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<a href="BioSQL-module.html">Package BioSQL</a> ::
<a href="BioSQL.BioSeq-module.html">Module BioSeq</a> ::
Class DBSeqRecord
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class DBSeqRecord</h1><p class="nomargin-top"><span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord">source code</a></span></p>
<pre class="base-tree">
<a href="Bio.SeqRecord.SeqRecord-class.html">Bio.SeqRecord.SeqRecord</a> --+
|
<strong class="uidshort">DBSeqRecord</strong>
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<p>BioSQL equivalent of the biopython SeqRecord object.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">adaptor</span>,
<span class="summary-sig-arg">primary_id</span>)</span><br />
Create a SeqRecord.</td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="__get_seq"></a><span class="summary-sig-name">__get_seq</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__get_seq">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__set_seq"></a><span class="summary-sig-name">__set_seq</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seq</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__set_seq">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__del_seq"></a><span class="summary-sig-name">__del_seq</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__del_seq">source code</a></span>
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<td><span class="summary-sig"><a name="__get_dbxrefs"></a><span class="summary-sig-name">__get_dbxrefs</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__get_dbxrefs">source code</a></span>
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<td><span class="summary-sig"><a name="__set_dbxrefs"></a><span class="summary-sig-name">__set_dbxrefs</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbxrefs</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__set_dbxrefs">source code</a></span>
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<td><span class="summary-sig"><a name="__del_dbxrefs"></a><span class="summary-sig-name">__del_dbxrefs</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__del_dbxrefs">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="__get_features"></a><span class="summary-sig-name">__get_features</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__get_features">source code</a></span>
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<td><span class="summary-sig"><a name="__set_features"></a><span class="summary-sig-name">__set_features</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">features</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__set_features">source code</a></span>
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<td><span class="summary-sig"><a name="__del_features"></a><span class="summary-sig-name">__del_features</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__del_features">source code</a></span>
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<td><span class="summary-sig"><a name="__get_annotations"></a><span class="summary-sig-name">__get_annotations</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__get_annotations">source code</a></span>
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<td><span class="summary-sig"><a name="__set_annotations"></a><span class="summary-sig-name">__set_annotations</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">annotations</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__set_annotations">source code</a></span>
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<span class="summary-type"> </span>
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<tr>
<td><span class="summary-sig"><a name="__del_annotations"></a><span class="summary-sig-name">__del_annotations</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__del_annotations">source code</a></span>
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<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.SeqRecord.SeqRecord-class.html">Bio.SeqRecord.SeqRecord</a></code></b>:
<code><a href="Bio.SeqRecord.SeqRecord-class.html#__len__">__len__</a></code>,
<code><a href="Bio.SeqRecord.SeqRecord-class.html#__nonzero__">__nonzero__</a></code>,
<code><a href="Bio.SeqRecord.SeqRecord-class.html#__repr__">__repr__</a></code>,
<code><a href="Bio.SeqRecord.SeqRecord-class.html#__str__">__str__</a></code>
</p>
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<!-- ==================== PROPERTIES ==================== -->
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<td align="left"><span class="table-header">Properties</span></td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="BioSQL.BioSeq.DBSeqRecord-class.html#seq" class="summary-name">seq</a><br />
Seq object
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="BioSQL.BioSeq.DBSeqRecord-class.html#dbxrefs" class="summary-name">dbxrefs</a><br />
Database cross references
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<span class="summary-type"> </span>
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<a href="BioSQL.BioSeq.DBSeqRecord-class.html#features" class="summary-name">features</a><br />
Features
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<span class="summary-type"> </span>
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<a href="BioSQL.BioSeq.DBSeqRecord-class.html#annotations" class="summary-name">annotations</a><br />
Annotations
</td>
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<!-- ==================== METHOD DETAILS ==================== -->
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">adaptor</span>,
<span class="sig-arg">primary_id</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeq-pysrc.html#DBSeqRecord.__init__">source code</a></span>
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<p>Create a SeqRecord.</p>
<p>Arguments: seq - Sequence, required (Seq object) id -
Sequence identifier, recommended (string) name - Sequence name,
optional (string) description - Sequence description, optional (string)
dbxrefs - Database cross references, optional (list of strings)
features - Any (sub)features, optional (list of SeqFeature
objects)</p>
<p>Note that while an id is optional, we strongly recommend you supply a
unique id string for each record. This is especially important if you
wish to write your sequences to a file.</p>
<p>You can create a 'blank' SeqRecord object, and then populated the
attributes later. Note that currently the annotations dictionary cannot
be specified when creating the SeqRecord.</p>
<dl class="fields">
<dt>Overrides:
<a href="Bio.SeqRecord.SeqRecord-class.html#__init__">Bio.SeqRecord.SeqRecord.__init__</a>
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<a name="seq"></a>
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<h3 class="epydoc">seq</h3>
<p>Seq object</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__get_seq" class="summary-sig-name" onclick="show_private();">__get_seq</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__set_seq" class="summary-sig-name" onclick="show_private();">__set_seq</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seq</span>)</span>
</dd>
<dt>Delete Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__del_seq" class="summary-sig-name" onclick="show_private();">__del_seq</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
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</div>
<a name="dbxrefs"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc">dbxrefs</h3>
<p>Database cross references</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__get_dbxrefs" class="summary-sig-name" onclick="show_private();">__get_dbxrefs</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__set_dbxrefs" class="summary-sig-name" onclick="show_private();">__set_dbxrefs</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbxrefs</span>)</span>
</dd>
<dt>Delete Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__del_dbxrefs" class="summary-sig-name" onclick="show_private();">__del_dbxrefs</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="features"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">features</h3>
<p>Features</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__get_features" class="summary-sig-name" onclick="show_private();">__get_features</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__set_features" class="summary-sig-name" onclick="show_private();">__set_features</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">features</span>)</span>
</dd>
<dt>Delete Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__del_features" class="summary-sig-name" onclick="show_private();">__del_features</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
<a name="annotations"></a>
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cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">annotations</h3>
<p>Annotations</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__get_annotations" class="summary-sig-name" onclick="show_private();">__get_annotations</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__set_annotations" class="summary-sig-name" onclick="show_private();">__set_annotations</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">annotations</span>)</span>
</dd>
<dt>Delete Method:</dt>
<dd class="value"><span class="summary-sig"><a href="BioSQL.BioSeq.DBSeqRecord-class.html#__del_annotations" class="summary-sig-name" onclick="show_private();">__del_annotations</a>(<span class="summary-sig-arg">self</span>)</span>
</dd>
</dl>
</td></tr></table>
</div>
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