Author: paperwing
Date: 2012-03-27 09:02:46 -0700 (Tue, 27 Mar 2012)
New Revision: 28663
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/AnimatorController.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/coordinator/BirdsEyeCoordinatorProcessor.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/view/DefaultValueVault.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/view/WindNetworkView.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/input/DebugInputHandler.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/layouts/SphericalLayoutAlgorithmTask.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/tools/NetworkToolkit.java
Log:
Renamed CyTableEntry references to CyIdentifiable, pressing C not only resets
camera but now also resets node z-coordinates to default values, fitInView()
method created in NetworkToolkit to allow the network view object to perform
fitting operations used in the toolbar, camera reference added to
WindNetworkView for taskbar zooming
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/AnimatorController.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/AnimatorController.java
2012-03-27 01:12:23 UTC (rev 28662)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/AnimatorController.java
2012-03-27 16:02:46 UTC (rev 28663)
@@ -116,7 +116,7 @@
return coordinator;
}
- private void startAnimator() {
+ public void startAnimator() {
animatorControl.start();
if (coordinator.isBirdsEyeClaimed() &&
coordinator.getBirdsEyeAnimatorControl() != null) {
@@ -124,7 +124,7 @@
}
}
- private void stopAnimator() {
+ public void stopAnimator() {
animatorControl.stop();
if (coordinator.isBirdsEyeClaimed() &&
coordinator.getBirdsEyeAnimatorControl() != null) {
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
2012-03-27 01:12:23 UTC (rev 28662)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/Graphics.java
2012-03-27 16:02:46 UTC (rev 28663)
@@ -24,6 +24,7 @@
import org.cytoscape.paperwing.internal.coordinator.CoordinatorProcessor;
import org.cytoscape.paperwing.internal.coordinator.ViewingCoordinator;
import
org.cytoscape.paperwing.internal.cytoscape.processing.CytoscapeDataProcessor;
+import org.cytoscape.paperwing.internal.cytoscape.view.WindNetworkView;
import org.cytoscape.paperwing.internal.data.GraphicsData;
import org.cytoscape.paperwing.internal.geometric.Vector3;
import org.cytoscape.paperwing.internal.input.InputProcessor;
@@ -260,6 +261,7 @@
component.addMouseWheelListener(controller);
graphicsData.setAnimatorController(controller);
+ ((WindNetworkView)
graphicsData.getNetworkView()).setAnimatorController(controller);
}
}
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/coordinator/BirdsEyeCoordinatorProcessor.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/coordinator/BirdsEyeCoordinatorProcessor.java
2012-03-27 01:12:23 UTC (rev 28662)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/coordinator/BirdsEyeCoordinatorProcessor.java
2012-03-27 16:02:46 UTC (rev 28663)
@@ -1,10 +1,14 @@
package org.cytoscape.paperwing.internal.coordinator;
+import java.util.Collection;
+
+import org.cytoscape.model.CyNode;
import org.cytoscape.paperwing.internal.data.CoordinatorData;
import org.cytoscape.paperwing.internal.data.GraphicsData;
import org.cytoscape.paperwing.internal.geometric.Vector3;
import org.cytoscape.paperwing.internal.tools.NetworkToolkit;
import org.cytoscape.paperwing.internal.tools.SimpleCamera;
+import org.cytoscape.view.model.View;
public class BirdsEyeCoordinatorProcessor implements CoordinatorProcessor {
@@ -98,6 +102,8 @@
// Update the birds eye view camera
camera.set(mainCameraCopy);
+ /*
+
Vector3 networkCenter =
NetworkToolkit.findNetworkCenter(graphicsData.getNetworkView(),
graphicsData.getDistanceScale());
Vector3 farthestNode =
NetworkToolkit.findFarthestNodeFromCenter(graphicsData.getNetworkView(),
networkCenter, graphicsData.getDistanceScale());
@@ -117,8 +123,14 @@
camera.moveTo(networkCenter.plus(offset));
camera.setDistance(newDistance);
+
+ */
+
+ NetworkToolkit.fitInView(camera,
graphicsData.getNetworkView().getNodeViews(), graphicsData.getDistanceScale(),
5.0);
}
+
+
@Override
public void unlinkCoordinator(ViewingCoordinator coordinator) {
coordinator.unlinkBirdsEye();
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/view/DefaultValueVault.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/view/DefaultValueVault.java
2012-03-27 01:12:23 UTC (rev 28662)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/view/DefaultValueVault.java
2012-03-27 16:02:46 UTC (rev 28663)
@@ -7,9 +7,9 @@
import java.util.Map.Entry;
import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
import org.cytoscape.view.model.VisualLexicon;
import org.cytoscape.view.model.VisualProperty;
import org.cytoscape.view.presentation.property.BasicVisualLexicon;
@@ -21,7 +21,7 @@
private Map<String, VisualPropertyValueHolder<?>> edgeDefaultValues;
private Map<String, VisualPropertyValueHolder<?>> networkDefaultValues;
- private Map<Class<? extends CyTableEntry>,
+ private Map<Class<? extends CyIdentifiable>,
Map<String, VisualPropertyValueHolder<?>>> defaultValueSets;
private VisualLexicon visualLexicon;
@@ -33,7 +33,7 @@
edgeDefaultValues = new HashMap<String,
VisualPropertyValueHolder<?>>();
networkDefaultValues = new HashMap<String,
VisualPropertyValueHolder<?>>();
- defaultValueSets = new HashMap<Class<? extends CyTableEntry>,
Map<String, VisualPropertyValueHolder<?>>>();
+ defaultValueSets = new HashMap<Class<? extends CyIdentifiable>,
Map<String, VisualPropertyValueHolder<?>>>();
defaultValueSets.put(CyNode.class, nodeDefaultValues);
defaultValueSets.put(CyEdge.class, edgeDefaultValues);
defaultValueSets.put(CyNetwork.class, networkDefaultValues);
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/view/WindNetworkView.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/view/WindNetworkView.java
2012-03-27 01:12:23 UTC (rev 28662)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/cytoscape/view/WindNetworkView.java
2012-03-27 16:02:46 UTC (rev 28663)
@@ -7,10 +7,12 @@
import java.util.Map;
import java.util.Set;
+import javax.media.opengl.GLAnimatorControl;
+
import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.SUIDFactory;
import org.cytoscape.model.events.AboutToRemoveEdgesEvent;
import org.cytoscape.model.events.AboutToRemoveEdgesListener;
@@ -20,8 +22,10 @@
import org.cytoscape.model.events.AddedEdgesListener;
import org.cytoscape.model.events.AddedNodesEvent;
import org.cytoscape.model.events.AddedNodesListener;
+import org.cytoscape.paperwing.internal.AnimatorController;
import org.cytoscape.paperwing.internal.geometric.Vector3;
import org.cytoscape.paperwing.internal.tools.NetworkToolkit;
+import org.cytoscape.paperwing.internal.tools.SimpleCamera;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.VisualLexicon;
@@ -40,6 +44,9 @@
private DefaultValueVault defaultValues;
private VisualMappingManager visualMappingManager;
+ private AnimatorController animatorController;
+ private SimpleCamera networkCamera = null;
+
// Assumes indices of nodes are unique
private Map<Integer, View<CyNode>> nodeViews;
private Map<Integer, View<CyEdge>> edgeViews;
@@ -104,8 +111,8 @@
}
@Override
- public Collection<View<? extends CyTableEntry>> getAllViews() {
- Collection<View<? extends CyTableEntry>> views = new
HashSet<View<? extends CyTableEntry>>();
+ public Collection<View<? extends CyIdentifiable>> getAllViews() {
+ Collection<View<? extends CyIdentifiable>> views = new
HashSet<View<? extends CyIdentifiable>>();
// Return views for Node, Edge, Network
views.addAll(getNodeViews());
@@ -278,7 +285,7 @@
// Update visual properties according to the current visual
style
VisualStyle visualStyle =
visualMappingManager.getVisualStyle(this);
- for (View<? extends CyTableEntry> view : getAllViews()) {
+ for (View<? extends CyIdentifiable> view : getAllViews()) {
for (VisualProperty<?> visualProperty :
visualLexicon.getAllVisualProperties()) {
if (view.getVisualProperty(visualProperty) !=
null
&&
visualStyle.getDefaultValue(visualProperty) != null
@@ -309,6 +316,22 @@
return defaultValues.getDefaultValue(visualProperty);
}
}
+
+ public void setAnimatorController(AnimatorController
animatorController) {
+ this.animatorController = animatorController;
+ }
+
+ public AnimatorController getAnimatorController() {
+ return animatorController;
+ }
+
+ public void setNetworkCamera(SimpleCamera networkCamera) {
+ this.networkCamera = networkCamera;
+ }
+
+ public SimpleCamera getNetworkCamera() {
+ return networkCamera;
+ }
// @Override
// public void handleEvent(AboutToRemoveNodesEvent e) {
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/input/DebugInputHandler.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/input/DebugInputHandler.java
2012-03-27 01:12:23 UTC (rev 28662)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/input/DebugInputHandler.java
2012-03-27 16:02:46 UTC (rev 28663)
@@ -2,7 +2,10 @@
import java.util.Set;
+import org.cytoscape.model.CyNode;
import org.cytoscape.paperwing.internal.data.GraphicsData;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.presentation.property.BasicVisualLexicon;
import com.jogamp.newt.event.KeyEvent;
@@ -26,9 +29,17 @@
graphicsData.setShowFPS(!graphicsData.getShowFPS());
}
+ // Toggle displaying all node labels or only for the
selected/hovered nodes
if (pressed.contains(KeyEvent.VK_L)) {
graphicsData.setShowAllNodeLabels(!graphicsData.getShowAllNodeLabels());
}
+
+ // Reset node z-coordinate values to default
+ if (pressed.contains(KeyEvent.VK_C)) {
+ for (View<CyNode> nodeView :
graphicsData.getNetworkView().getNodeViews()) {
+
nodeView.setVisualProperty(BasicVisualLexicon.NODE_Z_LOCATION, 0.0);
+ }
+ }
}
}
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/layouts/SphericalLayoutAlgorithmTask.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/layouts/SphericalLayoutAlgorithmTask.java
2012-03-27 01:12:23 UTC (rev 28662)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/layouts/SphericalLayoutAlgorithmTask.java
2012-03-27 16:02:46 UTC (rev 28663)
@@ -11,6 +11,7 @@
import org.cytoscape.model.CyEdge.Type;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.paperwing.internal.cytoscape.view.WindNetworkView;
import org.cytoscape.paperwing.internal.geometric.Vector3;
import org.cytoscape.paperwing.internal.tools.NetworkToolkit;
import org.cytoscape.view.layout.AbstractBasicLayoutTask;
@@ -60,6 +61,10 @@
}
arrangePartitions(partitions);
+
+ if (networkView instanceof WindNetworkView) {
+ ((WindNetworkView)
networkView).getAnimatorController().startAnimator();
+ }
}
private void arrangePartitions(Collection<Collection<View<CyNode>>>
partitions) {
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/tools/NetworkToolkit.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/tools/NetworkToolkit.java
2012-03-27 01:12:23 UTC (rev 28662)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/tools/NetworkToolkit.java
2012-03-27 16:02:46 UTC (rev 28663)
@@ -1,5 +1,6 @@
package org.cytoscape.paperwing.internal.tools;
+import java.util.Collection;
import java.util.Set;
import org.cytoscape.model.CyColumn;
@@ -17,6 +18,14 @@
private static final String SELECTED_COLUMN_NAME = "selected";
+ /**
+ * Find the average position of a given set of nodes.
+ *
+ * @param nodeIndices The indices of nodes whose average position is to
be found
+ * @param networkView The network view containing the nodes
+ * @param distanceScale The distance scaling used to convert between
Cytoscape and renderer coordinates.
+ * @return The average position
+ */
public static Vector3 findCenter(Set<Integer> nodeIndices,
CyNetworkView networkView, double distanceScale) {
if (nodeIndices.isEmpty()) {
return null;
@@ -43,7 +52,70 @@
return result;
}
+
+ /**
+ * Position the given camera as to fit all of the given nodes in the
current view.
+ *
+ * @param camera The camera to position
+ * @param nodeViews The node views to be fit into the current view
+ * @param distanceScale The distance scaling used to convert between
Cytoscape and render coordinates. Cytoscape coordinates
+ * are divided by this scale to obtain renderer coordinates.
+ * @param minDistance The minimum distance between the camera and the
average node position.
+ */
+ public static void fitInView(SimpleCamera camera,
Collection<View<CyNode>> nodeViews, double distanceScale, double minDistance) {
+ Vector3 center = NetworkToolkit.findCenter(nodeViews,
distanceScale);
+ Vector3 farthestNode =
NetworkToolkit.findFarthestNodeFromCenter(nodeViews, center, distanceScale);
+
+ double newDistance = farthestNode.distance(center);
+
+ // Further increase the distance needed
+ newDistance *= 3;
+
+ // Enforce minimum distance
+ newDistance = Math.max(newDistance, minDistance);
+
+ Vector3 offset = camera.getDirection().multiply(-newDistance);
+
+ camera.moveTo(center.plus(offset));
+ camera.setDistance(newDistance);
+ }
+
+ /**
+ * Obtain the average position of a set of nodes.
+ *
+ * @param nodeViews The node views whose average position is to be
obtained
+ * @param distanceScale The distance scaling used to convert between
Cytoscape and render coordinates. Cytoscape coordinates
+ * are divided by this scale to obtain renderer coordinates.
+ * @return The average position
+ */
+ public static Vector3 findCenter(Collection<View<CyNode>> nodeViews,
double distanceScale) {
+ double x = 0, y = 0, z = 0;
+ int visitedCount = 0;
+
+ for (View<CyNode> nodeView : nodeViews) {
+
+ if (nodeView != null) {
+ x +=
nodeView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
+ y +=
nodeView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION);
+ z +=
nodeView.getVisualProperty(BasicVisualLexicon.NODE_Z_LOCATION);
+ visitedCount++;
+ }
+ }
+
+ Vector3 result = new Vector3(x, y, z);
+ result.divideLocal(distanceScale * visitedCount);
+
+ return result;
+ }
+ /**
+ * Obtain the average position of nodes in a network.
+ *
+ * @param networkView The network to find the average position of
+ * @param distanceScale The distance scaling used to convert between
Cytoscape and render coordinates. Cytoscape coordinates
+ * are divided by this scale to obtain renderer coordinates.
+ * @return The average position
+ */
public static Vector3 findNetworkCenter(CyNetworkView networkView,
double distanceScale) {
double x = 0, y = 0, z = 0;
int visitedCount = 0;
@@ -70,17 +142,23 @@
return result;
}
- public static Vector3 findFarthestNodeFromCenter(CyNetworkView
networkView, Vector3 networkCenter, double distanceScale) {
+ /**
+ * Find the position of the node that is farthest from a given position.
+ *
+ * @param nodeViews The node views used to find the farthest node
+ * @param networkCenter The position used as the center, to determine
the farthest node
+ * @param distanceScale The distance scaling used to convert between
Cytoscape and render coordinates. Cytoscape coordinates
+ * are divided by this scale to obtain renderer coordinates.
+ * @return The position of the farthest node
+ */
+ public static Vector3
findFarthestNodeFromCenter(Collection<View<CyNode>> nodeViews, Vector3
networkCenter, double distanceScale) {
double currentDistanceSquared;
double maxDistanceSquared = 0;
Vector3 currentPosition = new Vector3();
Vector3 maxPosition = new Vector3();
- View<CyNode> nodeView;
-
- for (CyNode node : networkView.getModel().getNodeList()) {
- nodeView = networkView.getNodeView(node);
+ for (View<CyNode> nodeView : nodeViews) {
if (nodeView != null) {
@@ -100,11 +178,23 @@
return maxPosition;
}
+
+ public static Vector3 findFarthestNodeFromCenter(CyNetworkView
networkView, Vector3 networkCenter, double distanceScale) {
+ return findFarthestNodeFromCenter(networkView.getNodeViews(),
networkCenter, distanceScale);
+ }
public static Vector3 findFarthestNodeFromCenter(CyNetworkView
networkView, double distanceScale) {
return findFarthestNodeFromCenter(networkView,
findNetworkCenter(networkView, distanceScale), distanceScale);
}
+ /**
+ * Moves all of a given set of nodes by an amount specified by a
displacement vector.
+ *
+ * @param nodeIndices The indices of nodes to move
+ * @param networkView The network view containing the nodes
+ * @param distanceScale The distance scaling used to convert between
Cytoscape and renderer coordinates
+ * @param displacement The displacement vector
+ */
public static void displaceNodes(Set<Integer> nodeIndices,
CyNetworkView networkView, double distanceScale, Vector3 displacement) {
View<CyNode> nodeView;
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