<?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.ECell.ecell_format</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.ECell-module.html">Package ECell</a> ::
Module ecell_format
</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.ECell.ecell_format-module.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module ecell_format</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.ECell.ecell_format-pysrc.html">source code</a></span></p>
<pre class="literalblock">
Martel based parser to read ECell formatted files.
This is a huge regular regular expression for ECell, built using
the 'regular expressiona on steroids' capabilities of Martel.
http://www.bioinformatics.org/ecell2/
Notes:
Just so I remember -- the new end of line syntax is:
New regexp syntax - \R
\R means "
|
?"
[\R] means "[
]"
This helps us have endlines be consistent across platforms.
</pre>
<!-- ==================== 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>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="excluded_chars"></a><span class="summary-name">excluded_chars</span> = <code title="''' \t
\r'''"><code class="variable-quote">'</code><code class="variable-string"> \t\n\r</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="block_type"></a><span class="summary-name">block_type</span> = <code title="Group("block_type", Expression.NoCase(Str("Type")))">Group("block_type", Expression.NoCase(Str("Type")))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="header_line"></a><span class="summary-name">header_line</span> = <code title="Group("header_line", block_type+ ToEol())">Group("header_line", block_type+ ToEol())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="tab"></a><span class="summary-name">tab</span> = <code title="Group("tab", Str('\t'))">Group("tab", Str('\t'))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.ECell.ecell_format-module.html#system_tag" class="summary-name">system_tag</a> = <code title="Group("system_tag", Expression.NoCase(Str("system")))">Group("system_tag", Expression.NoCase(Str("system<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.ECell.ecell_format-module.html#reactor_tag" class="summary-name">reactor_tag</a> = <code title="Group("reactor_tag", Expression.NoCase(Str("Reactor")))">Group("reactor_tag", Expression.NoCase(Str("Reac<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.ECell.ecell_format-module.html#substance_tag" class="summary-name">substance_tag</a> = <code title="Group("substance_tag", Expression.NoCase(Str("Substance")))">Group("substance_tag", Expression.NoCase(Str("<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="system_line"></a><span class="summary-name">system_line</span> = <code title="Group("system_line", system_tag+ ToEol())">Group("system_line", system_tag+ ToEol())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reactor_line"></a><span class="summary-name">reactor_line</span> = <code title="Group("reactor_line", reactor_tag+ ToEol())">Group("reactor_line", reactor_tag+ ToEol())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="substance_line"></a><span class="summary-name">substance_line</span> = <code title="Group("substance_line", substance_tag+ ToEol())">Group("substance_line", substance_tag+ ToEol())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="continuation_line"></a><span class="summary-name">continuation_line</span> = <code title="Group("continuation_line", tab+ ToEol())">Group("continuation_line", tab+ ToEol())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="include_line"></a><span class="summary-name">include_line</span> = <code title="Group("include_line", Str('include')+ ToEol())">Group("include_line", Str('include')+ ToEol())</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.ECell.ecell_format-module.html#substance_multiline" class="summary-name">substance_multiline</a> = <code title="Group("substance_multiline", substance_line+ Rep(continuation_line))">Group("substance_multiline", substance_l<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.ECell.ecell_format-module.html#reactor_multiline" class="summary-name">reactor_multiline</a> = <code title="Group("reactor_multiline", reactor_line+ Rep(continuation_line))">Group("reactor_multiline", reactor_line+ R<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="system_block"></a><span class="summary-name">system_block</span> = <code title="Group("system_block", Rep1(system_line))">Group("system_block", Rep1(system_line))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="reactor_block"></a><span class="summary-name">reactor_block</span> = <code title="Group("reactor_block", Rep1(reactor_multiline))">Group("reactor_block", Rep1(reactor_multiline))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.ECell.ecell_format-module.html#substance_block" class="summary-name">substance_block</a> = <code title="Group("substance_block", Rep1(substance_multiline))">Group("substance_block", Rep1(substance_mult<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.ECell.ecell_format-module.html#valid_block" class="summary-name">valid_block</a> = <code title="Group("valid_block", header_line+ Alt(system_block, reactor_block, sub\
stance_block))">Group("valid_block", header_line+ Alt(system_blo<code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="valid_contents"></a><span class="summary-name">valid_contents</span> = <code title="Group("valid_contents", Rep1(valid_block))">Group("valid_contents", Rep1(valid_block))</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="ecell_record"></a><span class="summary-name">ecell_record</span> = <code title="Group("valid_contents", Rep1(valid_block))">Group("valid_contents", Rep1(valid_block))</code>
</td>
</tr>
</table>
<!-- ==================== 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="system_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">system_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("system_tag", Expression.NoCase(Str("system")))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reactor_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reactor_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reactor_tag", Expression.NoCase(Str("Reactor")))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="substance_tag"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">substance_tag</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("substance_tag", Expression.NoCase(Str("Substance")))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="substance_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">substance_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("substance_multiline", substance_line+ Rep(continuation_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="reactor_multiline"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">reactor_multiline</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("reactor_multiline", reactor_line+ Rep(continuation_line))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="substance_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">substance_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("substance_block", Rep1(substance_multiline))
</pre></td></tr></table>
</dd>
</dl>
</td></tr></table>
</div>
<a name="valid_block"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<h3 class="epydoc">valid_block</h3>
<dl class="fields">
</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
Group("valid_block", header_line+ Alt(system_block, reactor_block, sub<span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
stance_block))
</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 09:26:23 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>
