164 lines
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164 lines
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<a href="obitools-module.html">Package obitools</a> ::
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Module dot
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<h1 class="epydoc">Source Code for <a href="obitools.tree.dot-module.html">Module obitools.tree.dot</a></h1>
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<pre class="py-src">
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<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"> </tt>
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<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package obitools=obitools-module.html,Package obitools.unit.obitools=obitools.unit.obitools-module.html"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-0', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package obitools.utils=obitools.utils-module.html"><a title="obitools.utils" class="py-name" href="#" onclick="return doclink('link-1', 'utils', 'link-1');">utils</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Function obitools.utils.universalOpen()=obitools.utils-module.html#universalOpen"><a title="obitools.utils.universalOpen" class="py-name" href="#" onclick="return doclink('link-2', 'universalOpen', 'link-2');">universalOpen</a></tt> </tt>
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<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="obitools
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obitools.unit.obitools" class="py-name" href="#" onclick="return doclink('link-3', 'obitools', 'link-0');">obitools</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Module obitools.graph.tree=obitools.graph.tree-module.html,Module obitools.seqdb.genbank.graph.tree=obitools.seqdb.genbank.graph.tree-module.html,Package obitools.tree=obitools.tree-module.html"><a title="obitools.graph.tree
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obitools.seqdb.genbank.graph.tree
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obitools.tree" class="py-name" href="#" onclick="return doclink('link-4', 'tree', 'link-4');">tree</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class obitools.tree.Tree=obitools.tree.Tree-class.html"><a title="obitools.tree.Tree" class="py-name" href="#" onclick="return doclink('link-5', 'Tree', 'link-5');">Tree</a></tt><tt class="py-op">,</tt><tt id="link-6" class="py-name" targets="Class obitools.graph.tree.TreeNode=obitools.graph.tree.TreeNode-class.html,Class obitools.seqdb.genbank.graph.tree.TreeNode=obitools.seqdb.genbank.graph.tree.TreeNode-class.html,Class obitools.tree.TreeNode=obitools.tree.TreeNode-class.html"><a title="obitools.graph.tree.TreeNode
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obitools.seqdb.genbank.graph.tree.TreeNode
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obitools.tree.TreeNode" class="py-name" href="#" onclick="return doclink('link-6', 'TreeNode', 'link-6');">TreeNode</a></tt> </tt>
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<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"> </tt>
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<a name="nodeWriter"></a><div id="nodeWriter-def"><a name="L5"></a><tt class="py-lineno"> 5</tt> <a class="py-toggle" href="#" id="nodeWriter-toggle" onclick="return toggle('nodeWriter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.tree.dot-module.html#nodeWriter">nodeWriter</a><tt class="py-op">(</tt><tt class="py-param">tree</tt><tt class="py-op">,</tt><tt class="py-param">node</tt><tt class="py-op">,</tt><tt class="py-param">nodes</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="nodeWriter-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="nodeWriter-expanded"><a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
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<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">node</tt><tt class="py-op">.</tt><tt class="py-name">_parent</tt><tt class="py-op">:</tt> </tt>
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<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"> <tt class="py-name">data</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name" targets="Method obitools.align.Alignement.append()=obitools.align.Alignement-class.html#append,Method obitools.table.Table.append()=obitools.table.Table-class.html#append,Method obitools.table.TableRow.append()=obitools.table.TableRow-class.html#append,Method obitools.table._Row.append()=obitools.table._Row-class.html#append"><a title="obitools.align.Alignement.append
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obitools.table.Table.append
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obitools.table.TableRow.append
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obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-7', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt class="py-string">'%d -> %d '</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">nodes</tt><tt class="py-op">[</tt><tt class="py-name">node</tt><tt class="py-op">]</tt><tt class="py-op">,</tt><tt class="py-name">nodes</tt><tt class="py-op">[</tt><tt class="py-name">node</tt><tt class="py-op">.</tt><tt class="py-name">_parent</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"\n"</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt> </tt>
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</div><a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"> </tt>
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<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
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<a name="treeWriter"></a><div id="treeWriter-def"><a name="L12"></a><tt class="py-lineno">12</tt> <a class="py-toggle" href="#" id="treeWriter-toggle" onclick="return toggle('treeWriter');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="obitools.tree.dot-module.html#treeWriter">treeWriter</a><tt class="py-op">(</tt><tt class="py-param">tree</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
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</div><div id="treeWriter-collapsed" style="display:none;" pad="++" indent="++++"></div><div id="treeWriter-expanded"><a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"> <tt class="py-name">nodes</tt><tt class="py-op">=</tt><tt class="py-name">dict</tt><tt class="py-op">(</tt><tt class="py-name">map</tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt><tt id="link-8" class="py-name"><a title="obitools.graph.tree
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obitools.seqdb.genbank.graph.tree
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obitools.tree" class="py-name" href="#" onclick="return doclink('link-8', 'tree', 'link-4');">tree</a></tt><tt class="py-op">,</tt><tt class="py-name">xrange</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="obitools.graph.tree
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obitools.seqdb.genbank.graph.tree
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obitools.tree" class="py-name" href="#" onclick="return doclink('link-9', 'tree', 'link-4');">tree</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> <tt class="py-name">code</tt><tt class="py-op">=</tt><tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
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<a name="L15"></a><tt class="py-lineno">15</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">node</tt> <tt class="py-keyword">in</tt> <tt id="link-10" class="py-name"><a title="obitools.graph.tree
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obitools.seqdb.genbank.graph.tree
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obitools.tree" class="py-name" href="#" onclick="return doclink('link-10', 'tree', 'link-4');">tree</a></tt><tt class="py-op">:</tt> </tt>
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<a name="L16"></a><tt class="py-lineno">16</tt> <tt class="py-line"> <tt class="py-name">code</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name"><a title="obitools.align.Alignement.append
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obitools.table.Table.append
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obitools.table.TableRow.append
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obitools.table._Row.append" class="py-name" href="#" onclick="return doclink('link-11', 'append', 'link-7');">append</a></tt><tt class="py-op">(</tt><tt id="link-12" class="py-name" targets="Function obitools.phylogeny.newick.nodeWriter()=obitools.phylogeny.newick-module.html#nodeWriter,Function obitools.tree.dot.nodeWriter()=obitools.tree.dot-module.html#nodeWriter,Function obitools.tree.newick.nodeWriter()=obitools.tree.newick-module.html#nodeWriter"><a title="obitools.phylogeny.newick.nodeWriter
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obitools.tree.dot.nodeWriter
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obitools.tree.newick.nodeWriter" class="py-name" href="#" onclick="return doclink('link-12', 'nodeWriter', 'link-12');">nodeWriter</a></tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="obitools.graph.tree
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obitools.seqdb.genbank.graph.tree
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obitools.tree" class="py-name" href="#" onclick="return doclink('link-13', 'tree', 'link-4');">tree</a></tt><tt class="py-op">,</tt><tt class="py-name">node</tt><tt class="py-op">,</tt><tt class="py-name">nodes</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
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<a name="L17"></a><tt class="py-lineno">17</tt> <tt class="py-line"> <tt class="py-name">code</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">code</tt><tt class="py-op">)</tt> </tt>
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<a name="L18"></a><tt class="py-lineno">18</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">'digraph tree { node [shape=point]\n%s\n};'</tt> <tt class="py-op">%</tt> <tt class="py-name">code</tt> </tt>
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</div><a name="L19"></a><tt class="py-lineno">19</tt> <tt class="py-line"> </tt><script type="text/javascript">
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