Author: scooter
Date: 2010-11-29 10:12:20 -0800 (Mon, 29 Nov 2010)
New Revision: 23033
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/EisenCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NetworkColorDialog.java
Log:
Adapt to new ClusterSettingsDialog
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/EisenCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/EisenCluster.java
2010-11-29 18:11:12 UTC (rev 23032)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/EisenCluster.java
2010-11-29 18:12:20 UTC (rev 23033)
@@ -165,12 +165,12 @@
resetAttributes();
}
- public void setCreateGroups() { createGroups = true; }
- public void setIgnoreMissing() { ignoreMissing = true; }
- public void setSelectedOnly() { selectedOnly = true; }
- public void setAdjustDiagonals() { adjustDiagonals = true; }
- public void setZeroMissing() { zeroMissing = true; }
- public void setDebug() { debug = true; }
+ public void setCreateGroups(boolean val) { createGroups = val; }
+ public void setIgnoreMissing(boolean val) { ignoreMissing = val; }
+ public void setSelectedOnly(boolean val) { selectedOnly = val; }
+ public void setAdjustDiagonals(boolean val) { adjustDiagonals = val; }
+ public void setZeroMissing(boolean val) { zeroMissing = val; }
+ public void setDebug(boolean val) { debug = val; }
public String cluster(boolean transpose) {
String keyword = "GENE";
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
2010-11-29 18:11:12 UTC (rev 23032)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/hierarchical/HierarchicalCluster.java
2010-11-29 18:12:20 UTC (rev 23033)
@@ -291,16 +291,11 @@
}
private void setParameters(EisenCluster algorithm) {
- if (createGroups)
- algorithm.setCreateGroups();
- if (ignoreMissing)
- algorithm.setIgnoreMissing();
- if (selectedOnly)
- algorithm.setSelectedOnly();
- if (adjustDiagonals)
- algorithm.setAdjustDiagonals();
- if (zeroMissing)
- algorithm.setZeroMissing();
+ algorithm.setCreateGroups(createGroups);
+ algorithm.setIgnoreMissing(ignoreMissing);
+ algorithm.setSelectedOnly(selectedOnly);
+ algorithm.setAdjustDiagonals(adjustDiagonals);
+ algorithm.setZeroMissing(zeroMissing);
}
private void getAttributesList(List<String>attributeList, CyAttributes
attributes,
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
2010-11-29 18:11:12 UTC (rev 23032)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/ClusterSettingsDialog.java
2010-11-29 18:12:20 UTC (rev 23033)
@@ -241,7 +241,7 @@
}
private void updateAllSettings() {
- currentAlgorithm.updateSettings();
+ currentAlgorithm.updateSettings(true);
}
private void revertAllSettings() {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NetworkColorDialog.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NetworkColorDialog.java
2010-11-29 18:11:12 UTC (rev 23032)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/ui/NetworkColorDialog.java
2010-11-29 18:12:20 UTC (rev 23033)
@@ -256,17 +256,15 @@
}
// Get the right mapping, depending on whether we are mapping
an edge or a node
- byte mapping = ObjectMapping.NODE_MAPPING;
+ // byte mapping = ObjectMapping.NODE_MAPPING;
VisualPropertyType vizType = VisualPropertyType.NODE_FILL_COLOR;
if (edge) {
- mapping = ObjectMapping.EDGE_MAPPING;
+ // mapping = ObjectMapping.EDGE_MAPPING;
vizType = VisualPropertyType.EDGE_COLOR;
}
// Create the new continuous mapper
- ContinuousMapping colorMapping = new
ContinuousMapping(missingColor, mapping);
- colorMapping.setControllingAttributeName(attribute,
Cytoscape.getCurrentNetwork(), false);
- colorMapping.setInterpolator(new
LinearNumberToColorInterpolator());
+ ContinuousMapping colorMapping = new
ContinuousMapping(Color.class, attribute);
double minStep = minValue/5.0;
for (int i = 0; i < 5; i++) {
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