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<a href="BioSQL-module.html">Package BioSQL</a> ::
<a href="BioSQL.BioSeqDatabase-module.html">Module BioSeqDatabase</a> ::
Class Adaptor
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Adaptor</h1><p class="nomargin-top"><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor">source code</a></span></p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">conn</span>,
<span class="summary-sig-arg">dbutils</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="last_id"></a><span class="summary-sig-name">last_id</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">table</span>)</span></td>
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<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.last_id">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="BioSQL.BioSeqDatabase.Adaptor-class.html#autocommit" class="summary-sig-name">autocommit</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">y</span>=<span class="summary-sig-default">True</span>)</span><br />
Set the autocommit mode.</td>
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<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.autocommit">source code</a></span>
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<td><span class="summary-sig"><a name="commit"></a><span class="summary-sig-name">commit</span>(<span class="summary-sig-arg">self</span>)</span><br />
Commits the current transaction.</td>
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<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.commit">source code</a></span>
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<td><span class="summary-sig"><a name="rollback"></a><span class="summary-sig-name">rollback</span>(<span class="summary-sig-arg">self</span>)</span><br />
Rolls backs the current transaction.</td>
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<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.rollback">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.BioSeqDatabase.Adaptor-class.html#close" class="summary-sig-name">close</a>(<span class="summary-sig-arg">self</span>)</span><br />
Close the connection.</td>
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<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.close">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="fetch_dbid_by_dbname"></a><span class="summary-sig-name">fetch_dbid_by_dbname</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbname</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_dbid_by_dbname">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="fetch_seqid_by_display_id"></a><span class="summary-sig-name">fetch_seqid_by_display_id</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbid</span>,
<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqid_by_display_id">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="fetch_seqid_by_accession"></a><span class="summary-sig-name">fetch_seqid_by_accession</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbid</span>,
<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqid_by_accession">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="fetch_seqids_by_accession"></a><span class="summary-sig-name">fetch_seqids_by_accession</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbid</span>,
<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqids_by_accession">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="fetch_seqid_by_version"></a><span class="summary-sig-name">fetch_seqid_by_version</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbid</span>,
<span class="summary-sig-arg">name</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqid_by_version">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="fetch_seqid_by_identifier"></a><span class="summary-sig-name">fetch_seqid_by_identifier</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbid</span>,
<span class="summary-sig-arg">identifier</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.fetch_seqid_by_identifier">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="list_biodatabase_names"></a><span class="summary-sig-name">list_biodatabase_names</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_biodatabase_names">source code</a></span>
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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="list_bioentry_ids"></a><span class="summary-sig-name">list_bioentry_ids</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbid</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_bioentry_ids">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="list_bioentry_display_ids"></a><span class="summary-sig-name">list_bioentry_display_ids</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">dbid</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_bioentry_display_ids">source code</a></span>
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<td><span class="summary-sig"><a href="BioSQL.BioSeqDatabase.Adaptor-class.html#list_any_ids" class="summary-sig-name">list_any_ids</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sql</span>,
<span class="summary-sig-arg">args</span>)</span><br />
Return ids given a SQL statement to select for them.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_any_ids">source code</a></span>
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<td><span class="summary-sig"><a name="execute_one"></a><span class="summary-sig-name">execute_one</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sql</span>,
<span class="summary-sig-arg">args</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.execute_one">source code</a></span>
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<td><span class="summary-sig"><a name="execute"></a><span class="summary-sig-name">execute</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sql</span>,
<span class="summary-sig-arg">args</span>=<span class="summary-sig-default">None</span>)</span><br />
Just execute an sql command.</td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.execute">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_subseq_as_string"></a><span class="summary-sig-name">get_subseq_as_string</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">seqid</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.get_subseq_as_string">source code</a></span>
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<td><span class="summary-sig"><a name="execute_and_fetch_col0"></a><span class="summary-sig-name">execute_and_fetch_col0</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sql</span>,
<span class="summary-sig-arg">args</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.execute_and_fetch_col0">source code</a></span>
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<td><span class="summary-sig"><a name="execute_and_fetchall"></a><span class="summary-sig-name">execute_and_fetchall</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">sql</span>,
<span class="summary-sig-arg">args</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.execute_and_fetchall">source code</a></span>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">autocommit</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">y</span>=<span class="sig-default">True</span>)</span>
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><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.autocommit">source code</a></span>
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<p>Set the autocommit mode. True values enable; False value disable.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">close</span>(<span class="sig-arg">self</span>)</span>
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><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.close">source code</a></span>
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<p>Close the connection. No further activity possible.</p>
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<a name="list_any_ids"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">list_any_ids</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">sql</span>,
<span class="sig-arg">args</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="BioSQL.BioSeqDatabase-pysrc.html#Adaptor.list_any_ids">source code</a></span>
</td>
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<p>Return ids given a SQL statement to select for them.</p>
<p>This assumes that the given SQL does a SELECT statement that returns a
list of items. This parses them out of the 2D list they come as and just
returns them in a list.</p>
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