Author: pwang
Date: 2011-10-28 09:16:46 -0700 (Fri, 28 Oct 2011)
New Revision: 27325
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/ModFinder/HCSearch2.java
Log:
Refactored to work with Cy3
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/ModFinder/HCSearch2.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/ModFinder/HCSearch2.java
2011-10-27 23:51:47 UTC (rev 27324)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/ModFinder/HCSearch2.java
2011-10-28 16:16:46 UTC (rev 27325)
@@ -10,6 +10,7 @@
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
+import org.cytoscape.work.TaskMonitor;
import org.idekerlab.PanGIAPlugin.SearchTask;
import org.idekerlab.PanGIAPlugin.data.DoubleVector;
import org.idekerlab.PanGIAPlugin.networks.SFEdge;
@@ -22,17 +23,14 @@
import org.idekerlab.PanGIAPlugin.utilities.NumberFormatter;
import org.idekerlab.PanGIAPlugin.utilities.ThreadPriorityFactory;
-import cytoscape.task.Task;
-import cytoscape.task.TaskMonitor;
-
public class HCSearch2 {
/**
* @param percentAllocated up to what point to advance the task
monitor progress bar
*/
public static TypedLinkNetwork<TypedLinkNodeModule<String, BFEdge>,
BFEdge> search(
- SFNetwork pnet, SFNetwork gnet, HCScoringFunction sfunc, final
TaskMonitor taskMonitor,
+ SFNetwork pnet, SFNetwork gnet, HCScoringFunction sfunc,
TaskMonitor taskMonitor,
final float percentAllocated, SearchTask parentTask)
{
// The scoring function needs to load several lookup matricies
for the
@@ -41,7 +39,7 @@
MemoryReporter.reportMemoryUsage();
// Need to construct the ONetwork<HyperModule<String>,BFEdge>
object.
- taskMonitor.setStatus("1. Building merged network.");
+ taskMonitor.setStatusMessage("1. Building merged network.");
TypedLinkNetwork<TypedLinkNodeModule<String, BFEdge>, BFEdge>
results = constructBaseNetwork(
pnet, gnet);
@@ -52,7 +50,7 @@
MemoryReporter.reportMemoryUsage();
// Get the first-pass scores
- taskMonitor.setStatus("2. Obtaining primary scores.");
+ taskMonitor.setStatusMessage("2. Obtaining primary scores.");
computePrimaryScores(results, sfunc);
if (parentTask.needsToHalt()) return null;
@@ -61,7 +59,7 @@
MemoryReporter.reportMemoryUsage();
// Merge best tree-pairs together
- taskMonitor.setStatus("3. Forming clusters...");
+ taskMonitor.setStatusMessage("3. Forming clusters...");
// MemoryReporter.reportMemoryUsage();
@@ -166,8 +164,8 @@
for (TypedLinkNodeModule<String, BFEdge> m :
allc)
csizes.add(m.size());
final int percentCompleted =
Math.round((INITIAL_NODE_COUNT - results.numNodes()) * percentAllocated /
INITIAL_NODE_COUNT);
-
taskMonitor.setPercentCompleted(percentCompleted);
- taskMonitor.setStatus("3. Forming clusters (#
of clusters: "
+ taskMonitor.setProgress(percentCompleted/100.0);
+ taskMonitor.setStatusMessage("3. Forming
clusters (# of clusters: "
+ results.numNodes() + ",
largest cluster size: "
+ csizes.max(false) +
")");
}
@@ -175,7 +173,7 @@
iter++;
}
- taskMonitor.setPercentCompleted(Math.round(percentAllocated));
+ taskMonitor.setProgress(Math.round(percentAllocated/100.0));
System.out.println("Best score: " + global_scores.max(true));
System.out.println("Best score index: " + global_scores.maxI());
System.out.println("Number of edges before filtering:
"+results.numEdges());
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
