Class GraphTranslatorGraphML
- java.lang.Object
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- de.unirostock.sems.bives.ds.graph.GraphTranslator
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- de.unirostock.sems.bives.ds.graph.GraphTranslatorGraphML
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public class GraphTranslatorGraphML extends GraphTranslator
The Class GraphTranslatorGraphML to translate internal graph structures into GraphML. The resulting graph will look like:<graphml> <key attr.name="name" attr.type="string" for="node" id="name"/> <key attr.name="node set" attr.type="string" for="node" id="ns"> <default>species</default> </key> <key attr.name="version" attr.type="int" for="all" id="vers"> <default>0</default> </key> <key attr.name="modifier" attr.type="string" for="edge" id="mod"> <default>none</default> </key> <graph edgedefault="directed" id="G"> <node id="c1"> <data key="vers">0</data> <data key="name">compartment</data> <graph edgedefault="directed" id="G1"> <node id="s2"> <data key="ns">species</data> <data key="vers">0</data> <data key="name">sigb</data> </node> <node id="s1"> <data key="ns">species</data> <data key="vers">0</data> <data key="name">lacz</data> </node> <node id="r3"> <data key="ns">reaction</data> <data key="vers">2</data> <data key="name">sigb degr</data> </node> <!-- more nodes --> </graph> </node> <edge source="s2" target="r3"> <data key="mod">none</data> <data key="vers">0</data> </edge> <edge source="s4" target="r3"> <data key="mod">stimulator</data> <data key="vers">-1</data> </edge> <!-- more edges --> </graph> </graphml>
for more information see GraphmlFormatDescription- Author:
- Martin Scharm
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Constructor Summary
Constructors Constructor Description GraphTranslatorGraphML()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description org.jdom2.Document
getGraphmlDocument()
Gets the graphml document.String
translate(HierarchyNetwork hn)
Translate a hierarchy network.String
translate(ReactionNetwork rn)
Translate a reaction network.
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Method Detail
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translate
public String translate(HierarchyNetwork hn)
Description copied from class:GraphTranslator
Translate a hierarchy network. Might return null if not available.- Specified by:
translate
in classGraphTranslator
- Parameters:
hn
- the internal hierarchy network- Returns:
- the graph format
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translate
public String translate(ReactionNetwork rn)
Description copied from class:GraphTranslator
Translate a reaction network. Might return null if not available.- Specified by:
translate
in classGraphTranslator
- Parameters:
rn
- the internal reaction network- Returns:
- the graph format
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getGraphmlDocument
public org.jdom2.Document getGraphmlDocument()
Gets the graphml document.- Returns:
- the graphml document
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