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Class _FeatureConsumer
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class _FeatureConsumer</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer">source code</a></span></p>
<pre class="base-tree">
<a href="Bio.ParserSupport.AbstractConsumer-class.html">ParserSupport.AbstractConsumer</a> --+
|
<a href="Bio.GenBank._BaseGenBankConsumer-class.html">_BaseGenBankConsumer</a> --+
|
<strong class="uidshort">_FeatureConsumer</strong>
</pre>
<hr />
<p>Create a SeqRecord object with Features to return.</p>
<p>Attributes: o use_fuzziness - specify whether or not to parse with
fuzziness in feature locations. o feature_cleaner - a class that will be
used to provide specialized cleaning-up of feature values.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td align="left"><span class="table-header">Instance Methods</span></td>
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<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">use_fuzziness</span>,
<span class="summary-sig-arg">feature_cleaner</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.__init__">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="locus"></a><span class="summary-sig-name">locus</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">locus_name</span>)</span><br />
Set the locus name is set as the name of the Sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.locus">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="size"></a><span class="summary-sig-name">size</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.size">source code</a></span>
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<td><span class="summary-sig"><a name="residue_type"></a><span class="summary-sig-name">residue_type</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">type</span>)</span><br />
Record the sequence type so we can choose an appropriate alphabet.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.residue_type">source code</a></span>
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<td><span class="summary-sig"><a name="data_file_division"></a><span class="summary-sig-name">data_file_division</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">division</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.data_file_division">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="date"></a><span class="summary-sig-name">date</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">submit_date</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.date">source code</a></span>
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<td><span class="summary-sig"><a name="definition"></a><span class="summary-sig-name">definition</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">definition</span>)</span><br />
Set the definition as the description of the sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.definition">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#accession" class="summary-sig-name">accession</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">acc_num</span>)</span><br />
Set the accession number as the id of the sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.accession">source code</a></span>
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<td><span class="summary-sig"><a name="nid"></a><span class="summary-sig-name">nid</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.nid">source code</a></span>
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<td><span class="summary-sig"><a name="pid"></a><span class="summary-sig-name">pid</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.pid">source code</a></span>
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<td><span class="summary-sig"><a name="version"></a><span class="summary-sig-name">version</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">version_id</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.version">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#version_suffix" class="summary-sig-name">version_suffix</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">version</span>)</span><br />
Set the version to overwrite the id.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.version_suffix">source code</a></span>
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<td><span class="summary-sig"><a name="db_source"></a><span class="summary-sig-name">db_source</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.db_source">source code</a></span>
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<td><span class="summary-sig"><a name="gi"></a><span class="summary-sig-name">gi</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.gi">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="keywords"></a><span class="summary-sig-name">keywords</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.keywords">source code</a></span>
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<td><span class="summary-sig"><a name="segment"></a><span class="summary-sig-name">segment</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.segment">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="source"></a><span class="summary-sig-name">source</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.source">source code</a></span>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="organism"></a><span class="summary-sig-name">organism</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.organism">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="taxonomy"></a><span class="summary-sig-name">taxonomy</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span><br />
Records (another line of) the taxonomy lineage.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.taxonomy">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="reference_num"></a><span class="summary-sig-name">reference_num</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span><br />
Signal the beginning of a new reference object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.reference_num">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#reference_bases" class="summary-sig-name">reference_bases</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span><br />
Attempt to determine the sequence region the reference entails.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.reference_bases">source code</a></span>
</td>
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</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_split_reference_locations" class="summary-sig-name" onclick="show_private();">_split_reference_locations</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">location_string</span>)</span><br />
Get reference locations out of a string of reference information</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._split_reference_locations">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="authors"></a><span class="summary-sig-name">authors</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.authors">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="consrtm"></a><span class="summary-sig-name">consrtm</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.consrtm">source code</a></span>
</td>
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</td>
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<span class="summary-type"> </span>
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<tr>
<td><span class="summary-sig"><a name="title"></a><span class="summary-sig-name">title</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.title">source code</a></span>
</td>
</tr>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="journal"></a><span class="summary-sig-name">journal</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.journal">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="medline_id"></a><span class="summary-sig-name">medline_id</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.medline_id">source code</a></span>
</td>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="pubmed_id"></a><span class="summary-sig-name">pubmed_id</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.pubmed_id">source code</a></span>
</td>
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<td><span class="summary-sig"><a name="remark"></a><span class="summary-sig-name">remark</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.remark">source code</a></span>
</td>
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<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="comment"></a><span class="summary-sig-name">comment</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.comment">source code</a></span>
</td>
</tr>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="features_line"></a><span class="summary-sig-name">features_line</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span><br />
Get ready for the feature table when we reach the FEATURE line.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.features_line">source code</a></span>
</td>
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</table>
</td>
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<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="start_feature_table"></a><span class="summary-sig-name">start_feature_table</span>(<span class="summary-sig-arg">self</span>)</span><br />
Indicate we've got to the start of the feature table.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.start_feature_table">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_add_feature" class="summary-sig-name" onclick="show_private();">_add_feature</a>(<span class="summary-sig-arg">self</span>)</span><br />
Utility function to add a feature to the SeqRecord.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._add_feature">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="feature_key"></a><span class="summary-sig-name">feature_key</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.feature_key">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#location" class="summary-sig-name">location</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span><br />
Parse out location information from the location string.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.location">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_set_function" class="summary-sig-name" onclick="show_private();">_set_function</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">function</span>,
<span class="summary-sig-arg">cur_feature</span>)</span><br />
Set the location information based on a function.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._set_function">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_set_ordering_info" class="summary-sig-name" onclick="show_private();">_set_ordering_info</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">function</span>,
<span class="summary-sig-arg">cur_feature</span>)</span><br />
Parse a join or order and all of the information in it.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._set_ordering_info">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_set_location_info" class="summary-sig-name" onclick="show_private();">_set_location_info</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">parse_info</span>,
<span class="summary-sig-arg">cur_feature</span>)</span><br />
Set the location information for a feature from the parse info.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._set_location_info">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_set_location" class="summary-sig-name" onclick="show_private();">_set_location</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">location</span>,
<span class="summary-sig-arg">cur_feature</span>)</span><br />
Set the location information for a feature.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._set_location">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_get_location" class="summary-sig-name" onclick="show_private();">_get_location</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">range_info</span>)</span><br />
Return a (possibly fuzzy) location from a Range object.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._get_location">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_get_position" class="summary-sig-name" onclick="show_private();">_get_position</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">position</span>)</span><br />
Return a (possibly fuzzy) position for a single coordinate.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._get_position">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#_add_qualifier" class="summary-sig-name" onclick="show_private();">_add_qualifier</a>(<span class="summary-sig-arg">self</span>)</span><br />
Add a qualifier to the current feature without loss of info.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._add_qualifier">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#feature_qualifier_name" class="summary-sig-name">feature_qualifier_name</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content_list</span>)</span><br />
When we get a qualifier key, use it as a dictionary key.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.feature_qualifier_name">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="feature_qualifier_description"></a><span class="summary-sig-name">feature_qualifier_description</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.feature_qualifier_description">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="contig_location"></a><span class="summary-sig-name">contig_location</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span><br />
Deal with a location of CONTIG information.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.contig_location">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="origin_name"></a><span class="summary-sig-name">origin_name</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.origin_name">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="base_count"></a><span class="summary-sig-name">base_count</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.base_count">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="base_number"></a><span class="summary-sig-name">base_number</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.base_number">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.GenBank._FeatureConsumer-class.html#sequence" class="summary-sig-name">sequence</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span><br />
Add up sequence information as we get it.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.sequence">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="record_end"></a><span class="summary-sig-name">record_end</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">content</span>)</span><br />
Clean up when we've finished the record.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.record_end">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.GenBank._BaseGenBankConsumer-class.html">_BaseGenBankConsumer</a></code></b> (private):
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_clean_location" onclick="show_private();">_clean_location</a></code>,
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_convert_to_python_numbers" onclick="show_private();">_convert_to_python_numbers</a></code>,
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_normalize_spaces" onclick="show_private();">_normalize_spaces</a></code>,
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_remove_newlines" onclick="show_private();">_remove_newlines</a></code>,
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_remove_spaces" onclick="show_private();">_remove_spaces</a></code>,
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_split_accessions" onclick="show_private();">_split_accessions</a></code>,
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_split_keywords" onclick="show_private();">_split_keywords</a></code>,
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#_split_taxonomy" onclick="show_private();">_split_taxonomy</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.ParserSupport.AbstractConsumer-class.html">ParserSupport.AbstractConsumer</a></code></b>:
<code><a href="Bio.ParserSupport.AbstractConsumer-class.html#__getattr__">__getattr__</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.ParserSupport.AbstractConsumer-class.html">ParserSupport.AbstractConsumer</a></code></b> (private):
<code><a href="Bio.ParserSupport.AbstractConsumer-class.html#_unhandled" onclick="show_private();">_unhandled</a></code>,
<code><a href="Bio.ParserSupport.AbstractConsumer-class.html#_unhandled_section" onclick="show_private();">_unhandled_section</a></code>
</p></div>
</td>
</tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Class Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-ClassVariables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.GenBank._BaseGenBankConsumer-class.html">_BaseGenBankConsumer</a></code></b>:
<code><a href="Bio.GenBank._BaseGenBankConsumer-class.html#remove_space_keys">remove_space_keys</a></code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">use_fuzziness</span>,
<span class="sig-arg">feature_cleaner</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.__init__">source code</a></span>
</td>
</tr></table>
<dl class="fields">
<dt>Overrides:
<a href="Bio.GenBank._BaseGenBankConsumer-class.html#__init__">_BaseGenBankConsumer.__init__</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="accession"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">accession</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">acc_num</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.accession">source code</a></span>
</td>
</tr></table>
<p>Set the accession number as the id of the sequence.</p>
<p>If we have multiple accession numbers, the first one passed is
used.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="version_suffix"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">version_suffix</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">version</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.version_suffix">source code</a></span>
</td>
</tr></table>
<p>Set the version to overwrite the id.</p>
<p>Since the verison provides the same information as the accession
number, plus some extra info, we set this as the id if we have a
version.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="reference_bases"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">reference_bases</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">content</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.reference_bases">source code</a></span>
</td>
</tr></table>
<p>Attempt to determine the sequence region the reference entails.</p>
<p>Possible types of information we may have to deal with:</p>
<p>(bases 1 to 86436) (sites) (bases 1 to 105654; 110423 to 111122) 1
(residues 1 to 182)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_split_reference_locations"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_split_reference_locations</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">location_string</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._split_reference_locations">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Get reference locations out of a string of reference information
The passed string should be of the form:
1 to 20; 20 to 100
This splits the information out and returns a list of location objects
based on the reference locations.
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_add_feature"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_add_feature</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._add_feature">source code</a></span>
</td>
</tr></table>
<p>Utility function to add a feature to the SeqRecord.</p>
<p>This does all of the appropriate checking to make sure we haven't left
any info behind, and that we are only adding info if it exists.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="location"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">location</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">content</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.location">source code</a></span>
</td>
</tr></table>
<p>Parse out location information from the location string.</p>
<p>This uses Andrew's nice spark based parser to do the parsing for us,
and translates the results of the parse into appropriate Location
objects.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_set_function"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_set_function</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">function</span>,
<span class="sig-arg">cur_feature</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._set_function">source code</a></span>
</td>
</tr></table>
<p>Set the location information based on a function.</p>
<p>This handles all of the location functions like 'join', 'complement'
and 'order'.</p>
<p>Arguments: o function - A LocationParser.Function object specifying
the function we are acting on. o cur_feature - The feature to add
information to.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_set_ordering_info"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_set_ordering_info</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">function</span>,
<span class="sig-arg">cur_feature</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._set_ordering_info">source code</a></span>
</td>
</tr></table>
<p>Parse a join or order and all of the information in it.</p>
<p>This deals with functions that order a bunch of locations,
specifically 'join' and 'order'. The inner locations are added as
subfeatures of the top level feature</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_set_location_info"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_set_location_info</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">parse_info</span>,
<span class="sig-arg">cur_feature</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._set_location_info">source code</a></span>
</td>
</tr></table>
<p>Set the location information for a feature from the parse info.</p>
<p>Arguments: o parse_info - The classes generated by the LocationParser.
o cur_feature - The feature to add the information to.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_set_location"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_set_location</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">location</span>,
<span class="sig-arg">cur_feature</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._set_location">source code</a></span>
</td>
</tr></table>
<p>Set the location information for a feature.</p>
<p>Arguments: o location - An AbsoluteLocation object specifying the info
about the location. o cur_feature - The feature to add the information
to.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_location"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_get_location</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">range_info</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._get_location">source code</a></span>
</td>
</tr></table>
<p>Return a (possibly fuzzy) location from a Range object.</p>
<p>Arguments: o range_info - A location range (ie. something like
67..100). This may also be a single position (ie 27).</p>
<p>This returns a FeatureLocation object. If parser.use_fuzziness is set
at one, the positions for the end points will possibly be fuzzy.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_get_position"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_get_position</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">position</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._get_position">source code</a></span>
</td>
</tr></table>
<p>Return a (possibly fuzzy) position for a single coordinate.</p>
<p>Arguments: o position - This is a LocationParser.* object that
specifies a single coordinate. We will examine the object to determine
the fuzziness of the position.</p>
<p>This is used with _get_location to parse out a location of any
end_point of arbitrary fuzziness.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_add_qualifier"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_add_qualifier</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer._add_qualifier">source code</a></span>
</td>
</tr></table>
<p>Add a qualifier to the current feature without loss of info.</p>
<p>If there are multiple qualifier keys with the same name we would lose
some info in the dictionary, so we append a unique number to the end of
the name in case of conflicts.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="feature_qualifier_name"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">feature_qualifier_name</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">content_list</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.feature_qualifier_name">source code</a></span>
</td>
</tr></table>
<p>When we get a qualifier key, use it as a dictionary key.</p>
<p>We receive a list of keys, since you can have valueless keys such as
/pseudo which would be passed in with the next key (since no other tags
separate them in the file)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="sequence"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">sequence</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">content</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.GenBank-pysrc.html#_FeatureConsumer.sequence">source code</a></span>
</td>
</tr></table>
<p>Add up sequence information as we get it.</p>
<p>To try and make things speedier, this puts all of the strings into a
list of strings, and then uses string.join later to put them together.
Supposedly, this is a big time savings</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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