<?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.Graphics.DisplayRepresentation</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.Graphics-module.html">Package Graphics</a> ::
Module DisplayRepresentation
</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.Graphics.DisplayRepresentation-pysrc.html"
target="_top">no frames</a>]</span></td></tr>
</table>
</td>
</tr>
</table>
<h1 class="epydoc">Source Code for <a href="Bio.Graphics.DisplayRepresentation-module.html">Module Bio.Graphics.DisplayRepresentation</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-docstring">"""Represent information for graphical display.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-docstring">Classes in this module are designed to hold information in a way that</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-docstring">makes it easy to draw graphical figures.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># reportlab</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt class="py-name">reportlab</tt><tt class="py-op">.</tt><tt class="py-name">lib</tt> <tt class="py-keyword">import</tt> <tt class="py-name">colors</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"># local stuff</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Graphics=Bio.Graphics-module.html"><a title="Bio.Graphics" class="py-name" href="#" onclick="return doclink('link-1', 'Graphics', 'link-1');">Graphics</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.Graphics.BasicChromosome=Bio.Graphics.BasicChromosome-module.html"><a title="Bio.Graphics.BasicChromosome" class="py-name" href="#" onclick="return doclink('link-2', 'BasicChromosome', 'link-2');">BasicChromosome</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.Graphics.BasicChromosome.ChromosomeSegment=Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html"><a title="Bio.Graphics.BasicChromosome.ChromosomeSegment" class="py-name" href="#" onclick="return doclink('link-3', 'ChromosomeSegment', 'link-3');">ChromosomeSegment</a></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-4', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Graphics" class="py-name" href="#" onclick="return doclink('link-5', 'Graphics', 'link-1');">Graphics</a></tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.Graphics.BasicChromosome" class="py-name" href="#" onclick="return doclink('link-6', 'BasicChromosome', 'link-2');">BasicChromosome</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" class="py-name" targets="Class Bio.Graphics.BasicChromosome.TelomereSegment=Bio.Graphics.BasicChromosome.TelomereSegment-class.html"><a title="Bio.Graphics.BasicChromosome.TelomereSegment" class="py-name" href="#" onclick="return doclink('link-7', 'TelomereSegment', 'link-7');">TelomereSegment</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"># --- constants</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># This is a default color scheme based on the light spectrum.</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Based on my vague recollections from biology, this is our friend ROY G. BIV</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-8" class="py-name" targets="Variable Bio.Graphics.DisplayRepresentation.RAINBOW_COLORS=Bio.Graphics.DisplayRepresentation-module.html#RAINBOW_COLORS"><a title="Bio.Graphics.DisplayRepresentation.RAINBOW_COLORS" class="py-name" href="#" onclick="return doclink('link-8', 'RAINBOW_COLORS', 'link-8');">RAINBOW_COLORS</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">violet</tt><tt class="py-op">,</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-number">2</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">indigo</tt><tt class="py-op">,</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">blue</tt><tt class="py-op">,</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-number">4</tt><tt class="py-op">,</tt> <tt class="py-number">4</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">green</tt><tt class="py-op">,</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">yellow</tt><tt class="py-op">,</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-number">6</tt><tt class="py-op">,</tt> <tt class="py-number">6</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">orange</tt><tt class="py-op">,</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-number">7</tt><tt class="py-op">,</tt> <tt class="py-number">20</tt><tt class="py-op">)</tt> <tt class="py-op">:</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">red</tt><tt class="py-op">}</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> </tt>
<a name="ChromosomeCounts"></a><div id="ChromosomeCounts-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="ChromosomeCounts-toggle" onclick="return toggle('ChromosomeCounts');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html">ChromosomeCounts</a><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ChromosomeCounts-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-docstring">"""Represent a chromosome with count information.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"> This is used to display information about counts along a chromosome.</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring"> The segments are expected to have different count information, which</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-docstring"> will be displayed using a color scheme.</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-docstring"> I envision using this class when you think that certain regions of</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt class="py-docstring"> the chromosome will be especially abundant in the counts, and you</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-docstring"> want to pick those out.</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="ChromosomeCounts.__init__"></a><div id="ChromosomeCounts.__init__-def"><a name="L35"></a><tt class="py-lineno"> 35</tt> <a class="py-toggle" href="#" id="ChromosomeCounts.__init__-toggle" onclick="return toggle('ChromosomeCounts.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">segment_names</tt><tt class="py-op">,</tt> <tt class="py-param">color_scheme</tt> <tt class="py-op">=</tt> <tt id="link-9" class="py-name"><a title="Bio.Graphics.DisplayRepresentation.RAINBOW_COLORS" class="py-name" href="#" onclick="return doclink('link-9', 'RAINBOW_COLORS', 'link-8');">RAINBOW_COLORS</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ChromosomeCounts.__init__-expanded"><a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-docstring">"""Initialize a representation of chromosome counts.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-docstring"> o segment_names - An ordered list of all segment names along</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"> the chromosome. The count and other information will be added to</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> these.</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt class="py-docstring"> o color_scheme - A coloring scheme to use in the counts. This should</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> be a dictionary mapping count ranges to colors (specified in</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> reportlab.lib.colors).</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_names</tt> <tt class="py-op">=</tt> <tt class="py-name">segment_names</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_count_info</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_label_info</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scale_info</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-10" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-10', 'name', 'link-10');">name</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_names</tt><tt class="py-op">:</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_count_info</tt><tt class="py-op">[</tt><tt id="link-11" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-11', 'name', 'link-10');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_label_info</tt><tt class="py-op">[</tt><tt id="link-12" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-12', 'name', 'link-10');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scale_info</tt><tt class="py-op">[</tt><tt id="link-13" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-13', 'name', 'link-10');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_color_scheme</tt> <tt class="py-op">=</tt> <tt class="py-name">color_scheme</tt> </tt>
</div><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> </tt>
<a name="ChromosomeCounts.add_count"></a><div id="ChromosomeCounts.add_count-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="ChromosomeCounts.add_count-toggle" onclick="return toggle('ChromosomeCounts.add_count');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#add_count">add_count</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">segment_name</tt><tt class="py-op">,</tt> <tt class="py-param">count</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts.add_count-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ChromosomeCounts.add_count-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-docstring">"""Add counts to the given segment name.</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"> o segment_name - The name of the segment we should add counts to.</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> If the name is not present, a KeyError will be raised.</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"><tt class="py-docstring"> o count - The counts to add the current segment. This defaults to</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> a single count.</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_count_info</tt><tt class="py-op">[</tt><tt class="py-name">segment_name</tt><tt class="py-op">]</tt> <tt class="py-op">+=</tt> <tt id="link-14" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-14', 'count', 'link-14');">count</a></tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt class="py-string">"Segment name %s not found."</tt> <tt class="py-op">%</tt> <tt class="py-name">segment_name</tt><tt class="py-op">)</tt> </tt>
</div><a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> </tt>
<a name="ChromosomeCounts.scale_segment_value"></a><div id="ChromosomeCounts.scale_segment_value-def"><a name="L75"></a><tt class="py-lineno"> 75</tt> <a class="py-toggle" href="#" id="ChromosomeCounts.scale_segment_value-toggle" onclick="return toggle('ChromosomeCounts.scale_segment_value');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#scale_segment_value">scale_segment_value</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">segment_name</tt><tt class="py-op">,</tt> <tt class="py-param">scale_value</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts.scale_segment_value-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ChromosomeCounts.scale_segment_value-expanded"><a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-docstring">"""Divide the counts for a segment by some kind of scale value.</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"> This is useful if segments aren't represented by raw counts, but</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> are instead counts divided by some number.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_count_info</tt><tt class="py-op">[</tt><tt class="py-name">segment_name</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_count_info</tt><tt class="py-op">[</tt><tt class="py-name">segment_name</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">scale_value</tt><tt class="py-op">)</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt class="py-string">"Segment name %s not found."</tt> <tt class="py-op">%</tt> <tt class="py-name">segment_name</tt><tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="ChromosomeCounts.add_label"></a><div id="ChromosomeCounts.add_label-def"><a name="L87"></a><tt class="py-lineno"> 87</tt> <a class="py-toggle" href="#" id="ChromosomeCounts.add_label-toggle" onclick="return toggle('ChromosomeCounts.add_label');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#add_label">add_label</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">segment_name</tt><tt class="py-op">,</tt> <tt class="py-param">label</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts.add_label-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ChromosomeCounts.add_label-expanded"><a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-docstring">"""Add a label to a specfic segment.</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> Raises a KeyError is the specified segment name is not found.</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_label_info</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-15', 'has_key', 'link-15');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">segment_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_label_info</tt><tt class="py-op">[</tt><tt class="py-name">segment_name</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">label</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt class="py-string">"Segment name %s not found."</tt> <tt class="py-op">%</tt> <tt class="py-name">segment_name</tt><tt class="py-op">)</tt> </tt>
</div><a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> </tt>
<a name="ChromosomeCounts.set_scale"></a><div id="ChromosomeCounts.set_scale-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="ChromosomeCounts.set_scale-toggle" onclick="return toggle('ChromosomeCounts.set_scale');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#set_scale">set_scale</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">segment_name</tt><tt class="py-op">,</tt> <tt class="py-param">scale</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts.set_scale-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ChromosomeCounts.set_scale-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> <tt class="py-docstring">"""Set the scale for a specific chromosome segment.</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> By default all segments have the same scale -- this allows scaling</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> by the size of the segment.</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"><tt class="py-docstring"> Raises a KeyError is the specified segment name is not found.</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_label_info</tt><tt class="py-op">.</tt><tt id="link-16" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-16', 'has_key', 'link-15');">has_key</a></tt><tt class="py-op">(</tt><tt class="py-name">segment_name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scale_info</tt><tt class="py-op">[</tt><tt class="py-name">segment_name</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">scale</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">KeyError</tt><tt class="py-op">(</tt><tt class="py-string">"Segment name %s not found."</tt> <tt class="py-op">%</tt> <tt class="py-name">segment_name</tt><tt class="py-op">)</tt> </tt>
</div><a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> </tt>
<a name="ChromosomeCounts.get_segment_info"></a><div id="ChromosomeCounts.get_segment_info-def"><a name="L110"></a><tt class="py-lineno">110</tt> <a class="py-toggle" href="#" id="ChromosomeCounts.get_segment_info-toggle" onclick="return toggle('ChromosomeCounts.get_segment_info');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#get_segment_info">get_segment_info</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts.get_segment_info-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ChromosomeCounts.get_segment_info-expanded"><a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-docstring">"""Retrieve the color and label info about the segments.</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list consiting of two tuples specifying the counts and</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> label name for each segment. The list is ordered according to the</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> original listing of names. Labels are set as None if no label</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> was specified.</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-name">order_info</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">seg_name</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_names</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">order_info</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-17', 'append', 'link-17');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_count_info</tt><tt class="py-op">[</tt><tt class="py-name">seg_name</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_label_info</tt><tt class="py-op">[</tt><tt class="py-name">seg_name</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">order_info</tt> </tt>
</div><a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> </tt>
<a name="ChromosomeCounts.fill_chromosome"></a><div id="ChromosomeCounts.fill_chromosome-def"><a name="L126"></a><tt class="py-lineno">126</tt> <a class="py-toggle" href="#" id="ChromosomeCounts.fill_chromosome-toggle" onclick="return toggle('ChromosomeCounts.fill_chromosome');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#fill_chromosome">fill_chromosome</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">chromosome</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts.fill_chromosome-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ChromosomeCounts.fill_chromosome-expanded"><a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-docstring">"""Add the collected segment information to a chromosome for drawing.</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> Arguments:</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"> o chromosome - A Chromosome graphics object that we can add</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> chromosome segments to.</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"> This creates ChromosomeSegment (and TelomereSegment) objects to</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> fill in the chromosome. The information is derived from the</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> label and count information, with counts transformed to the</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> specified color map.</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> Returns the chromosome with all of the segments added.</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">seg_num</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_names</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-name">is_end_segment</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-comment"># make the top and bottom telomeres</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">seg_num</tt> <tt class="py-op">==</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-name">cur_segment</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Bio.Graphics.BasicChromosome.TelomereSegment" class="py-name" href="#" onclick="return doclink('link-18', 'TelomereSegment', 'link-7');">TelomereSegment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">is_end_segment</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">seg_num</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_names</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-name">cur_segment</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.Graphics.BasicChromosome.TelomereSegment" class="py-name" href="#" onclick="return doclink('link-19', 'TelomereSegment', 'link-7');">TelomereSegment</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"> <tt class="py-name">is_end_segment</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-comment"># otherwise, they are just regular segments</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-name">cur_segment</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="Bio.Graphics.BasicChromosome.ChromosomeSegment" class="py-name" href="#" onclick="return doclink('link-20', 'ChromosomeSegment', 'link-3');">ChromosomeSegment</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-name">seg_name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_names</tt><tt class="py-op">[</tt><tt class="py-name">seg_num</tt><tt class="py-op">]</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_count_info</tt><tt class="py-op">[</tt><tt class="py-name">seg_name</tt><tt class="py-op">]</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-name">color</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name" targets="Method Bio.Graphics.DisplayRepresentation.ChromosomeCounts._color_from_count()=Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#_color_from_count"><a title="Bio.Graphics.DisplayRepresentation.ChromosomeCounts._color_from_count" class="py-name" href="#" onclick="return doclink('link-21', '_color_from_count', 'link-21');">_color_from_count</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_count_info</tt><tt class="py-op">[</tt><tt class="py-name">seg_name</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">cur_segment</tt><tt class="py-op">.</tt><tt class="py-name">fill_color</tt> <tt class="py-op">=</tt> <tt class="py-name">color</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_label_info</tt><tt class="py-op">[</tt><tt class="py-name">seg_name</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">cur_segment</tt><tt class="py-op">.</tt><tt class="py-name">label</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_label_info</tt><tt class="py-op">[</tt><tt class="py-name">seg_name</tt><tt class="py-op">]</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-comment"># give end segments extra size so they look right</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">is_end_segment</tt><tt class="py-op">:</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">cur_segment</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt> <tt class="py-op">=</tt> <tt class="py-number">3</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-name">cur_segment</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_scale_info</tt><tt class="py-op">[</tt><tt class="py-name">seg_name</tt><tt class="py-op">]</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">chromosome</tt><tt class="py-op">.</tt><tt id="link-22" class="py-name" targets="Variable Bio.Affy.CelFile.add=Bio.Affy.CelFile-module.html#add,Method Bio.EUtils.POM.ElementNode.add()=Bio.EUtils.POM.ElementNode-class.html#add,Method Bio.GFF.easy.Location.add()=Bio.GFF.easy.Location-class.html#add,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.add()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#add,Variable Bio.LogisticRegression.add=Bio.LogisticRegression-module.html#add,Variable Bio.MarkovModel.add=Bio.MarkovModel-module.html#add,Variable Bio.MaxEntropy.add=Bio.MaxEntropy-module.html#add,Variable Bio.NaiveBayes.add=Bio.NaiveBayes-module.html#add,Method Bio.Nexus.Nexus.StepMatrix.add()=Bio.Nexus.Nexus.StepMatrix-class.html#add,Method Bio.Nexus.Nodes.Chain.add()=Bio.Nexus.Nodes.Chain-class.html#add,Method Bio.PDB.Entity.Entity.add()=Bio.PDB.Entity.Entity-class.html#add,Method Bio.PDB.Residue.DisorderedResidue.add()=Bio.PDB.Residue.DisorderedResidue-class.html#add,Method Bio.PDB.Residue.Residue.add()=Bio.PDB.Residue.Residue-class.html#add,Method Bio.Pathway.Rep.HashSet.HashSet.add()=Bio.Pathway.Rep.HashSet.HashSet-class.html#add,Method Bio.Restriction.Restriction.RestrictionBatch.add()=Bio.Restriction.Restriction.RestrictionBatch-class.html#add,Variable Bio.Statistics.lowess.add=Bio.Statistics.lowess-module.html#add,Method Bio.config.FormatRegistry.FormatGroup.add()=Bio.config.FormatRegistry.FormatGroup-class.html#add,Method Bio.config.Registry.RegisterableGroup.add()=Bio.config.Registry.RegisterableGroup-class.html#add,Variable Bio.distance.add=Bio.distance-module.html#add,Variable Bio.kNN.add=Bio.kNN-module.html#add,Method Martel.Dispatch.MulticallEnd.add()=Martel.Dispatch.MulticallEnd-class.html#add,Method Martel.Dispatch.MulticallStart.add()=Martel.Dispatch.MulticallStart-class.html#add"><a title="Bio.Affy.CelFile.add
Bio.EUtils.POM.ElementNode.add
Bio.GFF.easy.Location.add
Bio.Graphics.BasicChromosome._ChromosomeComponent.add
Bio.LogisticRegression.add
Bio.MarkovModel.add
Bio.MaxEntropy.add
Bio.NaiveBayes.add
Bio.Nexus.Nexus.StepMatrix.add
Bio.Nexus.Nodes.Chain.add
Bio.PDB.Entity.Entity.add
Bio.PDB.Residue.DisorderedResidue.add
Bio.PDB.Residue.Residue.add
Bio.Pathway.Rep.HashSet.HashSet.add
Bio.Restriction.Restriction.RestrictionBatch.add
Bio.Statistics.lowess.add
Bio.config.FormatRegistry.FormatGroup.add
Bio.config.Registry.RegisterableGroup.add
Bio.distance.add
Bio.kNN.add
Martel.Dispatch.MulticallEnd.add
Martel.Dispatch.MulticallStart.add" class="py-name" href="#" onclick="return doclink('link-22', 'add', 'link-22');">add</a></tt><tt class="py-op">(</tt><tt class="py-name">cur_segment</tt><tt class="py-op">)</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">chromosome</tt> </tt>
</div><a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> </tt>
<a name="ChromosomeCounts._color_from_count"></a><div id="ChromosomeCounts._color_from_count-def"><a name="L172"></a><tt class="py-lineno">172</tt> <a class="py-toggle" href="#" id="ChromosomeCounts._color_from_count-toggle" onclick="return toggle('ChromosomeCounts._color_from_count');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.DisplayRepresentation.ChromosomeCounts-class.html#_color_from_count">_color_from_count</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">count</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ChromosomeCounts._color_from_count-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="ChromosomeCounts._color_from_count-expanded"><a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-docstring">"""Translate the given count into a color using the color scheme.</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">count_start</tt><tt class="py-op">,</tt> <tt class="py-name">count_end</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_color_scheme</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.EUtils.MultiDict._BaseMultiDict.keys()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#keys,Method Bio.GenBank.NCBIDictionary.keys()=Bio.GenBank.NCBIDictionary-class.html#keys,Method Bio.Mindy.BaseDB.DictLookup.keys()=Bio.Mindy.BaseDB.DictLookup-class.html#keys,Method Bio.Mindy.BaseDB.OpenDB.keys()=Bio.Mindy.BaseDB.OpenDB-class.html#keys,Method Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys()=Bio.Mindy.BerkeleyDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys()=Bio.Mindy.BerkeleyDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryNamespace.keys()=Bio.Mindy.FlatDB.PrimaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.PrimaryTable.keys()=Bio.Mindy.FlatDB.PrimaryTable-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryNamespace.keys()=Bio.Mindy.FlatDB.SecondaryNamespace-class.html#keys,Method Bio.Mindy.FlatDB.SecondaryTable.keys()=Bio.Mindy.FlatDB.SecondaryTable-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Prosite.ExPASyDictionary.keys()=Bio.Prosite.ExPASyDictionary-class.html#keys,Method Bio.Prosite.Prodoc.ExPASyDictionary.keys()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#keys,Method Bio.PubMed.Dictionary.keys()=Bio.PubMed.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.Dictionary.keys()=Bio.SwissProt.SProt.Dictionary-class.html#keys,Method Bio.SwissProt.SProt.ExPASyDictionary.keys()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#keys,Method Bio.config.Registry.Registry.keys()=Bio.config.Registry.Registry-class.html#keys,Method BioSQL.BioSeqDatabase.BioSeqDatabase.keys()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#keys,Method BioSQL.BioSeqDatabase.DBServer.keys()=BioSQL.BioSeqDatabase.DBServer-class.html#keys,Method Martel.Parser.MartelAttributeList.keys()=Martel.Parser.MartelAttributeList-class.html#keys"><a title="Bio.Crystal.Crystal.keys
Bio.EUtils.MultiDict._BaseMultiDict.keys
Bio.GenBank.NCBIDictionary.keys
Bio.Mindy.BaseDB.DictLookup.keys
Bio.Mindy.BaseDB.OpenDB.keys
Bio.Mindy.BerkeleyDB.PrimaryNamespace.keys
Bio.Mindy.BerkeleyDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryNamespace.keys
Bio.Mindy.FlatDB.PrimaryTable.keys
Bio.Mindy.FlatDB.SecondaryNamespace.keys
Bio.Mindy.FlatDB.SecondaryTable.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Prosite.ExPASyDictionary.keys
Bio.Prosite.Prodoc.ExPASyDictionary.keys
Bio.PubMed.Dictionary.keys
Bio.SwissProt.SProt.Dictionary.keys
Bio.SwissProt.SProt.ExPASyDictionary.keys
Bio.config.Registry.Registry.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys
Martel.Parser.MartelAttributeList.keys" class="py-name" href="#" onclick="return doclink('link-23', 'keys', 'link-23');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-24" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-24', 'count', 'link-14');">count</a></tt> <tt class="py-op">>=</tt> <tt class="py-name">count_start</tt> <tt class="py-keyword">and</tt> <tt id="link-25" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-25', 'count', 'link-14');">count</a></tt> <tt class="py-op"><=</tt> <tt class="py-name">count_end</tt><tt class="py-op">:</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_color_scheme</tt><tt class="py-op">[</tt><tt class="py-op">(</tt><tt class="py-name">count_start</tt><tt class="py-op">,</tt> <tt class="py-name">count_end</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-comment"># if we got here we didn't find a color for the count</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Count value %s was not found in the color scheme."</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> <tt class="py-op">%</tt> <tt id="link-26" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-26', 'count', 'link-14');">count</a></tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt><script type="text/javascript">
<!--
expandto(location.href);
// -->
</script>
</pre>
<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 09:26:45 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>
