Author: scooter
Date: 2011-07-16 11:21:46 -0700 (Sat, 16 Jul 2011)
New Revision: 26198
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
Log:
Updates to heat map viewer and addition of K-Medoid
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
2011-07-15 23:40:16 UTC (rev 26197)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ClusterMaker.java
2011-07-16 18:21:46 UTC (rev 26198)
@@ -65,6 +65,7 @@
import clusterMaker.algorithms.ClusterAlgorithm;
import clusterMaker.algorithms.hierarchical.HierarchicalCluster;
import clusterMaker.algorithms.kmeans.KMeansCluster;
+import clusterMaker.algorithms.kmedoid.KMedoidCluster;
import clusterMaker.algorithms.FeatureVector.FeatureVectorCluster;
import clusterMaker.algorithms.TransClust.TransClustCluster;
import clusterMaker.algorithms.MCL.MCLCluster;
@@ -123,6 +124,7 @@
JMenu menu = new JMenu("Cluster");
addClusterAlgorithm(menu, new HierarchicalCluster());
addClusterAlgorithm(menu, new KMeansCluster());
+ addClusterAlgorithm(menu, new KMedoidCluster());
addClusterAlgorithm(menu, new FeatureVectorCluster());
addClusterAlgorithm(menu, new AutoSOMECluster(true));
// addClusterAlgorithm(menu, new QTCluster());
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
2011-07-15 23:40:16 UTC (rev 26197)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
2011-07-16 18:21:46 UTC (rev 26198)
@@ -261,7 +261,7 @@
}
if (monitor != null)
- monitor.setStatus("Initializaing");
+ monitor.setStatus("Initializing");
// Create a new clusterer
EisenCluster algorithm = new EisenCluster(attributeArray,
distanceMetric, clusterMethod,
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
2011-07-15 23:40:16 UTC (rev 26197)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
2011-07-16 18:21:46 UTC (rev 26198)
@@ -174,8 +174,8 @@
if (attributeArray == null || attributeArray.length == 0)
throw new CyCommandException("No attributes specified");
// Clone ourselves
- HeatMapView hmView = new HeatMapView();
- hmView.startup();
+ // HeatMapView hmView = new HeatMapView();
+ startup();
result.addMessage("Heat Map View displayed");
return result;
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
===================================================================
--- csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
2011-07-15 23:40:16 UTC (rev 26197)
+++ csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/KnnView.java
2011-07-16 18:21:46 UTC (rev 26198)
@@ -124,9 +124,11 @@
CyNetwork network = Cytoscape.getCurrentNetwork();
CyAttributes networkAttributes =
Cytoscape.getNetworkAttributes();
String netId = network.getIdentifier();
- if (networkAttributes.hasAttribute(netId,
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE) &&
- !networkAttributes.getStringAttribute(netId,
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE).equals("kmeans")) {
- return false;
+ if (networkAttributes.hasAttribute(netId,
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE)) {
+ String type =
networkAttributes.getStringAttribute(netId,
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE);
+ if (!networkAttributes.getStringAttribute(netId,
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE).equals("kmeans") &&
+ !networkAttributes.getStringAttribute(netId,
ClusterMaker.CLUSTER_TYPE_ATTRIBUTE).equals("kmedoid"))
+ return false;
}
if (networkAttributes.hasAttribute(netId,
ClusterMaker.CLUSTER_NODE_ATTRIBUTE) ||
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