<?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.Wise.psw</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.Wise-module.html">Package Wise</a> ::
Module psw
</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.Wise.psw-module.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module psw</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Wise.psw-pysrc.html">source code</a></span></p>
<hr />
<div class="fields"> <p><strong>Version:</strong>
$Revision: 1.5 $
</p>
</div><!-- ==================== CLASSES ==================== -->
<a name="section-Classes"></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">Classes</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Classes"
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">
<a href="Bio.Wise.psw.AlignmentColumnFullException-class.html" class="summary-name">AlignmentColumnFullException</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Wise.psw.Alignment-class.html" class="summary-name">Alignment</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Wise.psw.AlignmentColumn-class.html" class="summary-name">AlignmentColumn</a>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Wise.psw.ColumnUnit-class.html" class="summary-name">ColumnUnit</a>
</td>
</tr>
</table>
<!-- ==================== FUNCTIONS ==================== -->
<a name="section-Functions"></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">Functions</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Functions"
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="parse_line"></a><span class="summary-sig-name">parse_line</span>(<span class="summary-sig-arg">line</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Wise.psw-pysrc.html#parse_line">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.Wise.psw-module.html#parse" class="summary-sig-name">parse</a>(<span class="summary-sig-arg">iterable</span>)</span><br />
format</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Wise.psw-pysrc.html#parse">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="align"></a><span class="summary-sig-name">align</span>(<span class="summary-sig-arg">pair</span>,
<span class="summary-sig-arg">scores</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">gap_start</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">gap_extension</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">*args</span>,
<span class="summary-sig-arg">**keywds</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Wise.psw-pysrc.html#align">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="main"></a><span class="summary-sig-name">main</span>()</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Wise.psw-pysrc.html#main">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 name="_test"></a><span class="summary-sig-name">_test</span>(<span class="summary-sig-arg">*args</span>,
<span class="summary-sig-arg">**keywds</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Wise.psw-pysrc.html#_test">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
</table>
<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></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">Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Variables"
class="privatelink" onclick="toggle_private();"
>hide private</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">
<a name="_CMDLINE_PSW"></a><span class="summary-name">_CMDLINE_PSW</span> = <code title="['psw', '-l', '-F']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">psw</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">-l</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">-F</code><code class="variable-quote">'</code><code class="variable-group">]</code></code>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="_OPTION_GAP_START"></a><span class="summary-name">_OPTION_GAP_START</span> = <code title="'-g'"><code class="variable-quote">'</code><code class="variable-string">-g</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="_OPTION_GAP_EXTENSION"></a><span class="summary-name">_OPTION_GAP_EXTENSION</span> = <code title="'-e'"><code class="variable-quote">'</code><code class="variable-string">-e</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="_OPTION_SCORES"></a><span class="summary-name">_OPTION_SCORES</span> = <code title="'-m'"><code class="variable-quote">'</code><code class="variable-string">-m</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Wise.psw-module.html#_re_unit" class="summary-name" onclick="show_private();">_re_unit</a> = <code title="re.compile(r'^Unit +([01])- \[ *(-?\d+)- *(-?\d+)\] \[(\w+)\]$')">re.compile(r'^Unit <code class="re-op">+</code><code class="re-group">(</code><code class="re-group">[</code>01<code class="re-group">]</code><code class="re-group">)</code>- \[ <code class="re-op">*</code><code class="re-group">(</code>-<code class="re-op">?</code>\d<code class="re-op">+</code><code class="re-group">)</code>- <code class="re-op">*</code><code class="re-group">(</code>-<code class="re-op">?</code>\d<code class="re-op">+</code><code class="re-group">)</code>\]<code class="variable-ellipsis">...</code></code>
</td>
</tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></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">Function Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-FunctionDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="parse"></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">parse</span>(<span class="sig-arg">iterable</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Wise.psw-pysrc.html#parse">source code</a></span>
</td>
</tr></table>
<p>format</p>
<p>Column 0: Unit 0- [ -1- 0] [SEQUENCE] Unit 1- [ 85- 86]
[SEQUENCE]</p>
<p>means that seq1[0] == seq2[86] (0-based)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
<!-- ==================== VARIABLES DETAILS ==================== -->
<a name="section-VariablesDetails"></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">Variables Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-VariablesDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
</table>
<a name="_re_unit"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">_re_unit</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
re.compile(r'^Unit <code class="re-op">+</code><code class="re-group">(</code><code class="re-group">[</code>01<code class="re-group">]</code><code class="re-group">)</code>- \[ <code class="re-op">*</code><code class="re-group">(</code>-<code class="re-op">?</code>\d<code class="re-op">+</code><code class="re-group">)</code>- <code class="re-op">*</code><code class="re-group">(</code>-<code class="re-op">?</code>\d<code class="re-op">+</code><code class="re-group">)</code>\] \[<code class="re-group">(</code>\w<code class="re-op">+</code><code class="re-group">)</code>\]$')
</pre></td></tr></table>
</dd>
</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 09:26:26 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. So hide
// them unless we have a cookie that says to show them.
checkCookie();
// -->
</script>
</body>
</html>
