de.unirostock.sems.bives.ds.graph

Class GraphTranslatorGraphML

java.lang.Object

de.unirostock.sems.bives.ds.graph.GraphTranslator

de.unirostock.sems.bives.ds.graph.GraphTranslatorGraphML

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

Constructor Summary

Constructors

Constructor and Description
GraphTranslatorGraphML()

Method Summary

Modifier and Type	Method and 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GraphTranslatorGraphML

public GraphTranslatorGraphML()

Method Detail

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 class GraphTranslator

Parameters:

hn - the internal hierarchy network

Returns:

the graph format

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 class GraphTranslator

Parameters:

rn - the internal reaction network

Returns:

the graph format

getGraphmlDocument

public org.jdom2.Document getGraphmlDocument()

Gets the graphml document.

Returns:

the graphml document