Author: pwang
Date: 2011-10-28 18:03:01 -0700 (Fri, 28 Oct 2011)
New Revision: 27334
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/SearchTask.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/SearchTask.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/SearchTask.java
2011-10-29 01:02:29 UTC (rev 27333)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/SearchTask.java
2011-10-29 01:03:01 UTC (rev 27334)
@@ -23,30 +23,33 @@
import org.idekerlab.PanGIAPlugin.utilities.collections.ListOps;
import org.idekerlab.PanGIAPlugin.utilities.collections.SetUtil;
-import cytoscape.CyEdge;
-import cytoscape.CyNetwork;
-import cytoscape.Cytoscape;
-import cytoscape.data.CyAttributes;
-import cytoscape.task.Task;
-import cytoscape.task.TaskMonitor;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyEdge.Type;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableUtil;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.TaskMonitor;
//import cytoscape.util.ProbabilityScaler;
//import cytoscape.util.ScalingMethod;
import org.idekerlab.PanGIAPlugin.util.Scaler;
import org.idekerlab.PanGIAPlugin.util.ScalerFactory;
import javax.swing.*;
+import java.util.Iterator;
+import org.cytoscape.model.CyNode;
/**
* @author kono, ruschein, ghannum
*/
-public class SearchTask implements Task {
+public class SearchTask extends AbstractTask {
private static final float SEARCH_PERCENTAGE = 40.0f; // Progress
bar should go up to here for the search part.
private static final float COMPUTE_SIG_PERCENTAGE = 95.0f; // Progress
bar should go up to here for the permutations part.
protected static final String EDGE_TYPE_ATTR_NAME = "Module
Finder.Interaction Type";
- private TaskMonitor taskMonitor = null;
+// private TaskMonitor taskMonitor = null;
boolean needsToHalt = false;
static int numOfRuns = 1;
@@ -59,10 +62,17 @@
private long startTime;
- public void run() {
+ private TaskMonitor taskMonitor;
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ this.taskMonitor = taskMonitor;
+ this.taskMonitor.setTitle("Executing PanGIA task...");
+
+
startTime = System.nanoTime();
- taskMonitor.setPercentCompleted(1);
- taskMonitor.setStatus("Searching for modules...");
+ taskMonitor.setProgress(0.01);
+ taskMonitor.setStatusMessage("Searching for modules...");
if (needsToHalt) return;
@@ -90,13 +100,27 @@
List<SNodeModule> trainingComplexes = null;
if (parameters.getComplexTrainingPhysical() ||
parameters.getComplexTrainingGenetic() || parameters.getComplexAnnotation())
{
- final CyAttributes nodeAttr =
Cytoscape.getNodeAttributes();
+ final CyTable nodeAttr =
geneticInputNetwork.getDefaultNodeTable(); //Cytoscape.getNodeAttributes();
Map<String,Set<String>> annot_node = new
HashMap<String,Set<String>>(1000);
- for (String gnode : geneticNetwork.nodeIterator())
- for (Object annot :
nodeAttr.getListAttribute(gnode, parameters.getAnnotationAttrName()))
- HashMapUtil.updateMapSet(annot_node,
annot.toString(),
String.valueOf(nodeAttr.getAttribute(gnode,parameters.getNodeAttrName())));
-
+// for (String gnode : geneticNetwork.nodeIterator()) {
+// for (Object annot :
nodeAttr.getListAttribute(gnode, parameters.getAnnotationAttrName())) {
+// HashMapUtil.updateMapSet(annot_node,
annot.toString(),
String.valueOf(nodeAttr.getAttribute(gnode,parameters.getNodeAttrName())));
+// }
+// }
+
+ Iterator<CyNode> it =
geneticInputNetwork.getNodeList().iterator();
+ while(it.hasNext()){
+ CyNode node = it.next();
+
+ List<String> attList =
node.getCyRow().get(parameters.getAnnotationAttrName(), List.class);
+ for (Object annot :attList)
+ {
+ HashMapUtil.updateMapSet(annot_node,
annot.toString(),
String.valueOf(node.getCyRow().get(parameters.getNodeAttrName(), List.class)));
+ }
+
+ }
+
trainingComplexes = new
ArrayList<SNodeModule>(annot_node.size());
for (String annot : annot_node.keySet())
@@ -295,13 +319,13 @@
PanGIAPlugin.setModuleLabels(parameters.getNodeAttrName());
String networkName = "Module Overview Network";
- final NestedNetworkCreator nnCreator = new
NestedNetworkCreator(results, physicalInputNetwork, geneticInputNetwork, pNet,
gNet, pValueThreshold, taskMonitor, 100.0f - COMPUTE_SIG_PERCENTAGE,
module_name, networkName,isGNetSigned, parameters.getNodeAttrName(),
parameters.getGeneticEdgeAttrName());
+ final NestedNetworkCreator nnCreator = new
NestedNetworkCreator(results, physicalInputNetwork, geneticInputNetwork, pNet,
gNet, pValueThreshold, this.taskMonitor, 100.0f - COMPUTE_SIG_PERCENTAGE,
module_name, networkName,isGNetSigned, parameters.getNodeAttrName(),
parameters.getGeneticEdgeAttrName());
setStatus("Search finished!\n\n" + "Number of modules = " +
nnCreator.getOverviewNetwork().getNodeCount() + "\n\n" +
HCSearch2.report(results));
setPercentCompleted(100);
-
PanGIAPlugin.output.put(nnCreator.getOverviewNetwork().getIdentifier(),new
PanGIAOutput(nnCreator.getOverviewNetwork(), physicalInputNetwork,
geneticInputNetwork,parameters.getNodeAttrName(),parameters.getPhysicalEdgeAttrName(),parameters.getGeneticEdgeAttrName(),isGNetSigned));
+
PanGIAPlugin.output.put(nnCreator.getOverviewNetwork().getCyRow().get("name",
String.class),new PanGIAOutput(nnCreator.getOverviewNetwork(),
physicalInputNetwork,
geneticInputNetwork,parameters.getNodeAttrName(),parameters.getPhysicalEdgeAttrName(),parameters.getGeneticEdgeAttrName(),isGNetSigned));
/*
// Create an edge attribute "overlapScore", which is defined as
NumberOfSharedNodes/min(two network sizes)
@@ -367,17 +391,17 @@
private void setPercentCompleted(int percent) {
if (taskMonitor != null)
- taskMonitor.setPercentCompleted(percent);
+ taskMonitor.setProgress(percent/100.0);
}
private void setStatus(String message) {
if (taskMonitor != null)
- taskMonitor.setStatus(message);
+ taskMonitor.setStatusMessage(message);
}
private void setException(Throwable t, String message) {
- if (taskMonitor != null)
- taskMonitor.setException(t, message);
+// if (taskMonitor != null)
+// taskMonitor.setException(t, message);
}
//This function compute a p-value for each edge in the complex-complex
network
@@ -385,7 +409,7 @@
final double pValueThreshold, final int
numberOfSamples, final TaskMonitor taskMonitor, final float
startProgressPercentage,
final float endProgressPercentage)
{
- taskMonitor.setStatus("4. Computing permutations...");
+ taskMonitor.setStatusMessage("4. Computing permutations...");
Map<Integer,DoubleVector> numLinks2empiricalDist = new
HashMap<Integer,DoubleVector>(30);
TypedLinkNetwork<String,Float> gn = gnet.asTypedLinkNetwork();
@@ -451,8 +475,8 @@
final float permutationsFraction =
(float)currentEdgeNum / TOTAL_NUM_EDGES;
final float percentCompleted = startProgressPercentage
+ (endProgressPercentage - startProgressPercentage) * permutationsFraction;
-
taskMonitor.setPercentCompleted(Math.round(percentCompleted));
- taskMonitor.setStatus("4. Computing permutations: " +
Math.round(permutationsFraction * 100.0f) + "% completed.");
+
taskMonitor.setProgress(Math.round(percentCompleted/100.0));
+ taskMonitor.setStatusMessage("4. Computing
permutations: " + Math.round(permutationsFraction * 100.0f) + "% completed.");
}
results.removeAllEdgesWNodeUpdate(deleteSet);
}
@@ -466,14 +490,17 @@
private SFNetwork convertCyNetworkToSFNetwork(final CyNetwork
inputNetwork, String nodeAttrName, final String numericAttrName, final
ScalingMethodX scalingMethod)
throws IllegalArgumentException, ClassCastException
{
- CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ CyTable nodeAttr = inputNetwork.getDefaultNodeTable();
//Cytoscape.getNodeAttributes();
- @SuppressWarnings("unchecked") List<CyEdge> startingEdges =
(List<CyEdge>)inputNetwork.edgesList();
+ @SuppressWarnings("unchecked") List<CyEdge> startingEdges =
(List<CyEdge>)inputNetwork.getEdgeList();
List<CyEdge> netEdges = new
ArrayList<CyEdge>(startingEdges.size());
- for (final CyEdge edge : startingEdges)
- if
(nodeAttr.hasAttribute(edge.getSource().getIdentifier(), nodeAttrName) &&
nodeAttr.hasAttribute(edge.getTarget().getIdentifier(), nodeAttrName))
+ for (final CyEdge edge : startingEdges){
+// if
(nodeAttr.hasAttribute(edge.getSource().getCyRow().get("name", String.class),
nodeAttrName) && nodeAttr.hasAttribute(edge.getTarget().getCyRow().get("name",
String.class), nodeAttrName))
+// netEdges.add(edge);
+ if ( edge.getSource().getCyRow().getRaw(nodeAttrName)
!= null &&edge.getTarget().getCyRow().getRaw(nodeAttrName) != null)
netEdges.add(edge);
+ }
final FloatHashNetwork outputNetwork = new FloatHashNetwork(/*
selfOk = */false, /* directed = */false, /* startsize = */1);
@@ -487,31 +514,37 @@
float defaultScore =
-(float)Math.log(netEdges.size()/((float)numNodes*(numNodes-1)/2.0f));
for (final CyEdge edge : netEdges)
-
outputNetwork.add(edge.getSource().getIdentifier(),
edge.getTarget().getIdentifier(), defaultScore);
+
outputNetwork.add(edge.getSource().getCyRow().get("name", String.class),
edge.getTarget().getCyRow().get("name", String.class), defaultScore);
} else
{
// Validate that "numericAttrName" is a known numeric
edge attribute.
- final CyAttributes edgeAttributes =
Cytoscape.getEdgeAttributes();
- final byte edgeAttribType =
edgeAttributes.getType(numericAttrName);
- if (edgeAttribType != CyAttributes.TYPE_FLOATING &&
edgeAttribType != CyAttributes.TYPE_INTEGER)
+ final CyTable edgeAttributes =
inputNetwork.getDefaultEdgeTable(); //Cytoscape.getEdgeAttributes();
+ //final byte edgeAttribType =
edgeAttributes.getType(numericAttrName);
+ Class<?> edgeAttribType =
edgeAttributes.getColumn(numericAttrName).getType();
+
+ if (edgeAttribType != Double.class && edgeAttribType !=
Integer.class)
throw new IllegalArgumentException("\"" +
numericAttrName
+ "\" is not
the name of a known numeric edge attribute!");
List<CyEdge> edges = new
ArrayList<CyEdge>(netEdges.size());
- for (CyEdge e : netEdges)
- if
(edgeAttributes.getAttribute(e.getIdentifier(), numericAttrName)!=null)
edges.add(e);
+ for (CyEdge e : netEdges) {
+ //if
(edgeAttributes.getAttribute(e.getCyRow().get("name", String.class),
numericAttrName)!=null) edges.add(e);
+ if (e.getCyRow().isSet(numericAttrName)){
+ edges.add(e);
+ }
+ }
// Collect edge attribute values:
final float[] edgeAttribValues = new
float[edges.size()];
int edgeIndex = 0;
for (final CyEdge edge : edges) {
- final String edgeID = edge.getIdentifier();
- if (edgeAttribType ==
CyAttributes.TYPE_FLOATING) {
- final Double attrValue =
edgeAttributes.getDoubleAttribute(edgeID, numericAttrName);
+ final String edgeID =
edge.getCyRow().get("name", String.class);
+ if (edgeAttribType == Double.class) {
+ final Double attrValue =
edge.getCyRow().get(numericAttrName,Double.class);
//edgeAttributes.getDoubleAttribute(edgeID, numericAttrName);
if (attrValue != null)
edgeAttribValues[edgeIndex] = (float)(double)attrValue;
} else { // Assume we have an integer attribute.
- final Integer attrValue =
edgeAttributes.getIntegerAttribute(edgeID, numericAttrName);
+ final Integer attrValue =
edge.getCyRow().get(numericAttrName, Integer.class);
//edgeAttributes.getIntegerAttribute(edgeID, numericAttrName);
if (attrValue != null)
edgeAttribValues[edgeIndex] =
(float)(int)attrValue;
}
@@ -525,9 +558,10 @@
edgeIndex = 0;
for (final CyEdge edge : edges) {
- final String edgeID = edge.getIdentifier();
- if (edgeAttributes.getAttribute(edgeID,
numericAttrName) != null)
-
outputNetwork.add(edge.getSource().getIdentifier(),
edge.getTarget().getIdentifier(), scaledEdgeAttribValues[edgeIndex]);
+ //final String edgeID =
edge.getCyRow().get("name", String.class);
+ //if (edgeAttributes.getAttribute(edgeID,
numericAttrName) != null)
+ if (edge.getCyRow().get(numericAttrName,
Double.class) != null ||edge.getCyRow().get(numericAttrName, Integer.class) !=
null)
+
outputNetwork.add(edge.getSource().getCyRow().get("name", String.class),
edge.getTarget().getCyRow().get("name", String.class),
scaledEdgeAttribValues[edgeIndex]);
++edgeIndex;
}
}
@@ -586,7 +620,7 @@
b.add(networkName);
b.add("");
b.add("Physical network:");
- b.add(parameters.getPhysicalNetwork().getIdentifier());
+ b.add(parameters.getPhysicalNetwork().getCyRow().get("name",
String.class));
boolean isBinary = parameters.getPhysicalEdgeAttrName() == null
|| parameters.getPhysicalEdgeAttrName().length() == 0;
if (isBinary) b.add(parameters.getPhysicalEdgeAttrName()+"
(binary)");
else b.add("Edge score:
"+parameters.getPhysicalEdgeAttrName()+" (numeric,
scaling="+parameters.getPhysicalScalingMethod()+")");
@@ -597,7 +631,7 @@
b.add("");
b.add("Genetic network:");
- b.add(parameters.getGeneticNetwork().getIdentifier());
+ b.add(parameters.getGeneticNetwork().getCyRow().get("name",
String.class));
isBinary = parameters.getGeneticEdgeAttrName() == null ||
parameters.getGeneticEdgeAttrName().length() == 0;
if (isBinary) b.add(parameters.getGeneticEdgeAttrName()+"
(binary)");
else b.add("Edge score: "+parameters.getGeneticEdgeAttrName()+"
(numeric, scaling="+parameters.getGeneticScalingMethod()+")");
@@ -703,11 +737,19 @@
for (SNodeModule m : annots)
nodes.addAll(m.getMemberData());
- for (int i : geneticNetwork.getNodeIndicesArray())
- nodes.add(geneticNetwork.getNode(i).getIdentifier());
+// for (int i : geneticNetwork.getNodeIndicesArray())
+// nodes.add(geneticNetwork.getNode(i).getIdentifier());
+ Iterator<CyNode> nodeIt =
geneticNetwork.getNodeList().iterator();
+ while (nodeIt.hasNext()){
+ nodes.add(nodeIt.next().getCyRow().get("name",
String.class));
+ }
- for (int i : physicalNetwork.getNodeIndicesArray())
- nodes.add(physicalNetwork.getNode(i).getIdentifier());
+// for (int i : physicalNetwork.getNodeIndicesArray())
+//
nodes.add(physicalNetwork.getNode(i).getCyRow().get("name", String.class));
+ Iterator<CyNode> nodeIt2 =
physicalNetwork.getNodeList().iterator();
+ while (nodeIt2.hasNext()){
+ nodes.add(nodeIt2.next().getCyRow().get("name",
String.class));
+ }
int possible = nodes.size()*(nodes.size()-1)/2;
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