Author: ruschein
Date: 2010-09-10 14:58:48 -0700 (Fri, 10 Sep 2010)
New Revision: 21801
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/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/java/cytoscape/internal/task/CytoPanelTaskFactoryTunableAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkCollectionTaskFactoryTunableAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkTaskFactoryTunableAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkViewCollectionTaskFactoryTunableAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkViewTaskFactoryTunableAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/TaskFactoryTunableAction.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/CytoscapeMenuPopulator.java
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/NetworkPanel.java
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context-osgi.xml
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context.xml
cytoscape3/trunk/provision/pom.xml
Log:
Layouts are now Tasks and CyLayoutAlgorithm is now a TaskFactory.
Modified: cytoscape3/trunk/application/pom.xml
===================================================================
--- cytoscape3/trunk/application/pom.xml 2010-09-10 21:58:16 UTC (rev
21800)
+++ cytoscape3/trunk/application/pom.xml 2010-09-10 21:58:48 UTC (rev
21801)
@@ -103,6 +103,11 @@
</dependency>
<dependency>
<groupId>org.cytoscape</groupId>
+ <artifactId>event-api</artifactId>
+ <version>1.0-SNAPSHOT</version>
+ </dependency>
+ <dependency>
+ <groupId>org.cytoscape</groupId>
<artifactId>swing-util</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
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/DynamicLayoutMenu.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -131,7 +131,7 @@
layout.setSelectedOnly(false);
layout.setLayoutAttribute(null);
final Task layoutTask = new LayoutTask(layout,
view);
- tm.execute(new TaskIterator(layoutTask), null);
+ tm.execute(new TaskIterator(layoutTask));
}
}
}
@@ -204,7 +204,7 @@
}
public void actionPerformed(ActionEvent e) {
-
+/*
List<CyNetworkView> views =
netmgr.getSelectedNetworkViews();
for ( CyNetworkView netView : views ) {
@@ -227,8 +227,9 @@
layout.setLayoutAttribute(e.getActionCommand());
final Task layoutTask = new LayoutTask(layout,
netView);
- tm.execute(new TaskIterator(layoutTask), null);
+ tm.execute(new TaskIterator(layoutTask));
}
+*/
}
}
}
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
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutMenu.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -140,6 +140,7 @@
boolean enableMenuItem = checkEnabled();
+ /*
// Now, add each layout, as appropriate
for (CyLayoutAlgorithm layout:
menuMgr.getLayoutsInMenu(getText())) {
// Make sure we don't have any lingering locked nodes
@@ -154,6 +155,7 @@
super.add(new
StaticLayoutMenu(layout,enableMenuItem,netmgr,tm));
}
}
+ */
}
private boolean checkEnabled() {
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
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutSettingsDialog.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -38,8 +38,7 @@
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
import org.cytoscape.work.Tunable;
-import org.cytoscape.work.TaskManager;
-import org.cytoscape.work.swing.GUITunableInterceptor;
+import org.cytoscape.work.swing.GUITaskManager;
import javax.swing.*;
import javax.swing.border.Border;
@@ -75,15 +74,14 @@
private CySwingApplication desktop;
private LayoutMenuManager menuMgr;
private CyNetworkManager netmgr;
- private GUITunableInterceptor ti;
- private TaskManager tm;
+ private GUITaskManager taskManager;
/**
* Creates a new LayoutSettingsDialog object.
*/
public LayoutSettingsDialog(final CyLayouts cyLayouts, final
CySwingApplication desktop,
final LayoutMenuManager menuMgr, final
CyNetworkManager netmgr,
- final GUITunableInterceptor ti, final
TaskManager tm)
+ final GUITaskManager taskManager)
{
super(desktop.getJFrame(), "Layout Settings", false);
initializeOnce(); // Initialize the components we only do once
@@ -91,8 +89,7 @@
this.desktop = desktop;
this.menuMgr = menuMgr;
this.netmgr = netmgr;
- this.ti = ti;
- this.tm = tm;
+ this.taskManager = taskManager;
}
/**
@@ -104,12 +101,12 @@
// Are we the source of the event?
String command = e.getActionCommand();
- if (command.equals("done")) {
+ if (command.equals("done"))
setVisible(false);
- } else if (command.equals("execute")) {
- ti.setParent(algorithmPanel);
+ else if (command.equals("execute")) {
final Task layoutTask = new LayoutTask(currentLayout,
netmgr.getCurrentNetworkView());
- tm.execute(new TaskIterator(layoutTask), ti);
+ taskManager.setParent(algorithmPanel);
+ taskManager.execute(new TaskIterator(layoutTask));
} else {
// OK, initialize and display
initialize();
@@ -188,16 +185,12 @@
Object o = algorithmSelector.getSelectedItem();
// if it's a string, that means it's the instructions
if (!(o instanceof String)) {
- CyLayoutAlgorithm newLayout =
(CyLayoutAlgorithm)o;
- ti.loadTunables(newLayout);
- ti.setParent(algorithmPanel);
- try {
- ti.execUI(newLayout);
- } catch (Exception e1) {
- e1.printStackTrace();
+ final CyLayoutAlgorithm newLayout =
(CyLayoutAlgorithm)o;
+ taskManager.setParent(algorithmPanel);
+ if
(taskManager.getConfigurationPanel(newLayout) != null) {
+ pack();
+ currentLayout = newLayout;
}
- pack();
- currentLayout = newLayout;
}
}
}
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
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/LayoutTask.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -64,7 +64,7 @@
* Run the algorithm.
*/
public void run(TaskMonitor monitor) {
- layout.doLayout(view, monitor);
+// layout.doLayout(view, monitor);
}
@Override
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
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/SettingsAction.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -34,7 +34,7 @@
import cytoscape.view.CytoscapeAction;
import cytoscape.view.CySwingApplication;
import org.cytoscape.view.layout.CyLayouts;
-import org.cytoscape.work.TaskManager;
+import org.cytoscape.work.swing.GUITaskManager;
import org.cytoscape.work.swing.GUITunableInterceptor;
import javax.swing.event.MenuEvent;
@@ -47,23 +47,21 @@
private CyLayouts cyl;
private CySwingApplication desk;
private LayoutMenuManager menuMgr;
- private GUITunableInterceptor ti;
- private TaskManager tm;
+ private GUITaskManager tm;
public SettingsAction(final CyLayouts cyl, final CySwingApplication
desk, final LayoutMenuManager menuMgr,
- final CyNetworkManager netmgr, final
GUITunableInterceptor ti, final TaskManager tm)
+ final CyNetworkManager netmgr, final
GUITaskManager tm)
{
super("Settings...",netmgr);
setPreferredMenu("Layout");
this.cyl = cyl;
this.desk = desk;
this.menuMgr = menuMgr;
- this.ti = ti;
this.tm = tm;
}
public void actionPerformed(ActionEvent e) {
- LayoutSettingsDialog settingsDialog = new
LayoutSettingsDialog(cyl, desk, menuMgr, netmgr, ti, tm);
+ LayoutSettingsDialog settingsDialog = new
LayoutSettingsDialog(cyl, desk, menuMgr, netmgr, tm);
settingsDialog.actionPerformed(e);
}
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
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/layout/ui/StaticLayoutMenu.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -73,6 +73,6 @@
public void actionPerformed(ActionEvent e) {
layout.setSelectedOnly(false);
final Task layoutTask = new LayoutTask(layout,
netmgr.getCurrentNetworkView());
- tm.execute(new TaskIterator(layoutTask), null);
+ tm.execute(new TaskIterator(layoutTask));
}
}
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/CytoPanelTaskFactoryTunableAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/CytoPanelTaskFactoryTunableAction.java
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/CytoPanelTaskFactoryTunableAction.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -50,9 +50,8 @@
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TaskManager;
-import org.cytoscape.work.swing.GUITunableInterceptor;
import org.cytoscape.work.TunableValidator;
+import org.cytoscape.work.swing.GUITaskManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -69,13 +68,11 @@
*/
private static class ExecuteButtonListener implements ActionListener {
final private TaskFactory factory;
- final private TaskManager manager;
- final private GUITunableInterceptor interceptor;
+ final private GUITaskManager manager;
- ExecuteButtonListener(final GUITunableInterceptor interceptor,
final TaskFactory factory, final TaskManager manager) {
+ ExecuteButtonListener(final TaskFactory factory, final
GUITaskManager manager) {
this.factory = factory;
this.manager = manager;
- this.interceptor = interceptor;
}
public void actionPerformed(final ActionEvent event) {
@@ -95,33 +92,28 @@
}
}
- if (!interceptor.validateAndWriteBackTunables())
- return;
-
final TaskIterator taskIterator =
factory.getTaskIterator();
// execute the task in a separate thread
- manager.execute(taskIterator, interceptor);
+ manager.execute(taskIterator);
}
}
final private static CytoPanelName DEFAULT_CYTOPANEL =
CytoPanelName.WEST;
final private TaskFactory factory;
- final private TaskManager manager;
- final private GUITunableInterceptor interceptor;
+ final private GUITaskManager manager;
final private Map serviceProps;
private CytoPanel cytoPanel;
final private static Logger logger =
LoggerFactory.getLogger(CytoPanelTaskFactoryTunableAction.class);
- public CytoPanelTaskFactoryTunableAction(final TaskFactory factory,
final TaskManager manager,
- final GUITunableInterceptor
interceptor, final CySwingApplication app,
+ public CytoPanelTaskFactoryTunableAction(final TaskFactory factory,
final GUITaskManager manager,
+ final CySwingApplication app,
final Map serviceProps, final
CyNetworkManager netmgr)
{
super(serviceProps, netmgr);
this.factory = factory;
this.manager = manager;
- this.interceptor = interceptor;
this.serviceProps = serviceProps;
if (serviceProps.containsKey("preferredCytoPanel")) {
@@ -140,11 +132,7 @@
* Creates a new CytoPanel component and adds it to a CytoPanel.
*/
public void actionPerformed(final ActionEvent a) {
- // load the tunables from the object
- interceptor.loadTunables(factory);
-
- final JPanel innerPanel = interceptor.getUI(factory);
-
+ final JPanel innerPanel =
manager.getConfigurationPanel(factory);
if (innerPanel == null)
return;
@@ -189,7 +177,7 @@
outerPanel.add(innerPanel);
final JButton executeButton = new JButton("Execute");
- executeButton.addActionListener(new
ExecuteButtonListener(interceptor, factory, manager));
+ executeButton.addActionListener(new
ExecuteButtonListener(factory, manager));
outerPanel.add(executeButton);
final JButton closeButton = new JButton("Close");
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkCollectionTaskFactoryTunableAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkCollectionTaskFactoryTunableAction.java
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkCollectionTaskFactoryTunableAction.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -1,14 +1,6 @@
/*
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
-
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
@@ -33,28 +25,29 @@
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
-
package cytoscape.internal.task;
+
import java.awt.event.ActionEvent;
import java.util.Map;
import org.cytoscape.work.TaskFactory;
-import org.cytoscape.work.TunableInterceptor;
import org.cytoscape.work.TaskManager;
import cytoscape.view.CytoscapeAction;
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.task.NetworkCollectionTaskFactory;
+
public class NetworkCollectionTaskFactoryTunableAction
extends TaskFactoryTunableAction<NetworkCollectionTaskFactory> {
- public NetworkCollectionTaskFactoryTunableAction(TaskManager manager,
TunableInterceptor interceptor,
- NetworkCollectionTaskFactory factory, Map
serviceProps,
- CyNetworkManager netmgr) {
- super(manager, interceptor, factory, serviceProps, netmgr);
+ public NetworkCollectionTaskFactoryTunableAction(TaskManager manager,
+
NetworkCollectionTaskFactory factory,
+ Map serviceProps,
CyNetworkManager netmgr)
+ {
+ super(manager, factory, serviceProps, netmgr);
}
public void actionPerformed(ActionEvent a) {
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkTaskFactoryTunableAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkTaskFactoryTunableAction.java
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkTaskFactoryTunableAction.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -1,15 +1,8 @@
/*
File: NetworkTaskFactoryTunableAction.java
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
@@ -34,9 +27,9 @@
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
-
package cytoscape.internal.task;
+
import java.awt.event.ActionEvent;
import java.util.Map;
@@ -51,13 +44,15 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.task.NetworkTaskFactory;
+
public class NetworkTaskFactoryTunableAction
extends TaskFactoryTunableAction<NetworkTaskFactory> {
- public NetworkTaskFactoryTunableAction(TaskManager manager,
TunableInterceptor interceptor,
- NetworkTaskFactory factory, Map serviceProps,
- CyNetworkManager netmgr) {
- super(manager, interceptor, factory, serviceProps, netmgr);
+ public NetworkTaskFactoryTunableAction(TaskManager manager,
+ NetworkTaskFactory factory, Map
serviceProps,
+ CyNetworkManager netmgr)
+ {
+ super(manager, factory, serviceProps, netmgr);
}
public void actionPerformed(ActionEvent a) {
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkViewCollectionTaskFactoryTunableAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkViewCollectionTaskFactoryTunableAction.java
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkViewCollectionTaskFactoryTunableAction.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -33,9 +33,9 @@
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
-
package cytoscape.internal.task;
+
import java.awt.event.ActionEvent;
import java.util.Map;
@@ -48,13 +48,14 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.task.NetworkViewCollectionTaskFactory;
+
public class NetworkViewCollectionTaskFactoryTunableAction
extends TaskFactoryTunableAction<NetworkViewCollectionTaskFactory> {
- public NetworkViewCollectionTaskFactoryTunableAction(TaskManager
manager, TunableInterceptor interceptor,
+ public NetworkViewCollectionTaskFactoryTunableAction(TaskManager
manager,
NetworkViewCollectionTaskFactory factory, Map
serviceProps,
CyNetworkManager netmgr) {
- super(manager, interceptor, factory, serviceProps, netmgr);
+ super(manager, factory, serviceProps, netmgr);
}
public void actionPerformed(ActionEvent a) {
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkViewTaskFactoryTunableAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkViewTaskFactoryTunableAction.java
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/NetworkViewTaskFactoryTunableAction.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -1,15 +1,8 @@
/*
File: NetworkViewTaskFactoryTunableAction.java
- Copyright (c) 2006, The Cytoscape Consortium (www.cytoscape.org)
+ Copyright (c) 2006, 2010, The Cytoscape Consortium (www.cytoscape.org)
- The Cytoscape Consortium is:
- - Institute for Systems Biology
- - University of California San Diego
- - Memorial Sloan-Kettering Cancer Center
- - Institut Pasteur
- - Agilent Technologies
-
This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation; either version 2.1 of the License, or
@@ -34,9 +27,9 @@
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
-
package cytoscape.internal.task;
+
import java.awt.event.ActionEvent;
import java.util.Map;
@@ -49,13 +42,15 @@
import org.cytoscape.session.CyNetworkManager;
import org.cytoscape.task.NetworkViewTaskFactory;
+
public class NetworkViewTaskFactoryTunableAction
extends TaskFactoryTunableAction<NetworkViewTaskFactory> {
- public NetworkViewTaskFactoryTunableAction(TaskManager manager,
TunableInterceptor interceptor,
- NetworkViewTaskFactory factory, Map serviceProps,
- CyNetworkManager netmgr) {
- super(manager, interceptor, factory, serviceProps, netmgr);
+ public NetworkViewTaskFactoryTunableAction(TaskManager manager,
+ NetworkViewTaskFactory
factory, Map serviceProps,
+ CyNetworkManager netmgr)
+ {
+ super(manager, factory, serviceProps, netmgr);
}
public void actionPerformed(ActionEvent a) {
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/TaskFactoryTunableAction.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/TaskFactoryTunableAction.java
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/task/TaskFactoryTunableAction.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -37,7 +37,6 @@
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.Task;
import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TunableInterceptor;
import org.cytoscape.work.TaskManager;
import cytoscape.view.CytoscapeAction;
@@ -46,27 +45,24 @@
import org.slf4j.LoggerFactory;
import org.slf4j.Logger;
-public class TaskFactoryTunableAction<T extends TaskFactory> extends
CytoscapeAction {
+public class TaskFactoryTunableAction<T extends TaskFactory> extends
CytoscapeAction {
protected T factory;
- protected TunableInterceptor interceptor;
protected TaskManager manager;
-
private final static Logger logger = LoggerFactory.getLogger(
TaskFactoryTunableAction.class );
-
- public TaskFactoryTunableAction(final TaskManager manager, final
TunableInterceptor interceptor,
- final T factory, final Map
serviceProps, final CyNetworkManager netmgr)
+
+ public TaskFactoryTunableAction(final TaskManager manager, final T
factory,
+ final Map serviceProps, final
CyNetworkManager netmgr)
{
super(serviceProps,netmgr);
this.manager = manager;
this.factory = factory;
- this.interceptor = interceptor;
}
public void actionPerformed(ActionEvent a) {
logger.debug("About to execute task from factory: " +
factory.toString());
final TaskIterator taskIterator = factory.getTaskIterator();
// execute the task(s) in a separate thread
- manager.execute(taskIterator, interceptor);
+ manager.execute(taskIterator);
}
}
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/CytoscapeMenuPopulator.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/CytoscapeMenuPopulator.java
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/CytoscapeMenuPopulator.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -50,8 +50,7 @@
import java.util.HashMap;
import org.cytoscape.work.TaskFactory;
-import org.cytoscape.work.TaskManager;
-import org.cytoscape.work.swing.GUITunableInterceptor;
+import org.cytoscape.work.swing.GUITaskManager;
import org.cytoscape.task.NetworkTaskFactory;
import org.cytoscape.task.NetworkViewTaskFactory;
@@ -70,8 +69,7 @@
public class CytoscapeMenuPopulator {
final private CySwingApplication app;
final private CyMenus cyMenus;
- final private TaskManager taskManager;
- final private GUITunableInterceptor interceptor;
+ final private GUITaskManager taskManager;
final private CyNetworkManager netManager;
final private Map<TaskFactory, CyAction> taskMap;
@@ -81,23 +79,22 @@
* Creates a new CytoscapeMenus object. This will construct the basic
bar objects,
* but won't fill them with menu items and associated action listeners.
*/
- public CytoscapeMenuPopulator(final CySwingApplication app, final
TaskManager taskManager,
- final GUITunableInterceptor interceptor,
final CyNetworkManager netManager)
+ public CytoscapeMenuPopulator(final CySwingApplication app, final
GUITaskManager taskManager,
+ final CyNetworkManager netManager)
{
this.app = app;
this.cyMenus = app.getCyMenus();
this.taskManager = taskManager;
- this.interceptor = interceptor;
this.netManager = netManager;
taskMap = new HashMap<TaskFactory,CyAction>();
}
public void addTaskFactory(TaskFactory factory, Map props) {
- if (interceptor.hasTunables(factory))
- addFactory(new
CytoPanelTaskFactoryTunableAction(factory, taskManager, interceptor, app,
props, netManager), factory, props);
+ if (taskManager.hasTunables(factory))
+ addFactory(new
CytoPanelTaskFactoryTunableAction(factory, taskManager, app, props,
netManager), factory, props);
else
- addFactory(new
TaskFactoryTunableAction<TaskFactory>(taskManager, interceptor, factory, props,
netManager), factory, props);
+ addFactory(new
TaskFactoryTunableAction<TaskFactory>(taskManager, factory, props, netManager),
factory, props);
}
public void removeTaskFactory(TaskFactory factory, Map props) {
@@ -105,7 +102,7 @@
}
public void addNetworkTaskFactory(NetworkTaskFactory factory, Map
props) {
- addFactory(new NetworkTaskFactoryTunableAction(taskManager,
interceptor, factory, props, netManager), factory, props);
+ addFactory(new NetworkTaskFactoryTunableAction(taskManager,
factory, props, netManager), factory, props);
}
public void removeNetworkTaskFactory(NetworkTaskFactory factory, Map
props) {
@@ -113,7 +110,7 @@
}
public void addNetworkViewTaskFactory(NetworkViewTaskFactory factory,
Map props) {
- addFactory(new NetworkViewTaskFactoryTunableAction(taskManager,
interceptor, factory, props, netManager), factory, props);
+ addFactory(new NetworkViewTaskFactoryTunableAction(taskManager,
factory, props, netManager), factory, props);
}
public void removeNetworkViewTaskFactory(NetworkViewTaskFactory
factory, Map props) {
@@ -121,7 +118,7 @@
}
public void
addNetworkViewCollectionTaskFactory(NetworkViewCollectionTaskFactory factory,
Map props) {
- addFactory(new
NetworkViewCollectionTaskFactoryTunableAction(taskManager, interceptor,
factory, props, netManager), factory, props);
+ addFactory(new
NetworkViewCollectionTaskFactoryTunableAction(taskManager, factory, props,
netManager), factory, props);
}
public void
removeNetworkViewCollectionTaskFactory(NetworkViewCollectionTaskFactory
factory, Map props) {
@@ -129,7 +126,7 @@
}
public void
addNetworkCollectionTaskFactory(NetworkCollectionTaskFactory factory, Map
props) {
- addFactory(new
NetworkCollectionTaskFactoryTunableAction(taskManager, interceptor, factory,
props, netManager), factory, props);
+ addFactory(new
NetworkCollectionTaskFactoryTunableAction(taskManager, factory, props,
netManager), factory, props);
}
public void
removeNetworkCollectionTaskFactory(NetworkCollectionTaskFactory factory, Map
props) {
Modified:
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/NetworkPanel.java
===================================================================
---
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/NetworkPanel.java
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/java/cytoscape/internal/view/NetworkPanel.java
2010-09-10 21:58:48 UTC (rev 21801)
@@ -101,7 +101,6 @@
import org.cytoscape.util.swing.TreeTableModel;
import org.cytoscape.work.TaskFactory;
import org.cytoscape.work.TaskManager;
-import org.cytoscape.work.TunableInterceptor;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -137,7 +136,6 @@
private final TaskManager taskManager;
private Map<TaskFactory,JMenuItem> popupMap;
private Map<TaskFactory,CyAction> popupActions;
- private final TunableInterceptor tunableInterceptor;
private CyEventHelper eventHelper;
private Map<CyNetwork, RowSetMicroListener> nameListeners;
@@ -147,14 +145,13 @@
*
* @param desktop
*/
- public NetworkPanel( final CyNetworkManager netmgr, final
BirdsEyeViewHandler bird,
- final TaskManager taskManager,
- final TunableInterceptor tunableInterceptor,
- final CyEventHelper eventHelper) {
+ public NetworkPanel(final CyNetworkManager netmgr, final
BirdsEyeViewHandler bird,
+ final TaskManager taskManager, final CyEventHelper
eventHelper)
+ {
super();
+
this.netmgr = netmgr;
this.taskManager = taskManager;
- this.tunableInterceptor = tunableInterceptor;
this.eventHelper = eventHelper;
root = new NetworkTreeNode("Network Root", 0L);
@@ -236,7 +233,7 @@
}
public void addTaskFactory(TaskFactory factory, Map props) {
- addFactory(factory, new
TaskFactoryTunableAction(taskManager,tunableInterceptor,factory,props,netmgr));
+ addFactory(factory, new TaskFactoryTunableAction(taskManager,
factory, props, netmgr));
}
public void removeTaskFactory(TaskFactory factory, Map props) {
@@ -244,7 +241,7 @@
}
public void
addNetworkCollectionTaskFactory(NetworkCollectionTaskFactory factory, Map
props) {
- addFactory(factory,new
NetworkCollectionTaskFactoryTunableAction(taskManager,tunableInterceptor,factory,props,netmgr));
+ addFactory(factory,new
NetworkCollectionTaskFactoryTunableAction(taskManager, factory, props, netmgr));
}
public void
removeNetworkCollectionTaskFactory(NetworkCollectionTaskFactory factory, Map
props) {
@@ -253,7 +250,7 @@
public void
addNetworkViewCollectionTaskFactory(NetworkViewCollectionTaskFactory factory,
Map props) {
- addFactory(factory, new
NetworkViewCollectionTaskFactoryTunableAction(taskManager,tunableInterceptor,factory,props,netmgr));
+ addFactory(factory, new
NetworkViewCollectionTaskFactoryTunableAction(taskManager, factory, props,
netmgr));
}
public void
removeNetworkViewCollectionTaskFactory(NetworkViewCollectionTaskFactory
factory, Map props) {
@@ -261,7 +258,7 @@
}
public void addNetworkTaskFactory(NetworkTaskFactory factory, Map
props) {
- addFactory(factory, new
NetworkTaskFactoryTunableAction(taskManager,tunableInterceptor,factory,props,netmgr));
+ addFactory(factory, new
NetworkTaskFactoryTunableAction(taskManager, factory, props, netmgr));
}
public void removeNetworkTaskFactory(NetworkTaskFactory factory, Map
props) {
@@ -269,7 +266,7 @@
}
public void addNetworkViewTaskFactory(NetworkViewTaskFactory factory,
Map props) {
- addFactory(factory, new
NetworkViewTaskFactoryTunableAction(taskManager,tunableInterceptor,factory,props,netmgr));
+ addFactory(factory, new
NetworkViewTaskFactoryTunableAction(taskManager, factory, props, netmgr));
}
public void removeNetworkViewTaskFactory(NetworkViewTaskFactory
factory, Map props) {
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
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context-osgi.xml
2010-09-10 21:58:48 UTC (rev 21801)
@@ -15,7 +15,7 @@
<osgi:reference id="streamUtilServiceRef"
interface="org.cytoscape.io.util.StreamUtil" />
- <osgi:reference id="taskManagerServiceRef"
interface="org.cytoscape.work.TaskManager" />
+ <osgi:reference id="taskManagerServiceRef"
interface="org.cytoscape.work.swing.GUITaskManager" />
<osgi:reference id="cyServiceRegistrarServiceRef"
interface="org.cytoscape.service.util.CyServiceRegistrar" />
@@ -64,7 +64,10 @@
<osgi:reference id="cyTableManagerServiceRef"
interface="org.cytoscape.model.CyTableManager">
</osgi:reference>
+ <osgi:reference id="guiTaskManagerServiceRef"
interface="org.cytoscape.work.swing.GUITaskManager">
+ </osgi:reference>
+
<!-- define services that application provides -->
<!-- Props are manages in this service -->
Modified:
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context.xml
===================================================================
---
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context.xml
2010-09-10 21:58:16 UTC (rev 21800)
+++
cytoscape3/trunk/application/src/main/resources/META-INF/spring/bundle-context.xml
2010-09-10 21:58:48 UTC (rev 21801)
@@ -84,8 +84,7 @@
<bean name="networkPanel" class="cytoscape.internal.view.NetworkPanel">
<constructor-arg ref="cyNetworkManagerServiceRef" />
<constructor-arg ref="birdsEyeViewHandler" />
- <constructor-arg ref="taskManagerServiceRef" />
- <constructor-arg ref="tunableGUIInterceptorServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
<constructor-arg ref="cyEventHelperServiceRef" />
</bean>
@@ -159,13 +158,12 @@
<constructor-arg ref="cytoscapeMenus" />
<constructor-arg ref="cyLayoutsServiceRef" />
<constructor-arg ref="cyNetworkManagerServiceRef" />
- <constructor-arg ref="taskManagerServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
</bean>
<bean name="cytoscapeMenuPopulator"
class="cytoscape.internal.view.CytoscapeMenuPopulator">
<constructor-arg ref="cytoscapeDesktop" />
- <constructor-arg ref="taskManagerServiceRef" />
- <constructor-arg ref="tunableGUIInterceptorServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
<constructor-arg ref="cyNetworkManagerServiceRef" />
</bean>
@@ -174,8 +172,7 @@
<constructor-arg ref="cytoscapeDesktop" />
<constructor-arg ref="layoutMenuManager" />
<constructor-arg ref="cyNetworkManagerServiceRef" />
- <constructor-arg ref="tunableGUIInterceptorServiceRef" />
- <constructor-arg ref="taskManagerServiceRef" />
+ <constructor-arg ref="guiTaskManagerServiceRef" />
</bean>
<bean id="helpContentsTaskFactory"
class="cytoscape.internal.view.help.HelpContentsTaskFactory">
<constructor-arg ref="cyHelpBroker" />
Modified: cytoscape3/trunk/provision/pom.xml
===================================================================
--- cytoscape3/trunk/provision/pom.xml 2010-09-10 21:58:16 UTC (rev 21800)
+++ cytoscape3/trunk/provision/pom.xml 2010-09-10 21:58:48 UTC (rev 21801)
@@ -250,14 +250,16 @@
<!-- cytoscape layouts -->
+<!--
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>layout-cytoscape-impl</artifactId>
<version>1.0-SNAPSHOT</version>
</dependency>
+-->
-
<!-- jgraph layouts -->
+<!--
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>layout-jgraph-impl</artifactId>
@@ -278,9 +280,10 @@
<artifactId>org.jgraph.layouts</artifactId>
<version>5.10.0.2</version>
</dependency>
+-->
-
<!-- prefuse layouts -->
+<!--
<dependency>
<groupId>org.cytoscape</groupId>
<artifactId>layout-prefuse-impl</artifactId>
@@ -291,8 +294,8 @@
<artifactId>prefuse</artifactId>
<version>20071021</version>
</dependency>
+-->
-
<!-- linkout plugin -->
<dependency>
<groupId>org.cytoscape</groupId>
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