Author: pwang
Date: 2011-10-28 18:02:29 -0700 (Fri, 28 Oct 2011)
New Revision: 27333
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
Log:
Comment out some code
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
2011-10-28 21:36:34 UTC (rev 27332)
+++
csplugins/trunk/ucsd/ruschein/PanGIA-impl/src/main/java/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
2011-10-29 01:02:29 UTC (rev 27333)
@@ -1,7 +1,7 @@
package org.idekerlab.PanGIAPlugin;
-import giny.model.Node;
-import giny.view.NodeView;
+//import giny.model.Node;
+//import giny.view.NodeView;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
@@ -16,25 +16,25 @@
import java.util.Map.Entry;
import java.util.Set;
-import cytoscape.CyNode;
-import cytoscape.Cytoscape;
-import cytoscape.data.CyAttributes;
-import cytoscape.data.CyAttributesUtils;
-import cytoscape.layout.CyLayoutAlgorithm;
-import cytoscape.layout.CyLayouts;
-import cytoscape.view.CyNetworkView;
-import cytoscape.view.CytoscapeDesktop;
-import cytoscape.visual.EdgeAppearanceCalculator;
-import cytoscape.visual.NodeAppearanceCalculator;
-import cytoscape.visual.VisualPropertyType;
-import cytoscape.visual.VisualStyle;
-import cytoscape.visual.calculators.BasicCalculator;
-import cytoscape.visual.calculators.Calculator;
-import cytoscape.visual.mappings.BoundaryRangeValues;
-import cytoscape.visual.mappings.ContinuousMapping;
-import cytoscape.visual.mappings.ObjectMapping;
-import cytoscape.visual.mappings.PassThroughMapping;
-import cytoscape.visual.properties.EdgeOpacityProp;
+import org.cytoscape.model.CyNode;
+//import cytoscape.Cytoscape;
+import org.cytoscape.model.CyTable;
+//import cytoscape.data.CyAttributesUtils;
+//import cytoscape.layout.CyLayoutAlgorithm;
+//import cytoscape.layout.CyLayouts;
+import org.cytoscape.view.model.CyNetworkView;
+//import cytoscape.view.CytoscapeDesktop;
+//import cytoscape.visual.EdgeAppearanceCalculator;
+//import cytoscape.visual.NodeAppearanceCalculator;
+//import cytoscape.visual.VisualPropertyType;
+import org.cytoscape.view.vizmap.VisualStyle;
+//import cytoscape.visual.calculators.BasicCalculator;
+//import cytoscape.visual.calculators.Calculator;
+//import cytoscape.visual.mappings.BoundaryRangeValues;
+//import cytoscape.visual.mappings.ContinuousMapping;
+//import cytoscape.visual.mappings.ObjectMapping;
+//import cytoscape.visual.mappings.PassThroughMapping;
+//import cytoscape.visual.properties.EdgeOpacityProp;
/**
* Listening to the network creation event and override the visual style.
@@ -60,11 +60,11 @@
private static CyNetworkView overviewView;
- VisualStyleObserver() {
- styleMap = new HashMap<String, VisualStyle>();
-
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
- restoreVS();
- }
+// VisualStyleObserver() {
+// styleMap = new HashMap<String, VisualStyle>();
+//
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
+// restoreVS();
+// }
public static void setOverviewView(CyNetworkView overviewView)
{
@@ -74,166 +74,166 @@
private void restoreVS() {
// Load new styles.
- final VisualStyle currentStyle =
Cytoscape.getVisualMappingManager().getVisualStyle();
-
-
if(Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_MODULE_NAME)
== null ||
-
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_OVERVIEW_NAME)
== null) {
- Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED,
null, visualStypePropLocation);
- }
- overviewVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_OVERVIEW_NAME);
- moduleVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_MODULE_NAME);
-
-
Cytoscape.getVisualMappingManager().setVisualStyle(currentStyle);
- styleMap.put(NetworkType.OVERVIEW.name(), overviewVS);
- styleMap.put(NetworkType.MODULE.name(), moduleVS);
- styleMap.put(NetworkType.DETAILED.name(), moduleVS);
- System.out.println("#### Init VS finished.");
+// final VisualStyle currentStyle =
Cytoscape.getVisualMappingManager().getVisualStyle();
+//
+//
if(Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_MODULE_NAME)
== null ||
+//
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_OVERVIEW_NAME)
== null) {
+// Cytoscape.firePropertyChange(Cytoscape.VIZMAP_LOADED,
null, visualStypePropLocation);
+// }
+// overviewVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_OVERVIEW_NAME);
+// moduleVS =
Cytoscape.getVisualMappingManager().getCalculatorCatalog().getVisualStyle(VS_MODULE_NAME);
+//
+//
Cytoscape.getVisualMappingManager().setVisualStyle(currentStyle);
+// styleMap.put(NetworkType.OVERVIEW.name(), overviewVS);
+// styleMap.put(NetworkType.MODULE.name(), moduleVS);
+// styleMap.put(NetworkType.DETAILED.name(), moduleVS);
+// System.out.println("#### Init VS finished.");
}
public void setModuleLabels(String nattr)
{
- BasicCalculator calcLabel =
(BasicCalculator)moduleVS.getNodeAppearanceCalculator().getCalculator(VisualPropertyType.NODE_LABEL);
-
- if (calcLabel.getMapping(0) instanceof
cytoscape.visual.mappings.PassThroughMapping)
- {
- PassThroughMapping pm =
(PassThroughMapping)(calcLabel.getMapping(0));
-
- pm.setControllingAttributeName(nattr);
- }
-
+// BasicCalculator calcLabel =
(BasicCalculator)moduleVS.getNodeAppearanceCalculator().getCalculator(VisualPropertyType.NODE_LABEL);
+//
+// if (calcLabel.getMapping(0) instanceof
cytoscape.visual.mappings.PassThroughMapping)
+// {
+// PassThroughMapping pm =
(PassThroughMapping)(calcLabel.getMapping(0));
+//
+// pm.setControllingAttributeName(nattr);
+// }
+//
}
@SuppressWarnings({ "deprecation", "unchecked" })
public void propertyChange(PropertyChangeEvent evt) {
- if(evt.getPropertyName().equals(Cytoscape.SESSION_LOADED)) {
- restoreVS();
- return;
- }
-
-
if(evt.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_CREATED))
- {
- final Object newVal = evt.getNewValue();
- if(newVal == null || newVal instanceof CyNetworkView ==
false)
- return;
-
- final CyNetworkView view = (CyNetworkView) newVal;
-
- Object type =
Cytoscape.getNetworkAttributes().getAttribute(view.getNetwork().getIdentifier(),
NETWORK_TYPE_ATTRIBUTE_NAME);
-
- if(type == null)
- return;
-
- final VisualStyle style = styleMap.get(type.toString());
- if(style == null)
- return;
-
- if (style.getName().equals(VS_OVERVIEW_NAME))
- {
- overviewView = view;
-
- double min = Float.MAX_VALUE;
- double max = Float.MIN_VALUE;
-
- for (double f :
(Collection<Double>)CyAttributesUtils.getAttribute(NestedNetworkCreator.EDGE_SCORE,
Cytoscape.getEdgeAttributes()).values())
- {
- if (f<min) min = f;
- if (f>max) max = f;
- }
-
- EdgeAppearanceCalculator eac =
style.getEdgeAppearanceCalculator();
-
- // Set EDGE_OPACITY
- BasicCalculator cal = (BasicCalculator)
eac.getCalculator(VisualPropertyType.EDGE_OPACITY);
- if (cal.getMapping(0) instanceof
ContinuousMapping){
- ContinuousMapping c_m =
(ContinuousMapping)cal.getMapping(0);
- if
(c_m.getControllingAttributeName().equalsIgnoreCase(NestedNetworkCreator.EDGE_SCORE)){
- // Clear points
- for (int
i=c_m.getPointCount()-1; i>=0; i--){
- c_m.removePoint(i);
- }
- // Add new points
- c_m.addPoint(min, new
BoundaryRangeValues(30,30,30));
- c_m.addPoint(max, new
BoundaryRangeValues(255,255,255));
- }
-
- }
-
- //Set EDGE_LINE_WIDTH
- cal = (BasicCalculator)
eac.getCalculator(VisualPropertyType.EDGE_LINE_WIDTH);
- if (cal.getMapping(0) instanceof
ContinuousMapping){
- ContinuousMapping c_m =
(ContinuousMapping)cal.getMapping(0);
- if
(c_m.getControllingAttributeName().equalsIgnoreCase(NestedNetworkCreator.EDGE_SCORE)){
- // Clear points
- for (int
i=c_m.getPointCount()-1; i>=0; i--){
- c_m.removePoint(i);
- }
- // Add new points
- c_m.addPoint(min, new
BoundaryRangeValues(5,5,5));
- c_m.addPoint(max, new
BoundaryRangeValues(20,20,20));
- }
- }
-
- min = Float.MAX_VALUE;
- max = Float.MIN_VALUE;
-
- for (double f :
(Collection<Double>)CyAttributesUtils.getAttribute(NestedNetworkCreator.GENE_COUNT_SQRT,
Cytoscape.getNodeAttributes()).values())
- {
- if (f<min) min = f;
- if (f>max) max = f;
- }
-
- NodeAppearanceCalculator nac =
style.getNodeAppearanceCalculator();
-
- // Set Node Size
- cal = (BasicCalculator)
nac.getCalculator(VisualPropertyType.NODE_SIZE);
- if (cal.getMapping(0) instanceof
ContinuousMapping){
- ContinuousMapping c_m =
(ContinuousMapping)cal.getMapping(0);
- if
(c_m.getControllingAttributeName().equalsIgnoreCase(NestedNetworkCreator.GENE_COUNT_SQRT)){
- // Clear points
- for (int
i=c_m.getPointCount()-1; i>=0; i--){
- c_m.removePoint(i);
- }
- // Add new points
- c_m.addPoint(min, new
BoundaryRangeValues(20,20,20));
- double fs = Math.max(10*max,20);
- c_m.addPoint(max, new
BoundaryRangeValues(fs,fs,fs));
- }
- }
-
- //Set NODE_FONT_SIZE
- cal = (BasicCalculator)
nac.getCalculator(VisualPropertyType.NODE_FONT_SIZE);
- if (cal.getMapping(0) instanceof
ContinuousMapping){
- ContinuousMapping c_m =
(ContinuousMapping)cal.getMapping(0);
- if
(c_m.getControllingAttributeName().equalsIgnoreCase(NestedNetworkCreator.GENE_COUNT_SQRT)){
- // Clear points
- for (int
i=c_m.getPointCount()-1; i>=0; i--){
- c_m.removePoint(i);
- }
- // Add new points
- c_m.addPoint(min, new
BoundaryRangeValues(10,10,10));
- double fs = Math.max(max,10);
- c_m.addPoint(max, new
BoundaryRangeValues(fs,fs,fs));
- }
- }
- }
-
- view.setVisualStyle(style.getName());
-
if(Cytoscape.getVisualMappingManager().getVisualStyle().equals(style) == false)
-
Cytoscape.getVisualMappingManager().setVisualStyle(style);
-
- if (type.toString().equals(NetworkType.MODULE.name()))
- {
- CyLayoutAlgorithm alg =
cytoscape.layout.CyLayouts.getLayout("force-directed");
- view.applyLayout(alg);
-
- view.redrawGraph(true, true);
- }else if
(type.toString().equals(NetworkType.DETAILED.name()))
- {
- //DetailedViewLayout.layout(view, overviewView);
-
- }else view.redrawGraph(false, true);
- }
+// if(evt.getPropertyName().equals(Cytoscape.SESSION_LOADED)) {
+// restoreVS();
+// return;
+// }
+//
+//
if(evt.getPropertyName().equals(CytoscapeDesktop.NETWORK_VIEW_CREATED))
+// {
+// final Object newVal = evt.getNewValue();
+// if(newVal == null || newVal instanceof CyNetworkView ==
false)
+// return;
+//
+// final CyNetworkView view = (CyNetworkView) newVal;
+//
+// Object type =
Cytoscape.getNetworkAttributes().getAttribute(view.getNetwork().getIdentifier(),
NETWORK_TYPE_ATTRIBUTE_NAME);
+//
+// if(type == null)
+// return;
+//
+// final VisualStyle style = styleMap.get(type.toString());
+// if(style == null)
+// return;
+//
+// if (style.getName().equals(VS_OVERVIEW_NAME))
+// {
+// overviewView = view;
+//
+// double min = Float.MAX_VALUE;
+// double max = Float.MIN_VALUE;
+//
+// for (double f :
(Collection<Double>)CyAttributesUtils.getAttribute(NestedNetworkCreator.EDGE_SCORE,
Cytoscape.getEdgeAttributes()).values())
+// {
+// if (f<min) min = f;
+// if (f>max) max = f;
+// }
+//
+// EdgeAppearanceCalculator eac =
style.getEdgeAppearanceCalculator();
+//
+// // Set EDGE_OPACITY
+// BasicCalculator cal = (BasicCalculator)
eac.getCalculator(VisualPropertyType.EDGE_OPACITY);
+// if (cal.getMapping(0) instanceof
ContinuousMapping){
+// ContinuousMapping c_m =
(ContinuousMapping)cal.getMapping(0);
+// if
(c_m.getControllingAttributeName().equalsIgnoreCase(NestedNetworkCreator.EDGE_SCORE)){
+// // Clear points
+// for (int
i=c_m.getPointCount()-1; i>=0; i--){
+// c_m.removePoint(i);
+// }
+// // Add new points
+// c_m.addPoint(min, new
BoundaryRangeValues(30,30,30));
+// c_m.addPoint(max, new
BoundaryRangeValues(255,255,255));
+// }
+//
+// }
+//
+// //Set EDGE_LINE_WIDTH
+// cal = (BasicCalculator)
eac.getCalculator(VisualPropertyType.EDGE_LINE_WIDTH);
+// if (cal.getMapping(0) instanceof
ContinuousMapping){
+// ContinuousMapping c_m =
(ContinuousMapping)cal.getMapping(0);
+// if
(c_m.getControllingAttributeName().equalsIgnoreCase(NestedNetworkCreator.EDGE_SCORE)){
+// // Clear points
+// for (int
i=c_m.getPointCount()-1; i>=0; i--){
+// c_m.removePoint(i);
+// }
+// // Add new points
+// c_m.addPoint(min, new
BoundaryRangeValues(5,5,5));
+// c_m.addPoint(max, new
BoundaryRangeValues(20,20,20));
+// }
+// }
+//
+// min = Float.MAX_VALUE;
+// max = Float.MIN_VALUE;
+//
+// for (double f :
(Collection<Double>)CyAttributesUtils.getAttribute(NestedNetworkCreator.GENE_COUNT_SQRT,
Cytoscape.getNodeAttributes()).values())
+// {
+// if (f<min) min = f;
+// if (f>max) max = f;
+// }
+//
+// NodeAppearanceCalculator nac =
style.getNodeAppearanceCalculator();
+//
+// // Set Node Size
+// cal = (BasicCalculator)
nac.getCalculator(VisualPropertyType.NODE_SIZE);
+// if (cal.getMapping(0) instanceof
ContinuousMapping){
+// ContinuousMapping c_m =
(ContinuousMapping)cal.getMapping(0);
+// if
(c_m.getControllingAttributeName().equalsIgnoreCase(NestedNetworkCreator.GENE_COUNT_SQRT)){
+// // Clear points
+// for (int
i=c_m.getPointCount()-1; i>=0; i--){
+// c_m.removePoint(i);
+// }
+// // Add new points
+// c_m.addPoint(min, new
BoundaryRangeValues(20,20,20));
+// double fs = Math.max(10*max,20);
+// c_m.addPoint(max, new
BoundaryRangeValues(fs,fs,fs));
+// }
+// }
+//
+// //Set NODE_FONT_SIZE
+// cal = (BasicCalculator)
nac.getCalculator(VisualPropertyType.NODE_FONT_SIZE);
+// if (cal.getMapping(0) instanceof
ContinuousMapping){
+// ContinuousMapping c_m =
(ContinuousMapping)cal.getMapping(0);
+// if
(c_m.getControllingAttributeName().equalsIgnoreCase(NestedNetworkCreator.GENE_COUNT_SQRT)){
+// // Clear points
+// for (int
i=c_m.getPointCount()-1; i>=0; i--){
+// c_m.removePoint(i);
+// }
+// // Add new points
+// c_m.addPoint(min, new
BoundaryRangeValues(10,10,10));
+// double fs = Math.max(max,10);
+// c_m.addPoint(max, new
BoundaryRangeValues(fs,fs,fs));
+// }
+// }
+// }
+//
+// view.setVisualStyle(style.getName());
+//
if(Cytoscape.getVisualMappingManager().getVisualStyle().equals(style) == false)
+//
Cytoscape.getVisualMappingManager().setVisualStyle(style);
+//
+// if (type.toString().equals(NetworkType.MODULE.name()))
+// {
+// CyLayoutAlgorithm alg =
cytoscape.layout.CyLayouts.getLayout("force-directed");
+// view.applyLayout(alg);
+//
+// view.redrawGraph(true, true);
+// }else if
(type.toString().equals(NetworkType.DETAILED.name()))
+// {
+// //DetailedViewLayout.layout(view, overviewView);
+//
+// }else view.redrawGraph(false, true);
+// }
}
}
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