/*
Copyright (c) 2006, 2007, 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
any later version.
This library 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. The software and
documentation provided hereunder is on an "as is" basis, and the
Institute for Systems Biology and the Whitehead Institute
have no obligations to provide maintenance, support,
updates, enhancements or modifications. In no event shall the
Institute for Systems Biology and the Whitehead Institute
be liable to any party for direct, indirect, special,
incidental or consequential damages, including lost profits, arising
out of the use of this software and its documentation, even if the
Institute for Systems Biology and the Whitehead Institute
have been advised of the possibility of such damage. See
the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
package csplugins.id.mapping;
import csplugins.id.mapping.service.CyThesaurusNamespace;
import csplugins.id.mapping.service.IDMappingServiceSuppport;
import csplugins.id.mapping.ui.CyThesaurusDialog;
import cytoscape.Cytoscape;
import cytoscape.CytoscapeInit;
import cytoscape.plugin.CytoscapePlugin;
import cytoscape.task.Task;
import cytoscape.task.TaskMonitor;
import cytoscape.task.ui.JTaskConfig;
import cytoscape.task.util.TaskManager;
import cytoscape.util.CytoscapeAction;
import org.bridgedb.bio.BioDataSource;
import java.awt.event.ActionEvent;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeSupport;
import java.util.Map;
/**
* Plugin for attribute-based ID mapping
*
*
*/
public final class CyThesaurusPlugin extends CytoscapePlugin {
public static Map mapSrcAttrIDTypes = null;
public static double VERSION = 1.31;
public CyThesaurusPlugin() {
try {
BioDataSource.init();
addListeners();
IDMapperClientManager.cache();
IDMappingServiceSuppport.addService();
CyThesaurusNamespace.register(CyThesaurusNamespace.NAME);
} catch (Exception e) {
e.printStackTrace();
}
Cytoscape.getDesktop().getCyMenus().getOperationsMenu()
.add(new IDMappingAction());
// Cytoscape.getDesktop().getCyMenus().getOperationsMenu()
// .add(new IDMappingTestAction());
// Cytoscape.getDesktop().getCyMenus().getOperationsMenu()
// .add(new CyThesurrusServiceAttributeBasedIDMappingAction());
}
final class IDMappingTestAction extends CytoscapeAction {
public IDMappingTestAction() {
super("CyThesaurus test");
}
/**
* This method is called when the user selects the menu item.
*/
@Override
public void actionPerformed(final ActionEvent ae) {
java.util.List<String> nodeIds = new java.util.ArrayList<String>();
for (cytoscape.CyNode cn : (java.util.List<cytoscape.CyNode>) cytoscape.Cytoscape.getCurrentNetwork().nodesList()) {
nodeIds.add(cn.getIdentifier());
}
Map<String, Object> args = new java.util.HashMap<String, Object>();
args.put("sourceid", nodeIds);
args.put("sourcetype", "HGNC");
args.put("targettype", "Ensembl Human");
cytoscape.command.CyCommandResult result = null;
try {
result = cytoscape.command.CyCommandManager.execute(
"idmapping", "general mapping", args);
System.out.println("message:"+result.getMessages().get(0));
} catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
}
private void addListeners() {
PropertyChangeSupport pcs = Cytoscape.getPropertyChangeSupport();
pcs.addPropertyChangeListener(Cytoscape.CYTOSCAPE_INITIALIZED,
new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent evt) {
// IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
registerDefaultClients();
IDMapperClientManager.reCache();
mapSrcAttrIDTypes = null;
}
});
// pcs.addPropertyChangeListener(Cytoscape.SESSION_SAVED,
// new PropertyChangeListener() {
// public void propertyChange(PropertyChangeEvent evt) {
// // remove the old client but not the session properties
// IDMapperClientManager.removeAllClients(false);
//
// // reload the clients for this session (change the prop prefix)
// IDMapperClientManager.reloadFromCytoscapeSessionProperties();
// IDMapperClientManager.reCache();
// }
// });
// pcs.addPropertyChangeListener(Cytoscape.SESSION_LOADED,
// new PropertyChangeListener() {
// public void propertyChange(PropertyChangeEvent evt) {
// // remove the old client include session properties
// IDMapperClientManager.removeAllClients(true);
//
// // reload the clients for this session
// IDMapperClientManager.reloadFromCytoscapeSessionProperties();
//
// if (IDMapperClientManager.countClients()==0) {
// // load the default clients if no client
//// IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
// registerDefaultClients();
// }
//
// IDMapperClientManager.reCache();
//
// mapSrcAttrIDTypes = null;
// }
// });
// pcs.addPropertyChangeListener(Cytoscape.PREFERENCE_MODIFIED,
// new PropertyChangeListener() {
// public void propertyChange(PropertyChangeEvent evt) {
// if ((CytoscapeInit.getProperties().getProperty("defaultSpeciesName") == evt.getOldValue())
// || (CytoscapeInit.getProperties().getProperty("defaultSpeciesName") == evt.getNewValue())) {
// IDMapperClientManager.registerDefaultClient((String)evt.getNewValue(), (String)evt.getOldValue());
// IDMapperClientManager.reCache();
// }
// }
// });
}
private void registerDefaultClients() {
IDMapperClientManager.reloadFromCytoscapeGlobalProperties();
}
class IDMappingAction extends CytoscapeAction {
public IDMappingAction() {
super(FinalStaticValues.PLUGIN_NAME);
}
/**
* This method is called when the user selects the menu item.
*/
@Override
public void actionPerformed(final ActionEvent ae) {
NewDialogTask task = new NewDialogTask();
final JTaskConfig jTaskConfig = new JTaskConfig();
jTaskConfig.setOwner(Cytoscape.getDesktop());
jTaskConfig.displayCloseButton(false);
jTaskConfig.displayCancelButton(false);
jTaskConfig.displayStatus(true);
jTaskConfig.setAutoDispose(true);
jTaskConfig.setMillisToPopup(100); // always pop the task
// Execute Task in New Thread; pop open JTask Dialog Box.
TaskManager.executeTask(task, jTaskConfig);
final CyThesaurusDialog dialog = task.dialog();
dialog.setVisible(true);
//if (!dialog.isCancelled()) {
mapSrcAttrIDTypes = dialog.getMapSrcAttrIDTypes();
//}
}
}
private class NewDialogTask implements Task {
private TaskMonitor taskMonitor;
private CyThesaurusDialog dialog;
public NewDialogTask() {
}
/**
* Executes Task.
*/
//@Override
public void run() {
try {
taskMonitor.setStatus("Initializing...");
dialog = new CyThesaurusDialog(Cytoscape.getDesktop(), true);
dialog.setLocationRelativeTo(Cytoscape.getDesktop());
dialog.setMapSrcAttrIDTypes(mapSrcAttrIDTypes);
taskMonitor.setPercentCompleted(100);
} catch (Exception e) {
taskMonitor.setPercentCompleted(100);
taskMonitor.setStatus("Failed.\n");
e.printStackTrace();
}
}
public CyThesaurusDialog dialog() {
return dialog;
}
/**
* Halts the Task: Not Currently Implemented.
*/
//@Override
public void halt() {
}
/**
* Sets the Task Monitor.
*
* @param taskMonitor
* TaskMonitor Object.
*/
//@Override
public void setTaskMonitor(TaskMonitor taskMonitor) throws IllegalThreadStateException {
this.taskMonitor = taskMonitor;
}
/**
* Gets the Task Title.
*
* @return Task Title.
*/
//@Override
public String getTitle() {
return "Initializing...";
}
}
private class CyThesurrusServiceAttributeBasedIDMappingActionTest extends CytoscapeAction {
public static final String actionName = "Attribute ID mapping service example (See Tutorial)";
public CyThesurrusServiceAttributeBasedIDMappingActionTest() {
super(actionName); //TODO rename
}
/**
* This method is called when the user selects the menu item.
*/
@Override
public void actionPerformed(final ActionEvent ae) {
java.util.Set<String> srcAttrNames = new java.util.HashSet<String>();
srcAttrNames.add("ID");
srcAttrNames.add("EntrezGene ID");
String tgtIDType = "uniprot_swissprot_accession"; //biomart
// String tgtIDType = "RefSeq"; //bridgedb
Map<String,Object> args = new java.util.HashMap<String,Object>(5);
args.put("sourceattr", srcAttrNames);
args.put("targettype", tgtIDType);
cytoscape.command.CyCommandResult result = null;
try {
result = cytoscape.command.CyCommandManager.execute("idmapping", "attribute based mapping", args);
} catch (cytoscape.command.CyCommandException e) {
e.printStackTrace();
}
if (result.successful()) {
System.out.println(result.getMessages());
}
}
}
}