Author: rodche
Date: 2012-06-28 16:59:05 -0700 (Thu, 28 Jun 2012)
New Revision: 29722
Removed:
core3/samples/trunk/sample26/target/
Modified:
core3/impl/trunk/biopax-impl/pom.xml
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/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
Log:
Preferred layout related changes in biopax and cpath2 apps; ALSO deleted target
dir (committed by someone accidently)
Modified: core3/impl/trunk/biopax-impl/pom.xml
===================================================================
--- core3/impl/trunk/biopax-impl/pom.xml 2012-06-28 23:02:46 UTC (rev
29721)
+++ core3/impl/trunk/biopax-impl/pom.xml 2012-06-28 23:59:05 UTC (rev
29722)
@@ -53,6 +53,11 @@
<artifactId>swing-util-api</artifactId>
<scope>provided</scope>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>layout-api</artifactId>
+ <scope>provided</scope>
+ </dependency>
<dependency>
<groupId>org.biopax.paxtools</groupId>
<artifactId>paxtools-core</artifactId>
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
2012-06-28 23:02:46 UTC (rev 29721)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTask.java
2012-06-28 23:59:05 UTC (rev 29722)
@@ -1,21 +1,16 @@
package org.cytoscape.biopax.internal;
import java.io.InputStream;
-import java.util.Arrays;
-import java.util.HashSet;
import org.apache.commons.lang.StringEscapeUtils;
-import org.biopax.paxtools.controller.ModelUtils;
import org.biopax.paxtools.model.Model;
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.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
import org.slf4j.Logger;
@@ -35,8 +30,6 @@
private final CyNetworkFactory networkFactory;
private final CyNetworkViewFactory viewFactory;
private final CyNetworkNaming naming;
- private final VisualMappingManager mappingManager;
- private final BioPaxVisualStyleUtil bioPaxVisualStyleUtil;
private InputStream stream;
@@ -44,16 +37,6 @@
private CyNetwork network;
- /**
- * Constructor
- *
- * @param fileName File Name.
- */
-// public BioPaxReaderTask(String fileName) {
-// this.fileName = fileName;
-// this.model = null;
-// layout = getDefaultLayoutAlgorithm();
-// }
/**
* Constructor
@@ -61,16 +44,13 @@
*/
public BioPaxReaderTask(InputStream stream, String inputName,
CyNetworkFactory networkFactory, CyNetworkViewFactory
viewFactory,
- CyNetworkNaming naming, VisualMappingManager
mappingManager,
- BioPaxVisualStyleUtil bioPaxVisualStyleUtil)
+ CyNetworkNaming naming)
{
this.stream = stream;
this.inputName = inputName;
this.networkFactory = networkFactory;
this.viewFactory = viewFactory;
this.naming = naming;
- this.mappingManager = mappingManager;
- this.bioPaxVisualStyleUtil = bioPaxVisualStyleUtil;
}
@@ -142,28 +122,8 @@
@Override
public CyNetworkView buildCyNetworkView(CyNetwork network) {
- CyNetworkView view = viewFactory.createNetworkView(network);
-
- // 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();
-// bpContainer.showLegend();
-
- // add node's context menu
- // TODO: NodeViewTaskFactory?
-// BiopaxNodeCtxMenuListener nodeCtxMenuListener = new
BiopaxNodeCtxMenuListener();
-// view.addNodeContextMenuListener(nodeCtxMenuListener);
-
- return view;
+ return viewFactory.createNetworkView(network);
+ //there is a BioPAX Networks Tracker that listens to the
network added events and sets the visual style, layout, etc...
}
}
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
2012-06-28 23:02:46 UTC (rev 29721)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/BioPaxReaderTaskFactory.java
2012-06-28 23:59:05 UTC (rev 29722)
@@ -2,13 +2,11 @@
import java.io.InputStream;
-import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.io.CyFileFilter;
import org.cytoscape.io.read.AbstractInputStreamTaskFactory;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.work.TaskIterator;
public class BioPaxReaderTaskFactory extends AbstractInputStreamTaskFactory {
@@ -17,18 +15,13 @@
private final CyNetworkViewFactory viewFactory;
private final CyNetworkNaming naming;
- private VisualMappingManager mappingManager;
- private BioPaxVisualStyleUtil bioPaxVisualStyleUtil;
-
public BioPaxReaderTaskFactory(CyFileFilter filter, CyNetworkFactory
networkFactory,
- CyNetworkViewFactory viewFactory, CyNetworkNaming
naming,
- VisualMappingManager mappingManager,
BioPaxVisualStyleUtil bioPaxVisualStyleUtil) {
+ CyNetworkViewFactory viewFactory, CyNetworkNaming
naming)
+ {
super(filter);
this.networkFactory = networkFactory;
this.viewFactory = viewFactory;
this.naming = naming;
- this.mappingManager = mappingManager;
- this.bioPaxVisualStyleUtil = bioPaxVisualStyleUtil;
}
@@ -37,10 +30,9 @@
if(inputName == null)
inputName = "BioPAX_Network"; //default name fallback
- BioPaxReaderTask task = new BioPaxReaderTask(
- is, inputName, networkFactory, viewFactory,
naming,
- mappingManager, bioPaxVisualStyleUtil);
- return new TaskIterator(task);
+ return new TaskIterator(
+ new BioPaxReaderTask(is, inputName, networkFactory,
viewFactory, naming)
+ );
}
}
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
2012-06-28 23:02:46 UTC (rev 29721)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-06-28 23:59:05 UTC (rev 29722)
@@ -1,11 +1,13 @@
package org.cytoscape.biopax.internal;
-import org.biopax.paxtools.io.SimpleIOHandler;
-import org.biopax.paxtools.model.Model;
+//import org.biopax.paxtools.io.SimpleIOHandler;
+//import org.biopax.paxtools.model.Model;
import org.cytoscape.util.swing.OpenBrowser;
import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.io.util.StreamUtil;
+import org.cytoscape.property.CyProperty;
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
import org.cytoscape.application.swing.CySwingApplication;
@@ -16,6 +18,8 @@
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedListener;
import org.cytoscape.view.model.events.NetworkViewAddedListener;
+import org.cytoscape.work.TaskManager;
+import org.cytoscape.work.swing.DialogTaskManager;
import org.cytoscape.biopax.internal.BioPaxFilter;
import org.cytoscape.biopax.internal.action.BioPaxViewTracker;
@@ -59,18 +63,21 @@
VisualStyleFactory visualStyleFactoryRef =
getService(bc,VisualStyleFactory.class);
VisualMappingFunctionFactory discreteMappingFunctionFactoryRef
= getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=discrete)");
VisualMappingFunctionFactory
passthroughMappingFunctionFactoryRef =
getService(bc,VisualMappingFunctionFactory.class,"(mapping.type=passthrough)");
-
+ CyLayoutAlgorithmManager cyLayoutsRef =
getService(bc,CyLayoutAlgorithmManager.class);
+ TaskManager taskManagerRef = getService(bc,
DialogTaskManager.class);
+ CyProperty<Properties> cytoscapePropertiesServiceRef =
getService(bc, CyProperty.class, "(cyPropertyName=cytoscape3.props)");
+
BioPaxFilter bioPaxFilter = new BioPaxFilter(streamUtilRef);
LaunchExternalBrowser launchExternalBrowser = new
LaunchExternalBrowser(openBrowserRef);
BioPaxDetailsPanel bioPaxDetailsPanel = new
BioPaxDetailsPanel(launchExternalBrowser);
BioPaxContainer bioPaxContainer = new
BioPaxContainer(launchExternalBrowser,cyApplicationManagerRef,cyNetworkViewManagerRef,bioPaxDetailsPanel,cySwingApplicationRef);
BioPaxVisualStyleUtil bioPaxVisualStyleUtil = new
BioPaxVisualStyleUtil(visualStyleFactoryRef,visualMappingManagerRef,discreteMappingFunctionFactoryRef,passthroughMappingFunctionFactoryRef);
-
- BioPaxViewTracker bioPaxViewTracker = new
BioPaxViewTracker(bioPaxDetailsPanel,bioPaxContainer, cyApplicationManagerRef,
visualMappingManagerRef, bioPaxVisualStyleUtil);
- InputStreamTaskFactory inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,visualMappingManagerRef,bioPaxVisualStyleUtil);
+ BioPaxViewTracker bioPaxViewTracker = new
BioPaxViewTracker(bioPaxDetailsPanel,bioPaxContainer, cyApplicationManagerRef,
+ visualMappingManagerRef, bioPaxVisualStyleUtil,
cyLayoutsRef, taskManagerRef, cytoscapePropertiesServiceRef);
+ InputStreamTaskFactory inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef);
CytoPanelComponent cytoPanelComponent = new
BioPaxCytoPanelComponent(bioPaxContainer);
- // register/export core Cytoscape osgi service implementations
+ // register/export osgi services
registerService(bc,inputStreamTaskFactory,InputStreamTaskFactory.class, new
Properties());
registerService(bc,cytoPanelComponent,CytoPanelComponent.class,
new Properties());
registerService(bc,(RowsSetListener)bioPaxViewTracker,RowsSetListener.class,
new Properties());
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
2012-06-28 23:02:46 UTC (rev 29721)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/BioPaxViewTracker.java
2012-06-28 23:59:05 UTC (rev 29722)
@@ -3,6 +3,7 @@
import static org.cytoscape.biopax.internal.BioPaxMapper.BIOPAX_ENTITY_TYPE;
import java.util.Iterator;
+import java.util.Properties;
import javax.swing.SwingUtilities;
@@ -10,7 +11,6 @@
import org.cytoscape.application.events.SetCurrentNetworkViewEvent;
import org.cytoscape.application.events.SetCurrentNetworkViewListener;
import org.cytoscape.biopax.internal.BioPaxMapper;
-import org.cytoscape.biopax.internal.util.BioPaxUtil;
import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.biopax.internal.view.BioPaxContainer;
import org.cytoscape.biopax.internal.view.BioPaxDetailsPanel;
@@ -19,6 +19,9 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.events.RowsSetEvent;
import org.cytoscape.model.events.RowsSetListener;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
import org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedEvent;
@@ -28,6 +31,7 @@
import org.cytoscape.view.presentation.property.BasicVisualLexicon;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
+import org.cytoscape.work.TaskManager;
/**
@@ -44,23 +48,34 @@
private final CyApplicationManager cyApplicationManager;
private final VisualMappingManager visualMappingManager;
private final BioPaxVisualStyleUtil bioPaxVisualStyleUtil;
+ private final CyLayoutAlgorithmManager layoutAlgorithmManager;
+ private final TaskManager taskManagerRef;
+ private final CyProperty<Properties> prop;
/**
* Constructor.
*
* @param bpPanel BioPaxDetails Panel Object.
+ * @param taskManagerRef
+ * @param cytoscapePropertiesServiceRef
*/
public BioPaxViewTracker(BioPaxDetailsPanel bpPanel,
BioPaxContainer bpContainer,
CyApplicationManager cyApplicationManager,
VisualMappingManager visualMappingManager,
- BioPaxVisualStyleUtil bioPaxVisualStyleUtil)
+ BioPaxVisualStyleUtil bioPaxVisualStyleUtil,
+ CyLayoutAlgorithmManager layoutAlgorithmManager,
+ TaskManager taskManagerRef,
+ CyProperty<Properties> prop)
{
this.bpPanel = bpPanel;
this.bpContainer = bpContainer;
this.cyApplicationManager = cyApplicationManager;
this.visualMappingManager = visualMappingManager;
this.bioPaxVisualStyleUtil = bioPaxVisualStyleUtil;
+ this.layoutAlgorithmManager = layoutAlgorithmManager;
+ this.taskManagerRef = taskManagerRef;
+ this.prop = prop;
}
@@ -83,6 +98,24 @@
visualMappingManager.setVisualStyle(bioPaxVisualStyle, view);
bioPaxVisualStyle.apply(view);
view.updateView();
+
+ String pref =
CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME;
+ if (prop != null)
+ pref =
prop.getProperties().getProperty("preferredLayoutAlgorithm", pref);
+ final CyLayoutAlgorithm layout =
layoutAlgorithmManager.getLayout(pref);
+// final CyLayoutAlgorithm layout =
layoutAlgorithmManager.getDefaultLayout();
+ final Object context =
layout.getDefaultLayoutContext();
+ taskManagerRef.execute(
+ layout.createTaskIterator(view,
context, CyLayoutAlgorithm.ALL_NODE_VIEWS,""));
+
+//not yet migrated // set tooltips
+// setNodeToolTips(view);
+ // add node's context menu
+ // TODO: NodeViewTaskFactory?
+// BiopaxNodeCtxMenuListener nodeCtxMenuListener =
new BiopaxNodeCtxMenuListener();
+//
view.addNodeContextMenuListener(nodeCtxMenuListener);
+
+ view.updateView();
}
});
}
Modified:
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2012-06-28 23:02:46 UTC (rev 29721)
+++
core3/impl/trunk/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2012-06-28 23:59:05 UTC (rev 29722)
@@ -205,10 +205,11 @@
taskMonitor.setProgress(1.0);
}
- CyLayoutAlgorithmManager layoutManager =
cPathFactory.getCyLayoutAlgorithmManager();
- CyLayoutAlgorithm layout =
layoutManager.getDefaultLayout();
- Object context = layout.getDefaultLayoutContext();
-
insertTasksAfterCurrentTask(layout.createTaskIterator(view, context,
CyLayoutAlgorithm.ALL_NODE_VIEWS,""));
+// biopax/sif core apps will do
+// CyLayoutAlgorithmManager layoutManager =
cPathFactory.getCyLayoutAlgorithmManager();
+// CyLayoutAlgorithm layout =
layoutManager.getDefaultLayout();
+// Object context = layout.getDefaultLayoutContext();
+//
insertTasksAfterCurrentTask(layout.createTaskIterator(view, context,
CyLayoutAlgorithm.ALL_NODE_VIEWS,""));
} catch (IOException e) {
throw new Exception("Failed to retrieve records.", e);
--
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