de.unirostock.sems.bives.ds.graph

Class GraphTranslatorJson

java.lang.Object

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

de.unirostock.sems.bives.ds.graph.GraphTranslatorJson

public class GraphTranslatorJson
extends GraphTranslator

The Class GraphTranslatorJson to translate internal graph structures into JSON format. (e.g. to pass the graph to CytoscapeJS) The resulting graph will look like:

 {
        "elements": {
                "edges": [
                        {
                                "classes": "bives-ioedge",
                                "data": {
                                        "source": "s2",
                                        "target": "r3"
                                }
                        },
                        {
                                "classes": "bives-stimulator bives-deleted",
                                "data": {
                                        "source": "s4",
                                        "target": "r3"
                                }
                        },
                        [...]
                ],
                "nodes": [
                        {
                                "classes": "compartment",
                                "data": {
                                        "id": "c1",
                                        "name": "compartment"
                                }
                        },
                        {
                                "classes": "species",
                                "data": {
                                        "id": "s2",
                                        "name": "sigb",
                                        "parent": "c1"
                                }
                        },
                        {
                                "classes": "reaction bives-modified",
                                "data": {
                                        "id": "r3",
                                        "name": "sigb degr",
                                        "parent": "c1"
                                }
                        },
                        [...]
                ]
        }
 }
 

for more information see JsonGraphFormatDescription

Author:

Martin Scharm

Constructor Summary

Constructors

Constructor and Description
GraphTranslatorJson()

Method Summary

Modifier and Type	Method and Description
org.json.simple.JSONObject	getJsonGraph() Gets the JSON object.
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

GraphTranslatorJson

public GraphTranslatorJson()

Method Detail

getJsonGraph

public org.json.simple.JSONObject getJsonGraph()

Gets the JSON object.

Returns:

the JSON object representing the graph

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

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