Author: paperwing
Date: 2012-02-06 11:24:33 -0800 (Mon, 06 Feb 2012)
New Revision: 28197
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/presentation-impl.patch
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/swing-application-impl.patch
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/vizmap-gui-impl.patch
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/WindBirdsEyeRenderingEngine.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/WindMainRenderingEngine.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/coordinator/ViewingCoordinator.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/input/NetworkChangeInputHandler.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderArcEdgesProcedure.java
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderNodesProcedure.java
Log:
Updated patches for VizMapper to adjust position of nodes in the visual
property preview; removed System.println() statements; decreased apparent
shininess of edges to give a slightly cleaner appearance
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/presentation-impl.patch
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/presentation-impl.patch
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/presentation-impl.patch
2012-02-06 19:24:33 UTC (rev 28197)
@@ -1,6 +1,6 @@
Index:
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
===================================================================
----
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
(revision 28020)
+---
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
(revision 28196)
+++
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/RenderingEngineManagerImpl.java
(working copy)
@@ -19,7 +19,7 @@
private final Map<View<?>, RenderingEngine<?>> renderingEngineMap;
@@ -13,7 +13,7 @@
Index:
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
===================================================================
----
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
(revision 28020)
+---
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
(revision 28196)
+++
presentation-impl/src/main/java/org/cytoscape/view/presentation/internal/CyActivator.java
(working copy)
@@ -25,7 +25,6 @@
registerService(bc,renderingEngineManager,RenderingEngineManager.class,
renderingEngineManagerProps);
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/swing-application-impl.patch
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/swing-application-impl.patch
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/swing-application-impl.patch
2012-02-06 19:24:33 UTC (rev 28197)
@@ -1,8 +1,8 @@
Index:
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
===================================================================
----
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
(revision 28020)
+---
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
(revision 28196)
+++
swing-application-impl/src/main/java/org/cytoscape/internal/CyActivator.java
(working copy)
-@@ -169,10 +169,10 @@
+@@ -171,10 +171,10 @@
SubmenuTaskManager submenuTaskManagerServiceRef =
getService(bc, SubmenuTaskManager.class);
RenderingEngineFactory dingRenderingEngineFactoryServiceRef =
getService(bc,
RenderingEngineFactory.class,
@@ -17,9 +17,9 @@
BookmarksUtil bookmarksUtilServiceRef = getService(bc,
BookmarksUtil.class);
Index:
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
===================================================================
----
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
(revision 28020)
+---
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
(revision 28196)
+++
swing-application-impl/src/main/java/org/cytoscape/internal/view/NetworkViewManager.java
(working copy)
-@@ -123,7 +123,7 @@
+@@ -112,7 +112,7 @@
// TODO: for now, use this as default. But in the future, we should
provide
// UI to select presentation.
@@ -28,4 +28,3 @@
private final CyNetworkViewManager networkViewManager;
private final CyApplicationManager applicationManager;
-
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/vizmap-gui-impl.patch
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/vizmap-gui-impl.patch
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/misc/cytoscape-patches/vizmap-gui-impl.patch
2012-02-06 19:24:33 UTC (rev 28197)
@@ -1,6 +1,6 @@
Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
===================================================================
----
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
(revision 28020)
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
(revision 28196)
+++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewEditorImpl.java
(working copy)
@@ -201,7 +201,7 @@
@@ -22,9 +22,9 @@
propSet.add(vp);
Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
===================================================================
----
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
(revision 28020)
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
(revision 28196)
+++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/bypass/BypassManager.java
(working copy)
-@@ -44,7 +44,7 @@
+@@ -40,7 +40,7 @@
}
public void addBypass(RenderingEngineFactory<?> factory, Map props) {
@@ -33,9 +33,61 @@
return;
final VisualLexicon lexicon = factory.getVisualLexicon();
+Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
+===================================================================
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
(revision 28196)
++++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/DefaultViewPanelImpl.java
(working copy)
+@@ -57,6 +57,7 @@
+ import org.cytoscape.view.presentation.RenderingEngine;
+ import org.cytoscape.view.presentation.RenderingEngineFactory;
+ import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
++import org.cytoscape.view.presentation.property.RichVisualLexicon;
+ import org.cytoscape.view.vizmap.VisualStyle;
+ import org.cytoscape.view.vizmap.gui.DefaultViewPanel;
+ import org.cytoscape.view.vizmap.gui.SelectedVisualStyleManager;
+@@ -124,6 +125,10 @@
+ final CyNode source = dummyNet.addNode();
+ final CyNode target = dummyNet.addNode();
+
++ // Add dummy nodes to balance the z coordinates of the other
nodes
++ final CyNode balance1 = dummyNet.addNode();
++ final CyNode balance2 = dummyNet.addNode();
++
+ dummyNet.getRow(source).set(CyTableEntry.NAME, "Source");
+ dummyNet.getRow(target).set(CyTableEntry.NAME, "Target");
+
+@@ -135,11 +140,23 @@
+ .createNetworkView(dummyNet);
+
+ // Set node locations
+-
dummyview.getNodeView(source).setVisualProperty(NODE_X_LOCATION, 0d);
+-
dummyview.getNodeView(source).setVisualProperty(NODE_Y_LOCATION, 0d);
+-
dummyview.getNodeView(target).setVisualProperty(NODE_X_LOCATION, 150d);
+-
dummyview.getNodeView(target).setVisualProperty(NODE_Y_LOCATION, 20d);
+-
++
dummyview.getNodeView(source).setVisualProperty(NODE_X_LOCATION, -60.0);
++
dummyview.getNodeView(source).setVisualProperty(NODE_Y_LOCATION, -50.0);
++
dummyview.getNodeView(source).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
0.0);
++
++
dummyview.getNodeView(target).setVisualProperty(NODE_X_LOCATION, 60.0);
++
dummyview.getNodeView(target).setVisualProperty(NODE_Y_LOCATION, 50.0);
++
dummyview.getNodeView(target).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
0.0);
++
++
dummyview.getNodeView(balance1).setVisualProperty(NODE_X_LOCATION, -500.0);
++
dummyview.getNodeView(balance1).setVisualProperty(NODE_Y_LOCATION, -500.0);
++
dummyview.getNodeView(balance1).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
-450.0);
++
++
dummyview.getNodeView(balance2).setVisualProperty(NODE_X_LOCATION, 500.0);
++
dummyview.getNodeView(balance2).setVisualProperty(NODE_Y_LOCATION, 500.0);
++
dummyview.getNodeView(balance2).setVisualProperty(RichVisualLexicon.NODE_Z_LOCATION,
-450.0);
++
++
+ final VisualStyle currentStyle =
selectedManager.getCurrentVisualStyle();
+ currentStyle.apply(dummyview);
+
Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
===================================================================
----
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
(revision 28020)
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
(revision 28196)
+++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/CyActivator.java
(working copy)
@@ -74,8 +74,8 @@
CyApplicationConfiguration cyApplicationConfigurationServiceRef
= getService(bc,CyApplicationConfiguration.class);
@@ -50,7 +102,7 @@
CyApplicationManager cyApplicationManagerServiceRef =
getService(bc,CyApplicationManager.class);
Index:
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VisualPropertyFilter.java
===================================================================
----
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VisualPropertyFilter.java
(revision 28020)
+---
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VisualPropertyFilter.java
(revision 28196)
+++
vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/util/VisualPropertyFilter.java
(working copy)
@@ -12,8 +12,8 @@
@@ -65,7 +117,7 @@
Index: vizmap-gui-impl/src/main/resources/default_vizmap.xml
===================================================================
---- vizmap-gui-impl/src/main/resources/default_vizmap.xml (revision 28020)
+--- vizmap-gui-impl/src/main/resources/default_vizmap.xml (revision 28196)
+++ vizmap-gui-impl/src/main/resources/default_vizmap.xml (working copy)
@@ -458,7 +458,7 @@
<visualProperty name="NODE_TRANSPARENCY" default="255"/>
@@ -76,3 +128,21 @@
<visualProperty name="NODE_CUSTOMPAINT_5"
default="org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty$VisualizableImpl@69d41410"/>
<visualProperty name="NODE_CUSTOMPAINT_6"
default="org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty$VisualizableImpl@69d41410"/>
<visualProperty name="NODE_CUSTOMPAINT_7"
default="org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty$VisualizableImpl@69d41410"/>
+@@ -470,7 +470,7 @@
+ <visualProperty name="NODE_LABEL_FONT_FACE"
default="Dialog,plain,12"/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_SIZE_7" default="50.0"/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_8"/>
+- <visualProperty name="NODE_DEPTH" default="0.0"/>
++ <visualProperty name="NODE_DEPTH" default="70.0"/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_SIZE_9" default="50.0"/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_5"/>
+ <visualProperty name="NODE_SELECTED" default="false"/>
+@@ -495,7 +495,7 @@
+ <visualProperty name="NODE_TOOLTIP" default=""/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_POSITION_9"
default="C,C,c,0.00,0.00"/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_SIZE_6" default="50.0"/>
+- <visualProperty name="NODE_HEIGHT" default="40.0"/>
++ <visualProperty name="NODE_HEIGHT" default="70.0"/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_7"/>
+ <visualProperty name="NODE_CUSTOMPAINT_2"
default="org.cytoscape.view.presentation.property.DefaultVisualizableVisualProperty$VisualizableImpl@69d41410"/>
+ <visualProperty name="NODE_CUSTOMGRAPHICS_POSITION_6"
default="C,C,c,0.00,0.00"/>
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/WindBirdsEyeRenderingEngine.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/WindBirdsEyeRenderingEngine.java
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/WindBirdsEyeRenderingEngine.java
2012-02-06 19:24:33 UTC (rev 28197)
@@ -43,8 +43,6 @@
public WindBirdsEyeRenderingEngine(Object container, View<CyNetwork>
viewModel,
VisualLexicon visualLexicon) {
super(container, viewModel, visualLexicon);
-
- System.out.println("New WindBirdsEye engine: " + this);
}
@Override
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/WindMainRenderingEngine.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/WindMainRenderingEngine.java
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/WindMainRenderingEngine.java
2012-02-06 19:24:33 UTC (rev 28197)
@@ -41,8 +41,6 @@
public WindMainRenderingEngine(Object container, View<CyNetwork>
viewModel,
VisualLexicon visualLexicon) {
super(container, viewModel, visualLexicon);
-
- System.out.println("New WindMain engine: " + this);
}
@Override
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/coordinator/ViewingCoordinator.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/coordinator/ViewingCoordinator.java
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/coordinator/ViewingCoordinator.java
2012-02-06 19:24:33 UTC (rev 28197)
@@ -155,23 +155,11 @@
// Claim by a main window rendering object
public void claimMain() {
mainStatus = CoordinatorStatus.CLAIMED_AND_LINKED;
-
- //debug
- System.out.println("Coordinator main claimed: " + this);
- if (isBirdsEyeClaimed()) {
- System.out.println("Coordinator setup: " + this);
- }
}
// Claim by a birds eye view rendering object
public void claimBirdsEye() {
birdsEyeStatus = CoordinatorStatus.CLAIMED_AND_LINKED;
-
- //debug
- System.out.println("Coordinator birdsEye claimed: " + this);
- if (isMainClaimed()) {
- System.out.println("Coordinator setup: " + this);
- }
}
public boolean isMainClaimed() {
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/input/NetworkChangeInputHandler.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/input/NetworkChangeInputHandler.java
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/input/NetworkChangeInputHandler.java
2012-02-06 19:24:33 UTC (rev 28197)
@@ -43,9 +43,7 @@
Vector3 projection = GeometryToolkit.convertScreenTo3d(
mouse.x(), mouse.y(),
graphicsData.getScreenWidth(),
graphicsData.getScreenHeight(),
NODE_PLACEMENT_DISTANCE, camera);
-
- System.out.println("Node created at: " + projection);
-
+
CyNode added = networkView.getModel().addNode();
networkView.updateView();
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderArcEdgesProcedure.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderArcEdgesProcedure.java
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderArcEdgesProcedure.java
2012-02-06 19:24:33 UTC (rev 28197)
@@ -1,6 +1,7 @@
package org.cytoscape.paperwing.internal.rendering;
import java.awt.Color;
+import java.nio.FloatBuffer;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
@@ -29,7 +30,7 @@
public class RenderArcEdgesProcedure implements ReadOnlyGraphicsProcedure {
- private static final float SEGMENT_RADIUS = 0.007f; // 0.007 default
+ private static final float SEGMENT_RADIUS = 0.013f; // 0.007 default
private static final int SEGMENT_SLICES = 4;
private static final int SEGMENT_STACKS = 1;
@@ -42,7 +43,7 @@
private static final RenderColor DEFAULT_HOVER_COLOR =
new RenderColor(0.5, 0.5, 0.7);
- private static final float DASHED_EDGE_RADIUS = 0.006f;
+ private static final float DASHED_EDGE_RADIUS = 0.012f;
private static final float DASHED_EDGE_LENGTH = 0.05f;
private static final float DASHED_EDGE_SPACING = 0.07f;
@@ -173,6 +174,11 @@
CyNetworkView networkView = graphicsData.getNetworkView();
GL2 gl = graphicsData.getGlContext();
+ float[] specularReflection = { 0.1f, 0.1f, 0.1f, 1.0f };
+ gl.glMaterialfv(GL2.GL_FRONT, GL2.GL_SPECULAR,
+ FloatBuffer.wrap(specularReflection));
+ gl.glMateriali(GL2.GL_FRONT, GL2.GL_SHININESS, 1);
+
double distanceScale = graphicsData.getDistanceScale();
Set<EdgeViewContainer> edgeViewContainers =
analyzeEdges(networkView, distanceScale);
Modified:
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderNodesProcedure.java
===================================================================
---
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderNodesProcedure.java
2012-02-06 04:31:59 UTC (rev 28196)
+++
csplugins/trunk/toronto/yuedong/paperwing-impl/src/main/java/org/cytoscape/paperwing/internal/rendering/RenderNodesProcedure.java
2012-02-06 19:24:33 UTC (rev 28197)
@@ -1,6 +1,7 @@
package org.cytoscape.paperwing.internal.rendering;
import java.awt.Color;
+import java.nio.FloatBuffer;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -34,8 +35,8 @@
new RenderColor(0.5, 0.5, 0.7);
/** The default radius of the spherical nodes */
- private static final float NODE_SIZE_RADIUS = 0.102f; // 0.015f
-
+ private static final float NODE_SIZE_RADIUS = 0.322f; // 0.015f
+
private Map<NodeShape, ShapeType> cytoscapeShapeMap;
private ScalableShapeDrawer shapeDrawer;
@@ -59,6 +60,11 @@
public void execute(GraphicsData graphicsData) {
GL2 gl = graphicsData.getGlContext();
+ float[] specularReflection = { 0.46f, 0.46f, 0.46f, 1.0f };
+ gl.glMaterialfv(GL2.GL_FRONT, GL2.GL_SPECULAR,
+ FloatBuffer.wrap(specularReflection));
+ gl.glMateriali(GL2.GL_FRONT, GL2.GL_SHININESS, 21);
+
CyNetworkView networkView = graphicsData.getNetworkView();
float distanceScale = graphicsData.getDistanceScale();
Set<Integer> selectedNodeIndices =
graphicsData.getSelectionData()
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