Author: pwang
Date: 2011-10-21 16:39:10 -0700 (Fri, 21 Oct 2011)
New Revision: 27269
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
Log:
Fixed a bug
Modified:
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
===================================================================
---
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-10-21 23:38:07 UTC (rev 27268)
+++
csplugins/trunk/ucsd/pwang/jActiveModules31/src/main/java/csplugins/jActiveModules/ActivePaths.java
2011-10-21 23:39:10 UTC (rev 27269)
@@ -150,7 +150,12 @@
this.cyApplicationManagerService = cyApplicationManagerService;
this.cyEventHelperService = cyEventHelperService;
- MAX_NETWORK_VIEWS = new
Integer(this.cytoscapeProperties.getProperties().getProperty("defaultPluginDownloadUrl")).intValue();
+ try {
+ MAX_NETWORK_VIEWS = new
Integer(this.cytoscapeProperties.getProperties().getProperty("moduleNetworkViewCreationThreshold")).intValue();
+ }
+ catch (Exception e){
+ MAX_NETWORK_VIEWS = 5;
+ }
layoutAlgorithm =
this.cyLayoutsService.getLayout("force-directed");
//if (!eventFired){
// this.cyEventHelperService.fireEvent();
@@ -416,7 +421,7 @@
logger.info("Processing Expression Data into Hash");
HashMap tempHash = new HashMap();
logger.info("Do some testing of the ExpressionData object");
- CyTable nodeAttributes = this.cyNetwork.getDefaultNodeTable();
//Cytoscape.getNodeAttributes();
+ CyTable nodeAttributes = this.cyNetwork.getDefaultNodeTable();
// Create two identical lists of genes
List<CyNode> geneList = new ArrayList<CyNode>();
@@ -435,12 +440,14 @@
final Map<String, Integer> geneNameToIndexMap = new
HashMap<String, Integer>();
for (int i = 0; i < geneList.size(); i++) {
final String geneName =
geneList.get(i).getCyRow().get("name", String.class); //.getIdentifier();
+
geneNameToIndexMap.put(geneName, new Integer(i));
for (int j = 0; j < attrNames.length; j++)
{
//attribValues[j][i] =
nodeAttributes.get.getDoubleAttribute(geneName, attrNames[j]);
- Collection<CyRow> rows =
nodeAttributes.getMatchingRows(attrNames[j], geneName);
+ Collection<CyRow> rows =
nodeAttributes.getMatchingRows("name", geneName);
Object[] objs = rows.toArray();
+ // We assume name is unique, we expect one row
returned for each name
CyRow row = (CyRow) objs[0];
attribValues[j][i] = row.get(attrNames[j],
Double.class);
}
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