Author: rodche
Date: 2012-02-01 12:08:28 -0800 (Wed, 01 Feb 2012)
New Revision: 28177
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
Log:
Updated BioPAX visual style (node, arrow shapes, etc., which was broken since
ported to Cy3). Also fixed a NPE bug in the mapper, etc.
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-02-01 19:43:07 UTC (rev 28176)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxMapper.java
2012-02-01 20:08:28 UTC (rev 28177)
@@ -3,14 +3,7 @@
import java.awt.geom.Rectangle2D;
import java.awt.image.BufferedImage;
import java.io.ByteArrayOutputStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.Stack;
+import java.util.*;
import org.apache.commons.lang.StringUtils;
import org.biopax.paxtools.controller.AbstractTraverser;
@@ -20,26 +13,8 @@
import org.biopax.paxtools.io.SimpleIOHandler;
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.Model;
-import org.biopax.paxtools.model.level3.Catalysis;
-import org.biopax.paxtools.model.level3.CellularLocationVocabulary;
-import org.biopax.paxtools.model.level3.Complex;
-import org.biopax.paxtools.model.level3.Control;
-import org.biopax.paxtools.model.level3.ControlType;
-import org.biopax.paxtools.model.level3.Controller;
-import org.biopax.paxtools.model.level3.Conversion;
-import org.biopax.paxtools.model.level3.Entity;
-import org.biopax.paxtools.model.level3.Interaction;
-import org.biopax.paxtools.model.level3.Pathway;
-import org.biopax.paxtools.model.level3.PhysicalEntity;
+import org.biopax.paxtools.model.level3.*;
import org.biopax.paxtools.model.level3.Process;
-import org.biopax.paxtools.model.level3.PublicationXref;
-import org.biopax.paxtools.model.level3.RelationshipTypeVocabulary;
-import org.biopax.paxtools.model.level3.RelationshipXref;
-import org.biopax.paxtools.model.level3.SimplePhysicalEntity;
-import org.biopax.paxtools.model.level3.Stoichiometry;
-import org.biopax.paxtools.model.level3.UnificationXref;
-import org.biopax.paxtools.model.level3.XReferrable;
-import org.biopax.paxtools.model.level3.Xref;
import org.biopax.paxtools.util.ClassFilterSet;
import org.biopax.paxtools.util.Filter;
import org.cytoscape.biopax.internal.util.AttributeUtil;
@@ -53,7 +28,6 @@
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -204,6 +178,11 @@
createInteractionEdges(network);
createComplexEdges(network);
+ // TODO create pathwayComponent edges (requires pathway nodes)?
+
+ // create PE->memberPE edges (Arghhh!)?
+ createMemberEdges(network);
+
// Finally, set network attributes:
// name
@@ -229,6 +208,21 @@
}
+ private void createMemberEdges(CyNetwork network) {
+ // for each PE,
+ for (PhysicalEntity par :
model.getObjects(PhysicalEntity.class)) {
+ CyNode cyParentNode = uriToCyNodeMap.get(par);
+ // for each its member PE, add the directed edge
+ for (PhysicalEntity member :
par.getMemberPhysicalEntity())
+ {
+ CyNode cyMemberNode =
uriToCyNodeMap.get(member);
+ CyEdge edge = network.addEdge(cyParentNode,
cyMemberNode, true);
+ AttributeUtil.set(network, edge,
BIOPAX_EDGE_TYPE, "member", String.class);
+ }
+ }
+ }
+
+
private void createEntityNodes(CyNetwork network) {
taskMonitor.setStatusMessage("Creating nodes (first pass)...");
taskMonitor.setProgress(0);
@@ -236,9 +230,12 @@
int i = 0; //progress counter
Set<Entity> entities = model.getObjects(Entity.class);
for(Entity bpe: entities) {
- // skip for pathways
- if(bpe instanceof Pathway)
- continue;
+ // do not make nodes for top/main pathways
+ if(bpe instanceof Pathway) {
+ if(bpe.getParticipantOf().isEmpty()
+ &&
((Process)bpe).getPathwayComponentOf().isEmpty())
+ continue;
+ }
// Create node symbolizing the interaction
CyNode node = network.addNode();
@@ -343,7 +340,19 @@
{
// Note: getCyNode also assigns cellular location attribute...
CyNode nodeA = uriToCyNodeMap.get(bpeA);
+ if(nodeA == null) {
+ log.debug("linkNodes: no node was created for "
+ + bpeA.getModelInterface() + " " +
bpeA.getRDFId());
+ return; //e.g., we do not create any pathway nodes
currently...
+ }
+
CyNode nodeB = uriToCyNodeMap.get(bpeB);
+ if(nodeB == null) {
+ log.debug("linkNodes: no node was created for "
+ + bpeB.getModelInterface() + " " +
bpeB.getRDFId());
+ return; //e.g., we do not create any pathway nodes
currently...
+ }
+
CyEdge edge = null;
if (type.equals("right") || type.equals("cofactor")
|| type.equals("participant")) {
@@ -533,6 +542,9 @@
// add xref ids per database and per xref class
List<Xref> xList = BioPaxUtil.getXRefs(resource, Xref.class);
for (Xref link : xList) {
+ if(link.getDb() == null)
+ continue; // too bad (data issue...); skip it
+
// per db -
String key = BIOPAX_XREF_PREFIX +
link.getDb().toUpperCase();
// Set individual XRefs; Max of 1 per database.
@@ -541,7 +553,6 @@
AttributeUtil.set(network, node, key,
link.getId(), String.class);
}
-
StringBuffer temp = new StringBuffer();
if(!"CPATH".equalsIgnoreCase(link.getDb()))
@@ -589,8 +600,7 @@
{
Filter<PropertyEditor> filter = new Filter<PropertyEditor>() {
@Override
- // skips for entity-range properties
- // (which map to edges rather than attributes!),
+ // skips for entity-range properties (which map to
edges rather than attributes!),
// and several utility classes range ones
// (for which we do not want generate attributes or do
another way)
public boolean filter(PropertyEditor editor) {
@@ -904,92 +914,4 @@
}
- public static void customNodes(CyNetworkView networkView) {
- // grab node attributes
- CyNetwork cyNetwork = networkView.getModel();
-
- // iterate through the nodes
- Iterator<CyNode> nodesIt = cyNetwork.getNodeList().iterator();
- if (nodesIt.hasNext()) {
- // grab the node
- CyNode node = nodesIt.next();
-
- // get chemical modifications
- int count = 0;
- boolean isPhosphorylated = false;
- // TODO: MultiHashMap
-// MultiHashMapDefinition mhmdef =
nodeAttributes.getMultiHashMapDefinition();
-//
-// if
(mhmdef.getAttributeValueType(BIOPAX_CHEMICAL_MODIFICATIONS_MAP) != -1) {
-// MultiHashMap mhmap =
nodeAttributes.getMultiHashMap();
-// CountedIterator modsIt =
mhmap.getAttributeKeyspan(node.getIdentifier(),
-// BIOPAX_CHEMICAL_MODIFICATIONS_MAP, null);
-//
-// // do we have phosphorylation ?
-// while (modsIt.hasNext()) {
-// String modification = (String)
modsIt.next();
-//
-// if
(modification.equals(BioPaxUtil.PHOSPHORYLATION_SITE)) {
-// isPhosphorylated = true;
-//
-// Object[] key = {
BioPaxUtil.PHOSPHORYLATION_SITE };
-// String countStr = (String)
mhmap.getAttributeValue(node.getIdentifier(),
-// BIOPAX_CHEMICAL_MODIFICATIONS_MAP, key);
-// count = ((Integer)
Integer.valueOf(countStr)).intValue();
-//
-// break;
-// }
-// }
-// }
-
- // if phosphorylated, add custom node
- if (isPhosphorylated) {
- addCustomShapes(networkView, node,
"PHOSPHORYLATION_GRAPHICS", count);
- }
- }
- }
-
-
- /**
- * Based on given arguments, adds proper custom node shape to node.
- */
- private static void addCustomShapes(CyNetworkView networkView, CyNode
node, String shapeType,
- int modificationCount) {
- // TODO: Custom graphics
-// // create refs to help views
-// CyNetwork cyNetwork = networkView.getModel();
-// View<CyNode> nodeView = networkView.getNodeView(node);
-// DNodeView dingNodeView = (DNodeView) nodeView;
-//
-// // remove existing custom nodes
-// Iterator<CustomGraphic> it =
dingNodeView.customGraphicIterator();
-// while ( it.hasNext() ) {
-// dingNodeView.removeCustomGraphic( it.next() );
-// }
-//
-// for (int lc = 0; lc < modificationCount; lc++) {
-// // set image
-// BufferedImage image = null;
-//
-// if (shapeType.equals(PHOSPHORYLATION_GRAPHICS)) {
-// image = (cyNetwork.isSelected(node)) ?
customPhosGraphics[lc] : phosNode;
-// }
-//
-// // set rect
-// Rectangle2D rect = getCustomShapeRect(image, lc);
-//
-// // create our texture paint
-// Paint paint = null;
-//
-// try {
-// paint = new java.awt.TexturePaint(image, rect);
-// } catch (Exception exc) {
-// paint = java.awt.Color.black;
-// }
-//
-// // add the graphic
-// dingNodeView.addCustomGraphic(rect, paint,
NodeDetails.ANCHOR_CENTER);
-// }
- }
-
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
2012-02-01 19:43:07 UTC (rev 28176)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
2012-02-01 20:08:28 UTC (rev 28177)
@@ -1,18 +1,23 @@
package org.cytoscape.biopax.internal;
+import static org.cytoscape.biopax.internal.BioPaxMapper.BIOPAX_ENTITY_TYPE;
+
import java.io.InputStream;
import org.biopax.paxtools.controller.ModelUtils;
import org.biopax.paxtools.model.Model;
-import org.cytoscape.biopax.internal.action.BioPaxViewTracker;
import org.cytoscape.biopax.internal.util.BioPaxUtil;
import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.io.read.CyNetworkReader;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.model.View;
+import org.cytoscape.view.presentation.property.RichVisualLexicon;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
import org.cytoscape.work.AbstractTask;
@@ -36,7 +41,6 @@
private final CyNetworkNaming naming;
private final VisualMappingManager mappingManager;
private final BioPaxVisualStyleUtil bioPaxVisualStyleUtil;
- private final BioPaxViewTracker biopaxViewTracker;
private InputStream stream;
@@ -61,15 +65,14 @@
*/
public BioPaxReaderTask(InputStream stream, String inputName,
CyNetworkFactory networkFactory, CyNetworkViewFactory
viewFactory,
- CyNetworkNaming naming, BioPaxViewTracker
networkListener,
- VisualMappingManager mappingManager,
BioPaxVisualStyleUtil bioPaxVisualStyleUtil)
+ CyNetworkNaming naming, VisualMappingManager
mappingManager,
+ BioPaxVisualStyleUtil bioPaxVisualStyleUtil)
{
this.stream = stream;
this.inputName = inputName;
this.networkFactory = networkFactory;
this.viewFactory = viewFactory;
this.naming = naming;
- this.biopaxViewTracker = networkListener;
this.mappingManager = mappingManager;
this.bioPaxVisualStyleUtil = bioPaxVisualStyleUtil;
}
@@ -143,12 +146,15 @@
public CyNetworkView buildCyNetworkView(CyNetwork network) {
CyNetworkView view = viewFactory.createNetworkView(network);
- // Set-up the BioPax Visual Style
- VisualStyle bioPaxVisualStyle =
bioPaxVisualStyleUtil.getBioPaxVisualStyle();
-// // set tooltips
-// BioPaxVisualStyleUtil.setNodeToolTips(view);
-// // set style
- mappingManager.setVisualStyle(bioPaxVisualStyle, view);
+ // now everything's done in the listener (BioPaxViewTracker)
+
+// // Set-up the BioPax Visual Style
+// VisualStyle bioPaxVisualStyle =
bioPaxVisualStyleUtil.getBioPaxVisualStyle();
+// // set tooltips
+// setNodeToolTips(view);
+
+ // set style
+// mappingManager.setVisualStyle(bioPaxVisualStyle, view);
// Set up BP UI
// CytoscapeWrapper.initBioPaxPlugInUI();
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
2012-02-01 19:43:07 UTC (rev 28176)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
2012-02-01 20:08:28 UTC (rev 28177)
@@ -2,7 +2,6 @@
import java.io.InputStream;
-import org.cytoscape.biopax.internal.action.BioPaxViewTracker;
import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.read.InputStreamTaskFactory;
@@ -18,7 +17,6 @@
private final CyNetworkFactory networkFactory;
private final CyNetworkViewFactory viewFactory;
private final CyNetworkNaming naming;
- private final BioPaxViewTracker networkTracker;
private InputStream inputStream;
private String inputName;
@@ -26,13 +24,12 @@
private BioPaxVisualStyleUtil bioPaxVisualStyleUtil;
public BioPaxReaderTaskFactory(CyFileFilter filter, CyNetworkFactory
networkFactory,
- CyNetworkViewFactory viewFactory, CyNetworkNaming
naming, BioPaxViewTracker networkTracker,
+ CyNetworkViewFactory viewFactory, CyNetworkNaming
naming,
VisualMappingManager mappingManager,
BioPaxVisualStyleUtil bioPaxVisualStyleUtil) {
this.filter = filter;
this.networkFactory = networkFactory;
this.viewFactory = viewFactory;
this.naming = naming;
- this.networkTracker = networkTracker;
this.mappingManager = mappingManager;
this.bioPaxVisualStyleUtil = bioPaxVisualStyleUtil;
this.inputName = "BioPAX_Network"; //default name fallback
@@ -42,7 +39,7 @@
public TaskIterator createTaskIterator() {
BioPaxReaderTask task = new BioPaxReaderTask(
inputStream, inputName, networkFactory,
viewFactory, naming,
- networkTracker, mappingManager,
bioPaxVisualStyleUtil);
+ mappingManager, bioPaxVisualStyleUtil);
return new TaskIterator(task);
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-02-01 19:43:07 UTC (rev 28176)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-02-01 20:08:28 UTC (rev 28177)
@@ -7,7 +7,6 @@
import org.cytoscape.io.util.StreamUtil;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
-import org.cytoscape.application.swing.CyAction;
import org.cytoscape.application.swing.CySwingApplication;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
@@ -70,8 +69,8 @@
BioPaxContainer bioPaxContainer = new
BioPaxContainer(launchExternalBrowser,cyApplicationManagerRef,cyNetworkViewManagerRef,bioPaxDetailsPanel,cySwingApplicationRef);
BioPaxVisualStyleUtil bioPaxVisualStyleUtil = new
BioPaxVisualStyleUtil(visualStyleFactoryRef,visualMappingManagerRef,discreteMappingFunctionFactoryRef,passthroughMappingFunctionFactoryRef);
- BioPaxViewTracker bioPaxViewTracker = new
BioPaxViewTracker(bioPaxDetailsPanel,bioPaxContainer, cyApplicationManagerRef);
- InputStreamTaskFactory inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,bioPaxViewTracker,visualMappingManagerRef,bioPaxVisualStyleUtil);
+ BioPaxViewTracker bioPaxViewTracker = new
BioPaxViewTracker(bioPaxDetailsPanel,bioPaxContainer, cyApplicationManagerRef,
visualMappingManagerRef, bioPaxVisualStyleUtil);
+ InputStreamTaskFactory inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,visualMappingManagerRef,bioPaxVisualStyleUtil);
CytoPanelComponent cytoPanelComponent = new
BioPaxCytoPanelComponent(bioPaxContainer);
ExportAsBioPAXAction exportAsBioPAXAction = new
ExportAsBioPAXAction(fileUtilRef, cyApplicationManagerRef, bioPaxFilter,
taskManagerRef);
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
2012-02-01 19:43:07 UTC (rev 28176)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
2012-02-01 20:08:28 UTC (rev 28177)
@@ -1,59 +1,37 @@
-// $Id: BioPaxViewTracker.java,v 1.13 2006/06/15 22:02:52 grossb Exp $
-//------------------------------------------------------------------------------
-/** Copyright (c) 2006 Memorial Sloan-Kettering Cancer Center.
- **
- ** Code written by: Ethan Cerami
- ** Authors: Ethan Cerami, Gary Bader, Chris Sander
- **
- ** This library is free software; you can redistribute it and/or modify it
- ** under the terms of the GNU Lesser General Public License as published
- ** by the Free Software Foundation; either version 2.1 of the License, or
- ** any later version.
- **
- ** This library is distributed in the hope that it will be useful, but
- ** WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF
- ** MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and
- ** documentation provided hereunder is on an "as is" basis, and
- ** Memorial Sloan-Kettering Cancer Center
- ** has no obligations to provide maintenance, support,
- ** updates, enhancements or modifications. In no event shall
- ** Memorial Sloan-Kettering Cancer Center
- ** be liable to any party for direct, indirect, special,
- ** incidental or consequential damages, including lost profits, arising
- ** out of the use of this software and its documentation, even if
- ** Memorial Sloan-Kettering Cancer Center
- ** has been advised of the possibility of such damage. See
- ** the GNU Lesser General Public License for more details.
- **
- ** You should have received a copy of the GNU Lesser General Public License
- ** 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.biopax.internal.action;
+import static org.cytoscape.biopax.internal.BioPaxMapper.BIOPAX_ENTITY_TYPE;
+
+import java.util.Iterator;
+
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.application.events.SetCurrentNetworkViewEvent;
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
-import org.cytoscape.biopax.internal.BioPaxMapper;
import org.cytoscape.biopax.internal.view.BioPaxContainer;
import org.cytoscape.biopax.internal.util.BioPaxUtil;
+import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.biopax.internal.view.BioPaxDetailsPanel;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
import org.cytoscape.model.events.RowsSetEvent;
import org.cytoscape.model.events.RowsSetListener;
import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.model.View;
import org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedEvent;
import org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedListener;
import org.cytoscape.view.model.events.NetworkViewAddedEvent;
import org.cytoscape.view.model.events.NetworkViewAddedListener;
+import org.cytoscape.view.presentation.property.RichVisualLexicon;
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyle;
/**
* Listens for Network Events, and takes appropriate Actions.
* May be subclassed.
*
- * @author Ethan Cerami / Benjamin Gross / Igor Rodchenkov.
+ * @author Ethan Cerami, Gary Bader, Chris Sander, Benjamin Gross, Igor
Rodchenkov.
*/
public class BioPaxViewTracker implements NetworkViewAddedListener,
NetworkViewAboutToBeDestroyedListener, SetCurrentNetworkViewListener,
RowsSetListener {
@@ -61,17 +39,25 @@
private final BioPaxDetailsPanel bpPanel;
private final BioPaxContainer bpContainer;
private final CyApplicationManager cyApplicationManager;
+ private final VisualMappingManager visualMappingManager;
+ private final BioPaxVisualStyleUtil bioPaxVisualStyleUtil;
/**
* Constructor.
*
* @param bpPanel BioPaxDetails Panel Object.
*/
- public BioPaxViewTracker(BioPaxDetailsPanel bpPanel, BioPaxContainer
bpContainer, CyApplicationManager cyApplicationManager)
+ public BioPaxViewTracker(BioPaxDetailsPanel bpPanel,
+ BioPaxContainer bpContainer,
+ CyApplicationManager cyApplicationManager,
+ VisualMappingManager visualMappingManager,
+ BioPaxVisualStyleUtil bioPaxVisualStyleUtil)
{
this.bpPanel = bpPanel;
this.bpContainer = bpContainer;
this.cyApplicationManager = cyApplicationManager;
+ this.visualMappingManager = visualMappingManager;
+ this.bioPaxVisualStyleUtil = bioPaxVisualStyleUtil;
}
@@ -80,9 +66,17 @@
*/
@Override
public void handleEvent(NetworkViewAddedEvent e) {
- if(BioPaxUtil.isBioPAXNetwork(e.getNetworkView().getModel())) {
+ CyNetworkView view = e.getNetworkView();
+ if(BioPaxUtil.isBioPAXNetwork(view.getModel())) {
bpContainer.showLegend();
bpPanel.resetText();
+
+ // apply BioPAX visual style and set tool tips
+ setNodeToolTips(view);
+ VisualStyle bioPaxVisualStyle =
bioPaxVisualStyleUtil.getBioPaxVisualStyle();
+ visualMappingManager.setVisualStyle(bioPaxVisualStyle,
view);
+ bioPaxVisualStyle.apply(view);
+ view.updateView();
}
}
@@ -136,9 +130,110 @@
}
} finally {
// update custom nodes
- BioPaxMapper.customNodes(view);
+ customNodes(view);
}
}
}
+
+ private void setNodeToolTips(CyNetworkView networkView) {
+ // iterate through the nodes
+ CyNetwork network = networkView.getModel();
+ for (CyNode node : network.getNodeList()) {
+ CyRow row = network.getRow(node);
+ String tip = row.get(BIOPAX_ENTITY_TYPE, String.class)
+ "\n"
+ + row.get("/cellularLocation",
String.class);
+ View<CyNode> nodeView = networkView.getNodeView(node);
+ nodeView.setLockedValue(RichVisualLexicon.NODE_TOOLTIP,
tip);
+ }
+ }
+
+
+ private static void customNodes(CyNetworkView networkView) {
+ // grab node attributes
+ CyNetwork cyNetwork = networkView.getModel();
+
+ // iterate through the nodes
+ Iterator<CyNode> nodesIt = cyNetwork.getNodeList().iterator();
+ if (nodesIt.hasNext()) {
+ // grab the node
+ CyNode node = nodesIt.next();
+
+ // get chemical modifications
+ int count = 0;
+ boolean isPhosphorylated = false;
+ // TODO: MultiHashMap
+// MultiHashMapDefinition mhmdef =
nodeAttributes.getMultiHashMapDefinition();
+//
+// if
(mhmdef.getAttributeValueType(BIOPAX_CHEMICAL_MODIFICATIONS_MAP) != -1) {
+// MultiHashMap mhmap =
nodeAttributes.getMultiHashMap();
+// CountedIterator modsIt =
mhmap.getAttributeKeyspan(node.getIdentifier(),
+// BIOPAX_CHEMICAL_MODIFICATIONS_MAP, null);
+//
+// // do we have phosphorylation ?
+// while (modsIt.hasNext()) {
+// String modification = (String)
modsIt.next();
+//
+// if
(modification.equals(BioPaxUtil.PHOSPHORYLATION_SITE)) {
+// isPhosphorylated = true;
+//
+// Object[] key = {
BioPaxUtil.PHOSPHORYLATION_SITE };
+// String countStr = (String)
mhmap.getAttributeValue(node.getIdentifier(),
+// BIOPAX_CHEMICAL_MODIFICATIONS_MAP, key);
+// count = ((Integer)
Integer.valueOf(countStr)).intValue();
+//
+// break;
+// }
+// }
+// }
+
+ // if phosphorylated, add custom node
+ if (isPhosphorylated) {
+ addCustomShapes(networkView, node,
"PHOSPHORYLATION_GRAPHICS", count);
+ }
+ }
+ }
+
+
+ /**
+ * Based on given arguments, adds proper custom node shape to node.
+ */
+ private static void addCustomShapes(CyNetworkView networkView, CyNode
node, String shapeType,
+ int modificationCount) {
+ // TODO: Custom graphics
+// // create refs to help views
+// CyNetwork cyNetwork = networkView.getModel();
+// View<CyNode> nodeView = networkView.getNodeView(node);
+// DNodeView dingNodeView = (DNodeView) nodeView;
+//
+// // remove existing custom nodes
+// Iterator<CustomGraphic> it =
dingNodeView.customGraphicIterator();
+// while ( it.hasNext() ) {
+// dingNodeView.removeCustomGraphic( it.next() );
+// }
+//
+// for (int lc = 0; lc < modificationCount; lc++) {
+// // set image
+// BufferedImage image = null;
+//
+// if (shapeType.equals(PHOSPHORYLATION_GRAPHICS)) {
+// image = (cyNetwork.isSelected(node)) ?
customPhosGraphics[lc] : phosNode;
+// }
+//
+// // set rect
+// Rectangle2D rect = getCustomShapeRect(image, lc);
+//
+// // create our texture paint
+// Paint paint = null;
+//
+// try {
+// paint = new java.awt.TexturePaint(image, rect);
+// } catch (Exception exc) {
+// paint = java.awt.Color.black;
+// }
+//
+// // add the graphic
+// dingNodeView.addCustomGraphic(rect, paint,
NodeDetails.ANCHOR_CENTER);
+// }
+ }
}
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
2012-02-01 19:43:07 UTC (rev 28176)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/util/BioPaxVisualStyleUtil.java
2012-02-01 20:08:28 UTC (rev 28177)
@@ -36,16 +36,18 @@
import org.biopax.paxtools.model.BioPAXElement;
import org.biopax.paxtools.model.level3.Control;
+import org.biopax.paxtools.model.level3.ControlType;
import org.biopax.paxtools.model.level3.Interaction;
import org.biopax.paxtools.model.level3.PhysicalEntity;
import static org.cytoscape.biopax.internal.BioPaxMapper.*;
import org.cytoscape.model.CyNode;
-import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.presentation.property.ArrowShapeVisualProperty;
import org.cytoscape.view.presentation.property.MinimalVisualLexicon;
import org.cytoscape.view.presentation.property.NodeShapeVisualProperty;
import org.cytoscape.view.presentation.property.RichVisualLexicon;
+import org.cytoscape.view.presentation.property.values.ArrowShape;
import org.cytoscape.view.presentation.property.values.NodeShape;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualMappingManager;
@@ -155,13 +157,13 @@
//
style.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,false);
- createNodeShape(style);
createNodeSize(style);
createNodeLabel(style);
createNodeColor(style);
createNodeBorderColor(style);
createTargetArrows(style);
-
+ createNodeShape(style);
+
mappingManager.addVisualStyle(style);
}
}
@@ -171,10 +173,10 @@
private void createNodeShape(VisualStyle style) {
style.setDefaultValue(RichVisualLexicon.NODE_SHAPE,
- NodeShapeVisualProperty.RECTANGLE);
+ NodeShapeVisualProperty.ELLIPSE);
// create a discrete mapper, for mapping a biopax type to a
shape
- DiscreteMapping<String, NodeShape> function =
(DiscreteMapping<String, NodeShape>) discreteFactory
+ DiscreteMapping<String, NodeShape> shape =
(DiscreteMapping<String, NodeShape>) discreteFactory
.createVisualMappingFunction(
BIOPAX_ENTITY_TYPE,
String.class, null,
RichVisualLexicon.NODE_SHAPE);
@@ -183,11 +185,11 @@
for (Class<? extends BioPAXElement> claz :
BioPaxUtil.getSubclassNames(PhysicalEntity.class))
{
String name = claz.getSimpleName();
- function.putMapValue(name,
NodeShapeVisualProperty.ELLIPSE);
+ shape.putMapValue(name,
NodeShapeVisualProperty.ELLIPSE);
}
// hack for phosphorylated proteins
- function.putMapValue(BioPaxUtil.PROTEIN_PHOSPHORYLATED,
+ shape.putMapValue(BioPaxUtil.PROTEIN_PHOSPHORYLATED,
NodeShapeVisualProperty.ELLIPSE);
// map all interactions
@@ -196,14 +198,15 @@
for (Class<?> c :
BioPaxUtil.getSubclassNames(Interaction.class)) {
String entityName = c.getSimpleName();
if (Control.class.isAssignableFrom(c)) {
- function.putMapValue(entityName,
+ shape.putMapValue(entityName,
NodeShapeVisualProperty.TRIANGLE);
} else {
- function.putMapValue(entityName,
+ shape.putMapValue(entityName,
NodeShapeVisualProperty.RECTANGLE);
}
}
- style.addVisualMappingFunction(function);
+
+ style.addVisualMappingFunction(shape);
}
@@ -231,15 +234,13 @@
}
// map all complex to required size
-// for (Class c : BioPaxUtil.getSubclassNames(Complex.class)) {
- String entityName = "Complex";//c.getSimpleName();
- width.putMapValue(entityName,
- new
Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH
- *
BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE));
- height.putMapValue(entityName,
- new
Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT
- *
BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE));
-// }
+ String entityName = "Complex";//c.getSimpleName();
+ width.putMapValue(entityName,
+ new
Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_WIDTH
+ *
BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE));
+ height.putMapValue(entityName,
+ new
Double(BIO_PAX_VISUAL_STYLE_PHYSICAL_ENTITY_NODE_HEIGHT
+ *
BIO_PAX_VISUAL_STYLE_COMPLEX_NODE_SIZE_SCALE));
/*
* // hack for phosphorylated proteins - make them large so
label fits
@@ -277,14 +278,14 @@
// create a discrete mapper, for mapping biopax node type
// to a particular node color
- DiscreteMapping<String, Paint> function =
(DiscreteMapping<String, Paint>) discreteFactory
+ DiscreteMapping<String, Paint> color = (DiscreteMapping<String,
Paint>) discreteFactory
.createVisualMappingFunction(
BIOPAX_ENTITY_TYPE,
String.class, null,
MinimalVisualLexicon.NODE_FILL_COLOR);
// map all complex to black
- function.putMapValue("Complex", COMPLEX_NODE_COLOR);
- style.addVisualMappingFunction(function);
+ color.putMapValue("Complex", COMPLEX_NODE_COLOR);
+ style.addVisualMappingFunction(color);
}
@@ -304,67 +305,43 @@
style.addVisualMappingFunction(function);
}
- @Deprecated
+
private void createTargetArrows(VisualStyle style) {
- // DiscreteMapping discreteMapping = new
- // DiscreteMapping(ArrowShape.NONE,
- // BioPaxMapper.BIOPAX_EDGE_TYPE,
- // ObjectMapping.EDGE_MAPPING);
- //
- // discreteMapping.putMapValue(BioPaxMapper.RIGHT,
- // ArrowShape.DELTA);
- // discreteMapping.putMapValue(BioPaxMapper.CONTROLLED,
- // ArrowShape.DELTA);
- // discreteMapping.putMapValue(BioPaxMapper.COFACTOR,
- // ArrowShape.DELTA);
- // discreteMapping.putMapValue(BioPaxMapper.CONTAINS,
- // ArrowShape.CIRCLE);
- //
- // // Inhibition Edges
- // for (ControlType controlType : ControlType.values()) {
- // if(controlType.toString().startsWith("I")) {
- // discreteMapping.putMapValue(controlType.toString(),
ArrowShape.T);
- // }
- // }
- //
- // // Activation Edges
- // for (ControlType controlType : ControlType.values()) {
- // if(controlType.toString().startsWith("A")) {
- // discreteMapping.putMapValue(controlType.toString(),
- // ArrowShape.DELTA);
- // }
- // }
- //
- // Calculator edgeTargetArrowCalculator = new
- // BasicCalculator("BioPAX Target Arrows"
- // + VERSION_POST_FIX,
- // discreteMapping,
- // VisualPropertyType.EDGE_TGTARROW_SHAPE);
- // eac.setCalculator(edgeTargetArrowCalculator);
- }
+
+ DiscreteMapping<String, ArrowShape> tgtArrowShape =
+ (DiscreteMapping<String, ArrowShape>) discreteFactory
+ .createVisualMappingFunction(
+ BIOPAX_EDGE_TYPE, String.class,
null,
+
RichVisualLexicon.EDGE_TARGET_ARROW_SHAPE);
- @Deprecated
- public void setNodeToolTips(CyNetworkView networkView) {
- // // grab node attributes
- // CyAttributes nodeAttributes = Cytoscape.getNodeAttributes();
- //
- // // iterate through the nodes
- // Iterator<NodeView> nodesIt =
networkView.getNodeViewsIterator();
- // while (nodesIt.hasNext()) {
- // NodeView nodeView = nodesIt.next();
- // String id = nodeView.getNode().getIdentifier();
- // String tip =
- // nodeAttributes.getStringAttribute(id,
- // BioPaxMapper.BIOPAX_ENTITY_TYPE)
- // + "\n" +
- // nodeAttributes.getListAttribute(id,
- // BioPaxMapper.BIOPAX_CELLULAR_LOCATIONS);
- //
- // nodeView.setToolTip(tip);
- //
- // if(log.isDebugging())
- // log.debug("tooltip set "+ tip + " for node " + id);
- // }
- // networkView.updateView();
+ tgtArrowShape.putMapValue("right",
ArrowShapeVisualProperty.DELTA);
+ tgtArrowShape.putMapValue("controlled",
ArrowShapeVisualProperty.DELTA);
+ tgtArrowShape.putMapValue("cofactor",
ArrowShapeVisualProperty.DELTA);
+ tgtArrowShape.putMapValue("contains",
ArrowShapeVisualProperty.CIRCLE);
+
+ // Inhibition Edges
+ for (ControlType controlType : ControlType.values()) {
+ if (controlType.toString().startsWith("I")) {
+
tgtArrowShape.putMapValue(controlType.toString(),
+ ArrowShapeVisualProperty.T);
+ }
+ }
+
+ // Activation Edges
+ for (ControlType controlType : ControlType.values()) {
+ if (controlType.toString().startsWith("A")) {
+
tgtArrowShape.putMapValue(controlType.toString(),
+ ArrowShapeVisualProperty.DELTA);
+ }
+ }
+
+// old piece of code...
+// Calculator edgeTargetArrowCalculator = new BasicCalculator(
+// "BioPAX Target Arrows" + VERSION_POST_FIX,
tgtArrowShape,
+// VisualPropertyType.EDGE_TGTARROW_SHAPE);
+// eac.setCalculator(edgeTargetArrowCalculator);
+
+ style.addVisualMappingFunction(tgtArrowShape);
}
+
}
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