Author: kono
Date: 2010-08-12 17:14:19 -0700 (Thu, 12 Aug 2010)
New Revision: 21369
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/ViewChangeEdit.java
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DGraphView.java
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DNodeView.java
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DingNavigationRenderingEngineFactory.java
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DingRenderingEngineFactory.java
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
core3/ding-presentation-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractGraphPartition.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
core3/session-impl/trunk/src/main/java/org/cytoscape/session/internal/CyNetworkManagerImpl.java
core3/work-api/trunk/src/main/java/org/cytoscape/work/undo/AbstractUndoableEdit.java
core3/work-api/trunk/src/main/java/org/cytoscape/work/undo/UndoSupport.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/DeleteAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/RedoAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/UndoAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/util/undo/UndoMonitor.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/BirdsEyeViewHandler.java
Log:
Work API was broken and all dependent modules were broken. I fixed it by
re-organized the import and package name. This type of refactoring should be
done by IDE.
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/ViewChangeEdit.java
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/ViewChangeEdit.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/ViewChangeEdit.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,12 +36,12 @@
package org.cytoscape.ding;
+import javax.swing.undo.AbstractUndoableEdit;
+
import org.cytoscape.ding.impl.ViewState;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
-import javax.swing.undo.AbstractUndoableEdit;
-
/**
* A Ding specific undoable edit.
*/
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -240,7 +240,7 @@
if (returnThis.numAnchors() > 0)
return returnThis;
- final CyNetwork graph = m_view.m_perspective;
+ final CyNetwork graph = m_view.networkModel;
final CyEdge edgeObj = graph.getEdge(edge);
if (edgeObj.getSource() == edgeObj.getTarget()) { // Self-edge.
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DGraphView.java
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -104,7 +104,7 @@
import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
import org.cytoscape.work.TaskManager;
import org.cytoscape.work.TunableInterceptor;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
import phoebe.PhoebeCanvasDropListener;
import phoebe.PhoebeCanvasDroppable;
@@ -174,7 +174,7 @@
/**
* The graph model that will be viewed.
*/
- CyNetwork m_perspective;
+ CyNetwork networkModel;
/**
* Holds the NodeView data for the nodes that are visible. This will
change
@@ -332,10 +332,7 @@
*/
Paint m_lastTexturePaint = null;
- CyNetworkView cyNetworkView;
- RootVisualLexicon rootLexicon;
-
Map<NodeViewTaskFactory, Map> nodeViewTFs;
Map<EdgeViewTaskFactory, Map> edgeViewTFs;
Map<NetworkViewTaskFactory, Map> emptySpaceTFs;
@@ -348,6 +345,11 @@
private final CyServiceRegistrar cyServiceRegistrar;
private final CyTableManager tableMgr;
+
+ // This is the view model. This should be immutable.
+ final CyNetworkView cyNetworkView;
+
+ private final RootVisualLexicon rootLexicon;
/**
* Creates a new DGraphView object.
@@ -355,7 +357,7 @@
* @param perspective
* The graph model that we'll be creating a view for.
*/
- public DGraphView(CyNetworkView view, CyDataTableFactory dataFactory,
+ public DGraphView(final CyNetworkView view, CyDataTableFactory
dataFactory,
CyRootNetworkFactory cyRoot, UndoSupport undo,
SpacialIndex2DFactory spacialFactory, RootVisualLexicon
vpc,
VisualLexicon dingLexicon,
@@ -365,7 +367,10 @@
TunableInterceptor interceptor, TaskManager manager,
CyServiceRegistrar cyServiceRegistrar, CyTableManager
tableMgr) {
- m_perspective = view.getModel();
+ if(view == null)
+ throw new IllegalArgumentException("Network View Model
cannot be null.");
+
+ networkModel = view.getModel();
cyNetworkView = view;
cyServiceRegistrar.registerService(this,
ViewChangeListener.class, new Properties());
@@ -383,16 +388,16 @@
CyDataTable nodeCAM = dataFactory.createTable("node view",
false);
nodeCAM.createColumn("hidden", Boolean.class, false);
- tableMgr.getTableMap("NODE", m_perspective).put("VIEW",
nodeCAM);
+ tableMgr.getTableMap("NODE", networkModel).put("VIEW", nodeCAM);
//m_perspective.getNodeCyDataTables().put("VIEW", nodeCAM);
CyDataTable edgeCAM = dataFactory.createTable("edge view",
false);
edgeCAM.createColumn("hidden", Boolean.class, false);
- tableMgr.getTableMap("EDGE", m_perspective).put("VIEW",
edgeCAM);
+ tableMgr.getTableMap("EDGE", networkModel).put("VIEW", edgeCAM);
//m_perspective.getEdgeCyDataTables().put("VIEW", edgeCAM);
// creating empty subnetworks
- m_drawPersp =
cyRoot.convert(m_perspective).addMetaNode().getSubNetwork();
+ m_drawPersp =
cyRoot.convert(networkModel).addMetaNode().getSubNetwork();
m_spacial = spacialFactory.createSpacialIndex2D();
m_spacialA = spacialFactory.createSpacialIndex2D();
@@ -406,10 +411,10 @@
m_defaultNodeXMax = m_defaultNodeXMin + DNodeView.DEFAULT_WIDTH;
m_defaultNodeYMax = m_defaultNodeYMin +
DNodeView.DEFAULT_HEIGHT;
m_networkCanvas = new InnerCanvas(m_lock, this, undo);
- m_backgroundCanvas = new ArbitraryGraphicsCanvas(m_perspective,
this,
+ m_backgroundCanvas = new ArbitraryGraphicsCanvas(networkModel,
this,
m_networkCanvas, Color.white, true, true);
addViewportChangeListener(m_backgroundCanvas);
- m_foregroundCanvas = new ArbitraryGraphicsCanvas(m_perspective,
this,
+ m_foregroundCanvas = new ArbitraryGraphicsCanvas(networkModel,
this,
m_networkCanvas, Color.white, true, false);
addViewportChangeListener(m_foregroundCanvas);
m_selectedNodes = new IntBTree();
@@ -417,12 +422,12 @@
m_selectedAnchors = new IntBTree();
// from DingNetworkView
- this.title = m_perspective.attrs().get("name", String.class);
+ this.title = networkModel.attrs().get("name", String.class);
- for (CyNode nn : m_perspective.getNodeList())
+ for (CyNode nn : networkModel.getNodeList())
addNodeView(nn);
- for (CyEdge ee : m_perspective.getEdgeList())
+ for (CyEdge ee : networkModel.getEdgeList())
addEdgeView(ee);
// read in visual properties from view obj
@@ -441,11 +446,11 @@
* @return The GraphPerspective that the view was created for.
*/
public CyNetwork getGraphPerspective() {
- return m_perspective;
+ return networkModel;
}
public CyNetwork getNetwork() {
- return m_perspective;
+ return networkModel;
}
/**
@@ -873,11 +878,11 @@
final CyNode nnode;
synchronized (m_lock) {
- nnode = m_perspective.getNode(nodeInx);
+ nnode = networkModel.getNode(nodeInx);
// We have to query edges in the m_structPersp, not
m_drawPersp
// because what if the node is hidden?
- hiddenEdgeInx = m_perspective.getAdjacentEdgeList(nnode,
+ hiddenEdgeInx = networkModel.getAdjacentEdgeList(nnode,
CyEdge.Type.ANY);
// This isn't an error. Only if the nodeInx is invalid
will
@@ -984,7 +989,7 @@
final DEdgeView returnThis = (DEdgeView)
m_edgeViewMap.remove(Integer
.valueOf(edgeInx));
- CyEdge eedge = m_perspective.getEdge(edgeInx);
+ CyEdge eedge = networkModel.getEdge(edgeInx);
if (returnThis == null) {
return returnThis;
@@ -1176,7 +1181,7 @@
*/
public List<EdgeView> getEdgeViewsList(CyNode oneNode, CyNode
otherNode) {
synchronized (m_lock) {
- List<CyEdge> edges =
m_perspective.getConnectingEdgeList(oneNode,
+ List<CyEdge> edges =
networkModel.getConnectingEdgeList(oneNode,
otherNode, CyEdge.Type.ANY);
if (edges == null) {
@@ -1215,8 +1220,8 @@
CyNode n1;
CyNode n2;
synchronized (m_lock) {
- n1 = m_perspective.getNode(oneNodeInx);
- n2 = m_perspective.getNode(otherNodeInx);
+ n1 = networkModel.getNode(oneNodeInx);
+ n2 = networkModel.getNode(otherNodeInx);
}
return getEdgeViewsList(n1, n2);
}
@@ -1324,7 +1329,7 @@
synchronized (m_lock) {
final DNodeView nView = (DNodeView) obj;
nodeInx = nView.getRootGraphIndex();
- nnode = m_perspective.getNode(nodeInx);
+ nnode = networkModel.getNode(nodeInx);
edges = m_drawPersp.getAdjacentEdgeList(nnode,
CyEdge.Type.ANY);
if (edges == null || edges.size() <= 0) {
@@ -1386,7 +1391,7 @@
synchronized (m_lock) {
nodeInx = nView.getRootGraphIndex();
- CyNode nnode = m_perspective.getNode(nodeInx);
+ CyNode nnode = networkModel.getNode(nodeInx);
if (nnode == null) {
return false;
@@ -1418,7 +1423,7 @@
CyEdge newEdge;
synchronized (m_lock) {
- final CyEdge edge =
m_perspective.getEdge(((DEdgeView) obj)
+ final CyEdge edge =
networkModel.getEdge(((DEdgeView) obj)
.getRootGraphIndex());
if (edge == null) {
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DNodeView.java
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DNodeView.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DNodeView.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -156,7 +156,7 @@
*/
public CyNode getNode() {
synchronized (m_view.m_lock) {
- return m_view.m_perspective.getNode(m_inx);
+ return m_view.networkModel.getNode(m_inx);
}
}
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DingNavigationRenderingEngineFactory.java
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DingNavigationRenderingEngineFactory.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DingNavigationRenderingEngineFactory.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -26,7 +26,7 @@
import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.work.TaskManager;
import org.cytoscape.work.TunableInterceptor;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
/**
* RenderingEngineFactory for Navigation.
@@ -77,13 +77,18 @@
edgeViewTFs = new HashMap<EdgeViewTaskFactory, Map>();
emptySpaceTFs = new HashMap<NetworkViewTaskFactory, Map>();
}
+
+
public RenderingEngine<CyNetwork> render(Object visualizationContainer,
View<CyNetwork> view) {
- if (visualizationContainer == null || view == null)
+ if (visualizationContainer == null)
throw new IllegalArgumentException(
- "Both paramerts for render method
should not be null.");
+ "Visualization container is null. This
should be an JComponent for this rendering engine.");
+ if (view == null)
+ throw new IllegalArgumentException(
+ "View Model is null.");
if (!(visualizationContainer instanceof JComponent)
|| !(view instanceof CyNetworkView))
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DingRenderingEngineFactory.java
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DingRenderingEngineFactory.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/DingRenderingEngineFactory.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -9,7 +9,6 @@
import javax.swing.JDesktopPane;
import javax.swing.JInternalFrame;
-import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyDataTableFactory;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyTableManager;
@@ -29,7 +28,7 @@
import org.cytoscape.view.presentation.RenderingEngineFactory;
import org.cytoscape.work.TaskManager;
import org.cytoscape.work.TunableInterceptor;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
public class DingRenderingEngineFactory implements
RenderingEngineFactory<CyNetwork>, NetworkViewChangedListener {
Modified:
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/ding-presentation-impl/trunk/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,42 +36,16 @@
package org.cytoscape.ding.impl;
-import org.cytoscape.graph.render.export.ImageImposter;
-import org.cytoscape.graph.render.immed.EdgeAnchors;
-import org.cytoscape.graph.render.immed.GraphGraphics;
-import org.cytoscape.graph.render.stateful.GraphLOD;
-import org.cytoscape.graph.render.stateful.GraphRenderer;
-import org.cytoscape.util.intr.IntEnumerator;
-import org.cytoscape.util.intr.IntHash;
-import org.cytoscape.util.intr.IntStack;
-import org.cytoscape.util.swing.JMenuTracker;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.ding.EdgeView;
-import org.cytoscape.ding.GraphViewChangeListener;
-import org.cytoscape.ding.NodeView;
-import org.cytoscape.ding.ViewChangeEdit;
-import org.cytoscape.work.UndoSupport;
-import org.cytoscape.view.model.View;
-import org.cytoscape.task.NodeViewTaskFactory;
-import org.cytoscape.task.EdgeViewTaskFactory;
-import org.cytoscape.task.NetworkViewTaskFactory;
-import org.cytoscape.work.TaskFactory;
-import org.cytoscape.work.Task;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.TaskManager;
-import org.cytoscape.work.TunableInterceptor;
-import phoebe.PhoebeCanvasDropEvent;
-import phoebe.PhoebeCanvasDropListener;
-import phoebe.PhoebeCanvasDroppable;
-
-import javax.swing.*;
-import java.awt.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.Image;
+import java.awt.Point;
+import java.awt.Rectangle;
import java.awt.datatransfer.Transferable;
import java.awt.dnd.DnDConstants;
import java.awt.dnd.DropTarget;
-import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.awt.event.KeyListener;
import java.awt.event.MouseEvent;
@@ -87,10 +61,31 @@
import java.util.Enumeration;
import java.util.Iterator;
import java.util.Vector;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Map;
+import javax.swing.JComponent;
+import javax.swing.TransferHandler;
+
+import org.cytoscape.ding.EdgeView;
+import org.cytoscape.ding.GraphViewChangeListener;
+import org.cytoscape.ding.NodeView;
+import org.cytoscape.ding.ViewChangeEdit;
+import org.cytoscape.graph.render.export.ImageImposter;
+import org.cytoscape.graph.render.immed.EdgeAnchors;
+import org.cytoscape.graph.render.immed.GraphGraphics;
+import org.cytoscape.graph.render.stateful.GraphLOD;
+import org.cytoscape.graph.render.stateful.GraphRenderer;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.util.intr.IntEnumerator;
+import org.cytoscape.util.intr.IntHash;
+import org.cytoscape.util.intr.IntStack;
+import org.cytoscape.work.undo.UndoSupport;
+
+import phoebe.PhoebeCanvasDropEvent;
+import phoebe.PhoebeCanvasDropListener;
+import phoebe.PhoebeCanvasDroppable;
+
// AJK: 04/26/06 END
/**
*
@@ -236,7 +231,7 @@
synchronized (m_lock) {
if (m_view.m_contentChanged ||
m_view.m_viewportChanged) {
- m_lastRenderDetail =
GraphRenderer.renderGraph(m_view.m_perspective,
+ m_lastRenderDetail =
GraphRenderer.renderGraph(m_view.networkModel,
m_view.m_spacial, m_lod[0],
m_view.m_nodeDetails,
m_view.m_edgeDetails, m_hash,
@@ -303,7 +298,7 @@
m_backgroundColor.getBlue(), alpha);
synchronized (m_lock) {
- GraphRenderer.renderGraph(m_view.m_perspective,
m_view.m_spacial,
+ GraphRenderer.renderGraph(m_view.networkModel,
m_view.m_spacial,
m_view.m_printLOD,
m_view.m_nodeDetails,
m_view.m_edgeDetails, m_hash,
new GraphGraphics(img, false),
backgroundColor, m_xCenter,
m_yCenter, m_scaleFactor);
@@ -324,7 +319,7 @@
m_backgroundColor.getBlue(), alpha);
synchronized (m_lock) {
- GraphRenderer.renderGraph(m_view.m_perspective,
m_view.m_spacial,
+ GraphRenderer.renderGraph(m_view.networkModel,
m_view.m_spacial,
m_view.m_printLOD,
m_view.m_nodeDetails,
m_view.m_edgeDetails, m_hash,
new GraphGraphics(img, false),
backgroundColor, m_xCenter,
m_yCenter, m_scaleFactor);
@@ -1163,7 +1158,7 @@
stack.empty();
//final FixedGraph graph = (FixedGraph) m_view.m_perspective;
- final CyNetwork graph = m_view.m_perspective;
+ final CyNetwork graph = m_view.networkModel;
if ((m_lastRenderDetail & GraphRenderer.LOD_HIGH_DETAIL) == 0) {
// We won't need to look up arrows and their sizes.
Modified:
core3/ding-presentation-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
core3/ding-presentation-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/ding-presentation-impl/trunk/src/main/resources/META-INF/spring/bundle-context.xml
2010-08-13 00:14:19 UTC (rev 21369)
@@ -13,6 +13,7 @@
http://www.springframework.org/schema/lang
http://www.springframework.org/schema/lang/spring-lang-2.5.xsd
http://www.springframework.org/schema/osgi
http://www.springframework.org/schema/osgi/spring-osgi-1.0.xsd";
default-lazy-init="false">
+ <import resource="bundle-context-osgi.xml" />
<context:annotation-config />
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractGraphPartition.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractGraphPartition.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractGraphPartition.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -1,14 +1,14 @@
/* vim: set ts=2: */
package org.cytoscape.view.layout;
+import java.util.ArrayList;
+import java.util.List;
+
import org.cytoscape.model.CyNode;
import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
-import java.util.ArrayList;
-import java.util.List;
-
/**
* An abstract class that handles the partitioning of graphs so that
* the partitions will be laid out individually.
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/AbstractLayout.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,25 +36,21 @@
*/
package org.cytoscape.view.layout;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.model.View;
-// TODO find a replacement
-//import org.cytoscape.view.ViewChangeEdit;
-import org.cytoscape.work.UndoSupport;
-
-import javax.swing.*;
-import java.awt.*;
+import java.awt.Dimension;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.undo.UndoSupport;
+
/**
* The AbstractLayout provides nice starting point for Layouts
* written for Cytoscape.
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -41,7 +41,7 @@
import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableValidator;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
/**
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,16 +36,16 @@
package csplugins.layout.algorithms;
+import java.util.Collection;
+import java.util.Iterator;
+
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.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
-import java.util.Collection;
-import java.util.Iterator;
-
/**
*
*/
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutAlgorithm.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -32,20 +32,17 @@
*/
package csplugins.layout.algorithms.bioLayout;
-import org.cytoscape.view.layout.EdgeWeighter;
-import org.cytoscape.view.layout.LayoutPartition;
-import org.cytoscape.view.layout.AbstractGraphPartition;
-import org.cytoscape.model.CyRow;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
-
-import javax.swing.*;
-import java.awt.*;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.List;
import java.util.Set;
-import java.util.HashSet;
+import org.cytoscape.view.layout.AbstractGraphPartition;
+import org.cytoscape.view.layout.EdgeWeighter;
+import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.undo.UndoSupport;
+
/**
* Superclass for the two bioLayout algorithms (KK and FR).
*
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -32,15 +32,15 @@
*/
package csplugins.layout.algorithms.bioLayout;
+import java.awt.Dimension;
+import java.util.ArrayList;
+
import org.cytoscape.view.layout.LayoutEdge;
import org.cytoscape.view.layout.LayoutNode;
import org.cytoscape.view.layout.LayoutPartition;
import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
-import java.awt.*;
-import java.util.ArrayList;
-
/**
* Lays out the nodes in a graph using a modification of the
Fruchterman-Rheingold
* algorithm.
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -32,22 +32,22 @@
*/
package csplugins.layout.algorithms.bioLayout;
-import org.cytoscape.view.layout.LayoutEdge;
-import org.cytoscape.view.layout.LayoutNode;
-import org.cytoscape.view.layout.LayoutPartition;
-import csplugins.layout.Profile;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
-
-import java.awt.*;
+import java.awt.Dimension;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
+import org.cytoscape.view.layout.LayoutEdge;
+import org.cytoscape.view.layout.LayoutNode;
+import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.undo.UndoSupport;
+import csplugins.layout.Profile;
+
+
/**
* Lays out the nodes in a graph using a modification of the Kamada-Kawai
* algorithm.
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,24 +36,23 @@
package csplugins.layout.algorithms.circularLayout;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.layout.AbstractGraphPartition;
import org.cytoscape.view.layout.LayoutEdge;
import org.cytoscape.view.layout.LayoutNode;
import org.cytoscape.view.layout.LayoutPartition;
-import org.cytoscape.view.layout.AbstractGraphPartition;
-import csplugins.layout.algorithms.hierarchicalLayout.Edge;
-import csplugins.layout.algorithms.hierarchicalLayout.Graph;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
-import org.cytoscape.model.CyNode;
import org.cytoscape.view.model.View;
import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.undo.UndoSupport;
-import javax.swing.*;
-import java.awt.*;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.LinkedList;
+import csplugins.layout.algorithms.hierarchicalLayout.Edge;
+import csplugins.layout.algorithms.hierarchicalLayout.Graph;
/**
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/AttributeCircleLayout.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -32,22 +32,21 @@
*/
package csplugins.layout.algorithms.graphPartition;
-import org.cytoscape.view.layout.AbstractGraphPartition;
-import org.cytoscape.view.layout.LayoutNode;
-import org.cytoscape.view.layout.LayoutPartition;
-import org.cytoscape.model.CyDataTable;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
-
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import java.util.HashSet;
+import org.cytoscape.view.layout.AbstractGraphPartition;
+import org.cytoscape.view.layout.LayoutNode;
+import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.undo.UndoSupport;
+
/**
*
*/
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -3,22 +3,21 @@
import static org.cytoscape.model.GraphObject.NODE;
-import org.cytoscape.view.layout.AbstractGraphPartition;
-import org.cytoscape.view.layout.LayoutNode;
-import org.cytoscape.view.layout.LayoutPartition;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.List;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTableManager;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.view.layout.AbstractGraphPartition;
+import org.cytoscape.view.layout.LayoutNode;
+import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.work.undo.UndoSupport;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.List;
-
/**
*
*/
Modified:
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
===================================================================
---
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/graphPartition/ISOMLayout.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -4,26 +4,26 @@
*/
package csplugins.layout.algorithms.graphPartition;
+import java.util.Iterator;
+import java.util.List;
+
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.view.layout.AbstractGraphPartition;
+import org.cytoscape.view.layout.LayoutNode;
+import org.cytoscape.view.layout.LayoutPartition;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.undo.UndoSupport;
+
import cern.colt.list.IntArrayList;
import cern.colt.map.OpenIntIntHashMap;
import cern.colt.map.OpenIntObjectHashMap;
import cern.colt.map.PrimeFinder;
import cern.colt.matrix.DoubleMatrix1D;
import cern.colt.matrix.impl.DenseDoubleMatrix1D;
-import org.cytoscape.view.layout.AbstractGraphPartition;
-import org.cytoscape.view.layout.LayoutNode;
-import org.cytoscape.view.layout.LayoutPartition;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
-import java.util.Iterator;
-import java.util.List;
-
-
/**
*
*/
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
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-cytoscape-impl/trunk/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -39,16 +39,6 @@
**/
package csplugins.layout.algorithms.hierarchicalLayout;
-import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.view.layout.AbstractLayout;
-import org.cytoscape.model.CyDataTableUtil;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
-import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.TwoDVisualLexicon;
-
import java.awt.geom.Point2D;
import java.util.Arrays;
import java.util.HashMap;
@@ -56,7 +46,17 @@
import java.util.LinkedList;
import java.util.List;
+import org.cytoscape.model.CyDataTableUtil;
+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.TaskMonitor;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.undo.UndoSupport;
+
class HierarchyFlowLayoutOrderNode implements Comparable {
/**
*
Modified:
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
===================================================================
---
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-jgraph-impl/trunk/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,14 +36,22 @@
package csplugins.layout;
+import java.awt.geom.Rectangle2D;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Map;
+import java.util.Set;
+
+import javax.swing.JPanel;
+
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
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.UndoSupport;
-
+import org.cytoscape.work.undo.UndoSupport;
import org.jgraph.JGraph;
import org.jgraph.graph.CellView;
import org.jgraph.graph.ConnectionSet;
@@ -66,16 +74,7 @@
import org.jgraph.plugins.layouts.SugiyamaLayoutAlgorithm;
import org.jgraph.plugins.layouts.TreeLayoutAlgorithm;
-import javax.swing.*;
-import java.awt.geom.Rectangle2D;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Set;
-
/**
*
*/
Modified:
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
===================================================================
---
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/layout-prefuse-impl/trunk/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,14 +36,21 @@
package org.cytoscape.prefuse.layouts.internal;
+import java.awt.Dimension;
+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 org.cytoscape.view.layout.AbstractGraphPartition;
import org.cytoscape.view.layout.EdgeWeighter;
import org.cytoscape.view.layout.LayoutEdge;
import org.cytoscape.view.layout.LayoutNode;
import org.cytoscape.view.layout.LayoutPartition;
-import org.cytoscape.view.layout.AbstractGraphPartition;
-import org.cytoscape.model.CyRow;
import org.cytoscape.work.Tunable;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
import prefuse.util.force.DragForce;
import prefuse.util.force.EulerIntegrator;
@@ -54,15 +61,6 @@
import prefuse.util.force.RungeKuttaIntegrator;
import prefuse.util.force.SpringForce;
-import javax.swing.*;
-import java.awt.*;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.HashSet;
-
enum Integrators{
RUNGEKUTTA("RUNGEKUTTA"),
EULER("EULER");
Modified:
core3/session-impl/trunk/src/main/java/org/cytoscape/session/internal/CyNetworkManagerImpl.java
===================================================================
---
core3/session-impl/trunk/src/main/java/org/cytoscape/session/internal/CyNetworkManagerImpl.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/session-impl/trunk/src/main/java/org/cytoscape/session/internal/CyNetworkManagerImpl.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -63,6 +63,11 @@
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.presentation.RenderingEngine;
+/**
+ * An implementation of CyNetworkManager.
+ *
+ *
+ */
public class CyNetworkManagerImpl implements CyNetworkManager {
private final Map<Long, CyNetworkView> networkViewMap;
@@ -71,22 +76,26 @@
private final List<CyNetworkView> selectedNetworkViews;
private final List<CyNetwork> selectedNetworks;
- private final CyEventHelper eh;
+ private final CyEventHelper cyEventHelper;
private CyNetwork currentNetwork;
private CyNetworkView currentNetworkView;
+ private RenderingEngine<CyNetwork> currentRenderer;
+
- private RenderingEngine<CyNetwork> currentPresentation;
-
- public CyNetworkManagerImpl(final CyEventHelper eh) {
+ /**
+ *
+ * @param cyEventHelper
+ */
+ public CyNetworkManagerImpl(final CyEventHelper cyEventHelper) {
networkMap = new HashMap<Long, CyNetwork>();
networkViewMap = new HashMap<Long, CyNetworkView>();
selectedNetworkViews = new LinkedList<CyNetworkView>();
selectedNetworks = new LinkedList<CyNetwork>();
currentNetwork = null;
currentNetworkView = null;
- this.currentPresentation = null;
- this.eh = eh;
+ this.currentRenderer = null;
+ this.cyEventHelper = cyEventHelper;
}
public synchronized CyNetwork getCurrentNetwork() {
@@ -107,7 +116,7 @@
selectedNetworks.add(currentNetwork);
}
- eh.fireSynchronousEvent(new
SetCurrentNetworkEvent(CyNetworkManagerImpl.this,currentNetwork));
+ cyEventHelper.fireSynchronousEvent(new
SetCurrentNetworkEvent(CyNetworkManagerImpl.this,currentNetwork));
}
public synchronized Set<CyNetwork> getNetworkSet() {
@@ -157,7 +166,7 @@
selectedNetworkViews.add(currentNetworkView);
}
- eh.fireSynchronousEvent(new
SetCurrentNetworkViewEvent(CyNetworkManagerImpl.this,currentNetworkView));
+ cyEventHelper.fireSynchronousEvent(new
SetCurrentNetworkViewEvent(CyNetworkManagerImpl.this,currentNetworkView));
}
public synchronized List<CyNetworkView> getSelectedNetworkViews() {
@@ -187,7 +196,7 @@
}
}
- eh.fireSynchronousEvent(new
SetSelectedNetworkViewsEvent(CyNetworkManagerImpl.this, new
ArrayList<CyNetworkView>(selectedNetworkViews)));
+ cyEventHelper.fireSynchronousEvent(new
SetSelectedNetworkViewsEvent(CyNetworkManagerImpl.this, new
ArrayList<CyNetworkView>(selectedNetworkViews)));
}
public synchronized List<CyNetwork> getSelectedNetworks() {
@@ -215,7 +224,7 @@
selectedNetworks.add(cn);
}
- eh.fireSynchronousEvent(new
SetSelectedNetworksEvent(CyNetworkManagerImpl.this, new
ArrayList<CyNetwork>(selectedNetworks)));
+ cyEventHelper.fireSynchronousEvent(new
SetSelectedNetworksEvent(CyNetworkManagerImpl.this, new
ArrayList<CyNetwork>(selectedNetworks)));
}
// TODO
@@ -233,7 +242,7 @@
// TODO firing an event from within a lock!!!!
final CyNetwork toDestroy = network;
- eh.fireSynchronousEvent(new
NetworkAboutToBeDestroyedEvent(CyNetworkManagerImpl.this, toDestroy));
+ cyEventHelper.fireSynchronousEvent(new
NetworkAboutToBeDestroyedEvent(CyNetworkManagerImpl.this, toDestroy));
selectedNetworks.remove(network);
for (CyNode n : network.getNodeList())
@@ -262,7 +271,7 @@
}
// lets everyone know that *A* network is gone
- eh.fireSynchronousEvent(new NetworkDestroyedEvent(
CyNetworkManagerImpl.this ));
+ cyEventHelper.fireSynchronousEvent(new NetworkDestroyedEvent(
CyNetworkManagerImpl.this ));
}
public void destroyNetworkView(CyNetworkView view) {
@@ -279,7 +288,7 @@
// TODO firing an event from within a lock!!!!
final CyNetworkView toDestroy = view;
- eh.fireSynchronousEvent(new
NetworkViewAboutToBeDestroyedEvent(CyNetworkManagerImpl.this, toDestroy));
+ cyEventHelper.fireSynchronousEvent(new
NetworkViewAboutToBeDestroyedEvent(CyNetworkManagerImpl.this, toDestroy));
selectedNetworkViews.remove(view);
@@ -303,20 +312,22 @@
view = null;
}
- eh.fireSynchronousEvent(new NetworkViewDestroyedEvent(
CyNetworkManagerImpl.this ));
+ cyEventHelper.fireSynchronousEvent(new
NetworkViewDestroyedEvent( CyNetworkManagerImpl.this ));
}
+
public void addNetwork(final CyNetwork network) {
if (network == null)
- throw new NullPointerException("network is null");
+ throw new NullPointerException("Network is null");
synchronized (this) {
networkMap.put(network.getSUID(), network);
}
- eh.fireSynchronousEvent(new
NetworkAddedEvent(CyNetworkManagerImpl.this, network));
+ cyEventHelper.fireSynchronousEvent(new
NetworkAddedEvent(CyNetworkManagerImpl.this, network));
}
+
public void addNetworkView(final CyNetworkView view) {
if (view == null)
throw new NullPointerException("view is null");
@@ -331,14 +342,14 @@
networkViewMap.put(networkId, view);
}
- eh.fireSynchronousEvent(new NetworkViewAddedEvent(
CyNetworkManagerImpl.this, view));
+ cyEventHelper.fireSynchronousEvent(new NetworkViewAddedEvent(
CyNetworkManagerImpl.this, view));
}
public RenderingEngine getCurrentRenderingEngine() {
- return currentPresentation;
+ return currentRenderer;
}
public void setCurrentRenderingEngine(RenderingEngine engine) {
- this.currentPresentation = engine;
+ this.currentRenderer = engine;
}
}
Modified:
core3/work-api/trunk/src/main/java/org/cytoscape/work/undo/AbstractUndoableEdit.java
===================================================================
---
core3/work-api/trunk/src/main/java/org/cytoscape/work/undo/AbstractUndoableEdit.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
core3/work-api/trunk/src/main/java/org/cytoscape/work/undo/AbstractUndoableEdit.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -27,7 +27,7 @@
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
-package cytoscape.org.work.undo;
+package org.cytoscape.work.undo;
import javax.swing.undo.CannotUndoException;
Modified:
core3/work-api/trunk/src/main/java/org/cytoscape/work/undo/UndoSupport.java
===================================================================
--- core3/work-api/trunk/src/main/java/org/cytoscape/work/undo/UndoSupport.java
2010-08-12 23:38:49 UTC (rev 21368)
+++ core3/work-api/trunk/src/main/java/org/cytoscape/work/undo/UndoSupport.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -25,7 +25,7 @@
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
-package org.cytoscape.work;
+package org.cytoscape.work.undo;
import javax.swing.undo.UndoManager;
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/DeleteAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/DeleteAction.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/DeleteAction.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -28,7 +28,6 @@
*/
package cytoscape.internal.actions;
-import org.cytoscape.session.CyNetworkManager;
import java.awt.event.ActionEvent;
import java.awt.event.KeyEvent;
import java.util.HashSet;
@@ -44,10 +43,10 @@
import org.cytoscape.model.GraphObject;
import org.cytoscape.model.subnetwork.CyRootNetworkFactory;
import org.cytoscape.model.subnetwork.CySubNetwork;
+import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.work.UndoSupport;
+import org.cytoscape.work.undo.UndoSupport;
-import cytoscape.Cytoscape;
import cytoscape.view.CytoscapeAction;
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/RedoAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/RedoAction.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/RedoAction.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,17 +36,18 @@
*/
package cytoscape.internal.actions;
-import cytoscape.view.CytoscapeAction;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
-import org.cytoscape.work.UndoSupport;
-import org.cytoscape.session.CyNetworkManager;
-
-import javax.swing.*;
+import javax.swing.Action;
import javax.swing.event.MenuEvent;
import javax.swing.undo.CannotUndoException;
-import java.awt.event.ActionEvent;
-import java.awt.event.KeyEvent;
+import org.cytoscape.session.CyNetworkManager;
+import org.cytoscape.work.undo.UndoSupport;
+
+import cytoscape.view.CytoscapeAction;
+
/**
* An action that calls redo for the most recent edit in the
* undoable edit stack.
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/UndoAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/UndoAction.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/actions/UndoAction.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,17 +36,18 @@
*/
package cytoscape.internal.actions;
-import cytoscape.view.CytoscapeAction;
-import org.cytoscape.session.CyNetworkManager;
+import java.awt.event.ActionEvent;
+import java.awt.event.KeyEvent;
-import org.cytoscape.work.UndoSupport;
-
-import javax.swing.*;
+import javax.swing.Action;
import javax.swing.event.MenuEvent;
import javax.swing.undo.CannotUndoException;
-import java.awt.event.ActionEvent;
-import java.awt.event.KeyEvent;
+import org.cytoscape.session.CyNetworkManager;
+import org.cytoscape.work.undo.UndoSupport;
+
+import cytoscape.view.CytoscapeAction;
+
/**
* An action that calls undo for the most recent edit in the
* undoable edit stack.
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/util/undo/UndoMonitor.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/util/undo/UndoMonitor.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/util/undo/UndoMonitor.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -36,13 +36,12 @@
*/
package cytoscape.internal.util.undo;
-import org.cytoscape.work.UndoSupport;
+import java.util.Properties;
import org.cytoscape.session.events.SetCurrentNetworkViewEvent;
import org.cytoscape.session.events.SetCurrentNetworkViewListener;
+import org.cytoscape.work.undo.UndoSupport;
-import java.util.Properties;
-
/**
* This class monitors the undoable edit stack and implements whatever
* discard policy we might have. Currently, we discard all edits if
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/BirdsEyeViewHandler.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/BirdsEyeViewHandler.java
2010-08-12 23:38:49 UTC (rev 21368)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/BirdsEyeViewHandler.java
2010-08-13 00:14:19 UTC (rev 21369)
@@ -115,15 +115,17 @@
* The event triggering this method.
*/
public void handleEvent(SetCurrentNetworkEvent e) {
- RenderingEngine<CyNetwork> engine = bevFactory.render(bevHolder,
- netmgr.getCurrentNetworkView());
- setFocus();
+ //FIXME
+// RenderingEngine<CyNetwork> engine = bevFactory.render(bevHolder,
+// netmgr.getCurrentNetworkView());
+// setFocus();
}
public void handleEvent(SetCurrentNetworkViewEvent e) {
- RenderingEngine<CyNetwork> engine = bevFactory.render(bevHolder,
- netmgr.getCurrentNetworkView());
- setFocus();
+ //FIXME
+// RenderingEngine<CyNetwork> engine = bevFactory.render(bevHolder,
+// netmgr.getCurrentNetworkView());
+// setFocus();
}
public void handleEvent(NetworkViewDestroyedEvent e) {
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