Author: kono
Date: 2011-03-30 19:53:08 -0700 (Wed, 30 Mar 2011)
New Revision: 24638
Modified:
core3/layout-cytoscape-impl/trunk/pom.xml
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayoutTask.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/Layout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
Log:
Changed 2D visual lexicon to to minimal lexicon.
Modified: core3/layout-cytoscape-impl/trunk/pom.xml
===================================================================
--- core3/layout-cytoscape-impl/trunk/pom.xml 2011-03-31 02:20:57 UTC (rev
24637)
+++ core3/layout-cytoscape-impl/trunk/pom.xml 2011-03-31 02:53:08 UTC (rev
24638)
@@ -86,17 +86,17 @@
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>viewmodel-api</artifactId>
- <version>3.0.0-alpha3</version>
+ <version>3.0.0-alpha4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>layout-api</artifactId>
- <version>3.0.0-alpha1</version>
+ <version>3.0.0-alpha2-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>presentation-api</artifactId>
- <version>3.0.0-alpha1</version>
+ <version>3.0.0-alpha3-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>cytoscape-temp</groupId>
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java
2011-03-31 02:20:57 UTC (rev 24637)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/GroupAttributesLayoutTask.java
2011-03-31 02:53:08 UTC (rev 24638)
@@ -13,7 +13,7 @@
import org.cytoscape.view.layout.LayoutTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.model.CyNetwork;
@@ -242,8 +242,8 @@
if (partition.size() == 1) {
CyNode node = partition.get(0);
-
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
offsetx);
-
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
offsety);
+
networkView.getNodeView(node).setVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION,
offsetx);
+
networkView.getNodeView(node).setVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION,
offsety);
return 0.0;
}
@@ -259,8 +259,8 @@
for (CyNode node : partition) {
double x = offsetx + radius + (radius * Math.cos(phi));
double y = offsety + radius + (radius * Math.sin(phi));
-
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
x);
-
networkView.getNodeView(node).setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
y);
+
networkView.getNodeView(node).setVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION,
x);
+
networkView.getNodeView(node).setVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION,
y);
phi += phidelta;
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayoutTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayoutTask.java
2011-03-31 02:20:57 UTC (rev 24637)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayoutTask.java
2011-03-31 02:53:08 UTC (rev 24638)
@@ -10,7 +10,7 @@
import org.cytoscape.view.layout.LayoutTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
import org.cytoscape.work.TaskMonitor;
public class StackedNodeLayoutTask extends LayoutTask {
@@ -60,10 +60,10 @@
CyNode node = (CyNode) it.next();
View<CyNode> nodeView = networkView.getNodeView(node);
-
nodeView.setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION, x_position);
-
nodeView.setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION, yPosition);
+
nodeView.setVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION, x_position);
+
nodeView.setVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION, yPosition);
- int y = new
Float((nodeView.getVisualProperty(TwoDVisualLexicon.NODE_Y_SIZE).toString())).intValue();
+ int y = new
Float((nodeView.getVisualProperty(MinimalVisualLexicon.NODE_HEIGHT).toString())).intValue();
yPosition += y * 2;
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java
2011-03-31 02:20:57 UTC (rev 24637)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithmTask.java
2011-03-31 02:53:08 UTC (rev 24638)
@@ -13,7 +13,7 @@
import org.cytoscape.view.layout.LayoutPartition;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -199,8 +199,8 @@
while (iter.hasNext() && !cancelled) {
LayoutNode ln = (LayoutNode) (iter.next());
View<CyNode> nv = ln.getNodeView();
- double xPos =
nv.getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION);
- double yPos =
nv.getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION);
+ double xPos =
nv.getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
+ double yPos =
nv.getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
ln.setX(xPos);
ln.setY(yPos);
partition.moveNodeToLocation(ln);
@@ -276,8 +276,8 @@
innerDeltaAngle = (2 * Math.PI) / bc[compIndex].length;
if (firstTouched != -1) {
- pointX =
nodeViews.get(firstTouched).getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION);
- pointY =
nodeViews.get(firstTouched).getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION);
+ pointX =
nodeViews.get(firstTouched).getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
+ pointY =
nodeViews.get(firstTouched).getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
theAngle = Math.asin((startY - pointY) /
Math.sqrt(((pointX - startX) * (pointX
- startX))
+
((pointY - startY) * (pointY
@@ -330,8 +330,8 @@
if (noOfNeighbours == 0)
continue;
- pointX =
nodeViews.get(bc[compIndex][i]).getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION);
- pointY =
nodeViews.get(bc[compIndex][i]).getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION);
+ pointX =
nodeViews.get(bc[compIndex][i]).getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
+ pointY =
nodeViews.get(bc[compIndex][i]).getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
theAngle = Math.asin((startY - pointY) /
Math.sqrt(((pointX - startX) * (pointX
- startX))
@@ -418,8 +418,8 @@
continue;
}
- pointX =
nodeViews.get(currentNeighbour).getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION);
- pointY =
nodeViews.get(currentNeighbour).getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION);
+ pointX =
nodeViews.get(currentNeighbour).getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
+ pointY =
nodeViews.get(currentNeighbour).getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
theAngle = Math.asin((startY - pointY) /
Math.sqrt(((pointX - startX) * (pointX
- startX))
@@ -635,8 +635,8 @@
if (node2BiComp.containsKey(Integer.valueOf(nodeID))
&&
!drawnBiComps[node2BiComp.get(Integer.valueOf(nodeID)).intValue()]) {
int comp =
node2BiComp.get(Integer.valueOf(nodeID)).intValue();
- double centerX =
nodeViews.get(nodeID).getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION);
- double centerY =
nodeViews.get(nodeID).getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION);
+ double centerX =
nodeViews.get(nodeID).getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
+ double centerY =
nodeViews.get(nodeID).getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
double radius = (48 * bc[comp].length) / (2 * Math.PI);
double deltaAngle = (2 * Math.PI) / bc[comp].length;
double currAngle = theAngle - Math.PI - deltaAngle;
@@ -673,8 +673,8 @@
if (oneAtLeast) {
setOffset(nodeViews.get(nodeID),
-
nodeViews.get(nodeID).getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION) +
(Math.cos(theAngle) * 3 * radius),
-
nodeViews.get(nodeID).getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION) -
(Math.sin(theAngle) * 3 * radius));
+
nodeViews.get(nodeID).getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION) +
(Math.cos(theAngle) * 3 * radius),
+
nodeViews.get(nodeID).getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION) -
(Math.sin(theAngle) * 3 * radius));
SetOuterCircle(comp, radius, centerX, centerY,
nodeID);
}
@@ -756,14 +756,14 @@
rTry = r;
double hlp = 100.0;
- double startX =
nodeViews.get(nodeID).getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION);
- double startY =
nodeViews.get(nodeID).getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION);
+ double startX =
nodeViews.get(nodeID).getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
+ double startY =
nodeViews.get(nodeID).getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
if (neighboursCount > 2) {
setOffset(nodeViews.get(nodeID), startX +
(Math.cos(theAngle) * r * ((min2 + 1) % 100)),
startY -
(Math.sin(theAngle) * r * ((min2 + 1) % 100)));
- startX =
nodeViews.get(nodeID).getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION);
- startY =
nodeViews.get(nodeID).getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION);
+ startX =
nodeViews.get(nodeID).getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
+ startY =
nodeViews.get(nodeID).getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
//System.out.println("theAngle = " + theAngle +
", startAngle = " + startAngle + ", remStartAngle = " + remStartAngle + ",
deltaAngle = " + deltaAngle);
//System.out.println("min1Id = " + min1Id + ",
min2Id" + min2Id + ", maxId" + maxId);
@@ -1070,8 +1070,8 @@
}
private void setOffset(View<CyNode> nv, double x, double y){
- nv.setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION, x);
- nv.setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION, y);
+ nv.setVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION, x);
+ nv.setVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION, y);
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/Layout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/Layout.java
2011-03-31 02:20:57 UTC (rev 24637)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/Layout.java
2011-03-31 02:53:08 UTC (rev 24638)
@@ -42,7 +42,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
/**
* Class that represents the Layout of a given graph.
@@ -75,8 +75,8 @@
// initialize current values
if (load_current_values) {
for (View<CyNode>nv: view.getNodeViews()){
- setX(nv,
nv.getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION));
- setY(nv,
nv.getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION));
+ setX(nv,
nv.getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION));
+ setY(nv,
nv.getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION));
}
}
}
@@ -86,8 +86,8 @@
*/
public void applyLayout(CyNetworkView view) {
for (View<CyNode>nv: view.getNodeViews()){
- nv.setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
getX(nv));
- nv.setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
getY(nv));
+
nv.setVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION, getX(nv));
+
nv.setVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION, getY(nv));
}
}
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2011-03-31 02:20:57 UTC (rev 24637)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2011-03-31 02:53:08 UTC (rev 24638)
@@ -40,21 +40,8 @@
package csplugins.layout.algorithms.hierarchicalLayout;
-import java.awt.geom.Point2D;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
-import java.util.List;
-
-import org.cytoscape.model.CyTableUtil;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNode;
import org.cytoscape.view.layout.AbstractLayout;
-import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.undo.UndoSupport;
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
2011-03-31 02:20:57 UTC (rev 24637)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithmTask.java
2011-03-31 02:53:08 UTC (rev 24638)
@@ -15,7 +15,7 @@
import org.cytoscape.view.layout.LayoutTask;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
+import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -493,8 +493,8 @@
int currentRight;
if (currentView != null) {
- currentBottom = startLayerY +
currentView.getVisualProperty(TwoDVisualLexicon.NODE_Y_SIZE).intValue();
- currentRight = cleanLayerX +
currentView.getVisualProperty(TwoDVisualLexicon.NODE_X_SIZE).intValue();
+ currentBottom = startLayerY +
currentView.getVisualProperty(MinimalVisualLexicon.NODE_HEIGHT).intValue();
+ currentRight = cleanLayerX +
currentView.getVisualProperty(MinimalVisualLexicon.NODE_WIDTH).intValue();
} else {
currentBottom = startLayerY;
currentRight = cleanLayerX;
@@ -567,8 +567,8 @@
if (node.nodeView != null) {
View<CyNode> currentView = node.nodeView;
-
currentView.setVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION,
Double.valueOf((double)node.getXPos()));
-
currentView.setVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION,
Double.valueOf((double)node.getYPos()));
+
currentView.setVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION,
Double.valueOf((double)node.getXPos()));
+
currentView.setVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION,
Double.valueOf((double)node.getYPos()));
}
}
@@ -625,10 +625,10 @@
taskMonitor.setStatusMessage("hierarchical layout complete");
}
private double getXPositionOf(HashMap<Integer, View<CyNode>>
index2NodeView, int nodeIndex){
- return
index2NodeView.get(nodeIndex).getVisualProperty(TwoDVisualLexicon.NODE_X_LOCATION);
+ return
index2NodeView.get(nodeIndex).getVisualProperty(MinimalVisualLexicon.NODE_X_LOCATION);
}
private double getYPositionOf(HashMap<Integer, View<CyNode>>
index2NodeView, int nodeIndex){
- return
index2NodeView.get(nodeIndex).getVisualProperty(TwoDVisualLexicon.NODE_Y_LOCATION);
+ return
index2NodeView.get(nodeIndex).getVisualProperty(MinimalVisualLexicon.NODE_Y_LOCATION);
}
/**
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