Author: mes
Date: 2012-01-17 16:47:20 -0800 (Tue, 17 Jan 2012)
New Revision: 28036
Modified:
csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java
Log:
finally a working version
Modified:
csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java
===================================================================
---
csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java
2012-01-17 23:37:21 UTC (rev 28035)
+++
csplugins/trunk/ucsd/mes/gxp-reader/src/main/java/cytoscape/gxp/GXPGraphReader.java
2012-01-18 00:47:20 UTC (rev 28036)
@@ -75,16 +75,7 @@
public class GXPGraphReader extends AbstractGraphReader implements GraphReader
{
// node id from file -> node
private Map<String,CyNode> geneIdMap;
- private Map<String,CyNode> moduleIdMap;
- private Map<String,CyNode> regulatorIdMap;
- // module id from file -> list of nodes in module
- private Map<String,List<CyNode>> moduleMap;
-
- // regulator id from file -> list of nodes in regulator
- private Map<String,List<CyNode>> regulatorMap;
-
-
private List<Integer> nodeIds;
private List<Integer> edgeIds;
private URL fileURL;
@@ -129,8 +120,6 @@
edgeIds = new ArrayList<Integer>();
geneIdMap = new HashMap<String,CyNode>();
- moduleIdMap = new HashMap<String,CyNode>();
- regulatorIdMap = new HashMap<String,CyNode>();
try {
@@ -139,54 +128,32 @@
Document doc = builder.build(instream);
createGeneNodes( getTable(doc,"Genes") );
- createModuleNodes( getTable(doc,"Modules") );
- createRegulatorNodes(
getTable(doc,"Regulators_Regulators") );
-
- createGeneModuleEdges( getTable(doc,"Genes_Modules") );
- createModuleRegulatorEdges( getTable(doc,
"Modules_Regulator") );
+ createRegulatorsRegulatorsEdges(
getTable(doc,"Regulators_Regulators") );
-
} catch (JDOMException je) {
throw new IOException("JDOM failure parsing file.",je);
}
}
- private void createModuleRegulatorEdges(Element moduleRegulators) {
- for ( Object o :
moduleRegulators.getChildren("Module_Regulator") ) {
- Element moduleRegulator = (Element)o;
- String moduleId =
moduleRegulator.getAttributeValue("Module_Id");
- String regId =
moduleRegulator.getAttributeValue("Regulator_Id");
- if ( moduleId == null ||
- regId == null ||
- !moduleIdMap.containsKey(moduleId) ||
- !regulatorIdMap.containsKey(regId) )
- continue;
-
- CyNode na = moduleIdMap.get(moduleId);
- CyNode nb = regulatorIdMap.get(regId);
- CyEdge e =
Cytoscape.getCyEdge(na,nb,Semantics.INTERACTION,"regulates",true,true);
- edgeIds.add( e.getRootGraphIndex() );
- }
- }
-
- private void createGeneModuleEdges(Element geneModules) {
- for ( Object o : geneModules.getChildren("Gene_Module") ) {
- Element geneModule = (Element)o;
- String geneId = geneModule.getAttributeValue("Gene_Id");
- String moduleId =
geneModule.getAttributeValue("Module_Id");
- if ( moduleId == null ||
+ private void createRegulatorsRegulatorsEdges(Element
regulatorsRegulators) {
+ for ( Object o :
regulatorsRegulators.getChildren("Regulator_Gene") ) {
+ Element regulatorGene = (Element)o;
+ String regulatorId =
regulatorGene.getAttributeValue("Regulator_Id");
+ String geneId =
regulatorGene.getAttributeValue("Gene_Id");
+ if ( regulatorId == null ||
geneId == null ||
- !moduleIdMap.containsKey(moduleId) ||
+ !geneIdMap.containsKey(regulatorId) ||
!geneIdMap.containsKey(geneId) )
continue;
- CyNode na = moduleIdMap.get(moduleId);
+ CyNode na = geneIdMap.get(regulatorId);
CyNode nb = geneIdMap.get(geneId);
- CyEdge e =
Cytoscape.getCyEdge(na,nb,Semantics.INTERACTION,"contains",true,true);
+ CyEdge e =
Cytoscape.getCyEdge(na,nb,Semantics.INTERACTION,"regulates",true,true);
edgeIds.add( e.getRootGraphIndex() );
}
}
+
private void createGeneNodes(Element genes) {
for ( Object o : genes.getChildren("Gene") ) {
Element gene = (Element) o;
@@ -197,30 +164,6 @@
}
}
- private void createModuleNodes(Element modules) {
- for ( Object o : modules.getChildren("Module") ) {
- Element module = (Element) o;
- String id = module.getAttributeValue("Id");
- CyNode node =
Cytoscape.getCyNode(module.getAttributeValue("Name") + " - " + id,true);
- moduleIdMap.put(id,node);
- nodeIds.add( node.getRootGraphIndex() );
- }
- }
-
- private void createRegulatorNodes(Element regulators) {
- for ( Object o : regulators.getChildren("Regulator_Gene") ) {
- Element regulator = (Element) o;
- String id = regulator.getAttributeValue("Regulator_Id");
- CyNode node = Cytoscape.getCyNode("regulator: " +
-
regulator.getAttributeValue("Regulator_ORF") + " - " +
-
regulator.getAttributeValue("Gene_Id") + " - " +
-
regulator.getAttributeValue("Regulator") + " - " +
-
regulator.getAttributeValue("Gene_ORF"), true);
- regulatorIdMap.put(id,node);
- nodeIds.add( node.getRootGraphIndex() );
- }
- }
-
private Element getTable(Document doc, String tableName) {
for ( Object e : doc.getRootElement().getChildren("Table") )
if (
tableName.equals(((Element)e).getAttributeValue("Type")) )
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