Author: mes
Date: 2009-07-09 15:34:48 -0700 (Thu, 09 Jul 2009)
New Revision: 17313
Modified:
cytoscape3/trunk/application/pom.xml
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenu.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenuManager.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutTask.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/SettingsAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/StaticLayoutMenu.java
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context-osgi.xml
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/LayoutActivator.java
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
cytoscape3/trunk/biopax/src/main/java/org/mskcc/biopax_plugin/plugin/BioPaxGraphReader.java
cytoscape3/trunk/biopax/src/main/java/org/mskcc/biopax_plugin/util/cytoscape/LayoutUtil.java
cytoscape3/trunk/cpath/src/main/java/org/cytoscape/coreplugin/cpath/task/QueryCPathTask.java
cytoscape3/trunk/cpath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
cytoscape3/trunk/pom.xml
cytoscape3/trunk/provision/pom.xml
Log:
updated to add cytoscape layout implementations
Modified: cytoscape3/trunk/application/pom.xml
===================================================================
--- cytoscape3/trunk/application/pom.xml 2009-07-09 22:51:49 UTC (rev
17312)
+++ cytoscape3/trunk/application/pom.xml 2009-07-09 22:34:48 UTC (rev
17313)
@@ -109,7 +109,7 @@
<dependency>
<groupId>org.cytoscape</groupId>
- <artifactId>layout</artifactId>
+ <artifactId>layout-api</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -43,7 +43,7 @@
import org.cytoscape.model.CyRow;
import org.cytoscape.model.CyDataTableUtil;
import org.cytoscape.model.CyDataTable;
-import org.cytoscape.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.model.CyNetworkView;
import org.cytoscape.view.model.View;
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenu.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenu.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenu.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -41,7 +41,7 @@
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyDataTableUtil;
-import org.cytoscape.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.model.CyNetworkView;
import javax.swing.*;
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenuManager.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenuManager.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenuManager.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -36,8 +36,8 @@
*/
package cytoscape.internal.layout.ui;
-import org.cytoscape.layout.CyLayoutAlgorithm;
-import org.cytoscape.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.work.TaskManager;
import cytoscape.view.CyMenus;
import org.cytoscape.session.CyNetworkManager;
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -39,8 +39,8 @@
import org.cytoscape.session.CyNetworkManager;
import cytoscape.view.CySwingApplication;
-import org.cytoscape.layout.CyLayoutAlgorithm;
-import org.cytoscape.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.work.Tunable;
import org.cytoscape.work.TunableInterceptor;
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutTask.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutTask.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutTask.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -39,7 +39,7 @@
import cytoscape.Cytoscape;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.model.CyNetworkView;
import java.awt.Container;
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/SettingsAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/SettingsAction.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/SettingsAction.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -39,7 +39,7 @@
import org.cytoscape.session.CyNetworkManager;
import cytoscape.util.CytoscapeAction;
import cytoscape.view.CySwingApplication;
-import org.cytoscape.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.work.TunableInterceptor;
import org.cytoscape.work.TaskManager;
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/StaticLayoutMenu.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/StaticLayoutMenu.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/StaticLayoutMenu.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -38,7 +38,7 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.work.TaskManager;
-import org.cytoscape.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import javax.swing.*;
import java.awt.event.ActionEvent;
Modified:
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context-osgi.xml
===================================================================
---
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2009-07-09 22:34:48 UTC (rev 17313)
@@ -40,7 +40,7 @@
<osgi:reference id="cyRootNetworkFactoryServiceRef"
interface="org.cytoscape.model.subnetwork.CyRootNetworkFactory"
/>
- <osgi:reference id="cyLayoutsServiceRef"
interface="org.cytoscape.layout.CyLayouts">
+ <osgi:reference id="cyLayoutsServiceRef"
interface="org.cytoscape.view.layout.CyLayouts">
</osgi:reference>
<osgi:reference id="undoSupportServiceRef"
interface="org.cytoscape.work.UndoSupport">
Modified:
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
===================================================================
---
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/JGraphLayoutWrapper.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -39,7 +39,7 @@
import org.cytoscape.model.CyEdge;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNode;
-import org.cytoscape.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayout;
import org.cytoscape.view.NodeView;
import org.jgraph.JGraph;
import org.jgraph.graph.CellView;
Modified:
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/LayoutActivator.java
===================================================================
---
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/LayoutActivator.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/LayoutActivator.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -45,7 +45,7 @@
import csplugins.layout.algorithms.graphPartition.DegreeSortedCircleLayout;
import csplugins.layout.algorithms.graphPartition.ISOMLayout;
import
csplugins.layout.algorithms.hierarchicalLayout.HierarchicalLayoutAlgorithm;
-import org.cytoscape.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import org.osgi.framework.ServiceRegistration;
Modified:
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
===================================================================
---
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/GroupAttributesLayout.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -40,7 +40,7 @@
import cytoscape.CytoscapeInit;
import org.cytoscape.model.CyNode;
import org.cytoscape.model.CyRow;
-import org.cytoscape.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayout;
import org.cytoscape.tunable.ModuleProperties;
import org.cytoscape.tunable.Tunable;
import org.cytoscape.tunable.TunableFactory;
Modified:
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
===================================================================
---
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/StackedNodeLayout.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -37,7 +37,7 @@
package csplugins.layout.algorithms;
import org.cytoscape.model.CyNode;
-import org.cytoscape.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayout;
import org.cytoscape.view.NodeView;
import java.util.Collection;
Modified:
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
===================================================================
---
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/graphPartition/AbstractGraphPartition.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -5,7 +5,7 @@
import csplugins.layout.LayoutNode;
import csplugins.layout.LayoutPartition;
import org.cytoscape.model.CyNode;
-import org.cytoscape.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayout;
import java.util.ArrayList;
import java.util.List;
Modified:
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
===================================================================
---
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/automatic.layout/src/main/java/csplugins/layout/algorithms/hierarchicalLayout/HierarchicalLayoutAlgorithm.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -41,7 +41,7 @@
import cytoscape.CytoscapeInit;
import cytoscape.task.TaskMonitor;
-import org.cytoscape.layout.AbstractLayout;
+import org.cytoscape.view.layout.AbstractLayout;
import org.cytoscape.tunable.ModuleProperties;
import org.cytoscape.tunable.Tunable;
import org.cytoscape.tunable.TunableFactory;
Modified:
cytoscape3/trunk/biopax/src/main/java/org/mskcc/biopax_plugin/plugin/BioPaxGraphReader.java
===================================================================
---
cytoscape3/trunk/biopax/src/main/java/org/mskcc/biopax_plugin/plugin/BioPaxGraphReader.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/biopax/src/main/java/org/mskcc/biopax_plugin/plugin/BioPaxGraphReader.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -36,7 +36,7 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyRow;
-import org.cytoscape.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.GraphView;
import org.cytoscape.vizmap.VisualMappingManager;
import org.cytoscape.vizmap.VisualStyle;
Modified:
cytoscape3/trunk/biopax/src/main/java/org/mskcc/biopax_plugin/util/cytoscape/LayoutUtil.java
===================================================================
---
cytoscape3/trunk/biopax/src/main/java/org/mskcc/biopax_plugin/util/cytoscape/LayoutUtil.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/biopax/src/main/java/org/mskcc/biopax_plugin/util/cytoscape/LayoutUtil.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -37,7 +37,7 @@
import cytoscape.Cytoscape;
import cytoscape.task.TaskMonitor;
-import org.cytoscape.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.tunable.ModuleProperties;
import org.cytoscape.view.GraphView;
import org.cytoscape.view.NodeView;
Modified:
cytoscape3/trunk/cpath/src/main/java/org/cytoscape/coreplugin/cpath/task/QueryCPathTask.java
===================================================================
---
cytoscape3/trunk/cpath/src/main/java/org/cytoscape/coreplugin/cpath/task/QueryCPathTask.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/cpath/src/main/java/org/cytoscape/coreplugin/cpath/task/QueryCPathTask.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -50,7 +50,7 @@
import org.cytoscape.coreplugin.cpath.protocol.CPathProtocol;
import org.cytoscape.coreplugin.cpath.ui.Console;
import org.cytoscape.coreplugin.cpath.util.CPathProperties;
-import org.cytoscape.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
import org.cytoscape.view.GraphView;
import javax.swing.*;
Modified:
cytoscape3/trunk/cpath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
===================================================================
---
cytoscape3/trunk/cpath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
2009-07-09 22:51:49 UTC (rev 17312)
+++
cytoscape3/trunk/cpath2/src/main/java/org/cytoscape/coreplugin/cpath2/task/ExecuteGetRecordByCPathId.java
2009-07-09 22:34:48 UTC (rev 17313)
@@ -17,8 +17,8 @@
import org.cytoscape.coreplugin.cpath2.web_service.CPathResponseFormat;
import org.cytoscape.coreplugin.cpath2.web_service.CPathWebService;
import org.cytoscape.coreplugin.cpath2.web_service.EmptySetException;
-import org.cytoscape.layout.CyLayoutAlgorithm;
-import org.cytoscape.layout.CyLayouts;
+import org.cytoscape.view.layout.CyLayoutAlgorithm;
+import org.cytoscape.view.layout.CyLayouts;
import org.cytoscape.view.GraphView;
import org.cytoscape.view.GraphViewFactory;
import org.cytoscape.vizmap.VisualMappingManager;
Modified: cytoscape3/trunk/pom.xml
===================================================================
--- cytoscape3/trunk/pom.xml 2009-07-09 22:51:49 UTC (rev 17312)
+++ cytoscape3/trunk/pom.xml 2009-07-09 22:34:48 UTC (rev 17313)
@@ -205,6 +205,8 @@
<configuration>
<!-- some example Pax-Runner settings
-->
<provision>
+ <param>--log=NONE</param>
+
<param>--downloadFeedback=false</param>
<param>--platform=felix</param>
<param>--profiles=log</param>
<param>--noDownloadFeedback</param>
Modified: cytoscape3/trunk/provision/pom.xml
===================================================================
--- cytoscape3/trunk/provision/pom.xml 2009-07-09 22:51:49 UTC (rev 17312)
+++ cytoscape3/trunk/provision/pom.xml 2009-07-09 22:34:48 UTC (rev 17313)
@@ -329,6 +329,11 @@
<artifactId>editor-impl</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>layout-cytoscape-impl</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </dependency>
</dependencies>
</project>
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