Author: kono
Date: 2010-02-02 13:14:01 -0800 (Tue, 02 Feb 2010)
New Revision: 19143
Added:
coreplugins/trunk/NCBIClient/images/entrez_page_title.gif
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGeneDialog.java
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGenePanel.java
Modified:
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClientPlugin.java
Log:
NCBI Attribute Import GUI Plugin merged to NCBI Client Core.
Copied: coreplugins/trunk/NCBIClient/images/entrez_page_title.gif (from rev
19140, csplugins/trunk/ucsd/kono/NCBIUI/images/entrez_page_title.gif)
===================================================================
(Binary files differ)
Modified:
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClientPlugin.java
===================================================================
---
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClientPlugin.java
2010-02-02 20:57:16 UTC (rev 19142)
+++
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/NCBIClientPlugin.java
2010-02-02 21:14:01 UTC (rev 19143)
@@ -1,4 +1,3 @@
-
/*
Copyright (c) 2006, 2007, The Cytoscape Consortium (www.cytoscape.org)
@@ -32,23 +31,48 @@
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 edu.ucsd.bioeng.idekerlab.ncbiclient;
+import java.awt.event.ActionEvent;
+
+import javax.swing.AbstractAction;
+import javax.swing.JDialog;
+import javax.swing.JMenuItem;
+
+import cytoscape.Cytoscape;
import cytoscape.data.webservice.WebServiceClientManager;
import cytoscape.plugin.CytoscapePlugin;
+import edu.ucsd.bioeng.idekerlab.ncbiclient.ui.NCBIGeneDialog;
-
/**
* NCBI Entrez Web Service Client
*/
public class NCBIClientPlugin extends CytoscapePlugin {
+ private JDialog annotationDialog;
+
/**
* Register NCBIClientPlugin to the Web Service Client Manager.
*/
public NCBIClientPlugin() throws Exception {
// Register this client to the manager.
WebServiceClientManager.registerClient(NCBIClient.getClient());
+
+
Cytoscape.getDesktop().getCyMenus().getMenuBar().getMenu("File.Import")
+ .add(
+ new JMenuItem(new
AbstractAction(
+ "Import
Attributes from NCBI Entrez Gene...") {
+
+ private static final
long serialVersionUID = 3263699405477145319L;
+
+ public void
actionPerformed(ActionEvent e) {
+ if
(annotationDialog == null)
+
annotationDialog = new NCBIGeneDialog();
+
+
annotationDialog.setVisible(true);
+ }
+ }));
+
}
}
Copied:
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGeneDialog.java
(from rev 19140,
csplugins/trunk/ucsd/kono/NCBIUI/src/edu/ucsd/bioeng/idekerlab/ncbiclientui/ui/NCBIGeneDialog.java)
===================================================================
---
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGeneDialog.java
(rev 0)
+++
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGeneDialog.java
2010-02-02 21:14:01 UTC (rev 19143)
@@ -0,0 +1,37 @@
+package edu.ucsd.bioeng.idekerlab.ncbiclient.ui;
+
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+
+import javax.swing.JDialog;
+import javax.swing.JPanel;
+
+import cytoscape.Cytoscape;
+
+public class NCBIGeneDialog extends JDialog implements PropertyChangeListener {
+
+ private static final long serialVersionUID = -2609215983943863094L;
+
+ public NCBIGeneDialog() {
+ super(Cytoscape.getDesktop(), false);
+ setTitle("NCBI Entrez Gene");
+
+ try {
+ final JPanel panel = new NCBIGenePanel();
+ panel.addPropertyChangeListener(this);
+ add(panel);
+ pack();
+ setLocationRelativeTo(Cytoscape.getDesktop());
+ } catch (Exception e) {
+ e.printStackTrace();
+ }
+ }
+
+ public void propertyChange(PropertyChangeEvent evt) {
+ if(evt.getPropertyName().equals("CLOSE")) {
+ dispose();
+ }
+
+ }
+
+}
Copied:
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGenePanel.java
(from rev 19140,
csplugins/trunk/ucsd/kono/NCBIUI/src/edu/ucsd/bioeng/idekerlab/ncbiclientui/ui/NCBIGenePanel.java)
===================================================================
---
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGenePanel.java
(rev 0)
+++
coreplugins/trunk/NCBIClient/src/edu/ucsd/bioeng/idekerlab/ncbiclient/ui/NCBIGenePanel.java
2010-02-02 21:14:01 UTC (rev 19143)
@@ -0,0 +1,226 @@
+/*
+ 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 edu.ucsd.bioeng.idekerlab.ncbiclient.ui;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import cytoscape.Cytoscape;
+import cytoscape.data.webservice.AttributeImportQuery;
+import cytoscape.data.webservice.CyWebServiceEvent;
+import cytoscape.data.webservice.CyWebServiceException;
+import cytoscape.data.webservice.WebServiceClient;
+import cytoscape.data.webservice.WebServiceClientManager;
+import cytoscape.data.webservice.CyWebServiceEvent.WSEventType;
+import cytoscape.task.Task;
+import cytoscape.task.TaskMonitor;
+import cytoscape.task.ui.JTaskConfig;
+import cytoscape.task.util.TaskManager;
+import cytoscape.util.swing.AttributeImportPanel;
+import edu.ucsd.bioeng.idekerlab.ncbiclient.NCBIClient.AnnotationCategory;
+
+
+
+
+/**
+ * Simple attribute import GUI for Entrez Gene database
+ * This UI depends on
+ */
+public class NCBIGenePanel extends AttributeImportPanel {
+ protected static WebServiceClient ncbi =
WebServiceClientManager.getClient("ncbi_entrez");
+ private static final Icon LOGO = new
ImageIcon(NCBIGenePanel.class.getResource("/images/entrez_page_title.gif"));
+
+ /**
+ * Creates a new NCBIGenePanel object.
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public NCBIGenePanel() throws IOException {
+ this(LOGO, "", "Available Annotation Category");
+ }
+
+ /**
+ * Creates a new NCBIGenePanel object.
+ *
+ * @param logo DOCUMENT ME!
+ * @param title DOCUMENT ME!
+ * @param attrPanelName DOCUMENT ME!
+ *
+ * @throws IOException DOCUMENT ME!
+ */
+ public NCBIGenePanel(Icon logo, String title, String attrPanelName)
throws IOException {
+ super(logo, title, attrPanelName);
+ initDataSources();
+ this.setPreferredSize(new Dimension(550, 480));
+ }
+
+ private void initDataSources() {
+ this.databaseComboBox.addItem("NCBI Entrez Gene");
+ databaseComboBox.setEnabled(false);
+ setDataType();
+ }
+
+ private void setDataType() {
+ this.attributeTypeComboBox.addItem("Entrez Gene ID");
+ attributeTypeComboBox.setEnabled(false);
+
+ buildList();
+ }
+
+ protected void importButtonActionPerformed(ActionEvent e) {
+ importAttributes();
+ }
+
+ protected void resetButtonActionPerformed(ActionEvent e) {
+ buildList();
+ }
+
+ private void buildList() {
+ model = new DefaultListModel();
+ attrList.setModel(model);
+ for(AnnotationCategory dispAttrName :
AnnotationCategory.values()) {
+ model.addElement(dispAttrName.getName());
+ }
+ }
+
+
+
+ @Override
+ protected void databaseComboBoxActionPerformed(ActionEvent arg0) {
+ // TODO Auto-generated method stub
+ }
+
+ @Override
+ protected void importAttributes() {
+ String keyInHeader = null;
+ // Create Task
+ final ImportAttributeTask task = new
ImportAttributeTask(attributeComboBox.getSelectedItem().toString(),
keyInHeader);
+
+ // Configure JTask Dialog Pop-Up Box
+ final JTaskConfig jTaskConfig = new JTaskConfig();
+ jTaskConfig.setOwner(Cytoscape.getDesktop());
+ jTaskConfig.displayCloseButton(true);
+ jTaskConfig.displayCancelButton(true);
+ jTaskConfig.displayStatus(true);
+ jTaskConfig.setAutoDispose(false);
+
+ // Execute Task in New Thread; pop open JTask Dialog Box.
+ TaskManager.executeTask(task, jTaskConfig);
+
+ this.firePropertyChange("CLOSE", null, null);
+ }
+
+ private class ImportAttributeTask implements Task {
+
+ private String key;
+ private String keyAttrName;
+ private TaskMonitor taskMonitor;
+
+ public ImportAttributeTask(String key, String keyAttrName) {
+ this.key = key;
+ this.keyAttrName = keyAttrName;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getTitle() {
+ // TODO Auto-generated method stub
+ return "Loading Attributes from Web Service";
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void halt() {
+ Thread.currentThread().interrupt();
+ taskMonitor.setPercentCompleted(100);
+
+ // Kill the import task.
+ CyWebServiceEvent<String> cancelEvent = new
CyWebServiceEvent<String>(ncbi.getClientID(), WSEventType.CANCEL,
+ null,
+ null);
+ try {
+
WebServiceClientManager.getCyWebServiceEventSupport().fireCyWebServiceEvent(cancelEvent);
+ } catch (CyWebServiceException e) {
+ // TODO Auto-generated catch block
+ taskMonitor.setException(e, "Cancel Failed.");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run() {
+ taskMonitor.setStatus("Importing annotation from Entrez
Gene.\n\nIt may take a while.\nPlease wait...");
+ taskMonitor.setPercentCompleted(-1);
+
+ final Object[] selectedAttr =
attrList.getSelectedValues();
+
+ AttributeImportQuery qObj = new
AttributeImportQuery(selectedAttr, key, keyAttrName);
+
+ try {
+
WebServiceClientManager.getCyWebServiceEventSupport().fireCyWebServiceEvent(new
CyWebServiceEvent("ncbi_entrez", WSEventType.IMPORT_ATTRIBUTE, qObj));
+ } catch (Exception e) {
+ taskMonitor.setException(e, "Could not load
attributes from NCBI.");
+ }
+
+ taskMonitor.setPercentCompleted(100);
+ taskMonitor.setStatus("Attributes successfully
loaded.");
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param arg0 DOCUMENT ME!
+ *
+ * @throws IllegalThreadStateException DOCUMENT ME!
+ */
+ public void setTaskMonitor(TaskMonitor taskMonitor) throws
IllegalThreadStateException {
+ this.taskMonitor = taskMonitor;
+ }
+ }
+
+
+
+}
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