Author: mes
Date: 2011-04-29 16:23:23 -0700 (Fri, 29 Apr 2011)
New Revision: 24867
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/CyLayoutsImpl.java
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
Log:
Another update to Layout API
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/ApplyLayoutTask.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -18,7 +18,7 @@
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
// final CyLayoutAlgorithm layout =
layouts.getLayout(CyLayouts.DEFAULT_LAYOUT_NAME);
- final CyLayoutAlgorithm layout =
layouts.getDefaultLayout(util.appManager.getCurrentNetworkView());
+ final CyLayoutAlgorithm layout = layouts.getDefaultLayout();
layout.setNetworkView(util.appManager.getCurrentNetworkView());
insertTasksAfterCurrentTask(layout.getTaskIterator());
}
Modified:
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
===================================================================
---
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/io-impl/trunk/src/main/java/org/cytoscape/io/internal/read/sif/SIFNetworkViewReader.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -45,6 +45,7 @@
import org.cytoscape.model.CyTableEntry;
import org.cytoscape.model.events.RowsAboutToChangeEvent;
import org.cytoscape.model.events.RowsFinishedChangingEvent;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -183,7 +184,8 @@
final CyNetworkView view = cyNetworkViewFactory.getNetworkView(network);
- TaskFactory tf = layouts.getDefaultLayout(view);
+ CyLayoutAlgorithm tf = layouts.getDefaultLayout();
+ tf.setNetworkView(view);
TaskIterator ti = tf.getTaskIterator();
Task task = ti.next();
insertTasksAfterCurrentTask(task);
Modified:
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
===================================================================
---
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/io-impl/trunk/src/test/java/org/cytoscape/io/internal/read/AbstractNetworkViewReaderTester.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -54,7 +54,7 @@
when(def.getTaskIterator()).thenReturn(new TaskIterator(new
SimpleTask()));
layouts = mock(CyLayouts.class);
-
when(layouts.getDefaultLayout(any(CyNetworkView.class))).thenReturn(def);
+ when(layouts.getDefaultLayout()).thenReturn(def);
NetworkTestSupport nts = new NetworkTestSupport();
netFactory = nts.getNetworkFactory();
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/CyLayouts.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -46,7 +46,7 @@
Collection<CyLayoutAlgorithm> getAllLayouts();
- CyLayoutAlgorithm getDefaultLayout(CyNetworkView view);
+ CyLayoutAlgorithm getDefaultLayout();
String getMenuName(CyLayoutAlgorithm layout);
}
Modified:
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/CyLayoutsImpl.java
===================================================================
---
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/CyLayoutsImpl.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/layout-api/trunk/src/main/java/org/cytoscape/view/layout/internal/CyLayoutsImpl.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -112,7 +112,7 @@
*
* @return CyLayoutAlgorithm to use as the default layout algorithm
*/
- public CyLayoutAlgorithm getDefaultLayout(CyNetworkView view) {
+ public CyLayoutAlgorithm getDefaultLayout() {
// See if the user has set the layout.default property
// String defaultLayout =
CytoscapeInit.getProperties().getProperty("layout.default");
//
@@ -122,7 +122,6 @@
String defaultLayout = CyLayouts.DEFAULT_LAYOUT_NAME;
CyLayoutAlgorithm l = layoutMap.get(defaultLayout);
- l.setNetworkView(view);
return l;
}
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReader.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -14,6 +14,7 @@
import org.cytoscape.psi_mi.internal.data_mapper.MapPsiOneToInteractions;
import org.cytoscape.psi_mi.internal.data_mapper.MapPsiTwoFiveToInteractions;
import org.cytoscape.psi_mi.internal.model.Interaction;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -71,7 +72,8 @@
networkView = networkViewFactory.getNetworkView(network);
- TaskFactory taskFactory = layouts.getDefaultLayout(networkView);
+ CyLayoutAlgorithm taskFactory = layouts.getDefaultLayout();
+ taskFactory.setNetworkView(networkView);
TaskIterator taskIterator = taskFactory.getTaskIterator();
Task task = taskIterator.next();
insertTasksAfterCurrentTask(task);
Modified:
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
===================================================================
---
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/psi-mi-impl/trunk/src/main/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReader.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -6,6 +6,7 @@
import org.cytoscape.io.read.CyNetworkViewReader;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.CyNetworkViewFactory;
@@ -71,7 +72,8 @@
final CyNetworkView view =
cyNetworkViewFactory.getNetworkView(network);
- TaskFactory tf = layouts.getDefaultLayout(view);
+ CyLayoutAlgorithm tf = layouts.getDefaultLayout();
+ tf.setNetworkView(view);
TaskIterator ti = tf.getTaskIterator();
Task task = ti.next();
insertTasksAfterCurrentTask(task);
Modified:
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
===================================================================
---
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiNetworkViewReaderTest.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -39,7 +39,7 @@
public void setUp() {
MockitoAnnotations.initMocks(this);
-
when(layouts.getDefaultLayout(any(CyNetworkView.class))).thenReturn(layout);
+ when(layouts.getDefaultLayout()).thenReturn(layout);
when(layout.getTaskIterator()).thenReturn(new
TaskIterator(task));
networkFactory = new NetworkTestSupport().getNetworkFactory();
Modified:
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
===================================================================
---
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2011-04-29 23:14:12 UTC (rev 24866)
+++
core3/psi-mi-impl/trunk/src/test/java/org/cytoscape/psi_mi/internal/plugin/PsiMiTabReaderTest.java
2011-04-29 23:23:23 UTC (rev 24867)
@@ -45,7 +45,7 @@
public void setUp() throws Exception {
MockitoAnnotations.initMocks(this);
-
when(layouts.getDefaultLayout(any(CyNetworkView.class))).thenReturn(
+ when(layouts.getDefaultLayout()).thenReturn(
layout);
when(layout.getTaskIterator()).thenReturn(new
TaskIterator(task));
--
You received this message because you are subscribed to the Google Groups
"cytoscape-cvs" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/cytoscape-cvs?hl=en.
