Author: scooter
Date: 2011-03-28 21:15:35 -0700 (Mon, 28 Mar 2011)
New Revision: 24606
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractClusterAlgorithm.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractNetworkClusterer.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/ClusterAlgorithm.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterTask.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
Log:
Make task monitor have more rational defaults. Don't make the user click
"done" when there's no information...
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractClusterAlgorithm.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractClusterAlgorithm.java
2011-03-29 01:50:07 UTC (rev 24605)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractClusterAlgorithm.java
2011-03-29 04:15:35 UTC (rev 24606)
@@ -39,6 +39,7 @@
import cytoscape.groups.CyGroupManager;
import cytoscape.layout.Tunable;
import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
import java.lang.Math;
import java.util.ArrayList;
@@ -48,6 +49,8 @@
import java.beans.PropertyChangeSupport;
import javax.swing.JPanel;
+import clusterMaker.ui.ClusterTask;
+
// clusterMaker imports
public abstract class AbstractClusterAlgorithm implements ClusterAlgorithm {
@@ -122,6 +125,8 @@
public ClusterResults getResults() { return results; }
public PropertyChangeSupport getPropertyChangeSupport() {return pcs;}
+
+ public JTaskConfig getDefaultTaskConfig() { return
ClusterTask.getDefaultTaskConfig(false); }
public static double mean(Double[] vector) {
double result = 0.0;
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractNetworkClusterer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractNetworkClusterer.java
2011-03-29 01:50:07 UTC (rev 24605)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractNetworkClusterer.java
2011-03-29 04:15:35 UTC (rev 24606)
@@ -40,6 +40,7 @@
import cytoscape.groups.CyGroupManager;
import cytoscape.layout.Tunable;
import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
import java.lang.Math;
import java.util.ArrayList;
@@ -51,6 +52,7 @@
import javax.swing.JPanel;
import clusterMaker.ClusterMaker;
+import clusterMaker.ui.ClusterTask;
/**
* This abstract class is the base class for all of the network clusterers
provided by
@@ -74,6 +76,9 @@
}
}
+ // We don't want to autodispose our task monitors
+ public JTaskConfig getDefaultTaskConfig() { return
ClusterTask.getDefaultTaskConfig(true); }
+
protected List<List<CyNode>> createGroups(CyAttributes netAttributes,
String networkID,
CyAttributes nodeAttributes,
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/ClusterAlgorithm.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/ClusterAlgorithm.java
2011-03-29 01:50:07 UTC (rev 24605)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/ClusterAlgorithm.java
2011-03-29 04:15:35 UTC (rev 24606)
@@ -33,6 +33,7 @@
package clusterMaker.algorithms;
import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
import clusterMaker.ui.ClusterViz;
import java.beans.PropertyChangeSupport;
@@ -120,6 +121,13 @@
public void doCluster(TaskMonitor monitor);
/**
+ * This call returns a JTaskConfig option
+ *
+ * @return the JTaskconfig
+ */
+ public JTaskConfig getDefaultTaskConfig();
+
+ /**
* Hooks for the visualizer
*
* @return the visualizer or null if one doesn't exist
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
2011-03-29 01:50:07 UTC (rev 24605)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
2011-03-29 04:15:35 UTC (rev 24606)
@@ -132,7 +132,7 @@
// Cluster using the current layout
updateAllSettings();
TaskManager.executeTask( new
ClusterTask(currentAlgorithm, this),
-
ClusterTask.getDefaultTaskConfig() );
+
currentAlgorithm.getDefaultTaskConfig() );
} else if (command.equals("visualize")) {
visualizer.startViz();
// setVisible(false);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterTask.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterTask.java
2011-03-29 01:50:07 UTC (rev 24605)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterTask.java
2011-03-29 04:15:35 UTC (rev 24606)
@@ -84,7 +84,6 @@
cluster.doCluster(monitor);
if (dialog != null)
dialog.updateVizButton();
- monitor.setStatus("Clustering complete");
done = true;
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
2011-03-29 01:50:07 UTC (rev 24605)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/HeatMapView.java
2011-03-29 04:15:35 UTC (rev 24606)
@@ -67,6 +67,7 @@
import cytoscape.layout.Tunable;
import cytoscape.logger.CyLogger;
import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
import cytoscape.view.CyNetworkView;
import cytoscape.view.CytoscapeDesktop;
@@ -79,6 +80,7 @@
import clusterMaker.ClusterMaker;
import clusterMaker.algorithms.ClusterProperties;
import clusterMaker.algorithms.ClusterAlgorithm;
+import clusterMaker.ui.ClusterTask;
// TreeView imports
import clusterMaker.treeview.FileSet;
@@ -157,6 +159,8 @@
public String getName() { return "HeatMapView (unclustered)"; }
+ public JTaskConfig getDefaultTaskConfig() { return
ClusterTask.getDefaultTaskConfig(false); }
+
public void startViz() {
startup();
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2011-03-29 01:50:07 UTC (rev 24605)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NestedNetworkView.java
2011-03-29 04:15:35 UTC (rev 24606)
@@ -83,6 +83,7 @@
import clusterMaker.algorithms.AbstractNetworkClusterer;
import clusterMaker.algorithms.ClusterProperties;
import clusterMaker.algorithms.ClusterAlgorithm;
+import clusterMaker.ui.ClusterTask;
/**
* The ClusterViz class provides the primary interface to the
@@ -130,6 +131,8 @@
}
}
+ public JTaskConfig getDefaultTaskConfig() { return
ClusterTask.getDefaultTaskConfig(false); }
+
public void startViz() {
startup();
}
@@ -162,7 +165,7 @@
// Set up a new task
CreateNetworkTask task = new
CreateNetworkTask(clusterAttribute);
- TaskManager.executeTask( task, task.getDefaultTaskConfig() );
+ TaskManager.executeTask( task,
ClusterTask.getDefaultTaskConfig(false) );
}
protected void initialize() {
@@ -458,20 +461,6 @@
return "Creating new network";
}
- public JTaskConfig getDefaultTaskConfig() {
- JTaskConfig result = new JTaskConfig();
-
- result.displayCancelButton(false);
- result.displayCloseButton(false);
- result.displayStatus(true);
- result.displayTimeElapsed(false);
- result.setAutoDispose(true);
- result.setModal(false);
- result.setOwner(Cytoscape.getDesktop());
-
- return result;
- }
-
}
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
2011-03-29 01:50:07 UTC (rev 24605)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NewNetworkView.java
2011-03-29 04:15:35 UTC (rev 24606)
@@ -80,6 +80,7 @@
import clusterMaker.algorithms.ClusterProperties;
import clusterMaker.algorithms.ClusterAlgorithm;
import clusterMaker.algorithms.AbstractNetworkClusterer;
+import clusterMaker.ui.ClusterTask;
/**
* The ClusterViz class provides the primary interface to the
@@ -125,6 +126,8 @@
}
}
+ public JTaskConfig getDefaultTaskConfig() { return
ClusterTask.getDefaultTaskConfig(false); }
+
public void startViz() {
startup();
}
@@ -162,7 +165,7 @@
// Set up a new task
CreateNetworkTask task = new
CreateNetworkTask(clusterAttribute);
- TaskManager.executeTask( task, task.getDefaultTaskConfig() );
+ TaskManager.executeTask( task,
ClusterTask.getDefaultTaskConfig(false) );
}
protected void initialize() {
@@ -413,20 +416,6 @@
return "Creating new network";
}
- public JTaskConfig getDefaultTaskConfig() {
- JTaskConfig result = new JTaskConfig();
-
- result.displayCancelButton(false);
- result.displayCloseButton(false);
- result.displayStatus(true);
- result.displayTimeElapsed(false);
- result.setAutoDispose(true);
- result.setModal(false);
- result.setOwner(Cytoscape.getDesktop());
-
- return result;
- }
-
}
}
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