.html#__init__,Method obitools.zipfile.ZipFile.__init__()=obitools.zipfile.ZipFile-class.html#__init__,Method obitools.zipfile.ZipInfo.__init__()=obitools.zipfile.ZipInfo-class.html#__init__,Method obitools.zipfile._ZipDecrypter.__init__()=obitools.zipfile._ZipDecrypter-class.html#__init__"><a title="obitools.BioSequence.__init__
obitools.DNAComplementSequence.__init__
obitools.SVGdraw.SVGelement.__init__
obitools.SVGdraw.animate.__init__
obitools.SVGdraw.animateColor.__init__
obitools.SVGdraw.animateMotion.__init__
obitools.SVGdraw.animateTransform.__init__
obitools.SVGdraw.circle.__init__
obitools.SVGdraw.cursor.__init__
obitools.SVGdraw.defs.__init__
obitools.SVGdraw.description.__init__
obitools.SVGdraw.drawing.__init__
obitools.SVGdraw.ellipse.__init__
obitools.SVGdraw.group.__init__
obitools.SVGdraw.image.__init__
obitools.SVGdraw.line.__init__
obitools.SVGdraw.lineargradient.__init__
obitools.SVGdraw.link.__init__
obitools.SVGdraw.marker.__init__
obitools.SVGdraw.path.__init__
obitools.SVGdraw.pathdata.__init__
obitools.SVGdraw.pattern.__init__
obitools.SVGdraw.point.__init__
obitools.SVGdraw.polygon.__init__
obitools.SVGdraw.polyline.__init__
obitools.SVGdraw.radialgradient.__init__
obitools.SVGdraw.rect.__init__
obitools.SVGdraw.script.__init__
obitools.SVGdraw.set.__init__
obitools.SVGdraw.spannedtext.__init__
obitools.SVGdraw.stop.__init__
obitools.SVGdraw.style.__init__
obitools.SVGdraw.svg.__init__
obitools.SVGdraw.switch.__init__
obitools.SVGdraw.symbol.__init__
obitools.SVGdraw.text.__init__
obitools.SVGdraw.textpath.__init__
obitools.SVGdraw.title.__init__
obitools.SVGdraw.tref.__init__
obitools.SVGdraw.tspan.__init__
obitools.SVGdraw.use.__init__
obitools.SVGdraw.view.__init__
obitools.SubSequence.__init__
obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.homopolymere.HomoNucBioSeq.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.carto.Level.__init__
obitools.carto.Map.__init__
obitools.carto.MultiPartFeature.__init__
obitools.carto.SimpleFeature.__init__
obitools.carto.SubLevel.__init__
obitools.carto.TagFeature.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.annotation.EcoPCRDBAnnotationWriter.__init__
obitools.ecopcr.sequence.EcoPCRDBSequenceIterator.__init__
obitools.ecopcr.sequence.EcoPCRDBSequenceWriter.__init__
obitools.ecopcr.taxonomy.EcoTaxonomyDB.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.ecopcr.taxonomy.TaxonomyDump.__init__
obitools.ecotag.parser.EcoTagAbstractIterator.__init__
obitools.ecotag.parser.EcoTagFileIterator.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.format.ontology.go_obo.Entry.__init__
obitools.format.ontology.go_obo.Header.__init__
obitools.format.ontology.go_obo.OBOFile.__init__
obitools.format.ontology.go_obo.RelatedTerm.__init__
obitools.format.ontology.go_obo.Term.__init__
obitools.format.ontology.go_obo.Xref.__init__
obitools.genbank.ncbi.Genbank.__init__
obitools.goa.parser.GoAFileIterator.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.nucdb.genbank.ncbi.Genbank.__init__
obitools.obischemas.kb.Connection.__init__
obitools.obischemas.kb.Cursor.__init__
obitools.obischemas.kb.extern.Connection.__init__
obitools.obischemas.kb.extern.Cursor.__init__
obitools.obo.go.parser.GOTerm.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
obitools.sequenceencoder.SeqFragmentEncoder.__init__
obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
obitools.statistics.noncentralhypergeo.Interval.__init__
obitools.statistics.noncentralhypergeo.Product.__init__
obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tagmatcher.TagMatcherSequence.__init__
obitools.tagmatcher.parser.TagMatcherIterator.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-103', '__init__', 'link-103');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">reference</tt><tt class="py-op">,</tt><tt id="link-104" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-104', 'id', 'link-17');">id</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt id="link-105" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-105', 'definition', 'link-15');">definition</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-106" class="py-name"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-106', 'location', 'link-8');">location</a></tt><tt class="py-op">,</tt> <tt class="py-name">slice</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_location</tt> <tt class="py-op">=</tt> <tt id="link-107" class="py-name"><a title="obitools.location" class="py-name" href="#" onclick="return doclink('link-107', 'location', 'link-8');">location</a></tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-name">step</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">start</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt id="link-108" class="py-name" targets="Variable obitools.location.ComplementLocation.begin=obitools.location.ComplementLocation-class.html#begin,Variable obitools.location.CompositeLocation.begin=obitools.location.CompositeLocation-class.html#begin,Variable obitools.location.Location.begin=obitools.location.Location-class.html#begin,Variable obitools.location.PointLocation.begin=obitools.location.PointLocation-class.html#begin,Variable obitools.location.SimpleLocation.begin=obitools.location.SimpleLocation-class.html#begin,Variable obitools.location.feature.Feature.begin=obitools.location.feature.Feature-class.html#begin,Method obitools.statistics.noncentralhypergeo.Interval.begin()=obitools.statistics.noncentralhypergeo.Interval-class.html#begin"><a title="obitools.location.ComplementLocation.begin
obitools.location.CompositeLocation.begin
obitools.location.Location.begin
obitools.location.PointLocation.begin
obitools.location.SimpleLocation.begin
obitools.location.feature.Feature.begin
obitools.statistics.noncentralhypergeo.Interval.begin" class="py-name" href="#" onclick="return doclink('link-108', 'begin', 'link-108');">begin</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">;</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt id="link-109" class="py-name" targets="Class obitools.SVGdraw.stop=obitools.SVGdraw.stop-class.html"><a title="obitools.SVGdraw.stop" class="py-name" href="#" onclick="return doclink('link-109', 'stop', 'link-109');">stop</a></tt><tt class="py-op">,</tt><tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt id="link-110" class="py-name" targets="Variable obitools.location.ComplementLocation.end=obitools.location.ComplementLocation-class.html#end,Variable obitools.location.CompositeLocation.end=obitools.location.CompositeLocation-class.html#end,Variable obitools.location.Location.end=obitools.location.Location-class.html#end,Variable obitools.location.PointLocation.end=obitools.location.PointLocation-class.html#end,Variable obitools.location.SimpleLocation.end=obitools.location.SimpleLocation-class.html#end,Variable obitools.location.feature.Feature.end=obitools.location.feature.Feature-class.html#end,Method obitools.statistics.noncentralhypergeo.Interval.end()=obitools.statistics.noncentralhypergeo.Interval-class.html#end"><a title="obitools.location.ComplementLocation.end
obitools.location.CompositeLocation.end
obitools.location.Location.end
obitools.location.PointLocation.end
obitools.location.SimpleLocation.end
obitools.location.feature.Feature.end
obitools.statistics.noncentralhypergeo.Interval.end" class="py-name" href="#" onclick="return doclink('link-110', 'end', 'link-110');">end</a></tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">reference</tt><tt class="py-op">)</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_location</tt><tt class="py-op">=</tt><tt class="py-name">slice</tt><tt class="py-op">(</tt><tt class="py-name">start</tt><tt class="py-op">,</tt><tt id="link-111" class="py-name"><a title="obitools.SVGdraw.stop" class="py-name" href="#" onclick="return doclink('link-111', 'stop', 'link-109');">stop</a></tt><tt class="py-op">,</tt><tt class="py-name">step</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_indices</tt><tt class="py-op">=</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_location</tt><tt class="py-op">.</tt><tt class="py-name">indices</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-112', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_xrange</tt><tt class="py-op">=</tt><tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_indices</tt><tt class="py-op">)</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-113" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-113', '_info', 'link-14');">_info</a></tt><tt class="py-op">[</tt><tt class="py-string">'cut'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt class="py-string">'[%d,%d,%s]'</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_indices</tt> </tt>
</div><a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> </tt>
<a name="SubSequence.__len__"></a><div id="SubSequence.__len__-def"><a name="L317"></a><tt class="py-lineno">317</tt> <a class="py-toggle" href="#" id="SubSequence.__len__-toggle" onclick="return toggle('SubSequence.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.SubSequence-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubSequence.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubSequence.__len__-expanded"><a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_xrange</tt><tt class="py-op">)</tt> </tt>
</div><a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> </tt>
<a name="SubSequence.getStr"></a><div id="SubSequence.getStr-def"><a name="L320"></a><tt class="py-lineno">320</tt> <a class="py-toggle" href="#" id="SubSequence.getStr-toggle" onclick="return toggle('SubSequence.getStr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.SubSequence-class.html#getStr">getStr</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubSequence.getStr-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubSequence.getStr-expanded"><a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> </tt>
<a name="SubSequence.__iter__"></a><div id="SubSequence.__iter__-def"><a name="L323"></a><tt class="py-lineno">323</tt> <a class="py-toggle" href="#" id="SubSequence.__iter__-toggle" onclick="return toggle('SubSequence.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.SubSequence-class.html#__iter__">__iter__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubSequence.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubSequence.__iter__-expanded"><a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-114', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-115" class="py-name"><a title="obitools.BioSequence.getSymbolAt
obitools.DNAComplementSequence.getSymbolAt
obitools.WrappedBioSequence.getSymbolAt" class="py-name" href="#" onclick="return doclink('link-115', 'getSymbolAt', 'link-25');">getSymbolAt</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_indices</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> </tt>
<a name="SubSequence._posInWrapped"></a><div id="SubSequence._posInWrapped-def"><a name="L326"></a><tt class="py-lineno">326</tt> <a class="py-toggle" href="#" id="SubSequence._posInWrapped-toggle" onclick="return toggle('SubSequence._posInWrapped');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.SubSequence-class.html#_posInWrapped">_posInWrapped</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubSequence._posInWrapped-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubSequence._posInWrapped-expanded"><a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_xrange</tt><tt class="py-op">[</tt><tt class="py-name">position</tt><tt class="py-op">]</tt> </tt>
</div><a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> </tt>
<a name="SubSequence.complement"></a><div id="SubSequence.complement-def"><a name="L329"></a><tt class="py-lineno">329</tt> <a class="py-toggle" href="#" id="SubSequence.complement-toggle" onclick="return toggle('SubSequence.complement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.SubSequence-class.html#complement">complement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubSequence.complement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubSequence.complement-expanded"><a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-116', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-117" class="py-name"><a title="obitools.AASequence.isNucleotide
obitools.NucSequence.isNucleotide
obitools.WrappedBioSequence.isNucleotide" class="py-name" href="#" onclick="return doclink('link-117', 'isNucleotide', 'link-70');">isNucleotide</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-118" class="py-name"><a title="obitools.DNAComplementSequence" class="py-name" href="#" onclick="return doclink('link-118', 'DNAComplementSequence', 'link-57');">DNAComplementSequence</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AttributeError</tt> </tt>
</div></div><a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence"></a><div id="DNAComplementSequence-def"><a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <a class="py-toggle" href="#" id="DNAComplementSequence-toggle" onclick="return toggle('DNAComplementSequence');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html">DNAComplementSequence</a><tt class="py-op">(</tt><tt class="py-base-class">WrappedBioSequence</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="DNAComplementSequence-expanded"><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt id="link-119" class="py-name" targets="Variable obitools.DNAComplementSequence._comp=obitools.DNAComplementSequence-class.html#_comp,Variable obitools.location.ComplementLocation._comp=obitools.location.ComplementLocation-class.html#_comp,Variable obitools.sequenceencoder.DNAComplementEncoder._comp=obitools.sequenceencoder.DNAComplementEncoder-class.html#_comp"><a title="obitools.DNAComplementSequence._comp
obitools.location.ComplementLocation._comp
obitools.sequenceencoder.DNAComplementEncoder._comp" class="py-name" href="#" onclick="return doclink('link-119', '_comp', 'link-119');">_comp</a></tt><tt class="py-op">=</tt><tt class="py-op">{</tt><tt class="py-string">'a'</tt><tt class="py-op">:</tt> <tt class="py-string">'t'</tt><tt class="py-op">,</tt> <tt class="py-string">'c'</tt><tt class="py-op">:</tt> <tt class="py-string">'g'</tt><tt class="py-op">,</tt> <tt class="py-string">'g'</tt><tt class="py-op">:</tt> <tt class="py-string">'c'</tt><tt class="py-op">,</tt> <tt class="py-string">'t'</tt><tt class="py-op">:</tt> <tt class="py-string">'a'</tt><tt class="py-op">,</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-string">'r'</tt><tt class="py-op">:</tt> <tt class="py-string">'y'</tt><tt class="py-op">,</tt> <tt class="py-string">'y'</tt><tt class="py-op">:</tt> <tt class="py-string">'r'</tt><tt class="py-op">,</tt> <tt class="py-string">'k'</tt><tt class="py-op">:</tt> <tt class="py-string">'m'</tt><tt class="py-op">,</tt> <tt class="py-string">'m'</tt><tt class="py-op">:</tt> <tt class="py-string">'k'</tt><tt class="py-op">,</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-string">'s'</tt><tt class="py-op">:</tt> <tt class="py-string">'s'</tt><tt class="py-op">,</tt> <tt class="py-string">'w'</tt><tt class="py-op">:</tt> <tt class="py-string">'w'</tt><tt class="py-op">,</tt> <tt class="py-string">'b'</tt><tt class="py-op">:</tt> <tt class="py-string">'v'</tt><tt class="py-op">,</tt> <tt class="py-string">'d'</tt><tt class="py-op">:</tt> <tt class="py-string">'h'</tt><tt class="py-op">,</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-string">'h'</tt><tt class="py-op">:</tt> <tt class="py-string">'d'</tt><tt class="py-op">,</tt> <tt class="py-string">'v'</tt><tt class="py-op">:</tt> <tt class="py-string">'b'</tt><tt class="py-op">,</tt> <tt class="py-string">'n'</tt><tt class="py-op">:</tt> <tt class="py-string">'n'</tt><tt class="py-op">,</tt> <tt class="py-string">'u'</tt><tt class="py-op">:</tt> <tt class="py-string">'a'</tt><tt class="py-op">,</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-string">'-'</tt><tt class="py-op">:</tt> <tt class="py-string">'-'</tt><tt class="py-op">}</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence.__init__"></a><div id="DNAComplementSequence.__init__-def"><a name="L346"></a><tt class="py-lineno">346</tt> <a class="py-toggle" href="#" id="DNAComplementSequence.__init__-toggle" onclick="return toggle('DNAComplementSequence.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">reference</tt><tt class="py-op">,</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-param">id</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-param">definition</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-param">info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DNAComplementSequence.__init__-expanded"><a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt id="link-120" class="py-name"><a title="obitools.WrappedBioSequence" class="py-name" href="#" onclick="return doclink('link-120', 'WrappedBioSequence', 'link-102');">WrappedBioSequence</a></tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="obitools.BioSequence.__init__
obitools.DNAComplementSequence.__init__
obitools.SVGdraw.SVGelement.__init__
obitools.SVGdraw.animate.__init__
obitools.SVGdraw.animateColor.__init__
obitools.SVGdraw.animateMotion.__init__
obitools.SVGdraw.animateTransform.__init__
obitools.SVGdraw.circle.__init__
obitools.SVGdraw.cursor.__init__
obitools.SVGdraw.defs.__init__
obitools.SVGdraw.description.__init__
obitools.SVGdraw.drawing.__init__
obitools.SVGdraw.ellipse.__init__
obitools.SVGdraw.group.__init__
obitools.SVGdraw.image.__init__
obitools.SVGdraw.line.__init__
obitools.SVGdraw.lineargradient.__init__
obitools.SVGdraw.link.__init__
obitools.SVGdraw.marker.__init__
obitools.SVGdraw.path.__init__
obitools.SVGdraw.pathdata.__init__
obitools.SVGdraw.pattern.__init__
obitools.SVGdraw.point.__init__
obitools.SVGdraw.polygon.__init__
obitools.SVGdraw.polyline.__init__
obitools.SVGdraw.radialgradient.__init__
obitools.SVGdraw.rect.__init__
obitools.SVGdraw.script.__init__
obitools.SVGdraw.set.__init__
obitools.SVGdraw.spannedtext.__init__
obitools.SVGdraw.stop.__init__
obitools.SVGdraw.style.__init__
obitools.SVGdraw.svg.__init__
obitools.SVGdraw.switch.__init__
obitools.SVGdraw.symbol.__init__
obitools.SVGdraw.text.__init__
obitools.SVGdraw.textpath.__init__
obitools.SVGdraw.title.__init__
obitools.SVGdraw.tref.__init__
obitools.SVGdraw.tspan.__init__
obitools.SVGdraw.use.__init__
obitools.SVGdraw.view.__init__
obitools.SubSequence.__init__
obitools.WrappedBioSequence.__init__
obitools.WrapperSetIterator.__init__
obitools.align.homopolymere.HomoNucBioSeq.__init__
obitools.align.ssearch.SsearchParser.__init__
obitools.blast.Blast.__init__
obitools.blast.BlastCovMinFilter.__init__
obitools.blast.BlastResultIterator.__init__
obitools.blast.NetBlast.__init__
obitools.carto.Level.__init__
obitools.carto.Map.__init__
obitools.carto.MultiPartFeature.__init__
obitools.carto.SimpleFeature.__init__
obitools.carto.SubLevel.__init__
obitools.carto.TagFeature.__init__
obitools.cns.quality.QualitySequence.__init__
obitools.distances.DistanceMatrix.__init__
obitools.ecopcr.EcoPCRFile.__init__
obitools.ecopcr.annotation.EcoPCRDBAnnotationWriter.__init__
obitools.ecopcr.sequence.EcoPCRDBSequenceIterator.__init__
obitools.ecopcr.sequence.EcoPCRDBSequenceWriter.__init__
obitools.ecopcr.taxonomy.EcoTaxonomyDB.__init__
obitools.ecopcr.taxonomy.Taxonomy.__init__
obitools.ecopcr.taxonomy.TaxonomyDump.__init__
obitools.ecotag.parser.EcoTagAbstractIterator.__init__
obitools.ecotag.parser.EcoTagFileIterator.__init__
obitools.eutils.EFetch.__init__
obitools.eutils.EUtils.__init__
obitools.fast.Fast.__init__
obitools.format.genericparser.GenericParser.__init__
obitools.format.ontology.go_obo.Entry.__init__
obitools.format.ontology.go_obo.Header.__init__
obitools.format.ontology.go_obo.OBOFile.__init__
obitools.format.ontology.go_obo.RelatedTerm.__init__
obitools.format.ontology.go_obo.Term.__init__
obitools.format.ontology.go_obo.Xref.__init__
obitools.genbank.ncbi.Genbank.__init__
obitools.goa.parser.GoAFileIterator.__init__
obitools.graph.DiGraph.__init__
obitools.graph.Edge.__init__
obitools.graph.Graph.__init__
obitools.graph.Indexer.__init__
obitools.graph.Node.__init__
obitools.graph.UndirectedGraph.__init__
obitools.graph.dag.DAG.__init__
obitools.gzip.GzipFile.__init__
obitools.location.ComplementLocation.__init__
obitools.location.CompositeLocation.__init__
obitools.location.PointLocation.__init__
obitools.location.SimpleLocation.__init__
obitools.location.feature.Feature.__init__
obitools.nucdb.genbank.ncbi.Genbank.__init__
obitools.obischemas.kb.Connection.__init__
obitools.obischemas.kb.Cursor.__init__
obitools.obischemas.kb.extern.Connection.__init__
obitools.obischemas.kb.extern.Cursor.__init__
obitools.obo.go.parser.GOTerm.__init__
obitools.obo.parser.DefValue.__init__
obitools.obo.parser.NameValue.__init__
obitools.obo.parser.NamespaceValue.__init__
obitools.obo.parser.OBOEntry.__init__
obitools.obo.parser.OBOTerm.__init__
obitools.obo.parser.RelationshipValue.__init__
obitools.obo.parser.RemarkValue.__init__
obitools.obo.parser.SynonymValue.__init__
obitools.obo.parser.TaggedValue.__init__
obitools.obo.parser.TrailingModifier.__init__
obitools.obo.parser.Xref.__init__
obitools.obo.parser.XrefValue.__init__
obitools.parallel.Task.__init__
obitools.parallel.TaskPool.__init__
obitools.parallel.jobqueue.Job.__init__
obitools.parallel.jobqueue.JobIterator.__init__
obitools.parallel.jobqueue.JobPool.__init__
obitools.phylogeny.PhylogenicTree.__init__
obitools.seqdb.AnnotatedAASequence.__init__
obitools.seqdb.AnnotatedNucSequence.__init__
obitools.seqdb.AnnotatedSequence.__init__
obitools.seqdb.genbank.GpepSequence.__init__
obitools.seqdb.genbank.graph.DiGraph.__init__
obitools.seqdb.genbank.graph.Edge.__init__
obitools.seqdb.genbank.graph.Graph.__init__
obitools.seqdb.genbank.graph.Indexer.__init__
obitools.seqdb.genbank.graph.Node.__init__
obitools.seqdb.genbank.graph.UndirectedGraph.__init__
obitools.seqdb.genbank.graph.dag.DAG.__init__
obitools.seqdb.genbank.ncbi.NCBIAccession.__init__
obitools.seqdb.genbank.ncbi.NCBIGenbank.__init__
obitools.seqdb.genbank.ncbi.NCBIGenpep.__init__
obitools.sequenceencoder.SeqFragmentEncoder.__init__
obitools.solexa.SolexaFile.__init__
obitools.solexa.SolexaSequence.__init__
obitools.statistics.noncentralhypergeo.Interval.__init__
obitools.statistics.noncentralhypergeo.Product.__init__
obitools.svg.Circle.__init__
obitools.svg.Line.__init__
obitools.svg.Rectangle.__init__
obitools.svg.Scene.__init__
obitools.svg.Text.__init__
obitools.table.ProjectionIterator.__init__
obitools.table.SelectionIterator.__init__
obitools.table.Table.__init__
obitools.table.TableIterator.__init__
obitools.table.TableIteratorAsDict.__init__
obitools.table.TableRow.__init__
obitools.table.UnionIterator.__init__
obitools.table._Row.__init__
obitools.tagmatcher.TagMatcherSequence.__init__
obitools.tagmatcher.parser.TagMatcherIterator.__init__
obitools.tree.TreeNode.__init__
obitools.utils.CachedDB.__init__
obitools.utils.ColumnFile.__init__
obitools.zipfile.ZipExtFile.__init__
obitools.zipfile.ZipFile.__init__
obitools.zipfile.ZipInfo.__init__
obitools.zipfile._ZipDecrypter.__init__" class="py-name" href="#" onclick="return doclink('link-121', '__init__', 'link-103');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt><tt class="py-name">reference</tt><tt class="py-op">,</tt><tt id="link-122" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-122', 'id', 'link-17');">id</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt id="link-123" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-123', 'definition', 'link-15');">definition</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">reference</tt><tt class="py-op">.</tt><tt id="link-124" class="py-name"><a title="obitools.AASequence.isNucleotide
obitools.NucSequence.isNucleotide
obitools.WrappedBioSequence.isNucleotide" class="py-name" href="#" onclick="return doclink('link-124', 'isNucleotide', 'link-70');">isNucleotide</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-125" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder._info" class="py-name" href="#" onclick="return doclink('link-125', '_info', 'link-14');">_info</a></tt><tt class="py-op">[</tt><tt class="py-string">'complemented'</tt><tt class="py-op">]</tt><tt class="py-op">=</tt><tt id="link-126" class="py-name"><a title="obitools.SVGdraw.True" class="py-name" href="#" onclick="return doclink('link-126', 'True', 'link-58');">True</a></tt> </tt>
</div><a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence.getId"></a><div id="DNAComplementSequence.getId-def"><a name="L352"></a><tt class="py-lineno">352</tt> <a class="py-toggle" href="#" id="DNAComplementSequence.getId-toggle" onclick="return toggle('DNAComplementSequence.getId');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html#getId">getId</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence.getId-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DNAComplementSequence.getId-expanded"><a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_id</tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-string">"%s_CMP"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-127" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-127', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-128', 'id', 'link-17');">id</a></tt><tt class="py-op">)</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">d</tt> </tt>
</div><a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence.__len__"></a><div id="DNAComplementSequence.__len__-def"><a name="L356"></a><tt class="py-lineno">356</tt> <a class="py-toggle" href="#" id="DNAComplementSequence.__len__-toggle" onclick="return toggle('DNAComplementSequence.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DNAComplementSequence.__len__-expanded"><a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_wrapped</tt><tt class="py-op">)</tt> </tt>
</div><a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence.getStr"></a><div id="DNAComplementSequence.getStr-def"><a name="L359"></a><tt class="py-lineno">359</tt> <a class="py-toggle" href="#" id="DNAComplementSequence.getStr-toggle" onclick="return toggle('DNAComplementSequence.getStr');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html#getStr">getStr</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence.getStr-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DNAComplementSequence.getStr-expanded"><a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">''</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">x</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence.__iter__"></a><div id="DNAComplementSequence.__iter__-def"><a name="L362"></a><tt class="py-lineno">362</tt> <a class="py-toggle" href="#" id="DNAComplementSequence.__iter__-toggle" onclick="return toggle('DNAComplementSequence.__iter__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html#__iter__">__iter__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence.__iter__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DNAComplementSequence.__iter__-expanded"><a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="obitools.BioSequence.getSymbolAt
obitools.DNAComplementSequence.getSymbolAt
obitools.WrappedBioSequence.getSymbolAt" class="py-name" href="#" onclick="return doclink('link-129', 'getSymbolAt', 'link-25');">getSymbolAt</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">x</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence._posInWrapped"></a><div id="DNAComplementSequence._posInWrapped-def"><a name="L365"></a><tt class="py-lineno">365</tt> <a class="py-toggle" href="#" id="DNAComplementSequence._posInWrapped-toggle" onclick="return toggle('DNAComplementSequence._posInWrapped');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html#_posInWrapped">_posInWrapped</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence._posInWrapped-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DNAComplementSequence._posInWrapped-expanded"><a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-name">position</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
</div><a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence.getSymbolAt"></a><div id="DNAComplementSequence.getSymbolAt-def"><a name="L368"></a><tt class="py-lineno">368</tt> <a class="py-toggle" href="#" id="DNAComplementSequence.getSymbolAt-toggle" onclick="return toggle('DNAComplementSequence.getSymbolAt');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html#getSymbolAt">getSymbolAt</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt><tt class="py-param">position</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence.getSymbolAt-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DNAComplementSequence.getSymbolAt-expanded"><a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-130" class="py-name"><a title="obitools.DNAComplementSequence" class="py-name" href="#" onclick="return doclink('link-130', 'DNAComplementSequence', 'link-57');">DNAComplementSequence</a></tt><tt class="py-op">.</tt><tt id="link-131" class="py-name"><a title="obitools.DNAComplementSequence._comp
obitools.location.ComplementLocation._comp
obitools.sequenceencoder.DNAComplementEncoder._comp" class="py-name" href="#" onclick="return doclink('link-131', '_comp', 'link-119');">_comp</a></tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-132', 'wrapped', 'link-65');">wrapped</a></tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="obitools.BioSequence.getSymbolAt
obitools.DNAComplementSequence.getSymbolAt
obitools.WrappedBioSequence.getSymbolAt" class="py-name" href="#" onclick="return doclink('link-133', 'getSymbolAt', 'link-25');">getSymbolAt</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-134" class="py-name"><a title="obitools.WrappedBioSequence.posInWrapped" class="py-name" href="#" onclick="return doclink('link-134', 'posInWrapped', 'link-83');">posInWrapped</a></tt><tt class="py-op">(</tt><tt class="py-name">position</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
</div><a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> </tt>
<a name="DNAComplementSequence.complement"></a><div id="DNAComplementSequence.complement-def"><a name="L371"></a><tt class="py-lineno">371</tt> <a class="py-toggle" href="#" id="DNAComplementSequence.complement-toggle" onclick="return toggle('DNAComplementSequence.complement');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.DNAComplementSequence-class.html#complement">complement</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="DNAComplementSequence.complement-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="DNAComplementSequence.complement-expanded"><a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="obitools.WrappedBioSequence.wrapped" class="py-name" href="#" onclick="return doclink('link-135', 'wrapped', 'link-65');">wrapped</a></tt> </tt>
</div><a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt id="link-136" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-136', 'id', 'link-17');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">property</tt><tt class="py-op">(</tt><tt id="link-137" class="py-name"><a title="obitools.BioSequence.getId
obitools.DNAComplementSequence.getId
obitools.WrappedBioSequence.getId
obitools.cns.quality.QualitySequence.getId" class="py-name" href="#" onclick="return doclink('link-137', 'getId', 'link-55');">getId</a></tt><tt class="py-op">,</tt><tt id="link-138" class="py-name"><a title="obitools.BioSequence" class="py-name" href="#" onclick="return doclink('link-138', 'BioSequence', 'link-94');">BioSequence</a></tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="obitools.BioSequence.setId
obitools.cns.quality.QualitySequence.setId" class="py-name" href="#" onclick="return doclink('link-139', 'setId', 'link-56');">setId</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"Sequence Identifier"</tt><tt class="py-op">)</tt> </tt>
</div><a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> </tt>
<a name="_isNucSeq"></a><div id="_isNucSeq-def"><a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <a class="py-toggle" href="#" id="_isNucSeq-toggle" onclick="return toggle('_isNucSeq');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools-module.html#_isNucSeq">_isNucSeq</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_isNucSeq-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_isNucSeq-expanded"><a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-name">acgt</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-name">notnuc</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-name">ltot</tt> <tt class="py-op">=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-140" class="py-name" targets="Class obitools.SVGdraw.text=obitools.SVGdraw.text-class.html"><a title="obitools.SVGdraw.text" class="py-name" href="#" onclick="return doclink('link-140', 'text', 'link-140');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt id="link-141" class="py-name"><a title="obitools.SVGdraw.text" class="py-name" href="#" onclick="return doclink('link-141', 'text', 'link-140');">text</a></tt><tt class="py-op">.</tt><tt class="py-name">lower</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-keyword">in</tt> <tt class="py-string">'acgt-'</tt><tt class="py-op">:</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-name">acgt</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-142" class="py-name"><a title="obitools.sequenceencoder.DNAComplementEncoder" class="py-name" href="#" onclick="return doclink('link-142', 'DNAComplementEncoder', 'link-6');">DNAComplementEncoder</a></tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="obitools.DNAComplementSequence._comp
obitools.location.ComplementLocation._comp
obitools.sequenceencoder.DNAComplementEncoder._comp" class="py-name" href="#" onclick="return doclink('link-143', '_comp', 'link-119');">_comp</a></tt><tt class="py-op">:</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-name">notnuc</tt><tt class="py-op">+=</tt><tt class="py-number">1</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">notnuc</tt><tt class="py-op">==</tt><tt class="py-number">0</tt> <tt class="py-keyword">and</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">acgt</tt><tt class="py-op">)</tt><tt class="py-op">/</tt><tt class="py-name">ltot</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0.8</tt> </tt>
</div><a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt>
<a name="bioSeqGenerator"></a><div id="bioSeqGenerator-def"><a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <a class="py-toggle" href="#" id="bioSeqGenerator-toggle" onclick="return toggle('bioSeqGenerator');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools-module.html#bioSeqGenerator">bioSeqGenerator</a><tt class="py-op">(</tt><tt class="py-param">id</tt><tt class="py-op">,</tt><tt class="py-param">seq</tt><tt class="py-op">,</tt><tt class="py-param">definition</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-param">info</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="bioSeqGenerator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="bioSeqGenerator-expanded"><a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-144" class="py-name" targets="Function obitools._isNucSeq()=obitools-module.html#_isNucSeq"><a title="obitools._isNucSeq" class="py-name" href="#" onclick="return doclink('link-144', '_isNucSeq', 'link-144');">_isNucSeq</a></tt><tt class="py-op">(</tt><tt class="py-name">seq</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-145" class="py-name" targets="Class obitools.NucSequence=obitools.NucSequence-class.html"><a title="obitools.NucSequence" class="py-name" href="#" onclick="return doclink('link-145', 'NucSequence', 'link-145');">NucSequence</a></tt><tt class="py-op">(</tt><tt id="link-146" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-146', 'id', 'link-17');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">seq</tt><tt class="py-op">,</tt><tt id="link-147" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-147', 'definition', 'link-15');">definition</a></tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-148" class="py-name" targets="Class obitools.AASequence=obitools.AASequence-class.html"><a title="obitools.AASequence" class="py-name" href="#" onclick="return doclink('link-148', 'AASequence', 'link-148');">AASequence</a></tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="obitools.BioSequence.id
obitools.DNAComplementSequence.id
obitools.WrappedBioSequence.id
obitools.cns.quality.QualitySequence.id
obitools.obo.parser.OBOTerm.id" class="py-name" href="#" onclick="return doclink('link-149', 'id', 'link-17');">id</a></tt><tt class="py-op">,</tt><tt class="py-name">seq</tt><tt class="py-op">,</tt><tt id="link-150" class="py-name"><a title="obitools.BioSequence.definition
obitools.WrappedBioSequence.definition
obitools.cns.quality.QualitySequence.definition
obitools.obo.parser.OBOTerm.definition" class="py-name" href="#" onclick="return doclink('link-150', 'definition', 'link-15');">definition</a></tt><tt class="py-op">,</tt><tt class="py-op">**</tt><tt class="py-name">info</tt><tt class="py-op">)</tt> </tt>
</div><a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<br />
<!-- ==================== NAVIGATION BAR ==================== -->
<table class="navbar" border="0" width="100%" cellpadding="0"
bgcolor="#a0c0ff" cellspacing="0">
<tr valign="middle">
<!-- Home link -->
<th bgcolor="#70b0f0" class="navbar-select"
>&nbsp;&nbsp;&nbsp;Home&nbsp;&nbsp;&nbsp;</th>
<!-- Tree link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="module-tree.html">Trees</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Index link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="identifier-index.html">Indices</a>&nbsp;&nbsp;&nbsp;</th>
<!-- Help link -->
<th>&nbsp;&nbsp;&nbsp;<a
href="help.html">Help</a>&nbsp;&nbsp;&nbsp;</th>
<th class="navbar" width="100%"></th>
</tr>
</table>
<table border="0" cellpadding="0" cellspacing="0" width="100%%">
<tr>
<td align="left" class="footer">
Generated by Epydoc 3.0.1 on Tue May 19 23:26:55 2009
</td>
<td align="right" class="footer">
<a target="mainFrame" href="http://epydoc.sourceforge.net"
>http://epydoc.sourceforge.net</a>
</td>
</tr>
</table>
<script type="text/javascript">
<!--
// Private objects are initially displayed (because if
// javascript is turned off then we want them to be
// visible); but by default, we want to hide them. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
Reference in New Issue View Git Blame Copy Permalink