Author: scooter
Date: 2011-04-11 15:28:50 -0700 (Mon, 11 Apr 2011)
New Revision: 24742
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/EdgeAttributeHandler.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/autosome/AutoSOMECluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/kmeans/KMeansCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterViz.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:
Fix stupid bug introduced right before release.
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/EdgeAttributeHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/EdgeAttributeHandler.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/EdgeAttributeHandler.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -191,8 +191,6 @@
adjustLoops = ((Boolean) t.getValue()).booleanValue();
t = clusterProperties.get("attribute");
- attributeArray = getAllAttributes();
- t.setLowerBound((Object)attributeArray);
if ((t != null) && (t.valueChanged() || force)) {
if (attributeArray.length == 1) {
dataAttribute = attributeArray[0];
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/MCL/MCLCluster.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -200,9 +200,11 @@
clusteringThresh, maxResidual, maxThreads,
logger);
runMCL.setDebug(debug);
+ if (canceled) return;
// results = runMCL.run(monitor);
List<NodeCluster> clusters = runMCL.run(monitor);
+ if (clusters == null) return; // Canceled?
logger.info("Removing groups");
@@ -223,6 +225,7 @@
}
public void halt() {
+ canceled = true;
runMCL.halt();
}
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/autosome/AutoSOMECluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/autosome/AutoSOMECluster.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/autosome/AutoSOMECluster.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -455,8 +455,10 @@
t = clusterProperties.get("attributeList");
- attributeArray = getAllAttributes();
- t.setLowerBound(attributeArray);
+ if (force) {
+ attributeArray = getAllAttributes();
+ t.setLowerBound(attributeArray);
+ }
if ((t != null) && (t.valueChanged() || force)) {
dataAttribute = (String) t.getValue();
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -202,8 +202,6 @@
distanceMetric = distanceTypes[((Integer)
t.getValue()).intValue()];
t = clusterProperties.get("clusterAttributes");
- attributeArray = EisenCluster.getAllAttributes();
- t.setLowerBound((Object)attributeArray);
if ((t != null) && (t.valueChanged() || force))
clusterAttributes = ((Boolean)
t.getValue()).booleanValue();
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/kmeans/KMeansCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/kmeans/KMeansCluster.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/kmeans/KMeansCluster.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -202,8 +202,6 @@
distanceMetric = distanceTypes[((Integer)
t.getValue()).intValue()];
t = clusterProperties.get("clusterAttributes");
- attributeArray = EisenCluster.getAllAttributes();
- t.setLowerBound(attributeArray);
if ((t != null) && (t.valueChanged() || force))
clusterAttributes = ((Boolean)
t.getValue()).booleanValue();
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/commands/VizCommandHandler.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -82,6 +82,7 @@
if (command.equalsIgnoreCase(vizname)) {
// Get the algorithm
ClusterViz viz = vizMap.get(vizname);
+ viz.initializeProperties();
ClusterProperties props = viz.getSettings();
viz.updateSettings(true);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterViz.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterViz.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterViz.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -92,6 +92,13 @@
public ClusterProperties getSettings();
/**
+ * This method is used to re-initialize the properties for an
algorithm. This
+ * might be used, for example, by an external command, or when a new
network
+ * is loaded.
+ */
+ public void initializeProperties();
+
+ /**
* This is the main interface to trigger a ui to display
*
* @param monitor a TaskMonitor
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -312,8 +312,6 @@
clusterProperties.updateValues();
Tunable t = clusterProperties.get("attributeList");
- attributeArray = getAllAttributes();
- t.setLowerBound(attributeArray);
if ((t != null) && (t.valueChanged() || force)) {
dataAttributes = (String) t.getValue();
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
===================================================================
--- csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
2011-04-11 20:22:31 UTC (rev 24741)
+++ csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -118,6 +118,8 @@
public ClusterResults getResults() { return null; }
+ public void initializeProperties() {}
+
public boolean isAvailable() {
CyNetwork network = Cytoscape.getCurrentNetwork();
CyAttributes networkAttributes =
Cytoscape.getNetworkAttributes();
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -213,9 +213,6 @@
clusterProperties.updateValues();
Tunable t = clusterProperties.get("attribute");
- // Make sure to update the tunable while we're at it...
- attributeArray = getAllAttributes();
- t.setLowerBound(attributeArray);
if ((t != null) && (t.valueChanged() || force)) {
int val = ((Integer) t.getValue()).intValue();
clusterAttribute = attributeArray[val];
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
2011-04-11 20:22:31 UTC (rev 24741)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -211,9 +211,6 @@
clusterProperties.updateValues();
Tunable t = clusterProperties.get("attribute");
- // Make sure to update the tunable while we're at it...
- attributeArray = getAllAttributes();
- t.setLowerBound(attributeArray);
if ((t != null) && (t.valueChanged() || force)) {
int val = ((Integer) t.getValue()).intValue();
clusterAttribute = attributeArray[val];
@@ -270,22 +267,33 @@
CyNetwork net =
Cytoscape.createNetwork(currentNetwork.getTitle()+"--clustered",currentNetwork,false);
// Create the cluster Map
- HashMap<Integer, List<CyNode>> clusterMap = new HashMap();
+ HashMap<Object, List<CyNode>> clusterMap = new HashMap<Object,
List<CyNode>>();
for (CyNode node: (List<CyNode>)currentNetwork.nodesList()) {
// For each node -- see if it's in a cluster. If so,
add it to our map
if (nodeAttributes.hasAttribute(node.getIdentifier(),
clusterAttribute)) {
- Integer cluster =
nodeAttributes.getIntegerAttribute(node.getIdentifier(), clusterAttribute);
+ Object cluster =
nodeAttributes.getAttribute(node.getIdentifier(), clusterAttribute);
+ switch
(nodeAttributes.getType(clusterAttribute)) {
+ case CyAttributes.TYPE_SIMPLE_LIST:
+ // As a convenience, take the first
element of the list
+ List lObj =
nodeAttributes.getListAttribute(node.getIdentifier(), clusterAttribute);
+ if (lObj != null && lObj.size() > 0)
+ cluster = lObj.get(0);
+ else
+ continue;
+ }
if (!clusterMap.containsKey(cluster)) {
- clusterMap.put(cluster, new
ArrayList());
+ System.out.println("Creating new entry
for: "+cluster.toString());
+ clusterMap.put(cluster, new
ArrayList<CyNode>());
}
+ System.out.println("Adding node "+node+" to
"+cluster.toString());
clusterMap.get(cluster).add(node);
net.addNode(node);
}
}
- HashMap<CyEdge,CyEdge> edgeMap = new HashMap();
+ HashMap<CyEdge,CyEdge> edgeMap = new HashMap<CyEdge,CyEdge>();
- for (Integer cluster: clusterMap.keySet()) {
+ for (Object cluster: clusterMap.keySet()) {
// Get the list of nodes
List<CyNode> nodeList = clusterMap.get(cluster);
// Get the list of edges
@@ -386,7 +394,10 @@
String[] names = attributes.getAttributeNames();
for (int i = 0; i < names.length; i++) {
if (attributes.getType(names[i]) ==
CyAttributes.TYPE_FLOATING ||
- attributes.getType(names[i]) ==
CyAttributes.TYPE_INTEGER) {
+ attributes.getType(names[i]) ==
CyAttributes.TYPE_INTEGER ||
+ attributes.getType(names[i]) ==
CyAttributes.TYPE_BOOLEAN ||
+ attributes.getType(names[i]) ==
CyAttributes.TYPE_STRING ||
+ attributes.getType(names[i]) ==
CyAttributes.TYPE_SIMPLE_LIST) {
attributeList.add(prefix+names[i]);
}
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/TreeView.java
===================================================================
--- csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/TreeView.java
2011-04-11 20:22:31 UTC (rev 24741)
+++ csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/TreeView.java
2011-04-11 22:28:50 UTC (rev 24742)
@@ -148,6 +148,8 @@
public void updateSettings() {}
+ public void initializeProperties() {}
+
public void updateSettings(boolean force) {}
public ClusterProperties getSettings() { return null; }
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