Author: kono
Date: 2010-02-16 12:48:04 -0800 (Tue, 16 Feb 2010)
New Revision: 19335
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/BFEdge.java
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCScoringFunction.java
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCSearch2.java
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/MergeLinkRunner.java
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/SouravScore.java
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/NestedNetworkCreator.java
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/SearchTask.java
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/networks/linkedNetworks/TypedLinkNetwork.java
Log:
Wrong package names fixed.
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/BFEdge.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/BFEdge.java
2010-02-13 21:11:46 UTC (rev 19334)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/BFEdge.java
2010-02-16 20:48:04 UTC (rev 19335)
@@ -1,8 +1,10 @@
-package org.idekerlab.ModFindPlugin.networks.ModFinder;
+package org.idekerlab.ModFindPlugin.ModFinder;
-import java.util.*;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.Set;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.*;
+import org.idekerlab.ModFindPlugin.networks.linkedNetworks.Finalish;
/***
* An edge object for use with ONetworks to track statistics for the
HCNetsearch algorithm.
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCScoringFunction.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCScoringFunction.java
2010-02-13 21:11:46 UTC (rev 19334)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCScoringFunction.java
2010-02-16 20:48:04 UTC (rev 19335)
@@ -1,11 +1,15 @@
-package org.idekerlab.ModFindPlugin.networks.ModFinder;
+package org.idekerlab.ModFindPlugin.ModFinder;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.*;
+import org.idekerlab.ModFindPlugin.data.DoubleVector;
+import org.idekerlab.ModFindPlugin.networks.SFNetwork;
+import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNode;
+import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNodeModule;
import org.idekerlab.ModFindPlugin.networks.matrixNetworks.FloatMatrixNetwork;
-import org.idekerlab.ModFindPlugin.networks.*;
-import org.idekerlab.ModFindPlugin.data.DoubleVector;
public abstract class HCScoringFunction {
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCSearch2.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCSearch2.java
2010-02-13 21:11:46 UTC (rev 19334)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/HCSearch2.java
2010-02-16 20:48:04 UTC (rev 19335)
@@ -1,4 +1,4 @@
-package org.idekerlab.ModFindPlugin.networks.ModFinder;
+package org.idekerlab.ModFindPlugin.ModFinder;
import java.util.ArrayList;
import java.util.HashMap;
@@ -10,19 +10,19 @@
import java.util.concurrent.Executors;
import java.util.concurrent.TimeUnit;
-import cytoscape.task.TaskMonitor;
-
+import org.idekerlab.ModFindPlugin.data.DoubleVector;
import org.idekerlab.ModFindPlugin.networks.SFEdge;
import org.idekerlab.ModFindPlugin.networks.SFNetwork;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkEdge;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNetwork;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNode;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNodeModule;
-import org.idekerlab.ModFindPlugin.data.DoubleVector;
import org.idekerlab.ModFindPlugin.utilities.MemoryReporter;
import org.idekerlab.ModFindPlugin.utilities.ThreadPriorityFactory;
+import cytoscape.task.TaskMonitor;
+
public class HCSearch2 {
/**
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/MergeLinkRunner.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/MergeLinkRunner.java
2010-02-13 21:11:46 UTC (rev 19334)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/MergeLinkRunner.java
2010-02-16 20:48:04 UTC (rev 19335)
@@ -1,21 +1,18 @@
-package org.idekerlab.ModFindPlugin.networks.ModFinder;
+package org.idekerlab.ModFindPlugin.ModFinder;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkEdge;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNode;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNodeModule;
-public class MergeLinkRunner implements Runnable
-{
- private final TypedLinkEdge<TypedLinkNodeModule<String,BFEdge>,BFEdge>
ed;
-
- public
MergeLinkRunner(TypedLinkEdge<TypedLinkNodeModule<String,BFEdge>,BFEdge> ed)
- {
+public class MergeLinkRunner implements Runnable {
+ private final TypedLinkEdge<TypedLinkNodeModule<String, BFEdge>,
BFEdge> ed;
+
+ public MergeLinkRunner(
+ TypedLinkEdge<TypedLinkNodeModule<String, BFEdge>,
BFEdge> ed) {
this.ed = ed;
}
-
- public void run()
- {
+
+ public void run() {
HCSearch2.assignMergeLinkScore(ed);
}
-
+
}
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/SouravScore.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/SouravScore.java
2010-02-13 21:11:46 UTC (rev 19334)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/ModFinder/SouravScore.java
2010-02-16 20:48:04 UTC (rev 19335)
@@ -1,11 +1,11 @@
-package org.idekerlab.ModFindPlugin.networks.ModFinder;
+package org.idekerlab.ModFindPlugin.ModFinder;
import java.util.HashSet;
import java.util.Set;
import org.idekerlab.ModFindPlugin.networks.SFNetwork;
-import org.idekerlab.ModFindPlugin.networks.hashNetworks.*;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.*;
+import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNode;
+import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNodeModule;
public class SouravScore extends HCScoringFunction{
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/NestedNetworkCreator.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/NestedNetworkCreator.java
2010-02-13 21:11:46 UTC (rev 19334)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/NestedNetworkCreator.java
2010-02-16 20:48:04 UTC (rev 19335)
@@ -8,10 +8,11 @@
import java.util.PriorityQueue;
import java.util.Set;
-import org.idekerlab.ModFindPlugin.networks.ModFinder.BFEdge;
+import org.idekerlab.ModFindPlugin.ModFinder.BFEdge;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkEdge;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNetwork;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNodeModule;
+
import cytoscape.CyEdge;
import cytoscape.CyNetwork;
import cytoscape.CyNode;
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/SearchTask.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/SearchTask.java
2010-02-13 21:11:46 UTC (rev 19334)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/SearchTask.java
2010-02-16 20:48:04 UTC (rev 19335)
@@ -1,15 +1,13 @@
package org.idekerlab.ModFindPlugin;
-import java.util.ArrayList;
-
+import org.idekerlab.ModFindPlugin.ModFinder.BFEdge;
+import org.idekerlab.ModFindPlugin.ModFinder.HCScoringFunction;
+import org.idekerlab.ModFindPlugin.ModFinder.HCSearch2;
+import org.idekerlab.ModFindPlugin.ModFinder.SouravScore;
import org.idekerlab.ModFindPlugin.networks.SFNetwork;
-import org.idekerlab.ModFindPlugin.networks.ModFinder.BFEdge;
-import org.idekerlab.ModFindPlugin.networks.ModFinder.HCScoringFunction;
-import org.idekerlab.ModFindPlugin.networks.ModFinder.HCSearch2;
-import org.idekerlab.ModFindPlugin.networks.ModFinder.SouravScore;
-import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkEdge;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNetwork;
import org.idekerlab.ModFindPlugin.networks.linkedNetworks.TypedLinkNodeModule;
+
import cytoscape.CyNetwork;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
Modified:
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/networks/linkedNetworks/TypedLinkNetwork.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/networks/linkedNetworks/TypedLinkNetwork.java
2010-02-13 21:11:46 UTC (rev 19334)
+++
csplugins/trunk/ucsd/ruschein/ModFind/src/org/idekerlab/ModFindPlugin/networks/linkedNetworks/TypedLinkNetwork.java
2010-02-16 20:48:04 UTC (rev 19335)
@@ -1,9 +1,15 @@
package org.idekerlab.ModFindPlugin.networks.linkedNetworks;
-import java.util.*;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
import org.idekerlab.ModFindPlugin.utilities.IIterator;
import org.idekerlab.ModFindPlugin.utilities.files.FileIterator;
-import org.idekerlab.ModFindPlugin.networks.ModFinder.BFEdge;
/**
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