Author: kono
Date: 2012-05-04 17:36:53 -0700 (Fri, 04 May 2012)
New Revision: 29126
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/LayoutPartition.java
core3/api/trunk/session-api/src/main/java/org/cytoscape/session/CySession.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/MergeNetworkEdit.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/customgraphicsmgr/internal/ui/CustomGraphicsManagerDialog.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/AddEdgeStateMonitor.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DNodeDetails.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/ViewState.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/ClipboardManagerImpl.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CopyTaskFactory.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CutTaskFactory.java
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/PasteTask.java
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/QuickFindImpl.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/AbstractSessionReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/DirNetworkAnalyzer.java
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/model/AttributeMappingImpl.java
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/model/MatchingAttributeImpl.java
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/AttributeSetManager.java
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
Log:
fixes #928 All Maps using CyNode, CyEdge, and CyNetwork as key are replaced
with WeakHashMap. This means once Graph Objects are destroyed, managers will
release the values.
Modified:
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/LayoutPartition.java
===================================================================
---
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/LayoutPartition.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/api/trunk/layout-api/src/main/java/org/cytoscape/view/layout/LayoutPartition.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -41,6 +41,7 @@
import java.util.ListIterator;
import java.util.Map;
import java.util.Random;
+import java.util.WeakHashMap;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
@@ -95,7 +96,7 @@
public LayoutPartition(final int nodeCount, final int edgeCount) {
nodeList = new ArrayList<LayoutNode>(nodeCount);
edgeList = new ArrayList<LayoutEdge>(edgeCount);
- nodeToLayoutNode = new HashMap<CyNode,LayoutNode>(nodeCount);
+ nodeToLayoutNode = new
WeakHashMap<CyNode,LayoutNode>(nodeCount);
partitionNumber = 1;
}
@@ -118,7 +119,7 @@
// Initialize
nodeList = new
ArrayList<LayoutNode>(networkView.getModel().getNodeCount());
edgeList = new
ArrayList<LayoutEdge>(networkView.getModel().getEdgeCount());
- nodeToLayoutNode = new
HashMap<CyNode,LayoutNode>(networkView.getModel().getNodeCount());
+ nodeToLayoutNode = new
WeakHashMap<CyNode,LayoutNode>(networkView.getModel().getNodeCount());
// Now, walk the iterators and fill in the values
nodeListInitialize(networkView, nodeSet);
Modified:
core3/api/trunk/session-api/src/main/java/org/cytoscape/session/CySession.java
===================================================================
---
core3/api/trunk/session-api/src/main/java/org/cytoscape/session/CySession.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/api/trunk/session-api/src/main/java/org/cytoscape/session/CySession.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -34,6 +34,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.WeakHashMap;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -83,7 +84,7 @@
networks = Collections.unmodifiableSet( b.networks == null ?
new HashSet<CyNetwork>() : b.networks );
netViews = Collections.unmodifiableSet( b.netViews == null ?
new HashSet<CyNetworkView>() : b.netViews );
tables = Collections.unmodifiableSet( b.tables == null ? new
HashSet<CyTableMetadata>() : b.tables );
- vsMap = Collections.unmodifiableMap( b.vsMap == null ? new
HashMap<CyNetworkView, String>() : b.vsMap );
+ vsMap = Collections.unmodifiableMap( b.vsMap == null ? new
WeakHashMap<CyNetworkView, String>() : b.vsMap );
properties = Collections.unmodifiableSet( b.properties == null
? new HashSet<CyProperty<?>>() : b.properties );
visualStyles = Collections.unmodifiableSet( b.visualStyles ==
null ? new HashSet<VisualStyle>() : b.visualStyles );
appFiles = Collections.unmodifiableMap( b.appFiles == null ?
new HashMap<String, List<File>>() : b.appFiles );
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CloneNetworkTask.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -33,6 +33,7 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.WeakHashMap;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyColumn;
@@ -125,8 +126,8 @@
}
private void cloneNodes(CyNetwork origNet, CyNetwork newNet) {
- orig2NewNodeMap = new HashMap<CyNode, CyNode>();
- new2OrigNodeMap = new HashMap<CyNode, CyNode>();
+ orig2NewNodeMap = new WeakHashMap<CyNode, CyNode>();
+ new2OrigNodeMap = new WeakHashMap<CyNode, CyNode>();
for (final CyNode origNode : origNet.getNodeList()) {
final CyNode newNode = newNet.addNode();
orig2NewNodeMap.put(origNode, newNode);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/creation/CreateNetworkViewEdit.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -12,6 +12,7 @@
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
+import java.util.WeakHashMap;
import org.cytoscape.event.CyEventHelper;
import org.cytoscape.model.CyNetwork;
@@ -78,7 +79,7 @@
networkScaleFactor =
view.getVisualProperty(NETWORK_SCALE_FACTOR);
final Collection<View<CyNode>> nodeViews = view.getNodeViews();
- nodesAndLocations = new HashMap<CyNode,
NodeLocations>(nodeViews.size());
+ nodesAndLocations = new WeakHashMap<CyNode,
NodeLocations>(nodeViews.size());
for (final View<CyNode> nodeView : nodeViews)
nodesAndLocations.put(nodeView.getModel(), new
NodeLocations(nodeView));
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/MergeNetworkEdit.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/MergeNetworkEdit.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/cytoscape/MergeNetworkEdit.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -35,8 +35,8 @@
import java.awt.geom.Point2D;
import java.util.Collection;
-import java.util.HashMap;
import java.util.Map;
+import java.util.WeakHashMap;
import org.cytoscape.cpath2.internal.CPath2Factory;
import org.cytoscape.cpath2.internal.util.AttributeUtil;
@@ -90,7 +90,7 @@
this.cyNetwork = cyNetwork;
this.cyEdges = cyEdges;
- this.cyNodes = new HashMap<CyNode, Point2D.Double>();
+ this.cyNodes = new WeakHashMap<CyNode, Point2D.Double>();
final Collection<CyNetworkView> views =
factory.getCyNetworkViewManager().getNetworkViews(cyNetwork);
CyNetworkView view = null;
if(views.size() != 0)
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/customgraphicsmgr/internal/ui/CustomGraphicsManagerDialog.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/customgraphicsmgr/internal/ui/CustomGraphicsManagerDialog.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/customgraphicsmgr/internal/ui/CustomGraphicsManagerDialog.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -1,7 +1,6 @@
package org.cytoscape.ding.customgraphicsmgr.internal.ui;
import java.awt.Dimension;
-import java.awt.Frame;
import java.awt.image.BufferedImage;
import java.io.File;
import java.io.IOException;
@@ -18,7 +17,6 @@
import org.cytoscape.ding.customgraphics.CustomGraphicsManager;
import org.cytoscape.ding.customgraphics.CyCustomGraphics;
import org.cytoscape.ding.customgraphics.bitmap.URLImageCustomGraphics;
-import org.cytoscape.ding.customgraphicsmgr.internal.CustomGraphicsManagerImpl;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/AddEdgeStateMonitor.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/AddEdgeStateMonitor.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/AddEdgeStateMonitor.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -35,6 +35,7 @@
import java.awt.geom.Point2D;
import java.util.HashMap;
import java.util.Map;
+import java.util.WeakHashMap;
import org.cytoscape.model.CyNode;
import org.cytoscape.view.model.CyNetworkView;
@@ -58,8 +59,8 @@
private final InnerCanvas canvas;
private final DGraphView m_view;
- private static Map<CyNetworkView,CyNode> sourceNodes = new
HashMap<CyNetworkView,CyNode>();
- private static Map<CyNetworkView,Point2D> sourcePoints = new
HashMap<CyNetworkView,Point2D>();
+ private static Map<CyNetworkView,CyNode> sourceNodes = new
WeakHashMap<CyNetworkView,CyNode>();
+ private static Map<CyNetworkView,Point2D> sourcePoints = new
WeakHashMap<CyNetworkView,Point2D>();
AddEdgeStateMonitor(InnerCanvas canvas, DGraphView m_view) {
this.canvas = canvas;
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -36,6 +36,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.WeakHashMap;
import org.cytoscape.ding.DArrowShape;
import org.cytoscape.ding.DVisualLexicon;
@@ -58,33 +59,33 @@
final DGraphView m_view;
final Object m_deletedEntry = new Object();
- Map<CyEdge,Object> m_colorsLowDetail = new HashMap<CyEdge,Object>();
- Map<CyEdge,Object> m_selectedColorsLowDetail = new
HashMap<CyEdge,Object>();
+ Map<CyEdge,Object> m_colorsLowDetail = new WeakHashMap<CyEdge,Object>();
+ Map<CyEdge,Object> m_selectedColorsLowDetail = new
WeakHashMap<CyEdge,Object>();
- Map<CyEdge, Float> m_segmentThicknesses = new HashMap<CyEdge, Float>();
- Map<CyEdge, Stroke> m_segmentStrokes = new HashMap<CyEdge, Stroke>();
+ Map<CyEdge, Float> m_segmentThicknesses = new WeakHashMap<CyEdge,
Float>();
+ Map<CyEdge, Stroke> m_segmentStrokes = new WeakHashMap<CyEdge,
Stroke>();
- Map<CyEdge, Byte> m_sourceArrows = new HashMap<CyEdge, Byte>();
- Map<CyEdge, Paint> m_sourceArrowPaints = new HashMap<CyEdge, Paint>();
- Map<CyEdge, Byte> m_targetArrows = new HashMap<CyEdge, Byte>();
- Map<CyEdge, Paint> m_targetArrowPaints = new HashMap<CyEdge, Paint>();
+ Map<CyEdge, Byte> m_sourceArrows = new WeakHashMap<CyEdge, Byte>();
+ Map<CyEdge, Paint> m_sourceArrowPaints = new WeakHashMap<CyEdge,
Paint>();
+ Map<CyEdge, Byte> m_targetArrows = new WeakHashMap<CyEdge, Byte>();
+ Map<CyEdge, Paint> m_targetArrowPaints = new WeakHashMap<CyEdge,
Paint>();
- Map<CyEdge, Paint> m_targetArrowSelectedPaints = new HashMap<CyEdge,
Paint>();
+ Map<CyEdge, Paint> m_targetArrowSelectedPaints = new
WeakHashMap<CyEdge, Paint>();
- Map<CyEdge, Integer> m_labelCounts = new HashMap<CyEdge, Integer>();
- Map<CyEdge, String> m_labelTexts = new HashMap<CyEdge, String>();
- Map<CyEdge, Font> m_labelFonts = new HashMap<CyEdge, Font>();
- Map<CyEdge, Paint> m_labelPaints = new HashMap<CyEdge, Paint>();
- Map<CyEdge, Double> m_labelWidths = new HashMap<CyEdge, Double>();
+ Map<CyEdge, Integer> m_labelCounts = new WeakHashMap<CyEdge, Integer>();
+ Map<CyEdge, String> m_labelTexts = new WeakHashMap<CyEdge, String>();
+ Map<CyEdge, Font> m_labelFonts = new WeakHashMap<CyEdge, Font>();
+ Map<CyEdge, Paint> m_labelPaints = new WeakHashMap<CyEdge, Paint>();
+ Map<CyEdge, Double> m_labelWidths = new WeakHashMap<CyEdge, Double>();
- Map<CyEdge, Paint> m_unselectedPaints = new HashMap<CyEdge, Paint>();
- Map<CyEdge, Paint> m_selectedPaints = new HashMap<CyEdge, Paint>();
+ Map<CyEdge, Paint> m_unselectedPaints = new WeakHashMap<CyEdge,
Paint>();
+ Map<CyEdge, Paint> m_selectedPaints = new WeakHashMap<CyEdge, Paint>();
// Curved or not
- Map<CyEdge, Integer> m_lineType = new HashMap<CyEdge, Integer>();
+ Map<CyEdge, Integer> m_lineType = new WeakHashMap<CyEdge, Integer>();
// Edge Bends
- Map<CyEdge, Bend> m_edgeBends = new HashMap<CyEdge, Bend>();
+ Map<CyEdge, Bend> m_edgeBends = new WeakHashMap<CyEdge, Bend>();
private Byte m_sourceArrowDefault;
private Paint m_sourceArrowPaintDefault;
@@ -122,29 +123,29 @@
if (isCleared)
return;
- m_segmentThicknesses = new HashMap<CyEdge, Float>();
- m_segmentStrokes = new HashMap<CyEdge, Stroke>();
+ m_segmentThicknesses = new WeakHashMap<CyEdge, Float>();
+ m_segmentStrokes = new WeakHashMap<CyEdge, Stroke>();
- m_sourceArrows = new HashMap<CyEdge, Byte>();
- m_sourceArrowPaints = new HashMap<CyEdge, Paint>();
- m_targetArrows = new HashMap<CyEdge, Byte>();
- m_targetArrowPaints = new HashMap<CyEdge, Paint>();
- m_targetArrowSelectedPaints = new HashMap<CyEdge, Paint>();
- m_labelCounts = new HashMap<CyEdge, Integer>();
- m_labelTexts = new HashMap<CyEdge, String>();
- m_labelFonts = new HashMap<CyEdge, Font>();
- m_labelPaints = new HashMap<CyEdge, Paint>();
- m_labelWidths = new HashMap<CyEdge, Double>();
+ m_sourceArrows = new WeakHashMap<CyEdge, Byte>();
+ m_sourceArrowPaints = new WeakHashMap<CyEdge, Paint>();
+ m_targetArrows = new WeakHashMap<CyEdge, Byte>();
+ m_targetArrowPaints = new WeakHashMap<CyEdge, Paint>();
+ m_targetArrowSelectedPaints = new WeakHashMap<CyEdge, Paint>();
+ m_labelCounts = new WeakHashMap<CyEdge, Integer>();
+ m_labelTexts = new WeakHashMap<CyEdge, String>();
+ m_labelFonts = new WeakHashMap<CyEdge, Font>();
+ m_labelPaints = new WeakHashMap<CyEdge, Paint>();
+ m_labelWidths = new WeakHashMap<CyEdge, Double>();
- m_unselectedPaints = new HashMap<CyEdge, Paint>();
- m_selectedPaints = new HashMap<CyEdge, Paint>();
+ m_unselectedPaints = new WeakHashMap<CyEdge, Paint>();
+ m_selectedPaints = new WeakHashMap<CyEdge, Paint>();
- m_colorsLowDetail = new HashMap<CyEdge,Object>();
- m_selectedColorsLowDetail = new HashMap<CyEdge,Object>();
+ m_colorsLowDetail = new WeakHashMap<CyEdge,Object>();
+ m_selectedColorsLowDetail = new WeakHashMap<CyEdge,Object>();
- m_lineType = new HashMap<CyEdge, Integer>();
+ m_lineType = new WeakHashMap<CyEdge, Integer>();
- m_edgeBends = new HashMap<CyEdge, Bend>();
+ m_edgeBends = new WeakHashMap<CyEdge, Bend>();
isCleared = true;
}
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -59,6 +59,7 @@
import java.util.Map;
import java.util.Properties;
import java.util.Set;
+import java.util.WeakHashMap;
import javax.imageio.ImageIO;
import javax.swing.Icon;
@@ -471,8 +472,8 @@
m_edgeDetails = new DEdgeDetails(this);
m_nodeViewDefaultSupport = new
NodeViewDefaultSupport(m_nodeDetails, m_lock);
m_edgeViewDefaultSupport = new
EdgeViewDefaultSupport(m_edgeDetails, m_lock);
- m_nodeViewMap = new HashMap<CyNode, NodeView>();
- m_edgeViewMap = new HashMap<CyEdge, EdgeView>();
+ m_nodeViewMap = new WeakHashMap<CyNode, NodeView>();
+ m_edgeViewMap = new WeakHashMap<CyEdge, EdgeView>();
m_printLOD = new PrintLOD();
m_defaultNodeXMin = 0.0f;
m_defaultNodeYMin = 0.0f;
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DNodeDetails.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DNodeDetails.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DNodeDetails.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -39,6 +39,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.WeakHashMap;
import org.cytoscape.ding.DNodeShape;
import org.cytoscape.ding.DVisualLexicon;
@@ -69,35 +70,35 @@
final Object m_deletedEntry = new Object();
- Map<CyNode,Object> m_colorsLowDetail = new HashMap<CyNode,Object>();
- Map<CyNode,Object> m_selectedColorsLowDetail = new
HashMap<CyNode,Object>();
+ Map<CyNode,Object> m_colorsLowDetail = new WeakHashMap<CyNode,Object>();
+ Map<CyNode,Object> m_selectedColorsLowDetail = new
WeakHashMap<CyNode,Object>();
- Map<CyNode, Byte> m_shapes = new HashMap<CyNode, Byte>();
- Map<CyNode, Paint> m_unselectedPaints = new HashMap<CyNode, Paint>();
- Map<CyNode, Paint> m_selectedPaints = new HashMap<CyNode, Paint>();
+ Map<CyNode, Byte> m_shapes = new WeakHashMap<CyNode, Byte>();
+ Map<CyNode, Paint> m_unselectedPaints = new WeakHashMap<CyNode,
Paint>();
+ Map<CyNode, Paint> m_selectedPaints = new WeakHashMap<CyNode, Paint>();
- Map<CyNode, Float> m_borderWidths = new HashMap<CyNode, Float>();
- Map<CyNode, Paint> m_borderPaints = new HashMap<CyNode, Paint>();
- Map<CyNode, Integer> m_labelCounts = new HashMap<CyNode, Integer>();
+ Map<CyNode, Float> m_borderWidths = new WeakHashMap<CyNode, Float>();
+ Map<CyNode, Paint> m_borderPaints = new WeakHashMap<CyNode, Paint>();
+ Map<CyNode, Integer> m_labelCounts = new WeakHashMap<CyNode, Integer>();
- Map<CyNode, String> m_labelTexts = new HashMap<CyNode, String>();
- Map<CyNode, String> m_tooltipTexts = new HashMap<CyNode, String>();
+ Map<CyNode, String> m_labelTexts = new WeakHashMap<CyNode, String>();
+ Map<CyNode, String> m_tooltipTexts = new WeakHashMap<CyNode, String>();
- Map<CyNode, Font> m_labelFonts = new HashMap<CyNode, Font>();
- Map<CyNode, Paint> m_labelPaints = new HashMap<CyNode, Paint>();
- Map<CyNode, Double> m_labelWidths = new HashMap<CyNode, Double>();
+ Map<CyNode, Font> m_labelFonts = new WeakHashMap<CyNode, Font>();
+ Map<CyNode, Paint> m_labelPaints = new WeakHashMap<CyNode, Paint>();
+ Map<CyNode, Double> m_labelWidths = new WeakHashMap<CyNode, Double>();
- Map<CyNode, Integer> m_labelTextAnchors = new HashMap<CyNode,
Integer>();
- Map<CyNode, Integer> m_labelNodeAnchors = new HashMap<CyNode,
Integer>();
- Map<CyNode, Integer> m_labelJustifys = new HashMap<CyNode, Integer>();
- Map<CyNode, Double> m_labelOffsetXs = new HashMap<CyNode, Double>();
- Map<CyNode, Double> m_labelOffsetYs = new HashMap<CyNode, Double>();
+ Map<CyNode, Integer> m_labelTextAnchors = new WeakHashMap<CyNode,
Integer>();
+ Map<CyNode, Integer> m_labelNodeAnchors = new WeakHashMap<CyNode,
Integer>();
+ Map<CyNode, Integer> m_labelJustifys = new WeakHashMap<CyNode,
Integer>();
+ Map<CyNode, Double> m_labelOffsetXs = new WeakHashMap<CyNode, Double>();
+ Map<CyNode, Double> m_labelOffsetYs = new WeakHashMap<CyNode, Double>();
- Map<CyNode, Double> m_width = new HashMap<CyNode, Double>();
+ Map<CyNode, Double> m_width = new WeakHashMap<CyNode, Double>();
- Map<CyNode, List<CustomGraphic>> m_customGraphics = new HashMap<CyNode,
List<CustomGraphic>>();
+ Map<CyNode, List<CustomGraphic>> m_customGraphics = new
WeakHashMap<CyNode, List<CustomGraphic>>();
- private Set<CyNode> selected = new HashSet<CyNode>();
+ private final Set<CyNode> selected = new HashSet<CyNode>();
// Default values
private Color m_colorLowDetailDefault;
@@ -121,55 +122,45 @@
private Double m_labelOffsetVectorYDefault;
private Byte m_labelJustifyDefault;
private Double m_labelWidthDefault;
-
- private Map<CustomGraphicsVisualProperty,
CyCustomGraphics<CustomGraphic>> defaultCustomGraphicsMap;
- private Map<ObjectPositionVisualProperty, ObjectPosition>
defaultCustomGraphicsPositionMap;
-
- private List<CustomGraphic> defaultCGList;
+
private boolean isCleared = false;
DNodeDetails(final DGraphView view) {
this.m_view = view;
-
- defaultCustomGraphicsMap = new
HashMap<CustomGraphicsVisualProperty, CyCustomGraphics<CustomGraphic>>();
- defaultCustomGraphicsPositionMap = new
HashMap<ObjectPositionVisualProperty, ObjectPosition>();
}
void clear() {
if(isCleared)
return;
- m_colorsLowDetail = new HashMap<CyNode,Object>();
- m_selectedColorsLowDetail = new HashMap<CyNode,Object>();
+ m_colorsLowDetail = new WeakHashMap<CyNode,Object>();
+ m_selectedColorsLowDetail = new WeakHashMap<CyNode,Object>();
- m_shapes = new HashMap<CyNode, Byte>();
- m_unselectedPaints = new HashMap<CyNode, Paint>();
- m_borderWidths = new HashMap<CyNode, Float>();
- m_borderPaints = new HashMap<CyNode, Paint>();
- m_labelCounts = new HashMap<CyNode, Integer>();
- m_labelTexts = new HashMap<CyNode, String>();
- m_tooltipTexts = new HashMap<CyNode, String>();
- m_labelFonts = new HashMap<CyNode, Font>();
- m_labelPaints = new HashMap<CyNode, Paint>();
- m_labelWidths = new HashMap<CyNode, Double>();
+ m_shapes = new WeakHashMap<CyNode, Byte>();
+ m_unselectedPaints = new WeakHashMap<CyNode, Paint>();
+ m_borderWidths = new WeakHashMap<CyNode, Float>();
+ m_borderPaints = new WeakHashMap<CyNode, Paint>();
+ m_labelCounts = new WeakHashMap<CyNode, Integer>();
+ m_labelTexts = new WeakHashMap<CyNode, String>();
+ m_tooltipTexts = new WeakHashMap<CyNode, String>();
+ m_labelFonts = new WeakHashMap<CyNode, Font>();
+ m_labelPaints = new WeakHashMap<CyNode, Paint>();
+ m_labelWidths = new WeakHashMap<CyNode, Double>();
- m_labelTextAnchors = new HashMap<CyNode, Integer>();
- m_labelNodeAnchors = new HashMap<CyNode, Integer>();
- m_labelJustifys = new HashMap<CyNode, Integer>();
- m_labelOffsetXs = new HashMap<CyNode, Double>();
- m_labelOffsetYs = new HashMap<CyNode, Double>();
- m_width = new HashMap<CyNode, Double>();
+ m_labelTextAnchors = new WeakHashMap<CyNode, Integer>();
+ m_labelNodeAnchors = new WeakHashMap<CyNode, Integer>();
+ m_labelJustifys = new WeakHashMap<CyNode, Integer>();
+ m_labelOffsetXs = new WeakHashMap<CyNode, Double>();
+ m_labelOffsetYs = new WeakHashMap<CyNode, Double>();
+ m_width = new WeakHashMap<CyNode, Double>();
- m_selectedPaints = new HashMap<CyNode, Paint>();
+ m_selectedPaints = new WeakHashMap<CyNode, Paint>();
- m_customGraphics = new HashMap<CyNode, List<CustomGraphic>>();
+ m_customGraphics = new WeakHashMap<CyNode,
List<CustomGraphic>>();
+
- defaultCustomGraphicsMap = new
HashMap<CustomGraphicsVisualProperty, CyCustomGraphics<CustomGraphic>>();
- defaultCustomGraphicsPositionMap = new
HashMap<ObjectPositionVisualProperty, ObjectPosition>();
- defaultCGList = new ArrayList<CustomGraphic>();
-
// Clear all Custom Graphics
for(final View<CyNode> nv: m_view.getNodeViews())
((DNodeView) nv).removeAllCustomGraphics();
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/ViewState.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/ViewState.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/ViewState.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -41,6 +41,7 @@
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.WeakHashMap;
import org.cytoscape.ding.EdgeView;
import org.cytoscape.ding.GraphView;
@@ -82,7 +83,7 @@
// node views, which can disappear between when this edit
// is created and when it is used.
if (whatToSave == ViewChangeEdit.SavedObjs.ALL || whatToSave ==
ViewChangeEdit.SavedObjs.NODES) {
- points = new HashMap<CyNode, Point2D.Double>();
+ points = new WeakHashMap<CyNode, Point2D.Double>();
for (CyNode n: view.getNetwork().getNodeList()) {
NodeView nv = view.getDNodeView(n);
points.put(n, new
Point2D.Double(nv.getXPosition(), nv.getYPosition()));
@@ -90,8 +91,8 @@
}
if (whatToSave == ViewChangeEdit.SavedObjs.ALL || whatToSave ==
ViewChangeEdit.SavedObjs.EDGES) {
- anchors = new HashMap<CyEdge, List>();
- linetype = new HashMap<CyEdge, Integer>();
+ anchors = new WeakHashMap<CyEdge, List>();
+ linetype = new WeakHashMap<CyEdge, Integer>();
for (CyEdge e: view.getNetwork().getEdgeList()) {
EdgeView ev = view.getDEdgeView(e);
@@ -103,7 +104,7 @@
if (whatToSave == ViewChangeEdit.SavedObjs.SELECTED ||
whatToSave == ViewChangeEdit.SavedObjs.SELECTED_NODES ) {
- points = new HashMap<CyNode, Point2D.Double>();
+ points = new WeakHashMap<CyNode, Point2D.Double>();
Iterator<CyNode> nodeIter =
view.getSelectedNodes().iterator();
while (nodeIter.hasNext()) {
@@ -115,8 +116,8 @@
if (whatToSave == ViewChangeEdit.SavedObjs.SELECTED ||
whatToSave == ViewChangeEdit.SavedObjs.SELECTED_EDGES ) {
- anchors = new HashMap<CyEdge, List>();
- linetype = new HashMap<CyEdge, Integer>();
+ anchors = new WeakHashMap<CyEdge, List>();
+ linetype = new WeakHashMap<CyEdge, Integer>();
Iterator<CyEdge> edgeIter =
view.getSelectedEdges().iterator();
while (edgeIter.hasNext()) {
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/ClipboardManagerImpl.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/ClipboardManagerImpl.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/ClipboardManagerImpl.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -4,7 +4,7 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import java.util.Set;
+import java.util.WeakHashMap;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
@@ -20,20 +20,17 @@
import org.cytoscape.view.presentation.property.BasicVisualLexicon;
-public class ClipboardManagerImpl {
- CyNetworkView sourceView;
- List<View<CyNode>> nodeViews;
- List<View<CyEdge>> edgeViews;
+public final class ClipboardManagerImpl {
+ private CyNetworkView sourceView;
+ private List<View<CyNode>> nodeViews;
+ private List<View<CyEdge>> edgeViews;
// Row maps
- Map<CyIdentifiable, CyRow> oldDefaultRowMap;
- Map<CyIdentifiable, CyRow> oldHiddenRowMap;
+ private Map<CyIdentifiable, CyRow> oldDefaultRowMap;
+ private Map<CyIdentifiable, CyRow> oldHiddenRowMap;
- double xCenter, yCenter;
+ private double xCenter, yCenter;
- public ClipboardManagerImpl() {
- }
-
public boolean clipboardHasData() {
if (nodeViews != null && nodeViews.size() > 0)
return true;
@@ -45,8 +42,8 @@
CyNetwork sourceNetwork = sourceView.getModel();
nodeViews = new ArrayList<View<CyNode>>();
edgeViews = new ArrayList<View<CyEdge>>();
- oldDefaultRowMap = new HashMap<CyIdentifiable, CyRow>();
- oldHiddenRowMap = new HashMap<CyIdentifiable, CyRow>();
+ oldDefaultRowMap = new WeakHashMap<CyIdentifiable, CyRow>();
+ oldHiddenRowMap = new WeakHashMap<CyIdentifiable, CyRow>();
xCenter = 0.0;
yCenter = 0.0;
@@ -77,7 +74,7 @@
public List<CyIdentifiable> paste(CyNetworkView targetView, double x,
double y, boolean createColumns) {
List<CyIdentifiable> pastedObjects = new
ArrayList<CyIdentifiable>();
- Map<CyRow, CyRow> rowMap = new HashMap<CyRow, CyRow>();
+ final Map<CyRow, CyRow> rowMap = new HashMap<CyRow, CyRow>();
CyNetwork sourceNetwork = sourceView.getModel();
@@ -91,7 +88,7 @@
// nodes and add the edges.
// Pass 1: add the nodes
- Map<CyNode, CyNode> newNodeMap = new HashMap<CyNode, CyNode>();
+ final Map<CyNode, CyNode> newNodeMap = new HashMap<CyNode,
CyNode>();
for (View<CyNode> nodeView: nodeViews) {
CyNode node = nodeView.getModel();
CyNode newNode = null;
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CopyTaskFactory.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CopyTaskFactory.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CopyTaskFactory.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -1,11 +1,8 @@
package org.cytoscape.editor.internal;
-import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyNode;
import org.cytoscape.task.AbstractNetworkViewTaskFactory;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.View;
import org.cytoscape.work.TaskIterator;
public class CopyTaskFactory extends AbstractNetworkViewTaskFactory {
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CutTaskFactory.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CutTaskFactory.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/CutTaskFactory.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -1,11 +1,8 @@
package org.cytoscape.editor.internal;
-import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.model.CyNode;
import org.cytoscape.task.AbstractNetworkViewTaskFactory;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.View;
import org.cytoscape.work.TaskIterator;
public class CutTaskFactory extends AbstractNetworkViewTaskFactory {
Modified:
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/PasteTask.java
===================================================================
---
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/PasteTask.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/editor-impl/src/main/java/org/cytoscape/editor/internal/PasteTask.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -1,35 +1,26 @@
package org.cytoscape.editor.internal;
import java.awt.geom.Point2D;
-import java.util.List;
-import org.cytoscape.event.CyEventHelper;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyRow;
import org.cytoscape.task.AbstractNetworkViewTask;
import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.view.model.View;
-import org.cytoscape.view.presentation.property.BasicVisualLexicon;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.TaskMonitor;
-public class PasteTask extends AbstractNetworkViewTask{
+public class PasteTask extends AbstractNetworkViewTask {
private final VisualMappingManager vmm;
private final Point2D xformPt;
- private static int new_node_index =1;
private final ClipboardManagerImpl clipMgr;
-
- public PasteTask(final VisualMappingManager vmm, final CyNetworkView
view,final Point2D xformPt,
- final ClipboardManagerImpl clip) {
+
+ public PasteTask(final VisualMappingManager vmm, final CyNetworkView
view, final Point2D xformPt,
+ final ClipboardManagerImpl clip) {
super(view);
this.vmm = vmm;
this.xformPt = xformPt;
this.clipMgr = clip;
-
+
}
// TODO: add an isRead that is ready when we have something to paste
@@ -42,7 +33,7 @@
clipMgr.paste(view, xformPt.getX(), xformPt.getY(),
true);
view.updateView();
-
+
// Apply visual style
VisualStyle vs = vmm.getVisualStyle(view);
vs.apply(view);
Modified:
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/QuickFindImpl.java
===================================================================
---
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/QuickFindImpl.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/filter-impl/src/main/java/org/cytoscape/filter/internal/quickfind/util/QuickFindImpl.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -30,21 +30,19 @@
import java.util.ArrayList;
import java.util.Date;
-import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;
+import java.util.WeakHashMap;
import org.cytoscape.filter.internal.widgets.autocomplete.index.GenericIndex;
import org.cytoscape.filter.internal.widgets.autocomplete.index.Hit;
import org.cytoscape.filter.internal.widgets.autocomplete.index.IndexFactory;
import org.cytoscape.model.CyColumn;
-import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.work.TaskMonitor;
@@ -66,7 +64,7 @@
public QuickFindImpl() {
this.listenerList = new ArrayList<QuickFindListener>();
- this.networkMap = new HashMap<CyNetwork, GenericIndex>();
+ this.networkMap = new WeakHashMap<CyNetwork, GenericIndex>();
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/AbstractSessionReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/AbstractSessionReader.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/session/AbstractSessionReader.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -36,6 +36,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.WeakHashMap;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
@@ -68,7 +69,7 @@
protected final Set<CyNetwork> networks = new
LinkedHashSet<CyNetwork>();
protected final Set<CyNetworkView> networkViews = new
LinkedHashSet<CyNetworkView>();
protected final Set<VisualStyle> visualStyles = new
HashSet<VisualStyle>();
- protected final Map<CyNetworkView, String> visualStyleMap = new
HashMap<CyNetworkView, String>();
+ protected final Map<CyNetworkView, String> visualStyleMap = new
WeakHashMap<CyNetworkView, String>();
protected final Set<CyTableMetadata> tableMetadata = new
HashSet<CyTableMetadata>();
protected final Map<String, List<File>> appFileListMap = new
HashMap<String, List<File>>();
protected final Map<Class<? extends CyIdentifiable>, Map<Object, ?
extends CyIdentifiable>> objectMap = new HashMap<Class<? extends
CyIdentifiable>, Map<Object, ? extends CyIdentifiable>>();
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -30,6 +30,7 @@
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
+import java.util.WeakHashMap;
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyIdentifiable;
@@ -70,9 +71,9 @@
nodeByNameMap = new HashMap<Object, CyNode>();
- nodeLinkMap = new HashMap<CyNetwork, Set<Long>>();
- edgeLinkMap = new HashMap<CyNetwork, Set<Long>>();
- networkPointerMap = new HashMap<CyNode, Object>();
+ nodeLinkMap = new WeakHashMap<CyNetwork, Set<Long>>();
+ edgeLinkMap = new WeakHashMap<CyNetwork, Set<Long>>();
+ networkPointerMap = new WeakHashMap<CyNode, Object>();
}
public void dispose() {
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/write/xgmml/XGMMLWriter.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -42,6 +42,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.WeakHashMap;
import org.cytoscape.io.internal.read.xgmml.ObjectTypeMap;
import org.cytoscape.io.internal.util.UnrecognizedVisualPropertyManager;
@@ -132,9 +133,9 @@
private final CyNetworkManager networkMgr;
private final CyRootNetworkManager rootNetworkMgr;
- private HashMap<CyNode, CyNode> writtenNodeMap = new HashMap<CyNode,
CyNode>();
- private HashMap<CyEdge, CyEdge> writtenEdgeMap = new HashMap<CyEdge,
CyEdge>();
- private HashMap<CyNetwork, CyNetwork> writtenNetMap = new
HashMap<CyNetwork, CyNetwork>();
+ private final Map<CyNode, CyNode> writtenNodeMap = new WeakHashMap<CyNode,
CyNode>();
+ private final Map<CyEdge, CyEdge> writtenEdgeMap = new WeakHashMap<CyEdge,
CyEdge>();
+ private final Map<CyNetwork, CyNetwork> writtenNetMap = new
WeakHashMap<CyNetwork, CyNetwork>();
private int depth = 0;
private String indentString = "";
Modified:
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/DirNetworkAnalyzer.java
===================================================================
---
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/DirNetworkAnalyzer.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/network-analyzer-impl/src/main/java/de/mpg/mpi_inf/bioinf/netanalyzer/DirNetworkAnalyzer.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -26,6 +26,7 @@
import java.util.List;
import java.util.Map;
import java.util.Set;
+import java.util.WeakHashMap;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
@@ -81,8 +82,8 @@
this.numberOfIsolatedNodes = 0;
this.numberOfSelfLoops = 0;
this.multiEdgePartners = 0;
- this.nodeBetweenness = new HashMap<CyNode, NodeBetweenInfo>();
- this.edgeBetweenness = new HashMap<CyEdge, Double>();
+ this.nodeBetweenness = new WeakHashMap<CyNode,
NodeBetweenInfo>();
+ this.edgeBetweenness = new WeakHashMap<CyEdge, Double>();
this.stress = new HashMap<CyNode, Long>();
computeNB = true;
AttributeSetup.createDirectedNodeAttributes(aNetwork.getDefaultNodeTable());
Modified:
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/model/AttributeMappingImpl.java
===================================================================
---
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/model/AttributeMappingImpl.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/model/AttributeMappingImpl.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -48,6 +48,7 @@
import java.util.Map;
import java.util.HashMap;
import java.util.Iterator;
+import java.util.WeakHashMap;
import org.cytoscape.network.merge.internal.util.ColumnType;
@@ -65,10 +66,10 @@
private final String nullAttr = ""; // to hold a position in vector
standing that it's not a attribute
public AttributeMappingImpl() {
- attributeMapping = new HashMap<CyNetwork,List<String>>();
+ attributeMapping = new WeakHashMap<CyNetwork,List<String>>();
mergedAttributes = new ArrayList<String>();
mergedAttributeTypes = new ArrayList<ColumnType>();
- cyTables = new HashMap<CyNetwork,CyTable>();
+ cyTables = new WeakHashMap<CyNetwork,CyTable>();
}
Modified:
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/model/MatchingAttributeImpl.java
===================================================================
---
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/model/MatchingAttributeImpl.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/network-merge-impl/src/main/java/org/cytoscape/network/merge/internal/model/MatchingAttributeImpl.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -37,9 +37,9 @@
package org.cytoscape.network.merge.internal.model;
+import java.util.Map;
import java.util.Set;
-import java.util.Map;
-import java.util.HashMap;
+import java.util.WeakHashMap;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyNetwork;
@@ -55,7 +55,7 @@
private Map<CyNetwork,CyColumn> attributeForMatching; // network to
attribute name
public MatchingAttributeImpl() {
- attributeForMatching = new HashMap<CyNetwork,CyColumn>();
+ attributeForMatching = new WeakHashMap<CyNetwork,CyColumn>();
}
@Override
Modified:
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/AttributeSetManager.java
===================================================================
---
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/AttributeSetManager.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/vizmap-gui-impl/src/main/java/org/cytoscape/view/vizmap/gui/internal/AttributeSetManager.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -5,14 +5,15 @@
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
+import java.util.WeakHashMap;
import org.cytoscape.model.CyColumn;
import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkTableManager;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.events.ColumnCreatedEvent;
import org.cytoscape.model.events.ColumnCreatedListener;
import org.cytoscape.model.events.ColumnDeletedEvent;
@@ -43,8 +44,8 @@
public AttributeSetManager(final CyNetworkTableManager tableMgr) {
this.tableMgr = tableMgr;
- this.attrSets = new HashMap<CyNetwork, Map<Class<? extends
CyIdentifiable>, AttributeSet>>();
- this.tableSets = new HashMap<CyNetwork, Map<Class<? extends
CyIdentifiable>, Set<CyTable>>>();
+ this.attrSets = new WeakHashMap<CyNetwork, Map<Class<? extends
CyIdentifiable>, AttributeSet>>();
+ this.tableSets = new WeakHashMap<CyNetwork, Map<Class<? extends
CyIdentifiable>, Set<CyTable>>>();
}
public AttributeSet getAttributeSet(final CyNetwork network, final
Class<? extends CyIdentifiable> objectType) {
Modified:
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
===================================================================
---
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/vizmap-impl/impl/src/main/java/org/cytoscape/view/vizmap/internal/VisualMappingManagerImpl.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -65,8 +65,6 @@
// Default Style
private static final Color NETWORK_COLOR = Color.WHITE;
- private static final Color NETWORK_NODE_SELECTED_COLOR = Color.YELLOW;
- private static final Color NETWORK_EDGE_SELECTED_COLOR = Color.YELLOW;
private static final Color NODE_COLOR = new Color(0x4F, 0x94, 0xCD);
private static final Color NODE_LABEL_COLOR = Color.BLACK;
private static final Color EDGE_COLOR = new Color(50, 50, 50);
@@ -83,8 +81,8 @@
private final CyEventHelper cyEventHelper;
private final VisualLexiconManager lexManager;
- public VisualMappingManagerImpl(final CyEventHelper eventHelper,
- final VisualStyleFactory factory, final
VisualLexiconManager lexManager) {
+ public VisualMappingManagerImpl(final CyEventHelper eventHelper, final
VisualStyleFactory factory,
+ final VisualLexiconManager lexManager) {
if (eventHelper == null)
throw new NullPointerException("CyEventHelper cannot be
null");
@@ -131,7 +129,6 @@
style = getDefaultVisualStyle();
network2VisualStyleMap.put(nv, style);
}
-
return style;
}
Modified:
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
===================================================================
---
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
2012-05-04 23:42:07 UTC (rev 29125)
+++
core3/impl/trunk/webservice-psicquic-client-impl/src/main/java/org/cytoscape/webservice/psicquic/PSICQUICRestClient.java
2012-05-05 00:36:53 UTC (rev 29126)
@@ -11,6 +11,7 @@
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
+import java.util.WeakHashMap;
import java.util.concurrent.Callable;
import java.util.concurrent.CancellationException;
import java.util.concurrent.CompletionService;
@@ -261,7 +262,7 @@
this.serviceURL = serviceURL;
this.query = query;
this.mode = mode;
- this.returnThis = new HashMap<CyNetwork, String>();
+ this.returnThis = new WeakHashMap<CyNetwork, String>();
this.networkBuilder = new CyNetworkBuilder(factory);
}
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