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Module _Diagram
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<h1 class="epydoc">Source Code for <a href="Bio.Graphics.GenomeDiagram._Diagram-module.html" onclick="show_private();">Module Bio.Graphics.GenomeDiagram._Diagram</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">""" Diagram 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 Diagram - Container for information concerning the tracks to be</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-docstring"> drawn in a diagram, and the interface for defining the</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-docstring"> diagram (possibly split these functions in later version?)</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-docstring"> For drawing capabilities, this module uses reportlab to draw and write</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-docstring"> the diagram:</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt class="py-docstring"> http://www.reportlab.com</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"><tt class="py-docstring"> For dealing with biological information, the package expects BioPython</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt class="py-docstring"> objects - namely SeqRecord ojbects containing SeqFeature objects.</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt class="py-comment">#------------------------------------------------------------------------------</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"><tt class="py-comment"># IMPORTS</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"><tt class="py-comment"># ReportLab</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</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">graphics</tt> <tt class="py-keyword">import</tt> <tt class="py-name">renderPS</tt><tt class="py-op">,</tt> <tt class="py-name">renderPDF</tt><tt class="py-op">,</tt> <tt class="py-name">renderSVG</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</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">graphics</tt> <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Variable Bio.Graphics.GenomeDiagram._Diagram.renderPM=Bio.Graphics.GenomeDiagram._Diagram-module.html#renderPM"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-0', 'renderPM', 'link-0');">renderPM</a></tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">ImportError</tt><tt class="py-op">:</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-comment">#This is an optional part of ReportLab, so may not be installed.</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt id="link-1" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.renderPM" class="py-name" href="#" onclick="return doclink('link-1', 'renderPM', 'link-0');">renderPM</a></tt><tt class="py-op">=</tt><tt class="py-name">None</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</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">pagesizes</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"><tt class="py-comment"># GenomeDiagram</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-2" class="py-name" targets="Module Bio.Graphics.GenomeDiagram._LinearDrawer=Bio.Graphics.GenomeDiagram._LinearDrawer-module.html"><a title="Bio.Graphics.GenomeDiagram._LinearDrawer" class="py-name" href="#" onclick="return doclink('link-2', '_LinearDrawer', 'link-2');">_LinearDrawer</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Class Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer=Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html"><a title="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer" class="py-name" href="#" onclick="return doclink('link-3', 'LinearDrawer', 'link-3');">LinearDrawer</a></tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-4" class="py-name" targets="Module Bio.Graphics.GenomeDiagram._CircularDrawer=Bio.Graphics.GenomeDiagram._CircularDrawer-module.html"><a title="Bio.Graphics.GenomeDiagram._CircularDrawer" class="py-name" href="#" onclick="return doclink('link-4', '_CircularDrawer', 'link-4');">_CircularDrawer</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer=Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer-class.html"><a title="Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer" class="py-name" href="#" onclick="return doclink('link-5', 'CircularDrawer', 'link-5');">CircularDrawer</a></tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-6" class="py-name" targets="Module Bio.Graphics.GenomeDiagram._Track=Bio.Graphics.GenomeDiagram._Track-module.html"><a title="Bio.Graphics.GenomeDiagram._Track" class="py-name" href="#" onclick="return doclink('link-6', '_Track', 'link-6');">_Track</a></tt> <tt class="py-keyword">import</tt> <tt id="link-7" 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-7', 'Track', 'link-7');">Track</a></tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"><tt class="py-comment"># Builtins</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-8" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-8', 'Bio', 'link-8');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Package Bio.Graphics=Bio.Graphics-module.html"><a title="Bio.Graphics" class="py-name" href="#" onclick="return doclink('link-9', 'Graphics', 'link-9');">Graphics</a></tt> <tt class="py-keyword">import</tt> <tt id="link-10" class="py-name" targets="Function Bio.Graphics._write()=Bio.Graphics-module.html#_write,Method Bio.Motif._Motif.Motif._write()=Bio.Motif._Motif.Motif-class.html#_write"><a title="Bio.Graphics._write
Bio.Motif._Motif.Motif._write" class="py-name" href="#" onclick="return doclink('link-10', '_write', 'link-10');">_write</a></tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"><tt class="py-comment">#------------------------------------------------------------------------------</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"><tt class="py-comment"># CLASSES</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"><tt class="py-comment">#------------------------------------------------------------</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"><tt class="py-comment"># Diagram</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> </tt>
<a name="Diagram"></a><div id="Diagram-def"><a name="L56"></a><tt class="py-lineno"> 56</tt> <a class="py-toggle" href="#" id="Diagram-toggle" onclick="return toggle('Diagram');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html">Diagram</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="Diagram-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Diagram-expanded"><a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> <tt class="py-docstring">""" Diagram</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"><tt class="py-docstring"> Provides:</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"><tt class="py-docstring"> Attributes:</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"><tt class="py-docstring"> o name String, identifier for the diagram</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"><tt class="py-docstring"> o tracks List of Track objects comprising the diagram </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 format String, format of the diagram (circular/linear)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"><tt class="py-docstring"> o pagesize String, the pagesize of output</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-docstring"> o orientation String, the page orientation (landscape/portrait)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"><tt class="py-docstring"> o x Float, the proportion of the page to take up with even </tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-docstring"> X margins</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 y Float, the proportion of the page to take up with even </tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"><tt class="py-docstring"> Y margins</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 xl Float, the proportion of the page to take up with the </tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"><tt class="py-docstring"> left X margin</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"><tt class="py-docstring"> o xr Float, the proportion of the page to take up with the </tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"><tt class="py-docstring"> right X margin</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"><tt class="py-docstring"> o yt Float, the proportion of the page to take up with the </tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"><tt class="py-docstring"> top Y margin</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"><tt class="py-docstring"> o yb Float, the proportion of the page to take up with the </tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"><tt class="py-docstring"> bottom Y margin</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-docstring"> o start Int, the base/aa position to start the diagram at</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"><tt class="py-docstring"> o end Int, the base/aa position to end the diagram at</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 tracklines Boolean, True if track guidelines are to be drawn</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"><tt class="py-docstring"> o fragments Int, for a linear diagram, the number of equal divisions</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"><tt class="py-docstring"> into which the sequence is divided</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"><tt class="py-docstring"> o fragment_size Float, the proportion of the space available to each </tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"><tt class="py-docstring"> fragment that should be used in drawing</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 track_size Float, the proportion of the space available to each </tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"><tt class="py-docstring"> track that should be used in drawing</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"><tt class="py-docstring"> o circular Boolean, True if the genome/sequence to be drawn is, in </tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"><tt class="py-docstring"> reality, circular. </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"> Methods:</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 __init__(self, name=None) Called on instantiation</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 draw(self, format='circular', pagesize='A3', orientation='landscape',</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"><tt class="py-docstring"> x=0.05, y=0.05, xl=None, xr=None, yt=None, yb=None,</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"><tt class="py-docstring"> start=None, end=None, tracklines=0, fragments=10,</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"><tt class="py-docstring"> fragment_size=0.9, track_size=0.75) Instructs the package to draw</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"><tt class="py-docstring"> the diagram</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 write(self, filename='test1.ps', output='PS') Writes the drawn</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"><tt class="py-docstring"> diagram to a specified file, in a specified format.</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 add_track(self, track, track_level) Adds a Track object to the</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"><tt class="py-docstring"> diagram, with instructions to place it at a particular level on</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"><tt class="py-docstring"> the diagram</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"><tt class="py-docstring"> o del_track(self, track_level) Removes the track that is to be drawn</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"><tt class="py-docstring"> at a particular level on the diagram</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"><tt class="py-docstring"> o get_tracks(self) Returns the list of Track objects to be drawn</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"><tt class="py-docstring"> contained in the diagram</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"><tt class="py-docstring"> o renumber_tracks(self, low=1) Renumbers all tracks consecutively,</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"><tt class="py-docstring"> optionally from a passed lowest number</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"><tt class="py-docstring"> o get_levels(self) Returns a list of levels currently occupied by</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"><tt class="py-docstring"> Track objects</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"><tt class="py-docstring"> o get_drawn_levels(self) Returns a list of levels currently occupied</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"><tt class="py-docstring"> by Track objects that will be shown in the drawn diagram (i.e.</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"><tt class="py-docstring"> are not hidden)</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-docstring"> o range(self) Returns the lowest- and highest-numbered positions</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"><tt class="py-docstring"> contained within features in all tracks on the diagram as a tuple.</tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"><tt class="py-docstring"> o __getitem__(self, key) Returns the track contained at the level of</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"><tt class="py-docstring"> the passed key</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-docstring"> o __str__(self) Returns a formatted string describing the diagram</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="Diagram.__init__"></a><div id="Diagram.__init__-def"><a name="L151"></a><tt class="py-lineno">151</tt> <a class="py-toggle" href="#" id="Diagram.__init__-toggle" onclick="return toggle('Diagram.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-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">format</tt><tt class="py-op">=</tt><tt class="py-string">'circular'</tt><tt class="py-op">,</tt> <tt class="py-param">pagesize</tt><tt class="py-op">=</tt><tt class="py-string">'A3'</tt><tt class="py-op">,</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-param">orientation</tt><tt class="py-op">=</tt><tt class="py-string">'landscape'</tt><tt class="py-op">,</tt> <tt class="py-param">x</tt><tt class="py-op">=</tt><tt class="py-number">0.05</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">=</tt><tt class="py-number">0.05</tt><tt class="py-op">,</tt> <tt class="py-param">xl</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-param">xr</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">yt</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">yb</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt class="py-param">tracklines</tt><tt class="py-op">=</tt><tt class="py-name">False</tt><tt class="py-op">,</tt> <tt class="py-param">fragments</tt><tt class="py-op">=</tt><tt class="py-number">10</tt><tt class="py-op">,</tt> <tt class="py-param">fragment_size</tt><tt class="py-op">=</tt><tt class="py-number">0.9</tt><tt class="py-op">,</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-param">track_size</tt><tt class="py-op">=</tt><tt class="py-number">0.75</tt><tt class="py-op">,</tt> <tt class="py-param">circular</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Diagram.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.__init__-expanded"><a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-docstring">""" __init__(self, name=None)</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 name String describing the diagram</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 format String: 'circular' or 'linear', depending on the sort of</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"><tt class="py-docstring"> diagram required</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 pagesize String describing the ISO size of the image, or a tuple</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"><tt class="py-docstring"> of pixels</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 orientation String describing the required orientation of the</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"><tt class="py-docstring"> final drawing ('landscape' or 'portrait')</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 x Float (0->1) describing the relative size of the X</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"><tt class="py-docstring"> margins to the page</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 y Float (0->1) describing the relative size of the Y</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-docstring"> margins to the page</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 xl Float (0->1) describing the relative size of the left X</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"><tt class="py-docstring"> margin to the page (overrides x)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"><tt class="py-docstring"> o xl Float (0->1) describing the relative size of the left X</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"><tt class="py-docstring"> margin to the page (overrides x)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"><tt class="py-docstring"> o xr Float (0->1) describing the relative size of the right X</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"><tt class="py-docstring"> margin to the page (overrides x)</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"><tt class="py-docstring"> o yt Float (0->1) describing the relative size of the top Y</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"><tt class="py-docstring"> margin to the page (overrides y)</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"><tt class="py-docstring"> o yb Float (0->1) describing the relative size of the lower Y</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"><tt class="py-docstring"> margin to the page (overrides y)</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 start Int, the position to begin drawing the diagram at</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"><tt class="py-docstring"></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 end Int, the position to stop drawing the diagram at</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"><tt class="py-docstring"> o tracklines Boolean flag to show (or not) lines delineating </tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"><tt class="py-docstring"> tracks on the diagram</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"><tt class="py-docstring"> o fragments Int, for linear diagrams, the number of sections into</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"><tt class="py-docstring"> which to break the sequence being drawn</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"><tt class="py-docstring"> o fragment_size Float (0->1), for linear diagrams, describing </tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"><tt class="py-docstring"> the proportion of space in a fragment to take</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"><tt class="py-docstring"> up with tracks</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 track_size Float (0->1) describing the proportion of space</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"><tt class="py-docstring"> in a track to take up with sigils</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 circular Boolean flag to indicate whether the sequence being</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"><tt class="py-docstring"> drawn is circular</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"></tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># Holds all Track objects, keyed by level</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" 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-11', 'name', 'link-11');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-12', 'name', 'link-11');">name</a></tt> <tt class="py-comment"># Description of the diagram</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-comment"># Diagram page setup attributes</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method Bio.Align.Generic.Alignment.format()=Bio.Align.Generic.Alignment-class.html#format,Method Bio.Motif._Motif.Motif.format()=Bio.Motif._Motif.Motif-class.html#format,Method Bio.Phylo.BaseTree.Tree.format()=Bio.Phylo.BaseTree.Tree-class.html#format,Method Bio.Restriction.Restriction.RestrictionBatch.format()=Bio.Restriction.Restriction.RestrictionBatch-class.html#format,Method Bio.SeqRecord.SeqRecord.format()=Bio.SeqRecord.SeqRecord-class.html#format"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-13', 'format', 'link-13');">format</a></tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-14', 'format', 'link-13');">format</a></tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pagesize</tt> <tt class="py-op">=</tt> <tt class="py-name">pagesize</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orientation</tt> <tt class="py-op">=</tt> <tt class="py-name">orientation</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Variable Bio.Statistics.lowess.x=Bio.Statistics.lowess-module.html#x"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-15', 'x', 'link-15');">x</a></tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-16', 'x', 'link-15');">x</a></tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">y</tt> <tt class="py-op">=</tt> <tt class="py-name">y</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xl</tt> <tt class="py-op">=</tt> <tt class="py-name">xl</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xr</tt> <tt class="py-op">=</tt> <tt class="py-name">xr</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yt</tt> <tt class="py-op">=</tt> <tt class="py-name">yt</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yb</tt> <tt class="py-op">=</tt> <tt class="py-name">yb</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-17" class="py-name" targets="Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Variable Bio.SeqFeature.FeatureLocation.start=Bio.SeqFeature.FeatureLocation-class.html#start"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-17', 'start', 'link-17');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-18', 'start', 'link-17');">start</a></tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Variable Bio.SeqFeature.FeatureLocation.end=Bio.SeqFeature.FeatureLocation-class.html#end"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-19', 'end', 'link-19');">end</a></tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-20', 'end', 'link-19');">end</a></tt> </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">tracklines</tt> <tt class="py-op">=</tt> <tt class="py-name">tracklines</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">fragments</tt> <tt class="py-op">=</tt> <tt class="py-name">fragments</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fragment_size</tt> <tt class="py-op">=</tt> <tt class="py-name">fragment_size</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">track_size</tt> <tt class="py-op">=</tt> <tt class="py-name">track_size</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">circular</tt> <tt class="py-op">=</tt> <tt class="py-name">circular</tt> </tt>
</div><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> </tt>
<a name="Diagram.set_all_tracks"></a><div id="Diagram.set_all_tracks-def"><a name="L233"></a><tt class="py-lineno">233</tt> <a class="py-toggle" href="#" id="Diagram.set_all_tracks-toggle" onclick="return toggle('Diagram.set_all_tracks');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#set_all_tracks">set_all_tracks</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">attr</tt><tt class="py-op">,</tt> <tt class="py-param">value</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Diagram.set_all_tracks-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.set_all_tracks-expanded"><a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> <tt class="py-docstring">""" set_all_tracks(self, attr, value)</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"><tt class="py-docstring"> o attr An attribute of the Track class</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-docstring"> o value The value to set that attribute</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"><tt class="py-docstring"> Set the passed attribute of all tracks in the set to the</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-docstring"> passed value</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">track</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">.</tt><tt id="link-21" 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-21', 'values', 'link-21');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hasattr</tt><tt class="py-op">(</tt><tt class="py-name">track</tt><tt class="py-op">,</tt> <tt class="py-name">attr</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># If the feature has the attribute</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">getattr</tt><tt class="py-op">(</tt><tt class="py-name">track</tt><tt class="py-op">,</tt> <tt class="py-name">attr</tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt id="link-22" class="py-name" targets="Method Bio.Phylo.PhyloXMLIO.Writer.value()=Bio.Phylo.PhyloXMLIO.Writer-class.html#value"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-22', 'value', 'link-22');">value</a></tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">track</tt><tt class="py-op">,</tt> <tt class="py-name">attr</tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.value" class="py-name" href="#" onclick="return doclink('link-23', 'value', 'link-22');">value</a></tt><tt class="py-op">)</tt> <tt class="py-comment"># set it to the passed value </tt> </tt>
</div><a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> </tt>
<a name="Diagram.draw"></a><div id="Diagram.draw-def"><a name="L248"></a><tt class="py-lineno">248</tt> <a class="py-toggle" href="#" id="Diagram.draw-toggle" onclick="return toggle('Diagram.draw');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#draw">draw</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">format</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">pagesize</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">orientation</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-param">x</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">xl</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">xr</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">yt</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">yb</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-param">start</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">end</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">tracklines</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">fragments</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> <tt class="py-param">fragment_size</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">track_size</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-param">circular</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="Diagram.draw-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.draw-expanded"><a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-docstring">""" draw(self, format=None, pagesize=None, orientation=None,</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-docstring"> x=None, y=None, xl=None, xr=None, yt=None, yb=None,</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-docstring"> start=None, end=None, tracklines=None, fragments=None,</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-docstring"> fragment_size=None, track_size=None)</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-docstring"> Draws the diagram using the passed parameters, if any, to override</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-docstring"> previous settings for the diagram object.</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-comment"># Pass the parameters to the drawer objects that will build the </tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-comment"># diagrams. At the moment, we detect overrides with an or in the </tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> <tt class="py-comment"># Instantiation arguments, but I suspect there's a neater way to do </tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-comment"># this.</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-24" class="py-name"><a title="Bio.Align.Generic.Alignment.format
Bio.Motif._Motif.Motif.format
Bio.Phylo.BaseTree.Tree.format
Bio.Restriction.Restriction.RestrictionBatch.format
Bio.SeqRecord.SeqRecord.format" class="py-name" href="#" onclick="return doclink('link-24', 'format', 'link-13');">format</a></tt> <tt class="py-op">==</tt> <tt class="py-string">'linear'</tt><tt class="py-op">:</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-name">drawer</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer" class="py-name" href="#" onclick="return doclink('link-25', 'LinearDrawer', 'link-3');">LinearDrawer</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">pagesize</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pagesize</tt><tt class="py-op">,</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">orientation</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orientation</tt><tt class="py-op">,</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-26', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-27" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-27', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">xl</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xl</tt><tt class="py-op">,</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> <tt class="py-name">xr</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xr</tt><tt class="py-op">,</tt> <tt class="py-name">yt</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yt</tt><tt class="py-op">,</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">yb</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yb</tt><tt class="py-op">,</tt> <tt id="link-28" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-28', 'start', 'link-17');">start</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-29" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-29', 'start', 'link-17');">start</a></tt><tt class="py-op">,</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt id="link-30" class="py-name"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-30', 'end', 'link-19');">end</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-31" class="py-name"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-31', 'end', 'link-19');">end</a></tt><tt class="py-op">,</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">tracklines</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracklines</tt><tt class="py-op">,</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">fragments</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fragments</tt><tt class="py-op">,</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-name">fragment_size</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">fragment_size</tt><tt class="py-op">,</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">track_size</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">track_size</tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> <tt class="py-name">drawer</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer" class="py-name" href="#" onclick="return doclink('link-32', 'CircularDrawer', 'link-5');">CircularDrawer</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">pagesize</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pagesize</tt><tt class="py-op">,</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-name">orientation</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">orientation</tt><tt class="py-op">,</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"> <tt id="link-33" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-33', 'x', 'link-15');">x</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-34" class="py-name"><a title="Bio.Statistics.lowess.x" class="py-name" href="#" onclick="return doclink('link-34', 'x', 'link-15');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">y</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">y</tt><tt class="py-op">,</tt> <tt class="py-name">xl</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xl</tt><tt class="py-op">,</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt class="py-name">xr</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xr</tt><tt class="py-op">,</tt> <tt class="py-name">yt</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yt</tt><tt class="py-op">,</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">yb</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yb</tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-35', 'start', 'link-17');">start</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="Bio.Restriction._Update.RestrictionCompiler.start
Bio.SeqFeature.FeatureLocation.start" class="py-name" href="#" onclick="return doclink('link-36', 'start', 'link-17');">start</a></tt><tt class="py-op">,</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt id="link-37" class="py-name"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-37', 'end', 'link-19');">end</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-38" class="py-name"><a title="Bio.SeqFeature.FeatureLocation.end" class="py-name" href="#" onclick="return doclink('link-38', 'end', 'link-19');">end</a></tt><tt class="py-op">,</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-name">tracklines</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracklines</tt><tt class="py-op">,</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">track_size</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">track_size</tt><tt class="py-op">,</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-name">circular</tt> <tt class="py-keyword">or</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">circular</tt><tt class="py-op">)</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-name">drawer</tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Method Bio.Graphics.BasicChromosome.Chromosome.draw()=Bio.Graphics.BasicChromosome.Chromosome-class.html#draw,Method Bio.Graphics.BasicChromosome.ChromosomeSegment.draw()=Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html#draw,Method Bio.Graphics.BasicChromosome.Organism.draw()=Bio.Graphics.BasicChromosome.Organism-class.html#draw,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.draw()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#draw,Method Bio.Graphics.Distribution.BarChartDistribution.draw()=Bio.Graphics.Distribution.BarChartDistribution-class.html#draw,Method Bio.Graphics.Distribution.DistributionPage.draw()=Bio.Graphics.Distribution.DistributionPage-class.html#draw,Method Bio.Graphics.Distribution.LineDistribution.draw()=Bio.Graphics.Distribution.LineDistribution-class.html#draw,Method Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.draw()=Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer-class.html#draw,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.draw()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#draw,Method Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.draw()=Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw,Function Bio.Phylo._utils.draw()=Bio.Phylo._utils-module.html#draw"><a title="Bio.Graphics.BasicChromosome.Chromosome.draw
Bio.Graphics.BasicChromosome.ChromosomeSegment.draw
Bio.Graphics.BasicChromosome.Organism.draw
Bio.Graphics.BasicChromosome._ChromosomeComponent.draw
Bio.Graphics.Distribution.BarChartDistribution.draw
Bio.Graphics.Distribution.DistributionPage.draw
Bio.Graphics.Distribution.LineDistribution.draw
Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.draw
Bio.Graphics.GenomeDiagram._Diagram.Diagram.draw
Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.draw
Bio.Phylo._utils.draw" class="py-name" href="#" onclick="return doclink('link-39', 'draw', 'link-39');">draw</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># Tell the drawer to complete the drawing</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">drawing</tt> <tt class="py-op">=</tt> <tt class="py-name">drawer</tt><tt class="py-op">.</tt><tt class="py-name">drawing</tt> <tt class="py-comment"># Get the completed drawing</tt> </tt>
</div><a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="Diagram.write"></a><div id="Diagram.write-def"><a name="L288"></a><tt class="py-lineno">288</tt> <a class="py-toggle" href="#" id="Diagram.write-toggle" onclick="return toggle('Diagram.write');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write">write</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">filename</tt><tt class="py-op">=</tt><tt class="py-string">'test1.ps'</tt><tt class="py-op">,</tt> <tt class="py-param">output</tt><tt class="py-op">=</tt><tt class="py-string">'PS'</tt><tt class="py-op">,</tt> <tt class="py-param">dpi</tt><tt class="py-op">=</tt><tt class="py-number">72</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Diagram.write-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.write-expanded"><a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-docstring">""" write(self, filename='test1.ps', output='PS', dpi=72)</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"><tt class="py-docstring"> o filename String indicating the name of the output file,</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-docstring"> or a handle to write to.</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"><tt class="py-docstring"> o output String indicating output format, one of PS, PDF,</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"><tt class="py-docstring"> SVG, or provided the ReportLab renderPM module is</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"><tt class="py-docstring"> installed, one of the bitmap formats JPG, BMP,</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"><tt class="py-docstring"> GIF, PNG, TIFF or TIFF. The format can be given</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"><tt class="py-docstring"> in upper or lower case.</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"> o dpi Resolution (dots per inch) for bitmap formats.</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-docstring"> Write the completed drawing out to a file in a prescribed format</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"><tt class="py-docstring"> No return value.</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-40" class="py-name"><a title="Bio.Graphics._write
Bio.Motif._Motif.Motif._write" class="py-name" href="#" onclick="return doclink('link-40', '_write', 'link-10');">_write</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">drawing</tt><tt class="py-op">,</tt> <tt class="py-name">filename</tt><tt class="py-op">,</tt> <tt class="py-name">output</tt><tt class="py-op">,</tt> <tt class="py-name">dpi</tt><tt class="py-op">=</tt><tt class="py-name">dpi</tt><tt class="py-op">)</tt> </tt>
</div><a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> </tt>
<a name="Diagram.write_to_string"></a><div id="Diagram.write_to_string-def"><a name="L308"></a><tt class="py-lineno">308</tt> <a class="py-toggle" href="#" id="Diagram.write_to_string-toggle" onclick="return toggle('Diagram.write_to_string');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write_to_string">write_to_string</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">output</tt><tt class="py-op">=</tt><tt class="py-string">'PS'</tt><tt class="py-op">,</tt> <tt class="py-param">dpi</tt><tt class="py-op">=</tt><tt class="py-number">72</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Diagram.write_to_string-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.write_to_string-expanded"><a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-docstring">""" write(self, output='PS')</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"><tt class="py-docstring"> o output String indicating output format, one of PS, PDF,</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-docstring"> SVG, JPG, BMP, GIF, PNG, TIFF or TIFF (as</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"><tt class="py-docstring"> specified for the write method).</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"><tt class="py-docstring"> o dpi Resolution (dots per inch) for bitmap formats.</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-docstring"> Return the completed drawing as a string in a prescribed format</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"> <tt class="py-comment">#The ReportLab drawToString method, which this function used to call,</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-comment">#just uses a cStringIO or StringIO handle with the drawToFile method.</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-comment">#In order to put all our complicated file format specific code in one</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-comment">#place we'll just use a StringIO handle here:</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">from</tt> <tt class="py-name">StringIO</tt> <tt class="py-keyword">import</tt> <tt class="py-name">StringIO</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt id="link-41" class="py-name" targets="Variable Bio.UniGene.UniGene.handle=Bio.UniGene.UniGene-module.html#handle"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-41', 'handle', 'link-41');">handle</a></tt> <tt class="py-op">=</tt> <tt class="py-name">StringIO</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-42" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-42', 'write', 'link-42');">write</a></tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-43', 'handle', 'link-41');">handle</a></tt><tt class="py-op">,</tt> <tt class="py-name">output</tt><tt class="py-op">,</tt> <tt class="py-name">dpi</tt><tt class="py-op">)</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-44" class="py-name"><a title="Bio.UniGene.UniGene.handle" class="py-name" href="#" onclick="return doclink('link-44', 'handle', 'link-41');">handle</a></tt><tt class="py-op">.</tt><tt class="py-name">getvalue</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> </tt>
<a name="Diagram.add_track"></a><div id="Diagram.add_track-def"><a name="L328"></a><tt class="py-lineno">328</tt> <a class="py-toggle" href="#" id="Diagram.add_track-toggle" onclick="return toggle('Diagram.add_track');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#add_track">add_track</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">track</tt><tt class="py-op">,</tt> <tt class="py-param">track_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Diagram.add_track-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.add_track-expanded"><a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-docstring">""" add_track(self, track, track_level)</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"><tt class="py-docstring"> o track Track object to draw</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"><tt class="py-docstring"> o track_level Int, the level at which the track will be drawn</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-docstring"> (above an arbitrary baseline)</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"><tt class="py-docstring"> Add a pre-existing Track to the diagram at a given level</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">track</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt><tt class="py-op">(</tt><tt class="py-string">"Must specify track"</tt><tt class="py-op">)</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">track_level</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">:</tt> <tt class="py-comment"># No track at that level</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">track_level</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">track</tt> <tt class="py-comment"># so just add it</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># Already a track there, so shunt all higher tracks up one</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-name">occupied_levels</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.get_levels()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#get_levels"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.get_levels" class="py-name" href="#" onclick="return doclink('link-45', 'get_levels', 'link-45');">get_levels</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># Get list of occupied levels...</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt class="py-name">occupied_levels</tt><tt class="py-op">.</tt><tt id="link-46" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.sort()=Bio.Align.MultipleSeqAlignment-class.html#sort,Method Bio.PDB.Residue.DisorderedResidue.sort()=Bio.PDB.Residue.DisorderedResidue-class.html#sort,Method Bio.PDB.Residue.Residue.sort()=Bio.PDB.Residue.Residue-class.html#sort,Method Bio.Sequencing.Ace.ACEFileRecord.sort()=Bio.Sequencing.Ace.ACEFileRecord-class.html#sort"><a title="Bio.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-46', 'sort', 'link-46');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># ...sort it...</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-name">occupied_levels</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method Bio.Pathway.Reaction.reverse()=Bio.Pathway.Reaction-class.html#reverse,Method Bio.Seq.MutableSeq.reverse()=Bio.Seq.MutableSeq-class.html#reverse"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-47', 'reverse', 'link-47');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># ...reverse it (highest first)</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">occupied_levels</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-comment"># If track value >= that to be added</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">val</tt> <tt class="py-op">>=</tt> <tt class="py-name">track</tt><tt class="py-op">.</tt><tt class="py-name">track_level</tt><tt class="py-op">:</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">val</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">val</tt><tt class="py-op">]</tt> <tt class="py-comment"># ...increment by 1</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">track_level</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">track</tt> <tt class="py-comment"># And put the new track in</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">track_level</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">track_level</tt> <tt class="py-op">=</tt> <tt class="py-name">track_level</tt> </tt>
</div><a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> </tt>
<a name="Diagram.new_track"></a><div id="Diagram.new_track-def"><a name="L354"></a><tt class="py-lineno">354</tt> <a class="py-toggle" href="#" id="Diagram.new_track-toggle" onclick="return toggle('Diagram.new_track');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#new_track">new_track</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">track_level</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="Diagram.new_track-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.new_track-expanded"><a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-docstring">""" new_track(self, track_level) -> 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"> o track_level Int, the level at which the track will be drawn</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"><tt class="py-docstring"> (above an arbitrary baseline)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"><tt class="py-docstring"> Add a new Track to the diagram at a given level and returns it for</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"><tt class="py-docstring"> further user manipulation.</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"> <tt class="py-name">newtrack</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Track.Track" class="py-name" href="#" onclick="return doclink('link-48', 'Track', 'link-7');">Track</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</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="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">setattr</tt><tt class="py-op">(</tt><tt class="py-name">newtrack</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="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">track_level</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">:</tt> <tt class="py-comment"># No track at that level</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">track_level</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">newtrack</tt> <tt class="py-comment"># so just add it</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-comment"># Already a track there, so shunt all higher tracks up one</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-name">occupied_levels</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.get_levels" class="py-name" href="#" onclick="return doclink('link-49', 'get_levels', 'link-45');">get_levels</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># Get list of occupied levels...</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-name">occupied_levels</tt><tt class="py-op">.</tt><tt id="link-50" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-50', 'sort', 'link-46');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># ...sort it...</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-name">occupied_levels</tt><tt class="py-op">.</tt><tt id="link-51" class="py-name"><a title="Bio.Pathway.Reaction.reverse
Bio.Seq.MutableSeq.reverse" class="py-name" href="#" onclick="return doclink('link-51', 'reverse', 'link-47');">reverse</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># ...reverse (highest first)...</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">occupied_levels</tt><tt class="py-op">:</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">val</tt> <tt class="py-op">>=</tt> <tt class="py-name">track_level</tt><tt class="py-op">:</tt> <tt class="py-comment"># Track value >= that to be added</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">val</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">val</tt><tt class="py-op">]</tt> <tt class="py-comment"># ..increment by 1</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">track_level</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">newtrack</tt> <tt class="py-comment"># And put the new track in</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">track_level</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">track_level</tt> <tt class="py-op">=</tt> <tt class="py-name">track_level</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">newtrack</tt> </tt>
</div><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>
<a name="Diagram.del_track"></a><div id="Diagram.del_track-def"><a name="L380"></a><tt class="py-lineno">380</tt> <a class="py-toggle" href="#" id="Diagram.del_track-toggle" onclick="return toggle('Diagram.del_track');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#del_track">del_track</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">track_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Diagram.del_track-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.del_track-expanded"><a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-docstring">""" del_track(self, track_level)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"><tt class="py-docstring"> o track_level Int, the level of the track on the diagram to delete</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"><tt class="py-docstring"> Remove the track at the passed level from the diagram</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</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">tracks</tt><tt class="py-op">[</tt><tt class="py-name">track_level</tt><tt class="py-op">]</tt> </tt>
</div><a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> </tt>
<a name="Diagram.get_tracks"></a><div id="Diagram.get_tracks-def"><a name="L390"></a><tt class="py-lineno">390</tt> <a class="py-toggle" href="#" id="Diagram.get_tracks-toggle" onclick="return toggle('Diagram.get_tracks');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#get_tracks">get_tracks</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="Diagram.get_tracks-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.get_tracks-expanded"><a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-docstring">""" get_tracks(self) -> list</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"><tt class="py-docstring"> Returns a list of the tracks contained in the diagram</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</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">tracks</tt><tt class="py-op">.</tt><tt id="link-52" 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-52', 'values', 'link-21');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> </tt>
<a name="Diagram.move_track"></a><div id="Diagram.move_track-def"><a name="L398"></a><tt class="py-lineno">398</tt> <a class="py-toggle" href="#" id="Diagram.move_track-toggle" onclick="return toggle('Diagram.move_track');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#move_track">move_track</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">from_level</tt><tt class="py-op">,</tt> <tt class="py-param">to_level</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Diagram.move_track-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.move_track-expanded"><a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-docstring">""" move_track(self, from_level, to_level)</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"><tt class="py-docstring"> o from_level Int, the level at which the track to be moved is</tt> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"><tt class="py-docstring"> found</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"><tt class="py-docstring"> o to_level Int, the level to move the track to</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"><tt class="py-docstring"> Moves a track from one level on the diagram to another</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-name">aux</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">from_level</tt><tt class="py-op">]</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</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">tracks</tt><tt class="py-op">[</tt><tt class="py-name">from_level</tt><tt class="py-op">]</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-53" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.add_track()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#add_track"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.add_track" class="py-name" href="#" onclick="return doclink('link-53', 'add_track', 'link-53');">add_track</a></tt><tt class="py-op">(</tt><tt class="py-name">aux</tt><tt class="py-op">,</tt> <tt class="py-name">to_level</tt><tt class="py-op">)</tt> </tt>
</div><a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> </tt>
<a name="Diagram.renumber_tracks"></a><div id="Diagram.renumber_tracks-def"><a name="L413"></a><tt class="py-lineno">413</tt> <a class="py-toggle" href="#" id="Diagram.renumber_tracks-toggle" onclick="return toggle('Diagram.renumber_tracks');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#renumber_tracks">renumber_tracks</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">low</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-param">step</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Diagram.renumber_tracks-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.renumber_tracks-expanded"><a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-docstring">""" renumber_tracks(self, low=1, step=1)</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-docstring"> o low Int, the track number to start from</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"><tt class="py-docstring"> o step Int, the track interval for separation of tracks</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-docstring"> Reassigns all the tracks to run consecutively from the lowest</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"><tt class="py-docstring"> value (low)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-name">track</tt> <tt class="py-op">=</tt> <tt class="py-name">low</tt> <tt class="py-comment"># Start numbering from here</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">levels</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.get_levels" class="py-name" href="#" onclick="return doclink('link-54', 'get_levels', 'link-45');">get_levels</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-comment"># </tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">conversion</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> <tt class="py-comment"># Holds new set of levels</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">level</tt> <tt class="py-keyword">in</tt> <tt class="py-name">levels</tt><tt class="py-op">:</tt> <tt class="py-comment"># Starting at low...</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-name">conversion</tt><tt class="py-op">[</tt><tt class="py-name">track</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">tracks</tt><tt class="py-op">[</tt><tt class="py-name">level</tt><tt class="py-op">]</tt> <tt class="py-comment"># Add old tracks to new set</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-name">conversion</tt><tt class="py-op">[</tt><tt class="py-name">track</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">track_level</tt> <tt class="py-op">=</tt> <tt class="py-name">track</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> <tt class="py-name">track</tt> <tt class="py-op">+=</tt> <tt class="py-name">step</tt> <tt class="py-comment"># step interval</tt> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt> <tt class="py-op">=</tt> <tt class="py-name">conversion</tt> <tt class="py-comment"># Replace old set of levels with new set</tt> </tt>
</div><a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> </tt>
<a name="Diagram.get_levels"></a><div id="Diagram.get_levels-def"><a name="L433"></a><tt class="py-lineno">433</tt> <a class="py-toggle" href="#" id="Diagram.get_levels-toggle" onclick="return toggle('Diagram.get_levels');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#get_levels">get_levels</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="Diagram.get_levels-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.get_levels-expanded"><a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-docstring">""" get_levels(self) -> [int, int, ...]</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"><tt class="py-docstring"> Return a sorted list of levels occupied by tracks in the diagram</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-name">levels</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">.</tt><tt id="link-55" 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-55', 'keys', 'link-55');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-name">levels</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-56', 'sort', 'link-46');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">levels</tt> </tt>
</div><a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> </tt>
<a name="Diagram.get_drawn_levels"></a><div id="Diagram.get_drawn_levels-def"><a name="L443"></a><tt class="py-lineno">443</tt> <a class="py-toggle" href="#" id="Diagram.get_drawn_levels-toggle" onclick="return toggle('Diagram.get_drawn_levels');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#get_drawn_levels">get_drawn_levels</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="Diagram.get_drawn_levels-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.get_drawn_levels-expanded"><a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> <tt class="py-docstring">""" get_drawn_levels(self) -> [int, int, ...]</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-docstring"> Return a sorted list of levels occupied by tracks that are not</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-docstring"> explicitly hidden</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-name">drawn_levels</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">key</tt> <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">tracks</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><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-57', 'keys', 'link-55');">keys</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> <tt class="py-keyword">if</tt> \ </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">hide</tt><tt class="py-op">]</tt> <tt class="py-comment"># get list of shown levels</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt class="py-name">drawn_levels</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Align.MultipleSeqAlignment.sort
Bio.PDB.Residue.DisorderedResidue.sort
Bio.PDB.Residue.Residue.sort
Bio.Sequencing.Ace.ACEFileRecord.sort" class="py-name" href="#" onclick="return doclink('link-58', 'sort', 'link-46');">sort</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">drawn_levels</tt> </tt>
</div><a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> </tt>
<a name="Diagram.range"></a><div id="Diagram.range-def"><a name="L455"></a><tt class="py-lineno">455</tt> <a class="py-toggle" href="#" id="Diagram.range-toggle" onclick="return toggle('Diagram.range');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-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="Diagram.range-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.range-expanded"><a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-docstring">""" range(self) -> (int, int)</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"><tt class="py-docstring"> Returns the lowest and highest base (or mark) numbers containd in</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"><tt class="py-docstring"> track features as a tuple</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</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>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">track</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">.</tt><tt id="link-59" 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-59', 'values', 'link-21');">values</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt class="py-comment"># Get ranges for each track</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</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 class="py-name">track</tt><tt class="py-op">.</tt><tt id="link-60" 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-60', 'range', 'link-60');">range</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-name">lows</tt><tt class="py-op">.</tt><tt id="link-61" 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-61', 'append', 'link-61');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">low</tt><tt class="py-op">)</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-name">highs</tt><tt class="py-op">.</tt><tt id="link-62" 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-62', 'append', 'link-61');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">high</tt><tt class="py-op">)</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</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 extremes from all tracks</tt> </tt>
</div><a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> </tt>
<a name="Diagram.__getitem__"></a><div id="Diagram.__getitem__-def"><a name="L468"></a><tt class="py-lineno">468</tt> <a class="py-toggle" href="#" id="Diagram.__getitem__-toggle" onclick="return toggle('Diagram.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-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="Diagram.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.__getitem__-expanded"><a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-docstring">""" __getitem__(self, key) -> Track</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"><tt class="py-docstring"> o key The id of a track in the diagram</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"><tt class="py-docstring"> Return the Track object with the passed id</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</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">tracks</tt><tt class="py-op">[</tt><tt class="py-name">key</tt><tt class="py-op">]</tt> </tt>
</div><a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> </tt>
<a name="Diagram.__str__"></a><div id="Diagram.__str__-def"><a name="L477"></a><tt class="py-lineno">477</tt> <a class="py-toggle" href="#" id="Diagram.__str__-toggle" onclick="return toggle('Diagram.__str__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Graphics.GenomeDiagram._Diagram.Diagram-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="Diagram.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Diagram.__str__-expanded"><a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-docstring">""" __str__(self) -> ""</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"><tt class="py-docstring"> Returns a formatted string with information about the diagram</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"><tt class="py-docstring"> """</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</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-63" class="py-name"><a title="Bio.Phylo.PhyloXMLIO.Writer.name" class="py-name" href="#" onclick="return doclink('link-63', 'name', 'link-11');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-name">outstr</tt><tt class="py-op">.</tt><tt id="link-64" 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-64', 'append', 'link-61');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"%d tracks"</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">tracks</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">level</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.get_levels" class="py-name" href="#" onclick="return doclink('link-65', 'get_levels', 'link-45');">get_levels</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-name">outstr</tt><tt class="py-op">.</tt><tt id="link-66" 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-66', 'append', 'link-61');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">"Track %d: %s\n"</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tracks</tt><tt class="py-op">[</tt><tt class="py-name">level</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-name">outstr</tt> <tt class="py-op">=</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>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">outstr</tt> </tt>
</div></div><a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> </tt><script type="text/javascript">
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