Author: scooter
Date: 2011-04-07 09:38:29 -0700 (Thu, 07 Apr 2011)
New Revision: 24701
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/build.xml
csplugins/trunk/ucsf/scooter/clusterMaker/resources/plugin.props
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AP/APCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractNetworkClusterer.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/ConnectedComponents/ConnectedComponentsCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/GLay/GLayCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/RunMCL.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCODE/MCODECluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/SCPS/SCPSCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/TransClust/TransClustCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/autosome/AutoSOMECluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/ClusterCommandHandler.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/TreeView.java
Log:
Make sure short name is lower case everywhere, bump version to 1.9.
Modified: csplugins/trunk/ucsf/scooter/clusterMaker/build.xml
===================================================================
--- csplugins/trunk/ucsf/scooter/clusterMaker/build.xml 2011-04-07 05:54:16 UTC
(rev 24700)
+++ csplugins/trunk/ucsf/scooter/clusterMaker/build.xml 2011-04-07 16:38:29 UTC
(rev 24701)
@@ -23,10 +23,10 @@
<!-- The version of your plugin. To support plugin.props, make sure the
version is expressed in decimal notation, e.g. 3.0, 3.1, 3.14, etc.
-->
- <property name="version" value="1.8"/>
+ <property name="version" value="1.9"/>
<!-- The version of Cytoscape that you depend on. -->
- <property name="cytoscape.version" value="2.8.1-beta1-SNAPSHOT"/>
+ <property name="cytoscape.version" value="2.8.1"/>
</target>
Modified: csplugins/trunk/ucsf/scooter/clusterMaker/resources/plugin.props
===================================================================
--- csplugins/trunk/ucsf/scooter/clusterMaker/resources/plugin.props
2011-04-07 05:54:16 UTC (rev 24700)
+++ csplugins/trunk/ucsf/scooter/clusterMaker/resources/plugin.props
2011-04-07 16:38:29 UTC (rev 24701)
@@ -13,7 +13,7 @@
pluginDescription=Cluster Nodes and/or Edges
# Plugin version number, this must be two numbers separated by a decimlal.
Ex. 0.2, 14.03
-pluginVersion=1.8
+pluginVersion=1.9
# Compatible Cytoscape version
cytoscapeVersion=2.8
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -80,7 +80,7 @@
* Cytoscape plugin mechanism
*/
public class ClusterMaker extends CytoscapePlugin implements
PropertyChangeListener {
- static final double VERSION = 0.1;
+ static final double VERSION = 1.9;
HashMap<JMenuItem,ClusterViz> vizMenus;
HashMap<String, ClusterViz> vizMap;
HashMap<String, ClusterAlgorithm> algMap;
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AP/APCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AP/APCluster.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AP/APCluster.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -83,7 +83,7 @@
initializeProperties();
}
- public String getShortName() {return "AP";};
+ public String getShortName() {return "ap";};
public String getName() {return "Affinity Propagation cluster";};
public JPanel getSettingsPanel() {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractNetworkClusterer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractNetworkClusterer.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractNetworkClusterer.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -147,7 +147,7 @@
}
String cluster_type =
networkAttributes.getStringAttribute(netId,
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE);
- if (cluster_type != getShortName())
+ if (cluster_type == null ||
!cluster_type.toLowerCase().equals(getShortName()))
return false;
if (networkAttributes.hasAttribute(netId,
ClusterMaker.CLUSTER_ATTRIBUTE)) {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/ConnectedComponents/ConnectedComponentsCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/ConnectedComponents/ConnectedComponentsCluster.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/ConnectedComponents/ConnectedComponentsCluster.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -81,7 +81,7 @@
initializeProperties();
}
- public String getShortName() {return "ConnectedComponents";};
+ public String getShortName() {return "connectedcomponents";};
public String getName() {return "Connected Components cluster";};
public JPanel getSettingsPanel() {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/GLay/GLayCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/GLay/GLayCluster.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/GLay/GLayCluster.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -76,7 +76,7 @@
initializeProperties();
}
- public String getShortName() {return "GLay";};
+ public String getShortName() {return "glay";};
public String getName() {return "Community cluster (GLay)";};
public JPanel getSettingsPanel() {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -84,7 +84,7 @@
initializeProperties();
}
- public String getShortName() {return "MCL";};
+ public String getShortName() {return "mcl";};
public String getName() {return "MCL cluster";};
public JPanel getSettingsPanel() {
@@ -110,7 +110,7 @@
// Inflation Parameter
clusterProperties.add(new Tunable("inflation_parameter",
- "Density Parameter",
+ "Graularity Parameter
(inflation value)",
Tunable.DOUBLE, new
Double(2.5),
(Object)null, (Object)null,
0));
// Clustering Threshold
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/RunMCL.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/RunMCL.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/RunMCL.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -81,7 +81,7 @@
private DistanceMatrix distanceMatrix = null;
private DoubleMatrix2D matrix = null;
private boolean debug = false;
- final int NTHREADS = Runtime.getRuntime().availableProcessors();
+ final int NTHREADS = Runtime.getRuntime().availableProcessors()-1;
public RunMCL(DistanceMatrix dMat, double inflationParameter, int
num_iterations,
double clusteringThresh, double maxResidual, CyLogger
logger )
@@ -187,13 +187,16 @@
clusterCount = 0;
HashMap<Integer, NodeCluster> clusterMap = new HashMap();
matrix.forEachNonZero(new ClusterMatrix(clusterMap));
+ System.out.println("Cluster map has
"+clusterMap.keySet().size()+" clusters");
//Update node attributes in network to include clusters. Create
cygroups from clustered nodes
logger.info("Created "+clusterCount+" clusters");
+ logger.info("Cluster map has "+clusterMap.keySet().size()+"
clusters");
// debugln("Created "+clusterCount+" clusters:");
//
if (clusterCount == 0) {
logger.error("Created 0 clusters!!!!");
+ logger.error("Cluster map has
"+clusterMap.keySet().size()+" clusters");
return null;
}
@@ -536,11 +539,13 @@
NodeCluster rowCluster =
clusterMap.get(row);
if (rowCluster == columnCluster)
return value;
- // debugln("Joining cluster
"+columnCluster.getClusterNumber()+" and "+rowCluster.getClusterNumber());
+ clusterCount--;
+ logger.debug("Joining cluster
"+columnCluster.getClusterNumber()+" and "+rowCluster.getClusterNumber());
+ logger.debug("clusterCount =
"+clusterCount);
columnCluster.addAll(rowCluster);
- clusterCount--;
} else {
- // debugln("Adding "+row+" to
"+columnCluster.getClusterNumber());
+ logger.debug("Adding "+row+" to
"+columnCluster.getClusterNumber());
+ logger.debug("clusterCount =
"+clusterCount);
columnCluster.add(nodes, row);
}
updateClusters(columnCluster);
@@ -550,12 +555,14 @@
if (clusterMap.containsKey(row)) {
// Yes, just add column to row's cluster
rowCluster = clusterMap.get(row);
- // debugln("Adding "+column+" to
"+rowCluster.getClusterNumber());
+ logger.debug("Adding "+column+" to
"+rowCluster.getClusterNumber());
+ logger.debug("clusterCount =
"+clusterCount);
rowCluster.add(nodes, column);
} else {
clusterCount++;
rowCluster = new NodeCluster();
- // debugln("Created new cluster
"+rowCluster.getClusterNumber()+" with "+row+" and "+column);
+ logger.debug("Created new cluster
"+rowCluster.getClusterNumber()+" with "+row+" and "+column);
+ logger.debug("clusterCount =
"+clusterCount);
rowCluster.add(nodes, column);
rowCluster.add(nodes, row);
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCODE/MCODECluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCODE/MCODECluster.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCODE/MCODECluster.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -90,7 +90,7 @@
initializeProperties();
}
- public String getShortName() {return "MCODE";};
+ public String getShortName() {return "mcode";};
public String getName() {return "MCODE cluster";};
public JPanel getSettingsPanel() {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/SCPS/SCPSCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/SCPS/SCPSCluster.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/SCPS/SCPSCluster.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -84,7 +84,7 @@
initializeProperties();
}
- public String getShortName() {return "SCPS";};
+ public String getShortName() {return "scps";};
public String getName() {return "SCPS cluster";};
public JPanel getSettingsPanel() {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/TransClust/TransClustCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/TransClust/TransClustCluster.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/TransClust/TransClustCluster.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -58,7 +58,7 @@
initializeProperties();
}
- public String getShortName() {return "TransClust";};
+ public String getShortName() {return "transclust";};
public String getName() {return "Transitivity Clustering";};
public JPanel getSettingsPanel() {
@@ -303,4 +303,4 @@
runTransClust.halt();
}
-}
\ No newline at end of file
+}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/autosome/AutoSOMECluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/autosome/AutoSOMECluster.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/autosome/AutoSOMECluster.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -139,9 +139,9 @@
public String getShortName() {
if (heatmap)
- return "AutoSOME (HeatMap)";
+ return "autosome_heatmap";
else
- return "AutoSOME (Network)";
+ return "autosome_network";
};
public String getName() {return "AutoSOME "+((settings.distMatrix) ?
"Fuzzy " : "")+"Clustering";};
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/ClusterCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/ClusterCommandHandler.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/ClusterCommandHandler.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -61,11 +61,11 @@
import clusterMaker.algorithms.ClusterProperties;
enum BuiltIn {
- HASCLUSTER("hasCluster", "Test to see if this network has a cluster of
the requested type", "type"),
- GETNETCLUSTER("getNetworkCluster", "Get a cluster of the requested type
and the requested clustertype (node or attribute)",
+ HASCLUSTER("hascluster", "Test to see if this network has a cluster of
the requested type", "type"),
+ GETNETCLUSTER("getnetworkcluster", "Get a cluster of the requested type
and the requested clustertype (node or attribute)",
"type"),
- GETEISENCLUSTER("getCluster", "Get a cluster of the requested
clustertype (node or attribute)", "type=hierarchical|clustertype=node"),
- SHOWDIALOG("showDialog", "Show the clusterMaker dialog","type");
+ GETEISENCLUSTER("getcluster", "Get a cluster of the requested
clustertype (node or attribute)", "type=hierarchical|clustertype=node"),
+ SHOWDIALOG("showdialog", "Show the clusterMaker dialog","type");
private String command = null;
private String argList = null;
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -56,7 +56,7 @@
Map<String, ClusterViz> vizMap;
public VizCommandHandler (Map<String, ClusterViz>vizMap) {
- super("clusterViz");
+ super("clusterviz");
this.vizMap = vizMap;
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -155,7 +155,7 @@
}
// ClusterViz methods
- public String getShortName() { return "heatMapView"; }
+ public String getShortName() { return "heatmapview"; }
public String getName() { return "HeatMapView (unclustered)"; }
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
===================================================================
--- csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
2011-04-07 05:54:16 UTC (rev 24700)
+++ csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -109,7 +109,7 @@
}
// ClusterViz methods
- public String getShortName() { return "knnView"; }
+ public String getShortName() { return "knnview"; }
public String getName() { return "Eisen KnnView"; }
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -121,7 +121,7 @@
}
// ClusterViz methods
- public String getShortName() { return "NestedNetworkView"; }
+ public String getShortName() { return "nestednetworkview"; }
public String getName() {
if (checkForAvailability) {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
2011-04-07 05:54:16 UTC (rev 24700)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -116,7 +116,7 @@
}
// ClusterViz methods
- public String getShortName() { return "newNetworkView"; }
+ public String getShortName() { return "newnetworkview"; }
public String getName() {
if (checkForAvailability) {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/TreeView.java
===================================================================
--- csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/TreeView.java
2011-04-07 05:54:16 UTC (rev 24700)
+++ csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/TreeView.java
2011-04-07 16:38:29 UTC (rev 24701)
@@ -135,7 +135,7 @@
}
// ClusterViz methods
- public String getShortName() { return "treeView"; }
+ public String getShortName() { return "treeview"; }
public String getName() { return "Eisen TreeView"; }
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