<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Fasta.FastaAlign.FastaAlignment</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.Fasta-module.html">Package Fasta</a> :: <a href="Bio.Fasta.FastaAlign-module.html">Module FastaAlign</a> :: Class FastaAlignment </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Fasta.FastaAlign.FastaAlignment-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class FastaAlignment</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Fasta.FastaAlign-pysrc.html#FastaAlignment">source code</a></span></p> <pre class="base-tree"> <a href="Bio.Align.Generic.Alignment-class.html">Align.Generic.Alignment</a> --+ | <strong class="uidshort">FastaAlignment</strong> </pre> <hr /> <p>Work with the Fasta Alignment format.</p> <p>The fasta alignment format is basically the same as the regular ol' Fasta format we know and love, except the sequences have gaps (represented by -'s).</p> <!-- ==================== INSTANCE METHODS ==================== --> <a name="section-InstanceMethods"></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">Instance Methods</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-InstanceMethods" class="privatelink" onclick="toggle_private();" >hide private</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.Fasta.FastaAlign.FastaAlignment-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">Gapped(IUPACAmbiguousDNA(), '-')</span>)</span><br /> Initialize a new Alignment object.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Fasta.FastaAlign-pysrc.html#FastaAlignment.__init__">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.Fasta.FastaAlign.FastaAlignment-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br /> Print out a fasta version of the alignment info.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Fasta.FastaAlign-pysrc.html#FastaAlignment.__str__">source code</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.Align.Generic.Alignment-class.html">Align.Generic.Alignment</a></code></b>: <code><a href="Bio.Align.Generic.Alignment-class.html#__iter__">__iter__</a></code>, <code><a href="Bio.Align.Generic.Alignment-class.html#__repr__">__repr__</a></code>, <code><a href="Bio.Align.Generic.Alignment-class.html#add_sequence">add_sequence</a></code>, <code><a href="Bio.Align.Generic.Alignment-class.html#get_alignment_length">get_alignment_length</a></code>, <code><a href="Bio.Align.Generic.Alignment-class.html#get_all_seqs">get_all_seqs</a></code>, <code><a href="Bio.Align.Generic.Alignment-class.html#get_column">get_column</a></code>, <code><a href="Bio.Align.Generic.Alignment-class.html#get_seq_by_num">get_seq_by_num</a></code> </p> <div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Align.Generic.Alignment-class.html">Align.Generic.Alignment</a></code></b> (private): <code><a href="Bio.Align.Generic.Alignment-class.html#_str_line" onclick="show_private();">_str_line</a></code> </p></div> </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">alphabet</span>=<span class="sig-default">Gapped(IUPACAmbiguousDNA(), '-')</span>)</span> <br /><em class="fname">(Constructor)</em> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Fasta.FastaAlign-pysrc.html#FastaAlignment.__init__">source code</a></span> </td> </tr></table> <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"> <dt>Overrides: <a href="Bio.Align.Generic.Alignment-class.html#__init__">Align.Generic.Alignment.__init__</a> <dd><em class="note">(inherited documentation)</em></dd> </dt> </dl> </td></tr></table> </div> <a name="__str__"></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">__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.Fasta.FastaAlign-pysrc.html#FastaAlignment.__str__">source code</a></span> </td> </tr></table> <p>Print out a fasta version of the alignment info.</p> <dl class="fields"> <dt>Overrides: <a href="Bio.Align.Generic.Alignment-class.html#__str__">Align.Generic.Alignment.__str__</a> </dt> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table border="0" cellpadding="0" cellspacing="0" width="100%%"> <tr> <td align="left" class="footer"> Generated by Epydoc 3.0.1 on Mon Sep 15 09:26:34 2008 </td> <td align="right" class="footer"> <a target="mainFrame" href="http://epydoc.sourceforge.net" >http://epydoc.sourceforge.net</a> </td> </tr> </table> <script type="text/javascript"> <!-- // Private objects are initially displayed (because if // javascript is turned off then we want them to be // visible); but by default, we want to hide them. 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