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Module _Track
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<h1 class="epydoc">Source Code for <a href="Bio.Graphics.GenomeDiagram._Track-module.html" onclick="show_private();">Module Bio.Graphics.GenomeDiagram._Track</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2003-2008 by Leighton Pritchard. All rights reserved.</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"># Contact: Leighton Pritchard, Scottish Crop Research Institute,</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># Invergowrie, Dundee, Scotland, DD2 5DA, UK</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"># L.Pritchard@scri.ac.uk</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment">################################################################################</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-docstring">""" Track module</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-docstring"> Provides:</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-docstring"> o Track - Container for a single track on the diagram, containing</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> FeatureSet and GraphSet objects</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"> For drawing capabilities, this module uses reportlab to draw and write</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> the diagram:</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"> http://www.reportlab.com</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"> For dealing with biological information, the package expects BioPython</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> objects:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring"> http://www.biopython.org</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt class="py-comment"># ReportLab imports</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><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="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-comment"># GenomeDiagram imports</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Module Bio.Graphics.GenomeDiagram._FeatureSet=Bio.Graphics.GenomeDiagram._FeatureSet-module.html"><a title="Bio.Graphics.GenomeDiagram._FeatureSet" class="py-name" href="#" onclick="return doclink('link-0', '_FeatureSet', 'link-0');">_FeatureSet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-1" class="py-name" targets="Class Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html"><a title="Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet" class="py-name" href="#" onclick="return doclink('link-1', 'FeatureSet', 'link-1');">FeatureSet</a></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module Bio.Graphics.GenomeDiagram._GraphSet=Bio.Graphics.GenomeDiagram._GraphSet-module.html"><a title="Bio.Graphics.GenomeDiagram._GraphSet" class="py-name" href="#" onclick="return doclink('link-2', '_GraphSet', 'link-2');">_GraphSet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.Graphics.GenomeDiagram._GraphSet.GraphSet=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html"><a title="Bio.Graphics.GenomeDiagram._GraphSet.GraphSet" class="py-name" href="#" onclick="return doclink('link-3', 'GraphSet', 'link-3');">GraphSet</a></tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> </tt>
<a name="Track"></a><div id="Track-def"><a name="L37"></a><tt class="py-lineno"> 37</tt> <a class="py-toggle" href="#" id="Track-toggle" onclick="return toggle('Track');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html">Track</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Track-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Track-expanded"><a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-docstring">""" Track</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"> Provides:</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-docstring"> Methods:</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 __init__(self, name=None, height=1, hide=0, greytrack=0,</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-docstring"> greytrack_labels=5, greytrack_fontsize=8,</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-docstring"> greytrack_font='Helvetica', greytrack_font_rotation=0,</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"><tt class="py-docstring"> greytrack_fontcolor = colors.Color(0.6, 0.6, 0.6),</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-docstring"> scale=1, scale_color=colors.black, scale_font='Helvetica',</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"><tt class="py-docstring"> scale_fontsize=6,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-docstring"> scale_fontangle=45, scale_largeticks=0.5, scale_ticks=1,</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-docstring"> scale_smallticks=0.3, scale_largetick_interval=1e6,</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"><tt class="py-docstring"> scale_smalltick_interval=1e4, scale_largetick_labels=1,</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-docstring"> scale_smalltick_labels=0) Called on instantiation</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"><tt class="py-docstring"> o add_set(self, set) Add a FeatureSet or GraphSet to the diagram</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"><tt class="py-docstring"> o del_set(self, set_id) Delete a FeatureSet or GraphSet from the</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"> diagram</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"> o get_sets(self) Returns a list of the sets in the track</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"> o get_ids(self) Returns a list of the ids for sets in the track</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 range(self) Returns the base/position range covered by the data in</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> the track</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 to_string(self, verbose=0) Returns a string describing the data in</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"> the track</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-docstring"> o __getitem__(self, key) Returns the set with the passed id</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"> o __str__(self) Returns a formatted string describing the track</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"><tt class="py-docstring"> o height Int describing the relative height to other trackscale_fontsizes in the</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> diagram</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"><tt class="py-docstring"> o name String describing the track</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-docstring"> o hide Boolean, 0 if the track is not to be drawn</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack Boolean, 1 if a grey background to the track is to be</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"> drawn</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack_labels Int describing how many track-identifying labels</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"> should be placed on the track at regular intervals</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack_font String describing the font to use for the greytrack</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"> labels</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-docstring"> o greytrack_fontsize Int describing the font size to display the</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> labels on the grey track</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack_font_rotation Int describing the angle through which to</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"> rotate the grey track labels</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack_font_color colors.Color describing the color to draw</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"> the grey track labels</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> o scale Boolean, 1 if a scale is to be drawn on the track</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"> o scale_format String, defaults to None, when scale values are written</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> as numerals. Setting this to 'SInt' invokes SI</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"> unit-like multiples, such as Mbp, Kbp and so on.</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> o scale_color colors.Color to draw the elemnts of the scale</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"><tt class="py-docstring"> o scale_font String describing the font to use for the scale labels</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"><tt class="py-docstring"> o scale_fontsize Int describing the size of the scale label font</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"> o scale_fontangle Int describing the angle at which to draw the scale</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> labels (linear only)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> o scale_ticks Boolean, 1 if ticks should be drawn at all on the</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> scale</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"><tt class="py-docstring"> o scale_largeticks Float (0->1) describing the height of large</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> scale ticks relative to the track height.</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"><tt class="py-docstring"> o scale_smallticks Float (0->1) describing the height of large</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> scale ticks relative to the track height.</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"> o scale_largetick_interval Int, describing the number of bases that</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> should separate large ticks</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"> o scale_smalltick_interval Int, describing the number of bases that</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> should separate small ticks</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 scale_largetick_labels Boolean describing whether position labels</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> should be written over large ticks</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"> o scale_smalltick_labels Boolean describing whether position labels</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> should be written over small ticks</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"> o axis_labels Boolean describing whether the value labels should</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"> be placed on the Y axes</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Track.__init__"></a><div id="Track.__init__-def"><a name="L140"></a><tt class="py-lineno">140</tt> <a class="py-toggle" href="#" id="Track.__init__-toggle" onclick="return toggle('Track.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-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">name</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">height</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">hide</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">greytrack</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-param">greytrack_labels</tt><tt class="py-op">=</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-param">greytrack_fontsize</tt><tt class="py-op">=</tt><tt class="py-number">8</tt><tt class="py-op">,</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-param">greytrack_font</tt><tt class="py-op">=</tt><tt class="py-string">'Helvetica'</tt><tt class="py-op">,</tt> <tt class="py-param">greytrack_font_rotation</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-param">greytrack_font_color</tt> <tt class="py-op">=</tt> <tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">Color</tt><tt class="py-op">(</tt><tt class="py-number">0.6</tt><tt class="py-op">,</tt> <tt class="py-number">0.6</tt><tt class="py-op">,</tt> <tt class="py-number">0.6</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-param">scale</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">scale_format</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">scale_color</tt><tt class="py-op">=</tt><tt class="py-name">colors</tt><tt class="py-op">.</tt><tt class="py-name">black</tt><tt class="py-op">,</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-param">scale_font</tt><tt class="py-op">=</tt><tt class="py-string">'Helvetica'</tt><tt class="py-op">,</tt> <tt class="py-param">scale_fontsize</tt><tt class="py-op">=</tt><tt class="py-number">6</tt><tt class="py-op">,</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-param">scale_fontangle</tt><tt class="py-op">=</tt><tt class="py-number">45</tt><tt class="py-op">,</tt> <tt class="py-param">scale_largeticks</tt><tt class="py-op">=</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-param">scale_ticks</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-param">scale_smallticks</tt><tt class="py-op">=</tt><tt class="py-number">0.3</tt><tt class="py-op">,</tt> <tt class="py-param">scale_largetick_interval</tt><tt class="py-op">=</tt><tt class="py-number">1e6</tt><tt class="py-op">,</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-param">scale_smalltick_interval</tt><tt class="py-op">=</tt><tt class="py-number">1e4</tt><tt class="py-op">,</tt> <tt class="py-param">scale_largetick_labels</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-param">scale_smalltick_labels</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">axis_labels</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-param">greytrack_font_colour</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">scale_colour</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="Track.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.__init__-expanded"><a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-docstring">""" __init__(self, name=None, height=1)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-docstring"> o height Int describing the relative height to other tracks in the</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"><tt class="py-docstring"> diagram</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"><tt class="py-docstring"> o name String describing the track</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"><tt class="py-docstring"> o hide Boolean, 0 if the track is not to be drawn</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack Boolean, 1 if a grey background to the track is to be</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> drawn</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack_labels Int describing how many track-identifying labels</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> should be placed on the track at regular intervals</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack_font String describing the font to use for the greytrack</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> labels</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack_fontsize Int describing the font size to display the</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> labels on the grey track</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"><tt class="py-docstring"> o greytrack_font_rotation Int describing the angle through which to</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> rotate the grey track labels</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-docstring"> o greytrack_font_color colors.Color describing the color to draw</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> the grey track labels (overridden by</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"> backwards compatible argument with UK</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> spelling, colour).</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"> o scale Boolean, 1 if a scale is to be drawn on the track</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> o scale_color colors.Color to draw the elemnts of the scale</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"> (overridden by backwards compatible argument with UK</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"> spelling, colour).</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"> o scale_font String describing the font to use for the scale labels</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> o scale_fontsize Int describing the size of the scale label font</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"><tt class="py-docstring"> o scale_fontangle Int describing the angle at which to draw the scale</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"> labels (linear only)</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"><tt class="py-docstring"> o scale_ticks Boolean, 1 if ticks should be drawn at all on the</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"> scale</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> o scale_largeticks Float (0->1) describing the height of large</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"> scale ticks relative to the track height.</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring"> o scale_smallticks Float (0->1) describing the height of large</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-docstring"> scale ticks relative to the track height.</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> o scale_largetick_interval Int, describing the number of bases that</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> should separate large ticks</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"><tt class="py-docstring"> o scale_smalltick_interval Int, describing the number of bases that</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> should separate small ticks</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"><tt class="py-docstring"> o scale_largetick_labels Boolean describing whether position labels</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"> should be written over large ticks</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"><tt class="py-docstring"> o scale_smalltick_labels Boolean describing whether position labels</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> should be written over small ticks</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"><tt class="py-docstring"> o name String to help identify the track</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-docstring"> </tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-docstring"> o height Relative height to draw the track</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-docstring"> o axis_labels Boolean describing whether the value labels should</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-docstring"> be placed on the Y axes</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-comment">#Let the UK spelling (colour) override the USA spelling (color)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">greytrack_font_colour</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="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">greytrack_font_color</tt> <tt class="py-op">=</tt> <tt class="py-name">greytrack_font_colour</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">scale_colour</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="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">scale_color</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_colour</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_id</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> <tt class="py-comment"># This will count sets as they are added to the track</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sets</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># Holds sets, keyed by unique ID</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-comment"># Assign attribute values from instantiation</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">height</tt> <tt class="py-op">=</tt> <tt class="py-name">height</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-4" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.name()=Bio.Phylo.PhyloXMLIO.Writer-class.html#name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-4', 'name', 'link-4');">name</a></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="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-5', 'name', 'link-4');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-6" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-6', 'name', 'link-4');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-7', 'name', 'link-4');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"Track"</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">hide</tt> <tt class="py-op">=</tt> <tt class="py-name">hide</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"> <tt class="py-comment"># Attributes for the grey track background and labels</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">greytrack</tt> <tt class="py-op">=</tt> <tt class="py-name">greytrack</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">greytrack_labels</tt> <tt class="py-op">=</tt> <tt class="py-name">greytrack_labels</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">greytrack_fontsize</tt> <tt class="py-op">=</tt> <tt class="py-name">greytrack_fontsize</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">greytrack_font</tt> <tt class="py-op">=</tt> <tt class="py-name">greytrack_font</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">greytrack_font_rotation</tt> <tt class="py-op">=</tt> <tt class="py-name">greytrack_font_rotation</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">greytrack_fontcolor</tt> <tt class="py-op">=</tt> <tt class="py-name">greytrack_font_color</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-comment"># Attributes for the track scale</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale</tt> <tt class="py-op">=</tt> <tt class="py-name">scale</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_format</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_format</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_color</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_color</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_font</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_font</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_fontsize</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_fontsize</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_fontangle</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_fontangle</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_ticks</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_ticks</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_largeticks</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_largeticks</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_smallticks</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_smallticks</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_largetick_interval</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_largetick_interval</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_smalltick_interval</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_smalltick_interval</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_largetick_labels</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_largetick_labels</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">scale_smalltick_labels</tt> <tt class="py-op">=</tt> <tt class="py-name">scale_smalltick_labels</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">axis_labels</tt> <tt class="py-op">=</tt> <tt class="py-name">axis_labels</tt> </tt>
</div><a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> </tt>
<a name="Track.add_set"></a><div id="Track.add_set-def"><a name="L263"></a><tt class="py-lineno">263</tt> <a class="py-toggle" href="#" id="Track.add_set-toggle" onclick="return toggle('Track.add_set');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#add_set">add_set</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">set</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Track.add_set-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.add_set-expanded"><a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-docstring">""" add_set(self, set)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-docstring"> o set A FeatureSet or GraphSet object</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-docstring"> Add a preexisting FeatureSet or GraphSet object to the track</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt id="link-8" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.set()=Bio.Nexus.Nexus.StepMatrix-class.html#set,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#set"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-8', 'set', 'link-8');">set</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Parser.id()=Bio.Phylo.PhyloXMLIO.Parser-class.html#id,Method Bio.Phylo.PhyloXMLIO.Writer.id()=Bio.Phylo.PhyloXMLIO.Writer-class.html#id"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-9', 'id', 'link-9');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_id</tt> <tt class="py-comment"># Assign unique id to set</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt id="link-10" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-10', 'set', 'link-8');">set</a></tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> <tt class="py-comment"># Make set's parent this track</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sets</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_id</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-11" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-11', 'set', 'link-8');">set</a></tt> <tt class="py-comment"># Add set, keyed by unique id</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_id</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> <tt class="py-comment"># Increment unique set ids</tt> </tt>
</div><a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> </tt>
<a name="Track.new_set"></a><div id="Track.new_set-def"><a name="L276"></a><tt class="py-lineno">276</tt> <a class="py-toggle" href="#" id="Track.new_set-toggle" onclick="return toggle('Track.new_set');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#new_set">new_set</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">type</tt><tt class="py-op">=</tt><tt class="py-string">'feature'</tt><tt class="py-op">,</tt> <tt class="py-op">**</tt><tt class="py-param">args</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Track.new_set-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.new_set-expanded"><a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-docstring">""" new_set(self, type='feature') -> FeatureSet or GraphSet</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-docstring"> Create a new FeatureSet or GraphSet object, add it to the</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"><tt class="py-docstring"> track, and return for user manipulation</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">type_dict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">'feature'</tt><tt class="py-op">:</tt> <tt id="link-12" class="py-name"><a title="Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet" class="py-name" href="#" onclick="return doclink('link-12', 'FeatureSet', 'link-1');">FeatureSet</a></tt><tt class="py-op">,</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-string">'graph'</tt><tt class="py-op">:</tt> <tt id="link-13" class="py-name"><a title="Bio.Graphics.GenomeDiagram._GraphSet.GraphSet" class="py-name" href="#" onclick="return doclink('link-13', 'GraphSet', 'link-3');">GraphSet</a></tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-op">}</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt id="link-14" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-14', 'set', 'link-8');">set</a></tt> <tt class="py-op">=</tt> <tt class="py-name">type_dict</tt><tt class="py-op">[</tt><tt id="link-15" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type,Method Bio.Phylo.PhyloXMLIO.Writer.type()=Bio.Phylo.PhyloXMLIO.Writer-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-15', 'type', 'link-15');">type</a></tt><tt class="py-op">]</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">args</tt><tt class="py-op">:</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-16', 'set', 'link-8');">set</a></tt><tt class="py-op">,</tt> <tt class="py-name">key</tt><tt class="py-op">,</tt> <tt class="py-name">args</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt id="link-17" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-17', 'set', 'link-8');">set</a></tt><tt class="py-op">.</tt><tt id="link-18" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Parser.id
Bio.Phylo.PhyloXMLIO.Writer.id" class="py-name" href="#" onclick="return doclink('link-18', 'id', 'link-9');">id</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_id</tt> <tt class="py-comment"># Assign unique id to set</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt id="link-19" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-19', 'set', 'link-8');">set</a></tt><tt class="py-op">.</tt><tt class="py-name">parent</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt> <tt class="py-comment"># Make set's parent this track</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sets</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_id</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-20', 'set', 'link-8');">set</a></tt> <tt class="py-comment"># Add set, keyed by unique id</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_next_id</tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> <tt class="py-comment"># Increment unique set ids</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-21" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-21', 'set', 'link-8');">set</a></tt> </tt>
</div><a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> </tt>
<a name="Track.del_set"></a><div id="Track.del_set-def"><a name="L295"></a><tt class="py-lineno">295</tt> <a class="py-toggle" href="#" id="Track.del_set-toggle" onclick="return toggle('Track.del_set');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#del_set">del_set</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">set_id</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Track.del_set-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.del_set-expanded"><a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-docstring">""" del_set(self, set_id)</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> o set_id The unique id for the set in this track</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"><tt class="py-docstring"> Remove the set with the passed id from the track</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sets</tt><tt class="py-op">[</tt><tt id="link-22" class="py-name" targets="Method Bio.Nexus.Nodes.Node.set_id()=Bio.Nexus.Nodes.Node-class.html#set_id"><a title="Bio.Nexus.Nodes.Node.set_id" class="py-name" href="#" onclick="return doclink('link-22', 'set_id', 'link-22');">set_id</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> </tt>
<a name="Track.get_sets"></a><div id="Track.get_sets-def"><a name="L305"></a><tt class="py-lineno">305</tt> <a class="py-toggle" href="#" id="Track.get_sets-toggle" onclick="return toggle('Track.get_sets');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#get_sets">get_sets</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="Track.get_sets-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.get_sets-expanded"><a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-docstring">""" get_sets(self) -> FeatureSet or GraphSet</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"><tt class="py-docstring"> Return the sets contained in this track</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</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">_sets</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.Crystal.Crystal.values()=Bio.Crystal.Crystal-class.html#values,Method Bio.Phylo.PhyloXML.Events.values()=Bio.Phylo.PhyloXML.Events-class.html#values,Method Bio.SeqIO._index._IndexedSeqFileDict.values()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#values,Method BioSQL.BioSeqDatabase.BioSeqDatabase.values()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#values,Method BioSQL.BioSeqDatabase.DBServer.values()=BioSQL.BioSeqDatabase.DBServer-class.html#values"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-23', 'values', 'link-23');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> </tt>
<a name="Track.get_ids"></a><div id="Track.get_ids-def"><a name="L313"></a><tt class="py-lineno">313</tt> <a class="py-toggle" href="#" id="Track.get_ids-toggle" onclick="return toggle('Track.get_ids');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#get_ids">get_ids</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="Track.get_ids-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.get_ids-expanded"><a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-docstring">""" get_ids(self) -> [int, int, ...]</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-docstring"> Return the ids of all sets contained in this track</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</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">_sets</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Crystal.Crystal.keys()=Bio.Crystal.Crystal-class.html#keys,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#keys,Method Bio.Phylo.PhyloXML.Events.keys()=Bio.Phylo.PhyloXML.Events-class.html#keys,Method Bio.SeqIO._index._IndexedSeqFileDict.keys()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#keys,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.keys()=Bio.SeqIO._index._SQLiteManySeqFilesDict-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"><a title="Bio.Crystal.Crystal.keys
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.keys
Bio.Phylo.PhyloXML.Events.keys
Bio.SeqIO._index._IndexedSeqFileDict.keys
Bio.SeqIO._index._SQLiteManySeqFilesDict.keys
BioSQL.BioSeqDatabase.BioSeqDatabase.keys
BioSQL.BioSeqDatabase.DBServer.keys" class="py-name" href="#" onclick="return doclink('link-24', 'keys', 'link-24');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> </tt>
<a name="Track.range"></a><div id="Track.range-def"><a name="L321"></a><tt class="py-lineno">321</tt> <a class="py-toggle" href="#" id="Track.range-toggle" onclick="return toggle('Track.range');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#range">range</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="Track.range-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.range-expanded"><a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-docstring">""" range(self) -> (int, int)</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"><tt class="py-docstring"> Returns the lowest and highest base (or mark) numbers as a tuple</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-name">lows</tt><tt class="py-op">,</tt> <tt class="py-name">highs</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> <tt class="py-comment"># Holds set of low and high values from sets</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-25" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-25', 'set', 'link-8');">set</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sets</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name"><a title="Bio.Crystal.Crystal.values
Bio.Phylo.PhyloXML.Events.values
Bio.SeqIO._index._IndexedSeqFileDict.values
BioSQL.BioSeqDatabase.BioSeqDatabase.values
BioSQL.BioSeqDatabase.DBServer.values" class="py-name" href="#" onclick="return doclink('link-26', 'values', 'link-23');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">low</tt><tt class="py-op">,</tt> <tt class="py-name">high</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-27', 'set', 'link-8');">set</a></tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-28', 'range', 'link-28');">range</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># Get each set range</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">lows</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-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"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-29', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">low</tt><tt class="py-op">)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">highs</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-30', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">high</tt><tt class="py-op">)</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">lows</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">highs</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-comment"># Return lowest and highest values</tt> </tt>
</div><a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> </tt>
<a name="Track.to_string"></a><div id="Track.to_string-def"><a name="L334"></a><tt class="py-lineno">334</tt> <a class="py-toggle" href="#" id="Track.to_string-toggle" onclick="return toggle('Track.to_string');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#to_string">to_string</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">verbose</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Track.to_string-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.to_string-expanded"><a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-docstring">""" to_string(self, verbose=0) -> ""</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-docstring"> o verbose Boolean indicating whether a short or complete</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"><tt class="py-docstring"> account of the track is required</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"><tt class="py-docstring"> Returns a formatted string with information about the track</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">verbose</tt><tt class="py-op">:</tt> <tt class="py-comment"># Return the short description</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt> <tt class="py-comment"># Use __str__ method instead</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># Return the long desription</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-name">outstr</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"\n<%s: %s>"</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">__class__</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-31', 'name', 'link-4');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-name">outstr</tt><tt class="py-op">.</tt><tt id="link-32" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-32', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%d sets"</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">_sets</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">key</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sets</tt><tt class="py-op">:</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-name">outstr</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-33', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"set: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_sets</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">outstr</tt><tt class="py-op">)</tt> </tt>
</div><a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> </tt>
<a name="Track.__getitem__"></a><div id="Track.__getitem__-def"><a name="L352"></a><tt class="py-lineno">352</tt> <a class="py-toggle" href="#" id="Track.__getitem__-toggle" onclick="return toggle('Track.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">key</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Track.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.__getitem__-expanded"><a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-docstring">""" __getitem__(self, key) -> int</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"><tt class="py-docstring"> o key The id of a set in the track</tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"><tt class="py-docstring"> Return the set with the passed id</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</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">_sets</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> </tt>
<a name="Track.__str__"></a><div id="Track.__str__-def"><a name="L362"></a><tt class="py-lineno">362</tt> <a class="py-toggle" href="#" id="Track.__str__-toggle" onclick="return toggle('Track.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Track.Track-class.html#__str__">__str__</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="Track.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Track.__str__-expanded"><a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-docstring">""" __str__(self) -> ""</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-docstring"> Returns a formatted string with information about the Track</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">outstr</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-string">"\n<%s: %s>"</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">__class__</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-34', 'name', 'link-4');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">outstr</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-35', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%d sets"</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">_sets</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">outstr</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"><tt class="py-comment">################################################################################</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"><tt class="py-comment"># RUN AS SCRIPT</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"><tt class="py-comment">################################################################################</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-comment"># test code</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-36" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-36', 'Bio', 'link-36');">Bio</a></tt> <tt class="py-keyword">import</tt> <tt id="link-37" class="py-name" targets="Package Bio.GenBank=Bio.GenBank-module.html"><a title="Bio.GenBank" class="py-name" href="#" onclick="return doclink('link-37', 'GenBank', 'link-37');">GenBank</a></tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-38" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-38', 'Bio', 'link-36');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Module Bio.SeqFeature=Bio.SeqFeature-module.html,Class Bio.SeqFeature.SeqFeature=Bio.SeqFeature.SeqFeature-class.html"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-39', 'SeqFeature', 'link-39');">SeqFeature</a></tt> <tt class="py-keyword">import</tt> <tt id="link-40" class="py-name"><a title="Bio.SeqFeature
Bio.SeqFeature.SeqFeature" class="py-name" href="#" onclick="return doclink('link-40', 'SeqFeature', 'link-39');">SeqFeature</a></tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-41" class="py-name"><a title="Bio.Graphics.GenomeDiagram._FeatureSet" class="py-name" href="#" onclick="return doclink('link-41', '_FeatureSet', 'link-0');">_FeatureSet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-42" class="py-name"><a title="Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet" class="py-name" href="#" onclick="return doclink('link-42', 'FeatureSet', 'link-1');">FeatureSet</a></tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt id="link-43" class="py-name"><a title="Bio.Graphics.GenomeDiagram._GraphSet" class="py-name" href="#" onclick="return doclink('link-43', '_GraphSet', 'link-2');">_GraphSet</a></tt> <tt class="py-keyword">import</tt> <tt id="link-44" class="py-name"><a title="Bio.Graphics.GenomeDiagram._GraphSet.GraphSet" class="py-name" href="#" onclick="return doclink('link-44', 'GraphSet', 'link-3');">GraphSet</a></tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">random</tt> <tt class="py-keyword">import</tt> <tt class="py-name">normalvariate</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-name">parser</tt> <tt class="py-op">=</tt> <tt id="link-45" class="py-name"><a title="Bio.GenBank" class="py-name" href="#" onclick="return doclink('link-45', 'GenBank', 'link-37');">GenBank</a></tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Class Bio.GenBank.FeatureParser=Bio.GenBank.FeatureParser-class.html"><a title="Bio.GenBank.FeatureParser" class="py-name" href="#" onclick="return doclink('link-46', 'FeatureParser', 'link-46');">FeatureParser</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-name">fhandle</tt> <tt class="py-op">=</tt> <tt class="py-name">open</tt><tt class="py-op">(</tt><tt class="py-string">'/data/genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk'</tt><tt class="py-op">,</tt> <tt class="py-string">'r'</tt><tt class="py-op">)</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-name">genbank_entry</tt> <tt class="py-op">=</tt> <tt class="py-name">parser</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-47', 'parse', 'link-47');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">fhandle</tt><tt class="py-op">)</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-name">fhandle</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name" targets="Method Bio.SeqIO.SffIO._AddTellHandle.close()=Bio.SeqIO.SffIO._AddTellHandle-class.html#close,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.close()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#close,Method BioSQL.BioSeqDatabase.Adaptor.close()=BioSQL.BioSeqDatabase.Adaptor-class.html#close,Method BioSQL.BioSeqDatabase.DBServer.close()=BioSQL.BioSeqDatabase.DBServer-class.html#close"><a title="Bio.SeqIO.SffIO._AddTellHandle.close
Bio.SeqIO._index._SQLiteManySeqFilesDict.close
BioSQL.BioSeqDatabase.Adaptor.close
BioSQL.BioSeqDatabase.DBServer.close" class="py-name" href="#" onclick="return doclink('link-48', 'close', 'link-48');">close</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-name">gdfs1</tt> <tt class="py-op">=</tt> <tt id="link-49" class="py-name"><a title="Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet" class="py-name" href="#" onclick="return doclink('link-49', 'FeatureSet', 'link-1');">FeatureSet</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">'Nanoarchaeum equitans CDS - CDS'</tt><tt class="py-op">)</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-name">gdfs2</tt> <tt class="py-op">=</tt> <tt id="link-50" class="py-name"><a title="Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet" class="py-name" href="#" onclick="return doclink('link-50', 'FeatureSet', 'link-1');">FeatureSet</a></tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-string">'Nanoarchaeum equitans CDS - gene'</tt><tt class="py-op">)</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">feature</tt> <tt class="py-keyword">in</tt> <tt class="py-name">genbank_entry</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name" targets="Variable BioSQL.BioSeq.DBSeqRecord.features=BioSQL.BioSeq.DBSeqRecord-class.html#features"><a title="BioSQL.BioSeq.DBSeqRecord.features" class="py-name" href="#" onclick="return doclink('link-51', 'features', 'link-51');">features</a></tt><tt class="py-op">:</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">feature</tt><tt class="py-op">.</tt><tt id="link-52" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-52', 'type', 'link-15');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'CDS'</tt><tt class="py-op">:</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt class="py-name">gdfs1</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.add_feature()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#add_feature"><a title="Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.add_feature" class="py-name" href="#" onclick="return doclink('link-53', 'add_feature', 'link-53');">add_feature</a></tt><tt class="py-op">(</tt><tt class="py-name">feature</tt><tt class="py-op">)</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">feature</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type
Bio.Phylo.PhyloXMLIO.Writer.type" class="py-name" href="#" onclick="return doclink('link-54', 'type', 'link-15');">type</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'gene'</tt><tt class="py-op">:</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-name">gdfs2</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.add_feature" class="py-name" href="#" onclick="return doclink('link-55', 'add_feature', 'link-53');">add_feature</a></tt><tt class="py-op">(</tt><tt class="py-name">feature</tt><tt class="py-op">)</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-name">gdt</tt> <tt class="py-op">=</tt> <tt id="link-56" class="py-name" targets="Class Bio.Graphics.GenomeDiagram._Track.Track=Bio.Graphics.GenomeDiagram._Track.Track-class.html"><a title="Bio.Graphics.GenomeDiagram._Track.Track" class="py-name" href="#" onclick="return doclink('link-56', 'Track', 'link-56');">Track</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-name">gdt</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Track.Track.add_set()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#add_set"><a title="Bio.Graphics.GenomeDiagram._Track.Track.add_set" class="py-name" href="#" onclick="return doclink('link-57', 'add_set', 'link-57');">add_set</a></tt><tt class="py-op">(</tt><tt class="py-name">gdfs1</tt><tt class="py-op">)</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-name">gdt</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Track.Track.add_set" class="py-name" href="#" onclick="return doclink('link-58', 'add_set', 'link-57');">add_set</a></tt><tt class="py-op">(</tt><tt class="py-name">gdfs2</tt><tt class="py-op">)</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"> <tt class="py-name">graphdata</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">pos</tt> <tt class="py-keyword">in</tt> <tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">genbank_entry</tt><tt class="py-op">.</tt><tt id="link-59" class="py-name" targets="Variable Bio.SeqRecord.SeqRecord.seq=Bio.SeqRecord.SeqRecord-class.html#seq,Variable BioSQL.BioSeq.DBSeqRecord.seq=BioSQL.BioSeq.DBSeqRecord-class.html#seq"><a title="Bio.SeqRecord.SeqRecord.seq
BioSQL.BioSeq.DBSeqRecord.seq" class="py-name" href="#" onclick="return doclink('link-59', 'seq', 'link-59');">seq</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-number">1000</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-name">graphdata</tt><tt class="py-op">.</tt><tt id="link-60" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-60', 'append', 'link-29');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">normalvariate</tt><tt class="py-op">(</tt><tt class="py-number">0.5</tt><tt class="py-op">,</tt> <tt class="py-number">0.1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">gdgs</tt> <tt class="py-op">=</tt> <tt id="link-61" class="py-name"><a title="Bio.Graphics.GenomeDiagram._GraphSet.GraphSet" class="py-name" href="#" onclick="return doclink('link-61', 'GraphSet', 'link-3');">GraphSet</a></tt><tt class="py-op">(</tt><tt class="py-number">2</tt><tt class="py-op">,</tt> <tt class="py-string">'test data'</tt><tt class="py-op">)</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-name">gdgs</tt><tt class="py-op">.</tt><tt class="py-name">add_graph</tt><tt class="py-op">(</tt><tt class="py-name">graphdata</tt><tt class="py-op">,</tt> <tt class="py-string">'Test Data'</tt><tt class="py-op">)</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-name">gdt</tt><tt class="py-op">.</tt><tt id="link-62" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Track.Track.add_set" class="py-name" href="#" onclick="return doclink('link-62', 'add_set', 'link-57');">add_set</a></tt><tt class="py-op">(</tt><tt class="py-name">gdgs</tt><tt class="py-op">)</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">gdt</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.get_ids()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#get_ids,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.get_ids()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#get_ids,Method Bio.Graphics.GenomeDiagram._Track.Track.get_ids()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#get_ids"><a title="Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.get_ids
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.get_ids
Bio.Graphics.GenomeDiagram._Track.Track.get_ids" class="py-name" href="#" onclick="return doclink('link-63', 'get_ids', 'link-63');">get_ids</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-name">sets</tt> <tt class="py-op">=</tt> <tt class="py-name">gdt</tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Track.Track.get_sets()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#get_sets"><a title="Bio.Graphics.GenomeDiagram._Track.Track.get_sets" class="py-name" href="#" onclick="return doclink('link-64', 'get_sets', 'link-64');">get_sets</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-65" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-65', 'set', 'link-8');">set</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">sets</tt><tt class="py-op">:</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt id="link-66" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set" class="py-name" href="#" onclick="return doclink('link-66', 'set', 'link-8');">set</a></tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">gdt</tt><tt class="py-op">.</tt><tt class="py-name">get_element_limits</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> </tt><script type="text/javascript">
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