Author: rodche
Date: 2012-03-29 19:05:04 -0700 (Thu, 29 Mar 2012)
New Revision: 28704
Removed:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/ExportAsBioPAXAction.java
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
Log:
Removed unused classes (outdated; export to BioPAX was already disabled, not
ported; anyway, it worked in Cy 2.8x only for BioPAX networks and only to save
original BioPAX (modifications would be lost); biopax plugin has never been a
BioPAX editor, but reader/mapper only)
Modified:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-03-30 01:49:31 UTC (rev 28703)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/CyActivator.java
2012-03-30 02:05:04 UTC (rev 28704)
@@ -1,6 +1,5 @@
package org.cytoscape.biopax.internal;
-import org.cytoscape.work.TaskManager;
import org.cytoscape.util.swing.OpenBrowser;
import org.cytoscape.view.vizmap.VisualMappingManager;
import org.cytoscape.view.model.CyNetworkViewManager;
@@ -12,14 +11,12 @@
import org.cytoscape.view.vizmap.VisualMappingFunctionFactory;
import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.model.CyNetworkFactory;
-import org.cytoscape.util.swing.FileUtil;
import org.cytoscape.view.model.CyNetworkViewFactory;
import org.cytoscape.view.model.events.NetworkViewAboutToBeDestroyedListener;
import org.cytoscape.view.model.events.NetworkViewAddedListener;
import org.cytoscape.biopax.internal.BioPaxFilter;
import org.cytoscape.biopax.internal.action.BioPaxViewTracker;
-import org.cytoscape.biopax.internal.action.ExportAsBioPAXAction;
import org.cytoscape.biopax.internal.BioPaxReaderTaskFactory;
import org.cytoscape.biopax.internal.util.BioPaxVisualStyleUtil;
import org.cytoscape.biopax.internal.view.BioPaxContainer;
@@ -49,14 +46,12 @@
public void start(BundleContext bc) {
CySwingApplication cySwingApplicationRef =
getService(bc,CySwingApplication.class);
- TaskManager<?,?> taskManagerRef =
getService(bc,TaskManager.class);
OpenBrowser openBrowserRef = getService(bc,OpenBrowser.class);
CyApplicationManager cyApplicationManagerRef =
getService(bc,CyApplicationManager.class);
CyNetworkViewManager cyNetworkViewManagerRef =
getService(bc,CyNetworkViewManager.class);
CyNetworkNaming cyNetworkNamingRef =
getService(bc,CyNetworkNaming.class);
CyNetworkFactory cyNetworkFactoryRef =
getService(bc,CyNetworkFactory.class);
CyNetworkViewFactory cyNetworkViewFactoryRef =
getService(bc,CyNetworkViewFactory.class);
- FileUtil fileUtilRef = getService(bc,FileUtil.class);
StreamUtil streamUtilRef = getService(bc,StreamUtil.class);
VisualMappingManager visualMappingManagerRef =
getService(bc,VisualMappingManager.class);
VisualStyleFactory visualStyleFactoryRef =
getService(bc,VisualStyleFactory.class);
@@ -72,7 +67,6 @@
BioPaxViewTracker bioPaxViewTracker = new
BioPaxViewTracker(bioPaxDetailsPanel,bioPaxContainer, cyApplicationManagerRef,
visualMappingManagerRef, bioPaxVisualStyleUtil);
InputStreamTaskFactory inputStreamTaskFactory = new
BioPaxReaderTaskFactory(bioPaxFilter,cyNetworkFactoryRef,cyNetworkViewFactoryRef,cyNetworkNamingRef,visualMappingManagerRef,bioPaxVisualStyleUtil);
CytoPanelComponent cytoPanelComponent = new
BioPaxCytoPanelComponent(bioPaxContainer);
-// ExportAsBioPAXAction exportAsBioPAXAction = new
ExportAsBioPAXAction(fileUtilRef, cyApplicationManagerRef, bioPaxFilter,
taskManagerRef);
// register/export core Cytoscape osgi service implementations
registerService(bc,inputStreamTaskFactory,InputStreamTaskFactory.class, new
Properties());
@@ -82,8 +76,6 @@
registerService(bc,(NetworkViewAboutToBeDestroyedListener)bioPaxViewTracker,NetworkViewAboutToBeDestroyedListener.class,
new Properties());
registerService(bc,(SetCurrentNetworkViewListener)bioPaxViewTracker,SetCurrentNetworkViewListener.class,
new Properties());
- // the next CyAction service (export BioPAX) is disabled: TODO
needs refactoring; use ExportAsBioPAXTaskFactory as well...
- //registerService(bc, exportAsBioPAXAction, CyAction.class,
new Properties());
}
}
Deleted:
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/ExportAsBioPAXAction.java
===================================================================
---
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/ExportAsBioPAXAction.java
2012-03-30 01:49:31 UTC (rev 28703)
+++
core3/impl/trunk/biopax-impl/src/main/java/org/cytoscape/biopax/internal/action/ExportAsBioPAXAction.java
2012-03-30 02:05:04 UTC (rev 28704)
@@ -1,130 +0,0 @@
-/* Copyright 2008 - 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
- *
- * Authors: B. Arman Aksoy, Thomas Kelder, Emek Demir
- *
- * This file is part of PaxtoolsPlugin.
- *
- * PaxtoolsPlugin 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 3 of the License, or
- * (at your option) any later version.
- *
- * PaxtoolsPlugin is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this project. If not, see <http://www.gnu.org/licenses/>.
- */
-
-package org.cytoscape.biopax.internal.action;
-
-import java.awt.Component;
-import java.awt.event.ActionEvent;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import javax.swing.event.MenuEvent;
-
-import org.cytoscape.application.CyApplicationManager;
-import org.cytoscape.application.swing.AbstractCyAction;
-import org.cytoscape.biopax.internal.util.BioPaxUtil;
-import org.cytoscape.io.CyFileFilter;
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.util.swing.FileChooserFilter;
-import org.cytoscape.util.swing.FileUtil;
-import org.cytoscape.work.TaskIterator;
-import org.cytoscape.work.TaskManager;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-
-/**
- * This is currently an experimental feature.
- * Networks that were previously imported
- * from a BioPAX file or web services may be saved.
- * All the modifications to this network made
- * within Cytoscape will be lost.
- *
- * @author rodche
- *
- */
-public class ExportAsBioPAXAction extends AbstractCyAction {
-
- private Logger logger = LoggerFactory.getLogger(getClass());
-
- private final FileUtil fileUtil;
- private final CyApplicationManager applicationManager;
- private final CyFileFilter bioPaxFilter;
- private final TaskManager taskManager;
-
- public ExportAsBioPAXAction(FileUtil fileUtil, CyApplicationManager
applicationManager,
- CyFileFilter bioPaxFilter, TaskManager taskManager)
- {
- super("BioPAX", applicationManager,"network");
- setPreferredMenu("File.Export.Network");
- this.fileUtil = fileUtil;
- this.applicationManager = applicationManager;
- this.bioPaxFilter = bioPaxFilter;
- this.taskManager = taskManager;
- }
-
- /**
- * User-initiated action to save the current BioPAX network
- * to a user-specified file. If successfully saved, fires a
- * PropertyChange event with property=Cytoscape.NETWORK_SAVED,
- * old_value=null, and new_value=a three element Object array
containing:
- * <OL>
- * <LI>first element = CyNetwork saved
- * <LI>second element = URI of the location where saved
- * <LI>third element = an Integer representing the format in which the
- * Network was saved (e.g., Cytoscape.FILE_SIF).
- * </OL>
- * @param e ActionEvent Object.
- */
- public void actionPerformed(ActionEvent event) {
- Collection<FileChooserFilter> filters = new
ArrayList<FileChooserFilter>();
- filters.add(new FileChooserFilter("BioPAX format", "rdf"));
- File file = fileUtil.getFile((Component) event.getSource(),
- "Save BioPAX Network (experimental feature)",
FileUtil.SAVE, filters);
- if (file != null) {
- String fileName = file.getAbsolutePath();
-
- if (!fileName.endsWith(".xml"))
- fileName = fileName + ".xml";
-
- ExportAsBioPAXTaskFactory taskFactory = new
ExportAsBioPAXTaskFactory(fileName, bioPaxFilter);
- try {
- FileOutputStream stream = new
FileOutputStream(fileName);
- taskFactory.setOutputStream(stream);
- try {
- taskManager.execute(new
TaskIterator(taskFactory.getWriterTask()));
- } finally {
- stream.close();
- }
- } catch (IOException e) {
- logger.error("Unexpected error", e);
- }
- }
- }
-
- public void menuSelected(MenuEvent e) {
- CyNetwork cyNetwork = applicationManager.getCurrentNetwork();
-
- if( BioPaxUtil.isBioPAXNetwork(cyNetwork) )
- updateEnableState();
- else
- setEnabled(false);
- }
-}
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