Author: ghannum
Date: 2010-09-03 10:23:29 -0700 (Fri, 03 Sep 2010)
New Revision: 21684
Added:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/DetailedViewLayout.java
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
Log:
Added:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/DetailedViewLayout.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/DetailedViewLayout.java
(rev 0)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/DetailedViewLayout.java
2010-09-03 17:23:29 UTC (rev 21684)
@@ -0,0 +1,194 @@
+package org.idekerlab.PanGIAPlugin;
+
+import giny.model.Node;
+import giny.view.NodeView;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import org.idekerlab.PanGIAPlugin.data.DoubleVector;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.CyAttributes;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
+import cytoscape.view.CyNetworkView;
+
+public class DetailedViewLayout
+{
+ private static double BUFFER_RATIO = 1.2;
+
+ public static void layout(CyNetworkView view, CyNetworkView overview)
+ {
+ /*
+ CyLayoutAlgorithm alg =
CyLayouts.getLayout("attributes-layout");
+
+
alg.setLayoutAttribute(VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME);
+ alg.getSettings().updateValues();
+ alg.updateSettings();
+ view.applyLayout(alg);
+
+ view.redrawGraph(true, true);
+ */
+ //Get values of Parent Module attribute
+ CyAttributes nodeAttr = Cytoscape.getNodeAttributes();
+ Map<String,Set<Node>> module_nodes = new
HashMap<String,Set<Node>>();
+ for (int ni : view.getNetwork().getNodeIndicesArray())
+ {
+ String nodeID =
view.getNetwork().getNode(ni).getIdentifier();
+ String parent = nodeAttr.getAttribute(nodeID,
VisualStyleObserver.PARENT_MODULE_ATTRIBUTE_NAME).toString();
+
+ Set<Node> sset = module_nodes.get(parent);
+ if (sset==null)
+ {
+ sset = new HashSet<Node>();
+ sset.add(view.getNetwork().getNode(ni));
+ module_nodes.put(parent, sset);
+ }else sset.add(view.getNetwork().getNode(ni));
+ }
+
+ //For each parent module
+ for (Entry<String,Set<Node>> e : module_nodes.entrySet())
+ {
+ //Select all nodes with this attribute value
+ view.getNetwork().unselectAllNodes();
+ view.getNetwork().setSelectedNodeState(e.getValue(),
true);
+
+ //Perform force-directed layout of just the selected
+ CyLayoutAlgorithm fd =
CyLayouts.getLayout("force-directed");
+
+ fd.setSelectedOnly(true);
+ fd.getSettings().updateValues();
+ fd.updateSettings();
+ view.applyLayout(fd);
+
+ view.redrawGraph(true, true);
+ }
+ view.getNetwork().unselectAllNodes();
+
+ //Get the meanPosition and radius of each group
+ List<String> moduleList = new
ArrayList<String>(module_nodes.keySet());
+ double[] centerX = new double[moduleList.size()];
+ double[] centerY = new double[moduleList.size()];
+ double[] radius = new double[moduleList.size()];
+
+ for (int i=0;i<moduleList.size();i++)
+ {
+ Set<Node> nodes = module_nodes.get(moduleList.get(i));
+ double minX = Double.MAX_VALUE;
+ double maxX = Double.MIN_VALUE;
+ double minY = Double.MAX_VALUE;
+ double maxY = Double.MIN_VALUE;
+
+ for (Node n : nodes)
+ {
+ NodeView nv = view.getNodeView(n);
+ double x = nv.getXPosition();
+ double y = nv.getYPosition();
+
+ if (x<minX) minX = x;
+ else if (x>maxX) maxX = x;
+
+ if (y<minY) minY = y;
+ else if (y>maxY) maxY = y;
+ }
+
+ centerX[i] = (maxX+minX)/2.0;
+ centerY[i] = (maxY+minY)/2.0;
+
+ double diffX = maxX-centerX[i];
+ double diffY = maxY-centerY[i];
+ radius[i] = Math.sqrt(diffX*diffX+diffY*diffY);
+ }
+
+
+ //Get the map from module to overview node
+ Map<String,NodeView> module_overviewNode = new
HashMap<String,NodeView>(module_nodes.size(),1);
+
+ @SuppressWarnings("rawtypes")
+ List overviewNodes = overview.getSelectedNodes();
+ for (String mod : module_nodes.keySet())
+ for (Object n : overviewNodes)
+ if
(((NodeView)n).getNode().getIdentifier().equals(mod))
+ {
+ module_overviewNode.put(mod,
(NodeView)n);
+ break;
+ }
+
+
+ //Get the reference positions. Normalize to current scale
+ double minRadius = DoubleVector.min(radius);
+ double maxRadius = DoubleVector.max(radius);
+
+ double scale = BUFFER_RATIO*(minRadius+maxRadius);
+ minRadius = Math.max(minRadius, scale/100);
+ scale = BUFFER_RATIO*(minRadius+maxRadius);
+
+ for (int i=0;i<radius.length;i++)
+ if (radius[i]<minRadius) radius[i] = minRadius;
+
+ double[] newCenterX = new double[moduleList.size()];
+ double[] newCenterY = new double[moduleList.size()];
+
+ double minX = Double.MAX_VALUE;
+ double maxX = Double.MIN_VALUE;
+ double minY = Double.MAX_VALUE;
+ double maxY = Double.MIN_VALUE;
+
+ for (int i=0;i<radius.length;i++)
+ {
+ NodeView on =
module_overviewNode.get(moduleList.get(i));
+ double x = on.getXPosition();
+ double y = on.getYPosition();
+
+ newCenterX[i] = x;
+ newCenterY[i] = y;
+
+ if (x<minX) minX = x;
+ else if (x>maxX) maxX = x;
+
+ if (y<minY) minY = y;
+ else if (y>maxY) maxY = y;
+ }
+
+ newCenterX = DoubleVector.times(newCenterX, scale /
(maxX-minX));
+ newCenterY = DoubleVector.times(newCenterY, scale /
(maxY-minY));
+
+ double maxOverlapRatio = Double.MIN_VALUE;
+ for (int i=0;i<radius.length;i++)
+ for (int j=i+1;j<radius.length;j++)
+ {
+ double diffX = newCenterX[i]-newCenterX[j];
+ double diffY = newCenterY[i]-newCenterY[j];
+
+ double overlapRatio =
BUFFER_RATIO*(radius[i]+radius[j])/Math.sqrt(diffX*diffX+diffY*diffY);
+
+ if (overlapRatio>maxOverlapRatio)
maxOverlapRatio = overlapRatio;
+ }
+
+ newCenterX = DoubleVector.times(newCenterX, maxOverlapRatio);
+ newCenterY = DoubleVector.times(newCenterY, maxOverlapRatio);
+
+ //Shift nodes to the new centers
+ double[] shiftX = DoubleVector.subtract(newCenterX,centerX);
+ double[] shiftY = DoubleVector.subtract(newCenterY,centerY);
+
+ for (int i=0;i<radius.length;i++)
+ {
+ for (Node n : module_nodes.get(moduleList.get(i)))
+ {
+ NodeView on = view.getNodeView(n);
+ on.setXPosition(on.getXPosition()+shiftX[i]);
+ on.setYPosition(on.getYPosition()+shiftY[i]);
+ }
+ }
+
+ view.fitContent();
+ view.updateView();
+ }
+}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
2010-09-03 17:16:46 UTC (rev 21683)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
2010-09-03 17:23:29 UTC (rev 21684)
@@ -1,14 +1,17 @@
package org.idekerlab.PanGIAPlugin;
import giny.model.Node;
+import giny.view.NodeView;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.net.URL;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
+import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
@@ -54,6 +57,8 @@
private Map<String, VisualStyle> styleMap;
+ private CyNetworkView overviewView;
+
VisualStyleObserver() {
styleMap = new HashMap<String, VisualStyle>();
Cytoscape.getPropertyChangeSupport().addPropertyChangeListener(this);
@@ -107,6 +112,8 @@
if (style.getName().equals(VS_OVERVIEW_NAME))
{
+ overviewView = view;
+
double min = Float.MAX_VALUE;
double max = Float.MIN_VALUE;
@@ -174,51 +181,8 @@
view.redrawGraph(true, true);
}else if
(type.toString().equals(NetworkType.DETAILED.name()))
{
- CyLayoutAlgorithm alg =
CyLayouts.getLayout("attributes-layout");
+ DetailedViewLayout.layout(view, overviewView);
-
alg.setLayoutAttribute(PARENT_MODULE_ATTRIBUTE_NAME);
- alg.getSettings().updateValues();
- alg.updateSettings();
- view.applyLayout(alg);
-
- view.redrawGraph(true, true);
-
- //Get values of Parent Module attribute
- CyAttributes nodeAttr =
Cytoscape.getNodeAttributes();
- Map<String,Set<Node>> parentModules = new
HashMap<String,Set<Node>>();
- for (int ni :
view.getNetwork().getNodeIndicesArray())
- {
- String nodeID =
view.getNetwork().getNode(ni).getIdentifier();
- String parent =
nodeAttr.getAttribute(nodeID, PARENT_MODULE_ATTRIBUTE_NAME).toString();
-
- Set<Node> sset =
parentModules.get(parent);
- if (sset==null)
- {
- sset = new HashSet<Node>();
-
sset.add(view.getNetwork().getNode(ni));
- parentModules.put(parent, sset);
- }else
sset.add(view.getNetwork().getNode(ni));
- }
-
- //For each parent module
- for (Entry<String,Set<Node>> e :
parentModules.entrySet())
- {
- //Select all nodes with this attribute
value
- view.getNetwork().unselectAllNodes();
-
view.getNetwork().setSelectedNodeState(e.getValue(), true);
-
- //Perform force-directed layout of just
the selected
- CyLayoutAlgorithm fd =
CyLayouts.getLayout("force-directed");
-
- fd.setSelectedOnly(true);
- fd.getSettings().updateValues();
- fd.updateSettings();
- view.applyLayout(fd);
-
- view.redrawGraph(true, true);
- }
- view.getNetwork().unselectAllNodes();
-
}else view.redrawGraph(false, true);
}
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
2010-09-03 17:16:46 UTC (rev 21683)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ui/SearchPropertyPanel.java
2010-09-03 17:23:29 UTC (rev 21684)
@@ -550,7 +550,7 @@
edgeFilteringPanel.add(pValueThresholdLabel, gridBagConstraints);
*/
- edgeFilterSliderLabels.setText("More Less");
+ edgeFilterSliderLabels.setText("More
Less");
edgeFilterSliderLabels.setToolTipText("Strength of the edge filter. (0
returns all edges)");
edgeFilterSliderLabels.setFont(edgeFilterSliderLabels.getFont().deriveFont(12.0f));
edgeFilterSliderLabels.setEnabled(false);
@@ -570,7 +570,7 @@
edgeFilterSlider.setMajorTickSpacing(10);
edgeFilterSlider.setMinorTickSpacing(5);
edgeFilterSlider.setPaintLabels(false);
- edgeFilterSlider.setPaintTicks(true);
+ edgeFilterSlider.setPaintTicks(false);
edgeFilterSlider.setPaintTrack(true);
edgeFilterSlider.setEnabled(false);
edgeFilterSlider.addChangeListener(new
javax.swing.event.ChangeListener() {
@@ -832,8 +832,7 @@
private void closeButtonActionPerformed(java.awt.event.ActionEvent evt)
{
// Close parent tab
- final CytoPanel cytoPanel = Cytoscape.getDesktop().getCytoPanel(
-
SwingConstants.WEST);
+ final CytoPanel cytoPanel =
Cytoscape.getDesktop().getCytoPanel(SwingConstants.WEST);
cytoPanel.remove(this.getParent().getParent());
}
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