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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Align-module.html">Package Align</a> ::
<a href="Bio.Align.Generic-module.html">Module Generic</a> ::
Class Alignment
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Alignment</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment">source code</a></span></p>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.Clustalw.ClustalAlignment-class.html">Clustalw.ClustalAlignment</a></li><li>, <a href="Bio.Fasta.FastaAlign.FastaAlignment-class.html">Fasta.FastaAlign.FastaAlignment</a></li><li>, <a href="Bio.FSSP.FSSPTools.FSSPAlign-class.html">FSSP.FSSPTools.FSSPAlign</a></li> </ul>
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<hr />
<p>Represent a set of alignments.</p>
<p>This is a base class to represent alignments, which can be subclassed
to deal with an alignment in a specific format.</p>
<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">alphabet</span>)</span><br />
Initialize a new Alignment object.</td>
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<span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.__init__">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#__iter__" class="summary-sig-name">__iter__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Iterate over alignment rows as SeqRecord objects</td>
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#__repr__" class="summary-sig-name">__repr__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns a representation of the object for debugging.</td>
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Returns a multi-line string summary of the alignment.</td>
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#_str_line" class="summary-sig-name" onclick="show_private();">_str_line</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">record</span>)</span><br />
Returns a truncated string representation of a SeqRecord.</td>
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<span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment._str_line">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#add_sequence" class="summary-sig-name">add_sequence</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">descriptor</span>,
<span class="summary-sig-arg">sequence</span>,
<span class="summary-sig-arg">start</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">end</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">weight</span>=<span class="summary-sig-default">1.0</span>)</span><br />
Add a sequence to the alignment.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.add_sequence">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#get_alignment_length" class="summary-sig-name">get_alignment_length</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return the maximum length of the alignment.</td>
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<span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.get_alignment_length">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#get_all_seqs" class="summary-sig-name">get_all_seqs</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return all of the sequences involved in the alignment.</td>
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<span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.get_all_seqs">source code</a></span>
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<td><span class="summary-sig"><a name="get_column"></a><span class="summary-sig-name">get_column</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">col</span>)</span><br />
Returns a string containing a given column.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.get_column">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.Align.Generic.Alignment-class.html#get_seq_by_num" class="summary-sig-name">get_seq_by_num</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">number</span>)</span><br />
Retrieve a sequence by row number.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.get_seq_by_num">source code</a></span>
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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">alphabet</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.__init__">source code</a></span>
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<p>Initialize a new Alignment object.</p>
<p>Arguments: o alphabet - The alphabet to use for the sequence objects
that are created. This alphabet must be a gapped type.</p>
<dl class="fields">
</dl>
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<a name="__iter__"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__iter__</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.__iter__">source code</a></span>
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<pre class="literalblock">
Iterate over alignment rows as SeqRecord objects
e.g.
for record in align :
print record.id
print record.seq
</pre>
<dl class="fields">
</dl>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__repr__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.__repr__">source code</a></span>
</td>
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<p>Returns a representation of the object for debugging.</p>
<p>The representation cannot be used with eval() to recreate the object,
which is usually possible with simple python ojects. For example:</p>
<p><Bio.Align.Generic.Alignment instance (2 records of length 14,
SingleLetterAlphabet()) at a3c184c></p>
<p>The hex string is the memory address of the object, see help(id). This
provides a simple way to visually distinguish alignments of the same
size.</p>
<dl class="fields">
</dl>
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<a name="__str__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.__str__">source code</a></span>
</td>
</tr></table>
<p>Returns a multi-line string summary of the alignment.</p>
<p>This output is intended to be readable, but large alignments are shown
truncated. A maximum of 20 rows (sequences) and 50 columns are shown,
with the record identifiers. This should fit nicely on a single screen.
e.g.</p>
<p>DNAAlphabet() alignment with 3 rows and 14 columns ACGATCAGCTAGCT
Alpha CCGATCAGCTAGCT Beta ACGATGAGCTAGCT Gamma</p>
<dl class="fields">
</dl>
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<a name="_str_line"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_str_line</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">record</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment._str_line">source code</a></span>
</td>
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<p>Returns a truncated string representation of a SeqRecord.</p>
<p>This is a PRIVATE function used by the __str__ method.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="add_sequence"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">add_sequence</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">descriptor</span>,
<span class="sig-arg">sequence</span>,
<span class="sig-arg">start</span>=<span class="sig-default">None</span>,
<span class="sig-arg">end</span>=<span class="sig-default">None</span>,
<span class="sig-arg">weight</span>=<span class="sig-default">1.0</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.add_sequence">source code</a></span>
</td>
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<pre class="literalblock">
Add a sequence to the alignment.
This doesn't do any kind of alignment, it just adds in the sequence
object, which is assumed to be prealigned with the existing
sequences.
Arguments:
o descriptor - The descriptive id of the sequence being added.
This will be used as the resulting SeqRecord's
.id property (and, for historical compatibility,
also the .description property)
o sequence - A string with sequence info.
o start - You can explicitly set the start point of the sequence.
This is useful (at least) for BLAST alignments, which can just
be partial alignments of sequences.
o end - Specify the end of the sequence, which is important
for the same reason as the start.
o weight - The weight to place on the sequence in the alignment.
By default, all sequences have the same weight. (0.0 => no weight,
1.0 => highest weight)
</pre>
<dl class="fields">
</dl>
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</div>
<a name="get_alignment_length"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_alignment_length</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.get_alignment_length">source code</a></span>
</td>
</tr></table>
<p>Return the maximum length of the alignment.</p>
<p>All objects in the alignment should (hopefully) have the same length.
This function will go through and find this length by finding the maximum
length of sequences in the alignment.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_all_seqs"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_all_seqs</span>(<span class="sig-arg">self</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.get_all_seqs">source code</a></span>
</td>
</tr></table>
<p>Return all of the sequences involved in the alignment.</p>
<p>The return value is a list of SeqRecord objects.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="get_seq_by_num"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">get_seq_by_num</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">number</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Align.Generic-pysrc.html#Alignment.get_seq_by_num">source code</a></span>
</td>
</tr></table>
<p>Retrieve a sequence by row number.</p>
<p>Returns: o A Seq object for the requested sequence.</p>
<p>Raises: o IndexError - If the specified number is out of range.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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