Author: jm
Date: 2012-03-09 13:45:31 -0800 (Fri, 09 Mar 2012)
New Revision: 28473
Added:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutContext.java
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithmContext.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/core-task-impl/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReader.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayout.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/StackedNodeLayout.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayout.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayout.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-impl/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapper.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PSIMI10XMLNetworkViewReader.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PSIMI25XMLNetworkViewReader.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/performance/src/main/java/org/cytoscape/psi_mi/internal/PerfTest.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutMenuPopulator.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/UndoSupportTaskFactory.java
Log:
Cleaned up CyLayoutAlgorithm API
Introduced CyLayoutContext as base interface for layout algorithm settings
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithm.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -35,8 +35,6 @@
import java.util.List;
import java.util.Set;
-import org.cytoscape.view.model.CyNetworkView;
-import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TunableValidator;
import org.cytoscape.work.TunableValidator.ValidationState;
@@ -45,7 +43,7 @@
* The AbstractLayoutAlgorithm provides a basic implementation of a layout
TaskFactory.
* @CyAPI.Abstract.Class
*/
-abstract public class AbstractLayoutAlgorithm<T extends
AbstractLayoutAlgorithmContext> implements CyLayoutAlgorithm<T> {
+abstract public class AbstractLayoutAlgorithm<T extends CyLayoutContext>
implements CyLayoutAlgorithm<T> {
private final boolean supportsSelectedOnly;
private final String humanName;
@@ -125,21 +123,15 @@
return new ArrayList<String>();
}
- public boolean isReady(T tunableContext, CyNetworkView networkView) {
- tunableContext.setNetworkView(networkView);
+ @Override
+ public boolean isReady(T tunableContext) {
+ if (tunableContext.getNetworkView() == null) {
+ return false;
+ }
if (tunableContext instanceof TunableValidator) {
StringBuilder errors = new StringBuilder();
return ((TunableValidator)
tunableContext).getValidationState(errors) == ValidationState.OK;
}
return true;
}
-
- public final TaskIterator createTaskIterator(T tunableContext,
CyNetworkView networkView) {
- tunableContext.setNetworkView(networkView);
- if (tunableContext.useSelectedOnly())
- tunableContext.initStaticNodes(networkView);
- return createTaskIterator(tunableContext);
- }
-
- protected abstract TaskIterator createTaskIterator(T tunableContext);
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithmContext.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithmContext.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/AbstractLayoutAlgorithmContext.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -15,7 +15,7 @@
import org.cytoscape.work.Tunable;
import org.cytoscape.work.util.ListSingleSelection;
-public class AbstractLayoutAlgorithmContext {
+public class AbstractLayoutAlgorithmContext implements CyLayoutContext {
private static final String ALL_NODES = " All Nodes";
private static final String SELECTED_NODES_ONLY = " Selected Nodes
Only";
@@ -145,6 +145,10 @@
node_count = Math.sqrt(node_count);
node_count *= 100;
currentSize = new Dimension((int) node_count, (int) node_count);
+
+ if (useSelectedOnly()) {
+ initStaticNodes(networkView);
+ }
}
public CyNetworkView getNetworkView() {
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutAlgorithm.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -33,17 +33,16 @@
import java.util.List;
import java.util.Set;
-import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskIterator;
/**
* An extension of NetworkViewTaskFactory specific to layout algorithms.
* @CyAPI.Spi.Interface
*/
-public interface CyLayoutAlgorithm<T> {
- TaskIterator createTaskIterator(T tunableContext, CyNetworkView
networkView);
- boolean isReady(T tunableContext, CyNetworkView networkView);
- T createTunableContext();
+public interface CyLayoutAlgorithm<T extends CyLayoutContext> {
+ TaskIterator createTaskIterator(T layoutContext);
+ boolean isReady(T layoutContext);
+ T createLayoutContext();
/**
* Tests to see if this layout supports doing a layout on a subset of
the
Added:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutContext.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutContext.java
(rev 0)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/api/layout-api/src/main/java/org/cytoscape/view/layout/CyLayoutContext.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -0,0 +1,8 @@
+package org.cytoscape.view.layout;
+
+import org.cytoscape.view.model.CyNetworkView;
+
+public interface CyLayoutContext {
+ CyNetworkView getNetworkView();
+ void setNetworkView(CyNetworkView networkView);
+}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/core-task-impl/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/core-task-impl/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/core-task-impl/src/main/java/org/cytoscape/task/internal/layout/ApplyPreferredLayoutTask.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -33,6 +33,7 @@
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.undo.UndoSupport;
@@ -82,10 +83,11 @@
pref = props.getProperty("preferredLayoutAlgorithm",
DEF_LAYOUT);
tm.setProgress(0.2d);
final CyLayoutAlgorithm layout = layouts.getLayout(pref);
-
if (layout != null) {
tm.setProgress(0.6);
-
insertTasksAfterCurrentTask(layout.createTaskIterator(layout.createTunableContext(),
view));
+ CyLayoutContext context = layout.createLayoutContext();
+ context.setNetworkView(view);
+
insertTasksAfterCurrentTask(layout.createTaskIterator(context));
} else {
throw new IllegalArgumentException("Couldn't find
layout algorithm: " + pref);
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -2,6 +2,7 @@
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
@@ -21,9 +22,10 @@
// final CyLayoutAlgorithm layout =
layouts.getLayout(CyLayoutAlgorithmManager.DEFAULT_LAYOUT_NAME);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
taskMonitor.setProgress(0.1);
- Object context = layout.createTunableContext();
+ CyLayoutContext context = layout.createLayoutContext();
+ context.setNetworkView(util.appManager.getCurrentNetworkView());
taskMonitor.setProgress(0.2);
- insertTasksAfterCurrentTask(layout.createTaskIterator(context,
util.appManager.getCurrentNetworkView()));
+ insertTasksAfterCurrentTask(layout.createTaskIterator(context));
taskMonitor.setProgress(1.0);
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/cpath2-impl/src/main/java/org/cytoscape/cpath2/internal/task/ExecuteGetRecordByCPathId.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -42,6 +42,7 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.vizmap.VisualStyle;
@@ -207,7 +208,9 @@
CyLayoutAlgorithmManager layoutManager =
cPathFactory.getCyLayoutAlgorithmManager();
CyLayoutAlgorithm layout =
layoutManager.getDefaultLayout();
-
insertTasksAfterCurrentTask(layout.createTaskIterator(layout.createTunableContext(),
view));
+ CyLayoutContext context = layout.createLayoutContext();
+ context.setNetworkView(view);
+
insertTasksAfterCurrentTask(layout.createTaskIterator(context));
} catch (IOException e) {
throw new Exception("Failed to retrieve records.", e);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReader.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReader.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/graphml-impl/src/main/java/org/cytoscape/io/internal/read/graphml/GraphMLReader.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -14,8 +14,10 @@
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.model.subnetwork.CyRootNetworkManager;
+import org.cytoscape.view.layout.AbstractLayoutAlgorithmContext;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.vizmap.VisualStyle;
@@ -23,8 +25,6 @@
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.TaskMonitor;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
import org.xml.sax.InputSource;
import org.xml.sax.helpers.ParserAdapter;
@@ -99,9 +99,10 @@
final CyNetworkView view =
cyNetworkViewFactory.createNetworkView(network);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
-
+ CyLayoutContext context = layout.createLayoutContext();
+ context.setNetworkView(view);
// Force to run this task here to avoid concurrency problem.
- TaskIterator itr = layout.createTaskIterator(null, view);
+ TaskIterator itr = layout.createTaskIterator(context);
Task nextTask = itr.next();
try {
nextTask.run(taskMonitor);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkReader.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -45,6 +45,7 @@
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.Task;
@@ -190,9 +191,10 @@
final CyNetworkView view =
cyNetworkViewFactory.createNetworkView(network);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
-
+ CyLayoutContext context = layout.createLayoutContext();
+ context.setNetworkView(view);
// Force to run this task here to avoid concurrency problem.
- TaskIterator itr = layout.createTaskIterator(null, view);
+ TaskIterator itr = layout.createTaskIterator(context);
Task nextTask = itr.next();
try {
nextTask.run(parentTaskMonitor);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/impl/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -23,6 +23,7 @@
import org.cytoscape.property.SimpleCyProperty;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.AbstractTask;
@@ -51,8 +52,11 @@
public void setUp() throws Exception {
taskMonitor = mock(TaskMonitor.class);
+ CyLayoutContext context = mock(CyLayoutContext.class);
+
CyLayoutAlgorithm def = mock(CyLayoutAlgorithm.class);
- when(def.createTaskIterator(Mockito.any(),
Mockito.any(CyNetworkView.class))).thenReturn(new TaskIterator(new
SimpleTask()));
+ when(def.createLayoutContext()).thenReturn(context);
+
when(def.createTaskIterator(Mockito.any(CyLayoutContext.class))).thenReturn(new
TaskIterator(new SimpleTask()));
layouts = mock(CyLayoutAlgorithmManager.class);
when(layouts.getDefaultLayout()).thenReturn(def);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/io-impl/performance/src/main/java/org/cytoscape/io/read/sif/PerfTest.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -25,6 +25,7 @@
import org.cytoscape.property.SimpleCyProperty;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.model.subnetwork.CyRootNetwork;
@@ -56,7 +57,7 @@
taskMonitor = mock(TaskMonitor.class);
CyLayoutAlgorithm def = mock(CyLayoutAlgorithm.class);
- when(def.createTaskIterator(Mockito.any(),
Mockito.any(CyNetworkView.class))).thenReturn(new TaskIterator(new
SimpleTask()));
+
when(def.createTaskIterator(Mockito.any(CyLayoutContext.class))).thenReturn(new
TaskIterator(new SimpleTask()));
layouts = mock(CyLayoutAlgorithmManager.class);
when(layouts.getDefaultLayout()).thenReturn(def);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayout.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayout.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/GroupAttributesLayout.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -85,7 +85,7 @@
}
@Override
- public GroupAttributesLayoutContext createTunableContext() {
+ public GroupAttributesLayoutContext createLayoutContext() {
return new GroupAttributesLayoutContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/StackedNodeLayout.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/StackedNodeLayout.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/StackedNodeLayout.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -49,7 +49,7 @@
}
@Override
- public StackedNodeLayoutContext createTunableContext() {
+ public StackedNodeLayoutContext createLayoutContext() {
return new StackedNodeLayoutContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutFRAlgorithm.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -70,7 +70,7 @@
}
@Override
- public BioLayoutFRContext createTunableContext() {
+ public BioLayoutFRContext createLayoutContext() {
return new BioLayoutFRContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/bioLayout/BioLayoutKKAlgorithm.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -70,7 +70,7 @@
}
@Override
- public BioLayoutKKContext createTunableContext() {
+ public BioLayoutKKContext createLayoutContext() {
return new BioLayoutKKContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/circularLayout/CircularLayoutAlgorithm.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -20,7 +20,7 @@
}
@Override
- public CircularLayoutContext createTunableContext() {
+ public CircularLayoutContext createLayoutContext() {
return new CircularLayoutContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayout.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayout.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/AttributeCircleLayout.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -105,7 +105,7 @@
}
@Override
- public AttributeCircleLayoutContext createTunableContext() {
+ public AttributeCircleLayoutContext createLayoutContext() {
return new AttributeCircleLayoutContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/DegreeSortedCircleLayout.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -19,7 +19,7 @@
}
@Override
- public DegreeSortedCircleContext createTunableContext() {
+ public DegreeSortedCircleContext createLayoutContext() {
return new DegreeSortedCircleContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayout.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayout.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/graphPartition/ISOMLayout.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -22,7 +22,7 @@
}
@Override
- public ISOMLayoutContext createTunableContext() {
+ public ISOMLayoutContext createLayoutContext() {
return new ISOMLayoutContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-cytoscape-impl/src/main/java/csapps/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -80,7 +80,7 @@
}
@Override
- public HierarchicalLayoutContext createTunableContext() {
+ public HierarchicalLayoutContext createLayoutContext() {
return new HierarchicalLayoutContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-impl/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-impl/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-impl/src/main/java/org/cytoscape/view/layout/internal/algorithms/GridNodeLayout.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -52,7 +52,7 @@
}
@Override
- public GridNodeLayoutContext createTunableContext() {
+ public GridNodeLayoutContext createLayoutContext() {
return new GridNodeLayoutContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapper.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapper.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapper.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -161,7 +161,7 @@
}
@Override
- public AbstractLayoutAlgorithmContext createTunableContext() {
+ public AbstractLayoutAlgorithmContext createLayoutContext() {
return new
AbstractLayoutAlgorithmContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/layout-prefuse-impl/src/main/java/org/cytoscape/prefuse/layouts/internal/ForceDirectedLayout.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -41,7 +41,7 @@
}
@Override
- public ForceDirectedLayoutContext createTunableContext() {
+ public ForceDirectedLayoutContext createLayoutContext() {
return new ForceDirectedLayoutContext(supportsSelectedOnly(),
supportsNodeAttributes(), supportsEdgeAttributes());
}
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PSIMI10XMLNetworkViewReader.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PSIMI10XMLNetworkViewReader.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PSIMI10XMLNetworkViewReader.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -16,6 +16,7 @@
import org.cytoscape.psi_mi.internal.data_mapper.PSIMI25EntryMapper;
import org.cytoscape.psi_mi.internal.model.Interaction;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -109,8 +110,10 @@
public CyNetworkView buildCyNetworkView(final CyNetwork network) {
final CyNetworkView view =
networkViewFactory.createNetworkView(network);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
+ CyLayoutContext context = layout.createLayoutContext();
+ context.setNetworkView(view);
// Force to run this task here to avoid concurrency problem.
- TaskIterator itr = layout.createTaskIterator(null, view);
+ TaskIterator itr = layout.createTaskIterator(context);
Task nextTask = itr.next();
try {
nextTask.run(parentTaskMonitor);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PSIMI25XMLNetworkViewReader.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PSIMI25XMLNetworkViewReader.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PSIMI25XMLNetworkViewReader.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -7,6 +7,7 @@
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.psi_mi.internal.data_mapper.PSIMI25EntryMapper;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -84,8 +85,10 @@
public CyNetworkView buildCyNetworkView(final CyNetwork network) {
final CyNetworkView view =
networkViewFactory.createNetworkView(network);
final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
+ CyLayoutContext context = layout.createLayoutContext();
+ context.setNetworkView(view);
// Force to run this task here to avoid concurrency problem.
- TaskIterator itr = layout.createTaskIterator(null, view);
+ TaskIterator itr = layout.createTaskIterator(context);
Task nextTask = itr.next();
try {
nextTask.run(parentTaskMonitor);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -9,6 +9,7 @@
import org.cytoscape.model.CyNetworkFactory;
import org.cytoscape.property.CyProperty;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -82,9 +83,10 @@
pref =
prop.getProperties().getProperty("preferredLayoutAlgorithm", pref);
final CyLayoutAlgorithm layout = layouts.getLayout(pref);
-
+ CyLayoutContext context = layout.createLayoutContext();
+ context.setNetworkView(view);
// Force to run this task here to avoid concurrency problem.
- TaskIterator itr = layout.createTaskIterator(null, view);
+ TaskIterator itr = layout.createTaskIterator(context);
Task nextTask = itr.next();
try {
nextTask.run(parentTaskMonitor);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -16,7 +16,7 @@
import org.cytoscape.psi_mi.internal.plugin.PsiMiCyFileFilter.PSIMIVersion;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
-import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
@@ -50,7 +50,7 @@
MockitoAnnotations.initMocks(this);
when(layouts.getDefaultLayout()).thenReturn(layout);
- when(layout.createTaskIterator(Mockito.any(),
Mockito.any(CyNetworkView.class))).thenReturn(new TaskIterator(task));
+
when(layout.createTaskIterator(Mockito.any(CyLayoutContext.class))).thenReturn(new
TaskIterator(task));
networkFactory = new NetworkTestSupport().getNetworkFactory();
networkViewFactory = new
NetworkViewTestSupport().getNetworkViewFactory();
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/impl/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -18,7 +18,7 @@
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.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
@@ -53,7 +53,7 @@
when(layouts.getDefaultLayout()).thenReturn(
layout);
- when(layout.createTaskIterator(Mockito.any(),
Mockito.any(CyNetworkView.class))).thenReturn(new TaskIterator(task));
+
when(layout.createTaskIterator(Mockito.any(CyLayoutContext.class))).thenReturn(new
TaskIterator(task));
networkFactory = new NetworkTestSupport().getNetworkFactory();
networkViewFactory = new
NetworkViewTestSupport().getNetworkViewFactory();
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/performance/src/main/java/org/cytoscape/psi_mi/internal/PerfTest.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/performance/src/main/java/org/cytoscape/psi_mi/internal/PerfTest.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/psi-mi-impl/performance/src/main/java/org/cytoscape/psi_mi/internal/PerfTest.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -20,7 +20,7 @@
import org.cytoscape.psi_mi.internal.plugin.PsiMiTabReader;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
-import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskIterator;
@@ -47,7 +47,7 @@
public PerfTest() {
layout = mock(CyLayoutAlgorithm.class);
- when(layout.createTaskIterator(Mockito.any(),
Mockito.any(CyNetworkView.class))).thenReturn(new TaskIterator(new
SimpleTask()));
+
when(layout.createTaskIterator(Mockito.any(CyLayoutContext.class))).thenReturn(new
TaskIterator(new SimpleTask()));
layouts = mock(CyLayoutAlgorithmManager.class);
when(layouts.getLayout(anyString())).thenReturn(layout);
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutMenuPopulator.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutMenuPopulator.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutMenuPopulator.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -54,6 +54,7 @@
import org.cytoscape.view.layout.AbstractLayoutAlgorithm;
import org.cytoscape.view.layout.AbstractLayoutAlgorithmContext;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
@@ -100,7 +101,7 @@
// Implementors of CyLayoutAlgorithm would need to mimic
that
// somehow if they choose to implement from scratch.
UndoSupportTaskFactory<T> taskFactory = new
UndoSupportTaskFactory<T>((AbstractLayoutAlgorithm<T>) layout, undo,
eventHelper);
- T context = taskFactory.createTunableContext();
+ T context = taskFactory.createLayoutContext();
TaskFactory provisioner =
factoryProvisioner.createFor(wrapWithContext(taskFactory, context));
// get the submenu listener from the task manager
DynamicSubmenuListener submenu =
tm.getConfiguration(provisioner, context);
@@ -121,16 +122,18 @@
listenerMap.put(layout,ml);
}
- private <T> NetworkViewTaskFactory wrapWithContext(final
CyLayoutAlgorithm<T> layout, final T tunableContext) {
+ private <T extends CyLayoutContext> NetworkViewTaskFactory
wrapWithContext(final CyLayoutAlgorithm<T> layout, final T tunableContext) {
return new NetworkViewTaskFactory() {
@Override
public boolean isReady(CyNetworkView networkView) {
- return layout.isReady(tunableContext,
networkView);
+ tunableContext.setNetworkView(networkView);
+ return layout.isReady(tunableContext);
}
@Override
public TaskIterator createTaskIterator(CyNetworkView
networkView) {
- return
layout.createTaskIterator(tunableContext, networkView);
+ tunableContext.setNetworkView(networkView);
+ return
layout.createTaskIterator(tunableContext);
}
};
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -58,6 +58,7 @@
import org.cytoscape.task.TaskFactoryProvisioner;
import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.layout.CyLayoutContext;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskIterator;
@@ -358,7 +359,7 @@
// if it's a string, that means it's the instructions
if (!(o instanceof String)) {
final CyLayoutAlgorithm newLayout =
(CyLayoutAlgorithm)o;
- Object context =
newLayout.createTunableContext();
+ CyLayoutContext context =
newLayout.createLayoutContext();
TaskFactory provisioner =
factoryProvisioner.createFor(wrapWithContext(newLayout, context));
if (!provisioner.isReady()) {
throw new
IllegalArgumentException("Layout is not fully configured");
@@ -380,16 +381,18 @@
}
}
- private <T> NetworkViewTaskFactory wrapWithContext(final
CyLayoutAlgorithm<T> layout, final T tunableContext) {
+ private <T extends CyLayoutContext> NetworkViewTaskFactory
wrapWithContext(final CyLayoutAlgorithm<T> layout, final T tunableContext) {
return new NetworkViewTaskFactory() {
@Override
public boolean isReady(CyNetworkView networkView) {
- return layout.isReady(tunableContext,
networkView);
+ tunableContext.setNetworkView(networkView);
+ return layout.isReady(tunableContext);
}
@Override
public TaskIterator createTaskIterator(CyNetworkView
networkView) {
- return
layout.createTaskIterator(tunableContext, networkView);
+ tunableContext.setNetworkView(networkView);
+ return
layout.createTaskIterator(tunableContext);
}
};
}
Modified:
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/UndoSupportTaskFactory.java
===================================================================
---
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/UndoSupportTaskFactory.java
2012-03-09 21:44:57 UTC (rev 28472)
+++
csplugins/trunk/toronto/jm/cy3-stateless-taskfactory-alt1/impl/swing-application-impl/src/main/java/org/cytoscape/internal/layout/ui/UndoSupportTaskFactory.java
2012-03-09 21:45:31 UTC (rev 28473)
@@ -26,7 +26,7 @@
@Override
public TaskIterator createTaskIterator(T tunableContext) {
CyNetworkView networkView = tunableContext.getNetworkView();
- TaskIterator source =
delegate.createTaskIterator(tunableContext, networkView);
+ TaskIterator source =
delegate.createTaskIterator(tunableContext);
Task[] tasks = new Task[source.getNumTasks() + 1];
tasks[0] = new UndoSupportTask(name, undo, eventHelper,
networkView);
for (int i = 1; i < tasks.length; i++) {
@@ -35,12 +35,13 @@
return new TaskIterator(tasks.length, tasks);
}
- public boolean isReady(T tunableContext, CyNetworkView networkView) {
- return delegate.isReady(tunableContext, networkView);
+ @Override
+ public boolean isReady(T tunableContext) {
+ return delegate.isReady(tunableContext);
}
@Override
- public T createTunableContext() {
- return delegate.createTunableContext();
+ public T createLayoutContext() {
+ return delegate.createLayoutContext();
}
}
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