Author: kono
Date: 2011-12-08 13:11:24 -0800 (Thu, 08 Dec 2011)
New Revision: 27745
Modified:
core3/gui-distribution/trunk/features/src/main/resources/features.xml
core3/impl/trunk/core-task-impl/pom.xml
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/WelcomeScreenTaskFactory.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/CreateNewNetworkPanel.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/ShowWelcomeScreenTask.java
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/WelcomeScreenDialog.java
core3/impl/trunk/pom.xml
Log:
Welcome Screen uses DataSource manager.
Modified: core3/gui-distribution/trunk/features/src/main/resources/features.xml
===================================================================
--- core3/gui-distribution/trunk/features/src/main/resources/features.xml
2011-12-08 21:10:41 UTC (rev 27744)
+++ core3/gui-distribution/trunk/features/src/main/resources/features.xml
2011-12-08 21:11:24 UTC (rev 27745)
@@ -67,6 +67,7 @@
<bundle
start-level="110">mvn:org.cytoscape/webservice-api/${cytoscape.api.version}</bundle>
<bundle
start-level="110">mvn:org.cytoscape/application-api/${cytoscape.api.version}</bundle>
<bundle
start-level="110">mvn:org.cytoscape/biopax-api/${cytoscape.api.version}</bundle>
+ <bundle
start-level="110">mvn:org.cytoscape/datasource-api/${cytoscape.api.version}</bundle>
<bundle
start-level="115">mvn:org.cytoscape.distribution/cmdline-impl/${project.version}</bundle>
<bundle
start-level="115">mvn:org.cytoscape/property-impl/${cytoscape.impl.version}</bundle>
@@ -74,6 +75,7 @@
<bundle
start-level="115">mvn:org.cytoscape/util-intr/${cytoscape.impl.version}</bundle>
<bundle
start-level="115">mvn:org.cytoscape/spacial/${cytoscape.impl.version}</bundle>
+ <bundle
start-level="120">mvn:org.cytoscape/datasource-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="120">mvn:org.cytoscape/equations-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="120">mvn:org.cytoscape/event-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="120">mvn:org.cytoscape/swing-util-api/${cytoscape.api.version}</bundle>
@@ -89,6 +91,7 @@
<bundle
start-level="135">mvn:org.cytoscape/application-impl/${cytoscape.impl.version}</bundle>
+ <bundle
start-level="140">mvn:org.cytoscape/datasource-biogrid-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="140">mvn:org.cytoscape/session-impl/${cytoscape.impl.version}</bundle>
<bundle
start-level="140">mvn:org.cytoscape/ding-customgraphics-manager-impl/${cytoscape.impl.version}</bundle>
Modified: core3/impl/trunk/core-task-impl/pom.xml
===================================================================
--- core3/impl/trunk/core-task-impl/pom.xml 2011-12-08 21:10:41 UTC (rev
27744)
+++ core3/impl/trunk/core-task-impl/pom.xml 2011-12-08 21:11:24 UTC (rev
27745)
@@ -119,6 +119,11 @@
<groupId>org.cytoscape</groupId>
<artifactId>swing-application-api</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
+ <artifactId>datasource-api</artifactId>
+ </dependency>
+
<!-- Test Dependencies -->
<dependency>
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2011-12-08 21:10:41 UTC (rev 27744)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/CyActivator.java
2011-12-08 21:11:24 UTC (rev 27745)
@@ -1,127 +1,120 @@
package org.cytoscape.task.internal;
-import org.cytoscape.session.CySessionManager;
-import org.cytoscape.io.util.StreamUtil;
+import java.util.Properties;
+
import org.cytoscape.application.CyApplicationConfiguration;
-import org.cytoscape.model.subnetwork.CyRootNetworkManager;
-import org.cytoscape.model.CyEdge;
-import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.io.read.CyTableReaderManager;
-import org.cytoscape.model.CyNetworkManager;
-import org.cytoscape.util.swing.OpenBrowser;
-import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.datasource.DataSourceManager;
import org.cytoscape.event.CyEventHelper;
-import org.cytoscape.io.write.PresentationWriterManager;
-import org.cytoscape.view.presentation.RenderingEngineManager;
-import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.io.read.CyNetworkReaderManager;
import org.cytoscape.io.read.CySessionReaderManager;
+import org.cytoscape.io.read.CyTableReaderManager;
import org.cytoscape.io.read.VizmapReaderManager;
-import org.cytoscape.work.TaskManager;
-import org.cytoscape.work.SynchronousTaskManager;
-import org.cytoscape.property.CyProperty;
-import org.cytoscape.property.bookmark.Bookmarks;
-import org.cytoscape.property.bookmark.BookmarksUtil;
-import org.cytoscape.session.CyNetworkNaming;
-import org.cytoscape.io.write.CySessionWriterManager;
+import org.cytoscape.io.util.RecentlyOpenedTracker;
+import org.cytoscape.io.util.StreamUtil;
import org.cytoscape.io.write.CyNetworkViewWriterManager;
-import org.cytoscape.model.CyTableManager;
+import org.cytoscape.io.write.CySessionWriterManager;
import org.cytoscape.io.write.CyTableWriterManager;
-import org.cytoscape.view.model.CyNetworkViewFactory;
-import org.cytoscape.view.vizmap.VisualMappingManager;
-import org.cytoscape.view.model.CyNetworkViewManager;
-import org.cytoscape.work.undo.UndoSupport;
-import org.cytoscape.application.CyApplicationManager;
+import org.cytoscape.io.write.PresentationWriterManager;
import org.cytoscape.io.write.VizmapWriterManager;
-import org.cytoscape.io.read.CyNetworkReaderManager;
-import org.cytoscape.io.util.RecentlyOpenedTracker;
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNetworkFactory;
+import org.cytoscape.model.CyNetworkManager;
+import org.cytoscape.model.CyTableManager;
+import org.cytoscape.model.subnetwork.CyRootNetworkManager;
+import org.cytoscape.property.CyProperty;
+import org.cytoscape.service.util.AbstractCyActivator;
+import org.cytoscape.session.CyNetworkNaming;
+import org.cytoscape.session.CySessionManager;
+import org.cytoscape.task.NetworkCollectionTaskFactory;
+import org.cytoscape.task.NetworkTaskFactory;
+import org.cytoscape.task.NetworkViewCollectionTaskFactory;
+import org.cytoscape.task.NetworkViewTaskFactory;
+import org.cytoscape.task.NodeViewTaskFactory;
+import org.cytoscape.task.TableCellTaskFactory;
+import org.cytoscape.task.TableColumnTaskFactory;
+import org.cytoscape.task.TableTaskFactory;
import org.cytoscape.task.creation.LoadVisualStyles;
-
-import org.cytoscape.task.internal.export.vizmap.ExportVizmapTaskFactory;
-import org.cytoscape.task.internal.table.DeleteColumnTaskFactory;
-import
org.cytoscape.task.internal.loaddatatable.LoadAttributesURLTaskFactoryImpl;
+import org.cytoscape.task.creation.NewEmptyNetworkViewFactory;
+import org.cytoscape.task.internal.creation.CloneNetworkTaskFactory;
+import org.cytoscape.task.internal.creation.CreateNetworkViewTaskFactory;
+import org.cytoscape.task.internal.creation.NewEmptyNetworkTaskFactory;
+import
org.cytoscape.task.internal.creation.NewNetworkSelectedNodesEdgesTaskFactory;
+import
org.cytoscape.task.internal.creation.NewNetworkSelectedNodesOnlyTaskFactory;
+import org.cytoscape.task.internal.destruction.DestroyNetworkTaskFactory;
+import org.cytoscape.task.internal.destruction.DestroyNetworkViewTaskFactory;
import org.cytoscape.task.internal.edit.ConnectSelectedNodesTaskFactory;
+import
org.cytoscape.task.internal.export.graphics.ExportNetworkImageTaskFactory;
+import org.cytoscape.task.internal.export.network.ExportNetworkViewTaskFactory;
+import org.cytoscape.task.internal.export.table.ExportCurrentTableTaskFactory;
+import org.cytoscape.task.internal.export.table.ExportEdgeTableTaskFactory;
+import org.cytoscape.task.internal.export.table.ExportNodeTableTaskFactory;
+import org.cytoscape.task.internal.export.vizmap.ExportVizmapTaskFactory;
import org.cytoscape.task.internal.hide.HideSelectedEdgesTaskFactory;
-import org.cytoscape.task.internal.title.EditNetworkTitleTaskFactory;
+import org.cytoscape.task.internal.hide.HideSelectedNodesTaskFactory;
+import org.cytoscape.task.internal.hide.HideSelectedTaskFactory;
import org.cytoscape.task.internal.hide.UnHideAllEdgesTaskFactory;
-import org.cytoscape.task.internal.session.SaveSessionAsTaskFactory;
-import
org.cytoscape.task.internal.creation.NewNetworkSelectedNodesOnlyTaskFactory;
-import org.cytoscape.task.internal.quickstart.WelcomeScreenTaskFactory;
-import org.cytoscape.task.internal.export.table.ExportNodeTableTaskFactory;
+import org.cytoscape.task.internal.hide.UnHideAllNodesTaskFactory;
+import org.cytoscape.task.internal.hide.UnHideAllTaskFactory;
+import org.cytoscape.task.internal.layout.ApplyPreferredLayoutTaskFactory;
+import
org.cytoscape.task.internal.loaddatatable.LoadAttributesFileTaskFactoryImpl;
+import
org.cytoscape.task.internal.loaddatatable.LoadAttributesURLTaskFactoryImpl;
+import org.cytoscape.task.internal.loadnetwork.LoadNetworkFileTaskFactoryImpl;
+import org.cytoscape.task.internal.loadnetwork.LoadNetworkURLTaskFactoryImpl;
+import org.cytoscape.task.internal.loadvizmap.LoadVizmapFileTaskFactoryImpl;
+import
org.cytoscape.task.internal.networkobjects.DeleteSelectedNodesAndEdgesTaskFactory;
+import org.cytoscape.task.internal.proxysettings.ProxySettingsTaskFactory;
import org.cytoscape.task.internal.quickstart.ImportTaskUtil;
-import org.cytoscape.task.internal.select.InvertSelectedEdgesTaskFactory;
+import org.cytoscape.task.internal.quickstart.WelcomeScreenTaskFactory;
+import org.cytoscape.task.internal.quickstart.datasource.BioGridPreprocessor;
+import
org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor;
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
+import org.cytoscape.task.internal.select.DeselectAllEdgesTaskFactory;
import org.cytoscape.task.internal.select.DeselectAllNodesTaskFactory;
-import org.cytoscape.task.internal.creation.CloneNetworkTaskFactory;
-import org.cytoscape.task.internal.proxysettings.ProxySettingsTaskFactory;
import org.cytoscape.task.internal.select.DeselectAllTaskFactory;
-import org.cytoscape.task.internal.loadnetwork.LoadNetworkFileTaskFactoryImpl;
+import org.cytoscape.task.internal.select.InvertSelectedEdgesTaskFactory;
+import org.cytoscape.task.internal.select.InvertSelectedNodesTaskFactory;
+import org.cytoscape.task.internal.select.SelectAdjacentEdgesTaskFactory;
+import org.cytoscape.task.internal.select.SelectAllEdgesTaskFactory;
+import org.cytoscape.task.internal.select.SelectAllNodesTaskFactory;
+import org.cytoscape.task.internal.select.SelectAllTaskFactory;
+import org.cytoscape.task.internal.select.SelectConnectedNodesTaskFactory;
+import
org.cytoscape.task.internal.select.SelectFirstNeighborsNodeViewTaskFactory;
import org.cytoscape.task.internal.select.SelectFirstNeighborsTaskFactory;
-import org.cytoscape.task.internal.zoom.FitSelectedTaskFactory;
-import org.cytoscape.task.internal.setcurrent.SetCurrentNetworkTaskFactoryImpl;
-import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
-import org.cytoscape.task.internal.table.DeleteTableTaskFactory;
-import org.cytoscape.task.internal.destruction.DestroyNetworkViewTaskFactory;
-import org.cytoscape.task.internal.table.CopyValueToEntireColumnTaskFactory;
-import
org.cytoscape.task.internal.creation.NewNetworkSelectedNodesEdgesTaskFactory;
+import org.cytoscape.task.internal.select.SelectFromFileListTaskFactory;
import org.cytoscape.task.internal.session.NewSessionTaskFactory;
+import org.cytoscape.task.internal.session.OpenSessionTaskFactory;
+import org.cytoscape.task.internal.session.SaveSessionAsTaskFactory;
import org.cytoscape.task.internal.session.SaveSessionTaskFactory;
-import org.cytoscape.task.internal.creation.NewEmptyNetworkTaskFactory;
-import org.cytoscape.task.internal.export.table.ExportEdgeTableTaskFactory;
-import org.cytoscape.task.internal.hide.HideSelectedNodesTaskFactory;
-import org.cytoscape.task.internal.destruction.DestroyNetworkTaskFactory;
-import org.cytoscape.task.internal.export.network.ExportNetworkViewTaskFactory;
-import org.cytoscape.task.internal.quickstart.datasource.BioGridPreprocessor;
-import
org.cytoscape.task.internal.export.graphics.ExportNetworkImageTaskFactory;
-import org.cytoscape.task.internal.select.SelectAllTaskFactory;
-import org.cytoscape.task.internal.zoom.ZoomInTaskFactory;
-import org.cytoscape.task.internal.creation.CreateNetworkViewTaskFactory;
-import org.cytoscape.task.internal.zoom.FitContentTaskFactory;
-import org.cytoscape.task.internal.select.DeselectAllEdgesTaskFactory;
-import org.cytoscape.task.internal.zoom.ZoomOutTaskFactory;
-import org.cytoscape.task.internal.hide.UnHideAllNodesTaskFactory;
-import org.cytoscape.task.internal.layout.ApplyPreferredLayoutTaskFactory;
-import org.cytoscape.task.internal.select.SelectConnectedNodesTaskFactory;
+import org.cytoscape.task.internal.setcurrent.SetCurrentNetworkTaskFactoryImpl;
+import org.cytoscape.task.internal.table.CopyValueToEntireColumnTaskFactory;
+import org.cytoscape.task.internal.table.DeleteColumnTaskFactory;
+import org.cytoscape.task.internal.table.DeleteTableTaskFactory;
import org.cytoscape.task.internal.table.RenameColumnTaskFactory;
+import org.cytoscape.task.internal.title.EditNetworkTitleTaskFactory;
import org.cytoscape.task.internal.welcome.LoadMitabFileTaskFactory;
import org.cytoscape.task.internal.welcome.OpenSpecifiedSessionTaskFactory;
-import org.cytoscape.task.internal.welcome.ShowWelcomeScreenTask;
-import
org.cytoscape.task.internal.loaddatatable.LoadAttributesFileTaskFactoryImpl;
-import org.cytoscape.task.internal.select.InvertSelectedNodesTaskFactory;
-import org.cytoscape.task.internal.loadvizmap.LoadVizmapFileTaskFactoryImpl;
-import org.cytoscape.task.internal.export.table.ExportCurrentTableTaskFactory;
-import org.cytoscape.task.internal.select.SelectFromFileListTaskFactory;
-import
org.cytoscape.task.internal.networkobjects.DeleteSelectedNodesAndEdgesTaskFactory;
-import org.cytoscape.task.internal.hide.UnHideAllTaskFactory;
-import org.cytoscape.task.internal.session.OpenSessionTaskFactory;
-import org.cytoscape.task.internal.select.SelectAllNodesTaskFactory;
-import org.cytoscape.task.internal.hide.HideSelectedTaskFactory;
-import org.cytoscape.task.internal.select.SelectAdjacentEdgesTaskFactory;
-import org.cytoscape.task.internal.loadnetwork.LoadNetworkURLTaskFactoryImpl;
-import
org.cytoscape.task.internal.select.SelectFirstNeighborsNodeViewTaskFactory;
-import org.cytoscape.task.internal.select.SelectAllEdgesTaskFactory;
-
-import org.cytoscape.task.NetworkViewCollectionTaskFactory;
-import org.cytoscape.task.NodeViewTaskFactory;
-import org.cytoscape.task.NetworkTaskFactory;
-import org.cytoscape.task.NetworkViewTaskFactory;
-import org.cytoscape.task.TableTaskFactory;
-import org.cytoscape.task.TableCellTaskFactory;
-import org.cytoscape.task.NetworkCollectionTaskFactory;
-import org.cytoscape.work.TaskFactory;
-import org.cytoscape.task.TableColumnTaskFactory;
-import org.cytoscape.task.creation.NewEmptyNetworkViewFactory;
-
+import org.cytoscape.task.internal.zoom.FitContentTaskFactory;
+import org.cytoscape.task.internal.zoom.FitSelectedTaskFactory;
+import org.cytoscape.task.internal.zoom.ZoomInTaskFactory;
+import org.cytoscape.task.internal.zoom.ZoomOutTaskFactory;
+import org.cytoscape.util.swing.OpenBrowser;
+import org.cytoscape.view.layout.CyLayoutAlgorithmManager;
+import org.cytoscape.view.model.CyNetworkViewFactory;
+import org.cytoscape.view.model.CyNetworkViewManager;
+import org.cytoscape.view.presentation.RenderingEngineManager;
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
-import
org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor;
-
+import org.cytoscape.view.vizmap.VisualMappingManager;
+import org.cytoscape.view.vizmap.VisualStyleFactory;
+import org.cytoscape.work.SynchronousTaskManager;
+import org.cytoscape.work.TaskFactory;
+import org.cytoscape.work.TaskManager;
+import org.cytoscape.work.undo.UndoSupport;
import org.osgi.framework.BundleContext;
-import org.cytoscape.service.util.AbstractCyActivator;
-import java.util.Properties;
-
-
public class CyActivator extends AbstractCyActivator {
public CyActivator() {
super();
@@ -130,8 +123,7 @@
public void start(BundleContext bc) {
- CyProperty<Bookmarks> bookmarkServiceRef =
getService(bc,CyProperty.class,"(cyPropertyName=bookmarks)");
- BookmarksUtil bookmarksUtilServiceRef =
getService(bc,BookmarksUtil.class);
+ DataSourceManager dataSourceManagerServiceRef =
getService(bc,DataSourceManager.class);
OpenBrowser openBrowserServiceRef =
getService(bc,OpenBrowser.class);
CyEventHelper cyEventHelperRef =
getService(bc,CyEventHelper.class);
@@ -234,7 +226,7 @@
LoadMitabFileTaskFactory loadMitabFileTaskFactory = new
LoadMitabFileTaskFactory(cyNetworkReaderManagerServiceRef,cyNetworkManagerServiceRef,cyNetworkViewManagerServiceRef,cyPropertyServiceRef,cyNetworkNamingServiceRef);
- WelcomeScreenTaskFactory welcomeTaskFactory = new
WelcomeScreenTaskFactory(openBrowserServiceRef,
importTaskUtil,cyNetworkManagerServiceRef,subnetworkBuilderUtil,
recentlyOpenedTrackerServiceRef, taskManagerServiceRef,
openSpecifiedSessionTaskFactory, openSessionTaskFactory,
loadMitabFileTaskFactory, cyApplicationConfigurationServiceRef,
loadNetworkFileTaskFactory, bookmarksUtilServiceRef,
bookmarkServiceRef.getProperties());
+ WelcomeScreenTaskFactory welcomeTaskFactory = new
WelcomeScreenTaskFactory(openBrowserServiceRef,
importTaskUtil,cyNetworkManagerServiceRef,subnetworkBuilderUtil,
recentlyOpenedTrackerServiceRef, taskManagerServiceRef,
openSpecifiedSessionTaskFactory, openSessionTaskFactory,
loadMitabFileTaskFactory, cyApplicationConfigurationServiceRef,
loadNetworkFileTaskFactory, dataSourceManagerServiceRef);
BioGridPreprocessor bioGridPreprocessor = new
BioGridPreprocessor(cyPropertyServiceRef,cyApplicationConfigurationServiceRef);
ConnectSelectedNodesTaskFactory connectSelectedNodesTaskFactory
= new
ConnectSelectedNodesTaskFactory(undoSupportServiceRef,cyApplicationManagerServiceRef,cyEventHelperRef);
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/WelcomeScreenTaskFactory.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/WelcomeScreenTaskFactory.java
2011-12-08 21:10:41 UTC (rev 27744)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/WelcomeScreenTaskFactory.java
2011-12-08 21:11:24 UTC (rev 27745)
@@ -1,6 +1,7 @@
package org.cytoscape.task.internal.quickstart;
import org.cytoscape.application.CyApplicationConfiguration;
+import org.cytoscape.datasource.DataSourceManager;
import org.cytoscape.io.util.RecentlyOpenedTracker;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.property.bookmark.Bookmarks;
@@ -27,24 +28,21 @@
private final CyApplicationConfiguration config;
private final TaskFactory layoutTF;
- private final BookmarksUtil bkUtil;
- private final Bookmarks bookmarks;
+ private final DataSourceManager dsManager;
public WelcomeScreenTaskFactory(OpenBrowser openBrowserServiceRef,
final ImportTaskUtil util,
final CyNetworkManager networkManager, final
SubnetworkBuilderUtil subnetworkUtil,
RecentlyOpenedTracker fileTracker, TaskManager
guiTaskManager, OpenSpecifiedSessionTaskFactory taskFactory,
final OpenSessionTaskFactory openTaskFactory, final
LoadMitabFileTaskFactory loadTF,
- final CyApplicationConfiguration config, final
TaskFactory layoutTF, BookmarksUtil bkUtil,
- Bookmarks bookmarks) {
+ final CyApplicationConfiguration config, final
TaskFactory layoutTF, final DataSourceManager dsManager) {
super(util, networkManager, subnetworkUtil);
this.openBrowserServiceRef = openBrowserServiceRef;
this.fileTracker = fileTracker;
this.loadTF = loadTF;
this.config = config;
this.layoutTF = layoutTF;
+ this.dsManager = dsManager;
- this.bkUtil = bkUtil;
- this.bookmarks = bookmarks;
this.guiTaskManager = guiTaskManager;
this.taskFactory = taskFactory;
@@ -55,6 +53,6 @@
// return new TaskIterator(new StartTask(new QuickStartState(),
util,
// networkManager, subnetworkUtil, openBrowserServiceRef));
return new TaskIterator(new
ShowWelcomeScreenTask(openBrowserServiceRef, fileTracker, this.guiTaskManager,
- this.taskFactory, openTaskFactory, loadTF,
config, layoutTF, bkUtil, bookmarks));
+ this.taskFactory, openTaskFactory, loadTF,
config, layoutTF,dsManager));
}
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/CreateNewNetworkPanel.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/CreateNewNetworkPanel.java
2011-12-08 21:10:41 UTC (rev 27744)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/CreateNewNetworkPanel.java
2011-12-08 21:11:24 UTC (rev 27745)
@@ -12,9 +12,12 @@
import java.net.MalformedURLException;
import java.net.URISyntaxException;
import java.net.URL;
+import java.util.Collection;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.SortedSet;
+import java.util.TreeSet;
import javax.imageio.ImageIO;
import javax.swing.DefaultComboBoxModel;
@@ -26,9 +29,9 @@
import javax.swing.border.LineBorder;
import org.cytoscape.application.CyApplicationConfiguration;
-import org.cytoscape.property.bookmark.Bookmarks;
-import org.cytoscape.property.bookmark.BookmarksUtil;
-import org.cytoscape.property.bookmark.DataSource;
+import org.cytoscape.datasource.DataSource;
+import org.cytoscape.datasource.DataSourceManager;
+import org.cytoscape.io.DataCategory;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskManager;
@@ -51,43 +54,50 @@
private DownloadBiogridDataTaskFactory taskFactory;
private final TaskFactory loadNetworkFileTF;
- private final BookmarksUtil bkUtil;
- private final Bookmarks bookmarks;
+ private final DataSourceManager dsManager;
private final Map<String, String> dataSourceMap;
CreateNewNetworkPanel(Window parent, final TaskManager guiTaskManager,
final LoadMitabFileTaskFactory loadTF,
- final CyApplicationConfiguration config, final
TaskFactory loadNetworkFileTF, BookmarksUtil bkUtil,
- Bookmarks bookmarks) {
+ final CyApplicationConfiguration config, final
TaskFactory loadNetworkFileTF, final DataSourceManager dsManager) {
this.loadTF = loadTF;
this.parent = parent;
this.loadNetworkFileTF = loadNetworkFileTF;
this.guiTaskManager = guiTaskManager;
- this.bkUtil = bkUtil;
- this.bookmarks = bookmarks;
+ this.dsManager = dsManager;
+
this.dataSourceMap = new HashMap<String, String>();
this.networkList = new JComboBox();
// taskFactory = new DownloadBiogridDataTaskFactory(networkList,
// config);
// guiTaskManager.execute(taskFactory);
- setFromBookmark();
+ setFromDataSource();
initComponents();
}
- private void setFromBookmark() {
+ private void setFromDataSource() {
DefaultComboBoxModel theModel = new DefaultComboBoxModel();
// Extract the URL entries
- List<DataSource> dataSources =
bkUtil.getDataSourceList("network", bookmarks.getCategory());
+ final Collection<DataSource> dataSources =
dsManager.getDataSources(DataCategory.NETWORK);
+ final SortedSet<String> labelSet = new TreeSet<String>();
if (dataSources != null) {
for(DataSource ds: dataSources) {
- final String link = ds.getHref();
+ String link = null;
+ link = ds.getLocation().toString();
final String sourceName = ds.getName();
- dataSourceMap.put(sourceName, link);
- theModel.addElement(sourceName);
+ final String provider = ds.getProvider();
+ final String sourceLabel = provider + ":" +
sourceName;
+ dataSourceMap.put(sourceLabel, link);
+ labelSet.add(sourceLabel);
}
}
+
+ for(final String label: labelSet)
+ theModel.addElement(label);
+
+
this.networkList.setModel(theModel);
}
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/ShowWelcomeScreenTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/ShowWelcomeScreenTask.java
2011-12-08 21:10:41 UTC (rev 27744)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/ShowWelcomeScreenTask.java
2011-12-08 21:11:24 UTC (rev 27745)
@@ -4,6 +4,7 @@
import javax.swing.SwingUtilities;
import org.cytoscape.application.CyApplicationConfiguration;
+import org.cytoscape.datasource.DataSourceManager;
import org.cytoscape.io.util.RecentlyOpenedTracker;
import org.cytoscape.property.bookmark.Bookmarks;
import org.cytoscape.property.bookmark.BookmarksUtil;
@@ -26,22 +27,19 @@
private final CyApplicationConfiguration config;
private final TaskFactory layoutTF;
- private final BookmarksUtil bkUtil;
- private final Bookmarks bookmarks;
+ private final DataSourceManager dsManager;
public ShowWelcomeScreenTask(final OpenBrowser openBrowserServiceRef,
RecentlyOpenedTracker fileTracker,
TaskManager guiTaskManager,
OpenSpecifiedSessionTaskFactory taskFactory,
final OpenSessionTaskFactory openTaskFactory, final
LoadMitabFileTaskFactory loadTF,
- final CyApplicationConfiguration config, final
TaskFactory layoutTF, BookmarksUtil bkUtil,
- Bookmarks bookmarks) {
+ final CyApplicationConfiguration config, final
TaskFactory layoutTF, final DataSourceManager dsManager) {
this.openBrowserServiceRef = openBrowserServiceRef;
this.openTaskFactory = openTaskFactory;
this.loadTF = loadTF;
this.config = config;
this.layoutTF = layoutTF;
- this.bkUtil = bkUtil;
- this.bookmarks = bookmarks;
+ this.dsManager = dsManager;
this.fileTracker = fileTracker;
@@ -55,7 +53,7 @@
@Override
public void run() {
final JDialog welcome = new
WelcomeScreenDialog(null, openBrowserServiceRef, fileTracker,
- guiTaskManager, taskFactory,
openTaskFactory, loadTF, config, layoutTF, bkUtil, bookmarks);
+ guiTaskManager, taskFactory,
openTaskFactory, loadTF, config, layoutTF, dsManager);
welcome.setVisible(true);
}
});
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/WelcomeScreenDialog.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/WelcomeScreenDialog.java
2011-12-08 21:10:41 UTC (rev 27744)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/welcome/WelcomeScreenDialog.java
2011-12-08 21:11:24 UTC (rev 27745)
@@ -18,6 +18,7 @@
import javax.swing.border.LineBorder;
import org.cytoscape.application.CyApplicationConfiguration;
+import org.cytoscape.datasource.DataSourceManager;
import org.cytoscape.io.util.RecentlyOpenedTracker;
import org.cytoscape.property.bookmark.Bookmarks;
import org.cytoscape.property.bookmark.BookmarksUtil;
@@ -56,21 +57,18 @@
private final CyApplicationConfiguration config;
private final TaskFactory loadNetworkTF;
- private final BookmarksUtil bkUtil;
- private final Bookmarks bookmarks;
+ private final DataSourceManager dsManager;
WelcomeScreenDialog(Component parent, OpenBrowser
openBrowserServiceRef, RecentlyOpenedTracker fileTracker,
TaskManager guiTaskManager,
OpenSpecifiedSessionTaskFactory taskFactory,
final OpenSessionTaskFactory openTaskFactory, final
LoadMitabFileTaskFactory loadTF,
- final CyApplicationConfiguration config, final
TaskFactory layoutTF, BookmarksUtil bkUtil,
- Bookmarks bookmarks) {
+ final CyApplicationConfiguration config, final
TaskFactory layoutTF, final DataSourceManager dsManager) {
this.openBrowserServiceRef = openBrowserServiceRef;
this.loadTF = loadTF;
this.fileTracker = fileTracker;
this.config = config;
this.loadNetworkTF = layoutTF;
- this.bkUtil = bkUtil;
- this.bookmarks = bookmarks;
+ this.dsManager = dsManager;
this.guiTaskManager = guiTaskManager;
this.taskFactory = taskFactory;
@@ -149,7 +147,7 @@
buildHelpPanel(panel1, new OpenPanel(this, fileTracker,
guiTaskManager, taskFactory, openTaskFactory),
"Open a Recent Session");
- buildHelpPanel(panel2, new CreateNewNetworkPanel(this,
guiTaskManager, loadTF, config, loadNetworkTF, bkUtil, bookmarks), "Create New
Network");
+ buildHelpPanel(panel2, new CreateNewNetworkPanel(this,
guiTaskManager, loadTF, config, loadNetworkTF, dsManager), "Create New
Network");
buildHelpPanel(panel3, new HelpPanel(openBrowserServiceRef),
"Help");
buildHelpPanel(panel4, new LogoPanel(), "Latest News");
Modified: core3/impl/trunk/pom.xml
===================================================================
--- core3/impl/trunk/pom.xml 2011-12-08 21:10:41 UTC (rev 27744)
+++ core3/impl/trunk/pom.xml 2011-12-08 21:11:24 UTC (rev 27745)
@@ -58,6 +58,8 @@
<module>work-swing-impl</module>
<module>application-impl</module>
<module>webservice-psicquic-client-impl</module>
+ <module>datasource-impl</module>
+ <module>datasource-biogrid-impl</module>
</modules>
<properties>
@@ -189,6 +191,11 @@
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
+ <artifactId>datasource-api</artifactId>
+ <version>${cytoscape.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
<artifactId>core-task-api</artifactId>
<version>${cytoscape.api.version}</version>
<type>test-jar</type>
@@ -319,4 +326,4 @@
</plugins>
</build>
-</project>
+</project>
\ No newline at end of file
--
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.
