<?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.Application.AbstractCommandline</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.Application-module.html">Package Application</a> :: Class AbstractCommandline </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.Application.AbstractCommandline-class.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== CLASS DESCRIPTION ==================== --> <h1 class="epydoc">Class AbstractCommandline</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Application-pysrc.html#AbstractCommandline">source code</a></span></p> <dl><dt>Known Subclasses:</dt> <dd> <ul class="subclass-list"> <li><a href="Bio.AlignAce.Applications.AlignAceCommandline-class.html">AlignAce.Applications.AlignAceCommandline</a></li><li>, <a href="Bio.AlignAce.Applications.CompareAceCommandline-class.html">AlignAce.Applications.CompareAceCommandline</a></li><li>, <a href="Bio.Emboss.Applications.EConsenseCommandline-class.html">Emboss.Applications.EConsenseCommandline</a></li><li>, <a href="Bio.Emboss.Applications.EInvertedCommandline-class.html">Emboss.Applications.EInvertedCommandline</a></li><li>, <a href="Bio.Emboss.Applications.ENeighborCommandline-class.html">Emboss.Applications.ENeighborCommandline</a></li><li>, <a href="Bio.Emboss.Applications.EProtDistCommandline-class.html">Emboss.Applications.EProtDistCommandline</a></li><li>, <a href="Bio.Emboss.Applications.EProtParsCommandline-class.html">Emboss.Applications.EProtParsCommandline</a></li><li>, <a href="Bio.Emboss.Applications.ESeqBootCommandline-class.html">Emboss.Applications.ESeqBootCommandline</a></li><li>, <a href="Bio.Emboss.Applications.ETandemCommandline-class.html">Emboss.Applications.ETandemCommandline</a></li><li>, <a href="Bio.Emboss.Applications.Est2GenomeCommandline-class.html">Emboss.Applications.Est2GenomeCommandline</a></li><li>, <a href="Bio.Emboss.Applications.FuzznucCommandline-class.html">Emboss.Applications.FuzznucCommandline</a></li><li>, <a href="Bio.Emboss.Applications.PalindromeCommandline-class.html">Emboss.Applications.PalindromeCommandline</a></li><li>, <a href="Bio.Emboss.Applications.Primer3Commandline-class.html">Emboss.Applications.Primer3Commandline</a></li><li>, <a href="Bio.Emboss.Applications.PrimerSearchCommandline-class.html">Emboss.Applications.PrimerSearchCommandline</a></li><li>, <a href="Bio.Emboss.Applications.TranalignCommandline-class.html">Emboss.Applications.TranalignCommandline</a></li><li>, <a href="Bio.Emboss.Applications.WaterCommandline-class.html">Emboss.Applications.WaterCommandline</a></li><li>, <a href="Bio.Blast.Applications.BlastallCommandline-class.html">Blast.Applications.BlastallCommandline</a></li><li>, <a href="Bio.Blast.Applications.FastacmdCommandline-class.html">Blast.Applications.FastacmdCommandline</a></li> </ul> </dd></dl> <hr /> <p>Generic interface for running applications from biopython.</p> <p>This class shouldn't be called directly; it should be subclassed to provide an implementation for a specific application.</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 name="__init__"></a><span class="summary-sig-name">__init__</span>(<span class="summary-sig-arg">self</span>)</span></td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Application-pysrc.html#AbstractCommandline.__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 name="__str__"></a><span class="summary-sig-name">__str__</span>(<span class="summary-sig-arg">self</span>)</span><br /> Make the commandline with the currently set options.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Application-pysrc.html#AbstractCommandline.__str__">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.Application.AbstractCommandline-class.html#_check_value" class="summary-sig-name" onclick="show_private();">_check_value</a>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">value</span>, <span class="summary-sig-arg">name</span>, <span class="summary-sig-arg">check_function</span>)</span><br /> Check whether the given value is valid.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Application-pysrc.html#AbstractCommandline._check_value">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="set_parameter"></a><span class="summary-sig-name">set_parameter</span>(<span class="summary-sig-arg">self</span>, <span class="summary-sig-arg">name</span>, <span class="summary-sig-arg">value</span>=<span class="summary-sig-default">None</span>)</span><br /> Set a commandline option for a program.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Application-pysrc.html#AbstractCommandline.set_parameter">source code</a></span> </td> </tr> </table> </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="_check_value"></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">_check_value</span>(<span class="sig-arg">self</span>, <span class="sig-arg">value</span>, <span class="sig-arg">name</span>, <span class="sig-arg">check_function</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Application-pysrc.html#AbstractCommandline._check_value">source code</a></span> </td> </tr></table> <p>Check whether the given value is valid.</p> <p>This uses the passed function 'check_function', which can either return a [0, 1] (bad, good) value or raise an error. Either way this function will raise an error if the value is not valid, or finish silently otherwise.</p> <dl class="fields"> </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 09:26:30 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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