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[Cdk-commits] CVS: cdk-plugins/wwmmplugin/src/uk/ac/cam/ch/wwmm WWMMCDKPlugin.java,1.2,1.3 WWMMCDKPluginQueryFrame.java,1.1,1.2
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From: Yong Z. <yz...@us...> - 2003-12-03 21:09:39
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Update of /cvsroot/cdk/cdk-plugins/wwmmplugin/src/uk/ac/cam/ch/wwmm
In directory sc8-pr-cvs1:/tmp/cvs-serv24856/src/uk/ac/cam/ch/wwmm
Modified Files:
WWMMCDKPlugin.java WWMMCDKPluginQueryFrame.java
Log Message:
Add create IChI and lookup wwmm xindice database
Index: WWMMCDKPlugin.java
===================================================================
RCS file: /cvsroot/cdk/cdk-plugins/wwmmplugin/src/uk/ac/cam/ch/wwmm/WWMMCDKPlugin.java,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- WWMMCDKPlugin.java 3 Dec 2003 17:12:55 -0000 1.2
+++ WWMMCDKPlugin.java 3 Dec 2003 21:09:34 -0000 1.3
@@ -1,8 +1,5 @@
package uk.ac.cam.ch.wwmm;
-import org.openscience.cdk.applications.plugin.*;
-import org.openscience.cdk.tools.LoggingTool;
-
import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
@@ -14,8 +11,16 @@
import javax.swing.JMenuItem;
import javax.swing.JPanel;
+import org.openscience.cdk.applications.plugin.*;
+import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.ChemModel;
+import org.openscience.cdk.Molecule;
+//import org.openscience.cdk.graph.invariant.IChIGenerator;
+import org.openscience.cdk.tools.ChemModelManipulator;
+import org.openscience.cdk.tools.LoggingTool;
import org.openscience.jchempaint.JChemPaint;
+import uk.ac.cam.ch.wwmm.IChIGenerator;
import uk.ac.cam.ch.wwmm.WWMMCDKPluginQueryFrame;
/**
@@ -26,6 +31,7 @@
*/
public class WWMMCDKPlugin implements CDKPluginInterface {
+ private JChemPaint jcp = null;
private JPanel pluginPanel = null;
private CDKEditBus editBus = null;
private LoggingTool logger = null;
@@ -80,15 +86,28 @@
*/
public JMenu getMenu(){
JMenu menu = new JMenu();
+
JMenuItem item0 = new JMenuItem("Query WWMM");
- QueryWWMMEvent qweUCC =new QueryWWMMEvent();
- qweUCC.setServer(pluginProps.getProperty("WWMMServer","http://wwmm.ch.cam.ac.uk/Bob"));
- item0.addActionListener(qweUCC);
+ QueryWWMMEvent qwe =new QueryWWMMEvent();
+ qwe.setServer(pluginProps.getProperty("WWMMServer","wwmm.ch.cam.ac.uk"));
+ item0.addActionListener(qwe);
menu.add(item0);
- JMenuItem item2 = new JMenuItem("Create IChI");
+ JMenuItem item1 = new JMenuItem("Create IChI");
+ CreateIChIEvent cie = new CreateIChIEvent();
+ item1.addActionListener(cie);
+ menu.add(item1);
+
+ JMenuItem item2 = new JMenuItem("Lookup UCC Xindice Database");
+ LookupWWMMEvent lweUCC =new LookupWWMMEvent();
+ lweUCC.setServer(pluginProps.getProperty("WWMMServer","wwmm.ch.cam.ac.uk"));
+ item2.addActionListener(lweUCC);
menu.add(item2);
- JMenuItem item3 = new JMenuItem("Lookup UCC WWMM");
+
+ JMenuItem item3 = new JMenuItem("Lookup Local Xindice Database");
+ LookupWWMMEvent lweLocal =new LookupWWMMEvent();
+ lweLocal.setServer(pluginProps.getProperty("LocalServer","localhost:8080"));
+ item3.addActionListener(lweLocal);
menu.add(item3);
return menu;
@@ -106,10 +125,103 @@
}
public void actionPerformed(ActionEvent event) {
- WWMMCDKPluginQueryFrame frame = new WWMMCDKPluginQueryFrame((JChemPaint)editBus);
- ((JChemPaint)editBus).getDesktopPane().add(frame);
- frame.pack();
- frame.show();
+ WWMMCDKPluginQueryFrame frame = new WWMMCDKPluginQueryFrame((JChemPaint)editBus);
+ ((JChemPaint)editBus).getDesktopPane().add(frame);
+ frame.pack();
+ frame.show();
+ }
+ }
+
+ class CreateIChIEvent extends AbstractAction {
+ public void actionPerformed(ActionEvent e) {
+ jcp = (JChemPaint)editBus;
+ logger.debug("Trying to create IChI: ");
+ IChIGenerator generator = new IChIGenerator();
+ String IChI = "";
+ logger.debug("IChI = " + IChI);
+ try {
+ ChemModel model = (ChemModel)jcp.getCurrentModel().getChemModel();
+ AtomContainer container = ChemModelManipulator.getAllInOneContainer(model);
+ Molecule molecule = new Molecule(container);
+ System.out.println("Before runing IChI generater: ");
+ IChI = generator.createIChI(molecule);
+ System.out.println("After runing IChI generater: " + IChI);
+
+ //JOptionPane.showMessageDialog(jcp, message);
+ TextFrame frame = new TextFrame(IChI);
+ frame.pack();
+ frame.setVisible(true);
+ } catch(Exception exc) {
+ logger.error(exc.toString());
+ }
+ }
+ }
+
+ class LookupWWMMEvent extends AbstractAction {
+ private String server = "";
+
+ public String getServer() {
+ return this.server;
+ }
+
+ public void setServer(String server) {
+ this.server = server;
+ }
+
+ public void actionPerformed(ActionEvent event) {
+ TextFrame frame = null;
+ jcp = (JChemPaint)editBus;
+ logger.debug("Trying to create IChI: ");
+ IChIGenerator generator = new IChIGenerator();
+ String IChI = "";
+ logger.debug("IChI = " + IChI);
+ try {
+ ChemModel model = (ChemModel)jcp.getCurrentModel().getChemModel();
+ AtomContainer container = ChemModelManipulator.getAllInOneContainer(model);
+ Molecule molecule = new Molecule(container);
+ logger.debug("Before runing IChI generater: ");
+ IChI = generator.createIChI(molecule);
+ String message = "Generated IChI: " + IChI;
+ logger.debug(message);
+ String server = this.server;
+ String collection = "nci/entry";
+ String basic = new GetIChIBasic().GetBasic(IChI);
+ String query = "//entry[//basic[.='" + basic + "']]";
+
+ XindiceReader xr = new XindiceReader();
+ try {
+ xr.sendAndReceiveQuery(server, collection, query);
+ int count = xr.getResultCount();
+ if (count == 0) {
+ JOptionPane.showMessageDialog(jcp, "No molecule is found in WWMM database.\n IChI Basic='" + basic + "'");
+ return;
+ } else if (count == -1) {
+ JOptionPane.showMessageDialog(jcp, "The result is null.\n IChI Basic='" + basic + "'");
+ return;
+ } else if (count == 1) {
+ JOptionPane.showMessageDialog(jcp, "There is 1 molecule in WWMM database.\n IChI Basic='" + basic + "'");
+ Molecule m = xr.readMolecules().getMolecule(0);
+ new Utils().displayInJmol(m);
+ String result = xr.getResult();
+ frame = new TextFrame(result);
+ frame.pack();
+ frame.setVisible(true);
+ } else {
+ JOptionPane.showMessageDialog(jcp, "There are "+ Integer.toString(count) + " molecules in WWMM database.\n IChI Basic='" + basic + "'");
+ Molecule m = xr.readMolecules().getMolecule(0);
+ new Utils().displayInJmol(m);
+ String result = xr.getResult();
+ frame = new TextFrame(result);
+ frame.pack();
+ frame.setVisible(true);
+ }
+ } catch (Exception eXindice) {
+ eXindice.printStackTrace();
+ }
+
+ } catch(Exception exc) {
+ logger.error(exc.toString());
+ }
}
}
@@ -150,5 +262,36 @@
}
}
return pluginProps;
+ }
+
+ private class TextFrame extends JFrame {
+ public TextFrame(String ichi) {
+ super("IChI");
+
+ //Create a text area.
+ JTextArea textArea = new JTextArea(ichi);
+ textArea.setFont(new Font("Monospaced", Font.BOLD, 16));
+ textArea.setLineWrap(true);
+ textArea.setWrapStyleWord(true);
+ JScrollPane areaScrollPane = new JScrollPane(textArea);
+ areaScrollPane.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
+ areaScrollPane.setPreferredSize(new Dimension(1000, 700));
+ areaScrollPane.setBorder(
+ BorderFactory.createCompoundBorder(
+ BorderFactory.createCompoundBorder(
+ BorderFactory.createTitledBorder("IChI string"),
+ BorderFactory.createEmptyBorder(5,5,5,5)),
+ areaScrollPane.getBorder()));
+
+ JPanel contentPane = new JPanel();
+ BoxLayout box = new BoxLayout(contentPane, BoxLayout.X_AXIS);
+ contentPane.setLayout(box);
+ contentPane.add(areaScrollPane);
+ setContentPane(contentPane);
+ }
+
+ public void closeFrame() {
+ dispose();
+ }
}
}
Index: WWMMCDKPluginQueryFrame.java
===================================================================
RCS file: /cvsroot/cdk/cdk-plugins/wwmmplugin/src/uk/ac/cam/ch/wwmm/WWMMCDKPluginQueryFrame.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- WWMMCDKPluginQueryFrame.java 3 Dec 2003 17:11:44 -0000 1.1
+++ WWMMCDKPluginQueryFrame.java 3 Dec 2003 21:09:34 -0000 1.2
@@ -302,7 +302,7 @@
//Create a text area.
JTextArea textArea = new JTextArea(entry);
- textArea.setFont(new Font("Courier", Font.BOLD, 16));
+ textArea.setFont(new Font("Monospaced", Font.BOLD, 16));
textArea.setLineWrap(true);
textArea.setWrapStyleWord(true);
JScrollPane areaScrollPane = new JScrollPane(textArea);
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