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biopython-doc-1.47-2mdv2008.1.x86_64.rpm

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        Bio ::
        GenBank ::
        _RecordConsumer ::
        Class&nbsp;_RecordConsumer
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class _RecordConsumer</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer">source&nbsp;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">_RecordConsumer</strong>
</pre>

<hr />
<p>Create a GenBank Record object from scanner generated information.</p>

<!-- ==================== INSTANCE METHODS ==================== -->
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          <td><span class="summary-sig"><a href="Bio.GenBank._RecordConsumer-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>)</span></td>
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.__init__">source&nbsp;code</a></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>,
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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>,
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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>,
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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>,
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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>,
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.definition">source&nbsp;code</a></span>
            
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          <td><span class="summary-sig"><a name="accession"></a><span class="summary-sig-name">accession</span>(<span class="summary-sig-arg">self</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>,
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.pid">source&nbsp;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>,
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.version">source&nbsp;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>,
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.db_source">source&nbsp;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>,
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.gi">source&nbsp;code</a></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>,
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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>,
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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>,
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.source">source&nbsp;code</a></span>
            
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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#_RecordConsumer.organism">source&nbsp;code</a></span>
            
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          <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></td>
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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 />
      Grab the reference number and signal the start of a new reference.</td>
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          <td><span class="summary-sig"><a name="reference_bases"></a><span class="summary-sig-name">reference_bases</span>(<span class="summary-sig-arg">self</span>,
        <span class="summary-sig-arg">content</span>)</span></td>
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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>,
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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">
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          <td><span class="summary-sig"><a name="title"></a><span class="summary-sig-name">title</span>(<span class="summary-sig-arg">self</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>,
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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>
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.medline_id">source&nbsp;code</a></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>
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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>,
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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>
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            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.comment">source&nbsp;code</a></span>
            
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          <td><span class="summary-sig"><a name="primary_ref_line"></a><span class="summary-sig-name">primary_ref_line</span>(<span class="summary-sig-arg">self</span>,
        <span class="summary-sig-arg">content</span>)</span><br />
      Data for the PRIMARY line</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.primary_ref_line">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="primary"></a><span class="summary-sig-name">primary</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#_RecordConsumer.primary">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</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#_RecordConsumer.features_line">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</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 />
      Signal the start of the feature table.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.start_feature_table">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</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><br />
      Grab the key of the feature and signal the start of a new feature.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.feature_key">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr class="private">
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="Bio.GenBank._RecordConsumer-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 Record.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer._add_feature">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a name="location"></a><span class="summary-sig-name">location</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#_RecordConsumer.location">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="Bio.GenBank._RecordConsumer-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 />
      Deal with qualifier names</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.feature_qualifier_name">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</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#_RecordConsumer.feature_qualifier_description">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</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#_RecordConsumer.base_count">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</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#_RecordConsumer.origin_name">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</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 />
      Signal that we have contig information to add to the record.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.contig_location">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="Bio.GenBank._RecordConsumer-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 sequence information to a list of sequence strings.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.sequence">source&nbsp;code</a></span>
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</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 />
      Signal the end of the record and do any necessary clean-up.</td>
          <td align="right" valign="top">
            <span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.record_end">source&nbsp;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 ==================== -->
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       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%">
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        <td align="right" valign="top"
         ><span class="options">[<a href="#section-ClassVariables"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
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  <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>
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<!-- ==================== 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>
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<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>
    <br /><em class="fname">(Constructor)</em>
  </h3>
  </td><td align="right" valign="top"
    ><span class="codelink"><a href="Bio.GenBank-pysrc.html#_RecordConsumer.__init__">source&nbsp;code</a></span>&nbsp;
    </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="_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#_RecordConsumer._add_feature">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Utility function to add a feature to the Record.</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="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#_RecordConsumer.feature_qualifier_name">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Deal with qualifier names</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#_RecordConsumer.sequence">source&nbsp;code</a></span>&nbsp;
    </td>
  </tr></table>
  
  <p>Add sequence information to a list of sequence strings.</p>
  <p>This removes spaces in the data and uppercases the sequence, and then 
  adds it to a list of sequences. Later on we'll join this list together to
  make the final sequence. This is faster than adding on the new string 
  every time.</p>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<br />
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