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[Cdk-commits] SF.net SVN: cdk: [8672] trunk/cdk-taverna
|
From: <mar...@us...> - 2007-08-08 19:19:37
|
Revision: 8672
http://cdk.svn.sourceforge.net/cdk/?rev=8672&view=rev
Author: mario_baseda
Date: 2007-08-08 12:19:30 -0700 (Wed, 08 Aug 2007)
Log Message:
-----------
Classes modified/added
Modified Paths:
--------------
trunk/cdk-taverna/.project
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateEMCluster.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateJ48WModel.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateKMeanCluster.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateKMeanClusterAction.java
trunk/cdk-taverna/src/main/resources/META-INF/services/org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI
Added Paths:
-----------
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateEMClusterAction.java
trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateJ48WModelAction.java
Modified: trunk/cdk-taverna/.project
===================================================================
--- trunk/cdk-taverna/.project 2007-08-07 15:20:11 UTC (rev 8671)
+++ trunk/cdk-taverna/.project 2007-08-08 19:19:30 UTC (rev 8672)
@@ -1,23 +1,13 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>cdk-taverna</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.maven.ide.eclipse.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.maven.ide.eclipse.maven2Nature</nature>
- </natures>
-</projectDescription>
+<projectDescription>
+ <name>cdk-taverna</name>
+ <comment/>
+ <projects/>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>
\ No newline at end of file
Modified: trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateEMCluster.java
===================================================================
--- trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateEMCluster.java 2007-08-07 15:20:11 UTC (rev 8671)
+++ trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateEMCluster.java 2007-08-08 19:19:30 UTC (rev 8672)
@@ -35,6 +35,13 @@
import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException;
import org.embl.ebi.escience.baclava.DataThing;
+import org.embl.ebi.escience.scufl.DuplicatePortNameException;
+import org.embl.ebi.escience.scufl.InputPort;
+import org.embl.ebi.escience.scufl.OutputPort;
+import org.embl.ebi.escience.scufl.PortCreationException;
+import org.embl.ebi.escience.scufl.XScufl;
+import org.jdom.Attribute;
+import org.jdom.Element;
import org.openscience.cdk.libio.weka.Weka;
import org.openscience.cdk.qsar.model.weka.EMCluster;
@@ -42,6 +49,9 @@
import org.openscience.cdk.applications.taverna.LocalWorkerCDK;
import org.openscience.cdk.applications.taverna.qsar.model.weka.Selection;
import org.openscience.cdk.applications.taverna.qsar.model.weka.Standardise;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.CDKLocalWorkerWithPorts;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.CDKProcessor;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.XMLExtensible;
/**
* GenerateEMCluster assigns a probability distribution to each instance which indicates the probability of it
@@ -66,7 +76,7 @@
* @cdk.keyword clusterers
* @cdk.keyword EM
*/
-public class GenerateEMCluster implements LocalWorkerCDK{
+public class GenerateEMCluster implements LocalWorkerCDK, CDKLocalWorkerWithPorts, XMLExtensible{
// new instance of EM cluster
private EMCluster em = new EMCluster();
// Contains the possible class attributs
@@ -75,6 +85,7 @@
private String[] y = null;
// Contains the dacriptor titles to select the descriptor values, which was chosen before
private String[] title;
+ private String[] options;
private String[] inputNames = new String[] { "matrix" };
private String[] outputNames = new String[] { "ModelsNumericAtts", "LogDensityPerCluster", "NumberOfCluster",
"ClusterPriorsProbability", "ClusterPriors", "MaxIterations", "MinStdDev", "NumClusters", "Seed"};
@@ -95,13 +106,40 @@
return new String[] {LocalWorkerCDK.ListOfListOfDoubleList, LocalWorkerCDK.ListOfDoubleList, LocalWorkerCDK.DOUBLE, LocalWorkerCDK.DoubleList,
LocalWorkerCDK.DoubleList, LocalWorkerCDK.DOUBLE, LocalWorkerCDK.DOUBLE, LocalWorkerCDK.DOUBLE, LocalWorkerCDK.DOUBLE};
}
+
+// Region: XML tags/attributes
+ private static final String EXTENSIONS = "extensions";
+ private static final String GenerateEMCluster = "generateemcluster";
+ private static final String OPTIONS = "options";
+
/**
* Constructor of the GenerateEMCluster object
*
*/
public GenerateEMCluster(){}
-
+
+ public List<InputPort> inputPorts(CDKProcessor processor) throws DuplicatePortNameException, PortCreationException {
+ List<InputPort> input = new ArrayList<InputPort>();
+ InputPort inPort;
+ for (int i = 0; i < inputNames.length; i++) {
+ inPort = new InputPort(processor, inputNames[i]);
+ inPort.setSyntacticType(inputTypes()[i]);
+ input.add(inPort);
+ }
+ return input;
+ }
+ public List<OutputPort> outputPorts(CDKProcessor processor) throws DuplicatePortNameException, PortCreationException {
+ List<OutputPort> output = new ArrayList<OutputPort>();
+ OutputPort outPort;
+ for (int i = 0; i < outputNames.length; i++) {
+ outPort = new OutputPort(processor, outputNames[i]);
+ outPort.setSyntacticType(outputTypes()[i]);
+ output.add(outPort);
+ }
+ return output;
+ }
+
/**
* Set the specific cluster options.
* Valid options are (according weka library):
@@ -116,6 +154,7 @@
*/
public void setOptions(String[] options) throws Exception{
em.setOptions(options);
+ this.options = options;
}
/**Set the class attributs. That are the possible dependent values
@@ -359,17 +398,46 @@
return new Double (em.getSeed());
}
- /**
- * Gets the current settings of the cluster
- *
- * @return list A List which contains the current settings as String
+ /**Returns the specific cluster options.
+ * @return A string[] which contains the the specific cluster options
*/
- public List getOptions(){
- List list = new ArrayList();
- String[] object = em.getOptions();
- for (String string : object) {
- list.add(string);
+ public String[] getOptions(){
+ return this.options;
+ }
+
+// Region: XML processing methods
+
+ public void consumeXML(Element element) {
+ List list = element.getChildren(GenerateEMCluster, XScufl.XScuflNS);
+ String[] temp = new String[list.size()];
+ Attribute attribute;
+ int i = 0;
+ for (Iterator iter = list.iterator(); iter.hasNext();) {
+ Element elements = (Element) iter.next();
+ attribute = elements.getAttribute(OPTIONS + (i + 1), XScufl.XScuflNS);
+ temp[i] = attribute.getValue();
+ i++;
}
- return list;
+ try {
+ setOptions(temp);
+ } catch (Exception ex) {
+ System.out.println("consumeXML_Exeption" + ex.toString());
+ // TODO: handle exception
+ }
}
-}
+
+ public Element provideXML() {
+ Element extensions = new Element(EXTENSIONS, XScufl.XScuflNS);
+ String[] temp = getOptions();
+ if (temp == null) return extensions;
+ Element options;
+ for (int i = 0; i < temp.length; i++){
+ options = new Element(GenerateEMCluster, XScufl.XScuflNS);
+ options.setAttribute(OPTIONS + (i + 1), temp[i], XScufl.XScuflNS);
+ extensions.addContent(options);
+ }
+ return extensions;
+ }
+
+ // End of region
+}
\ No newline at end of file
Modified: trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateJ48WModel.java
===================================================================
--- trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateJ48WModel.java 2007-08-07 15:20:11 UTC (rev 8671)
+++ trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateJ48WModel.java 2007-08-08 19:19:30 UTC (rev 8672)
@@ -35,6 +35,13 @@
import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException;
import org.embl.ebi.escience.baclava.DataThing;
+import org.embl.ebi.escience.scufl.DuplicatePortNameException;
+import org.embl.ebi.escience.scufl.InputPort;
+import org.embl.ebi.escience.scufl.OutputPort;
+import org.embl.ebi.escience.scufl.PortCreationException;
+import org.embl.ebi.escience.scufl.XScufl;
+import org.jdom.Attribute;
+import org.jdom.Element;
import org.openscience.cdk.libio.weka.Weka;
import org.openscience.cdk.qsar.model.weka.J48WModel;
@@ -42,6 +49,9 @@
import org.openscience.cdk.applications.taverna.LocalWorkerCDK;
import org.openscience.cdk.applications.taverna.qsar.model.weka.Selection;
import org.openscience.cdk.applications.taverna.qsar.model.weka.Standardise;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.CDKLocalWorkerWithPorts;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.CDKProcessor;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.XMLExtensible;
/**
* A modeling class that provides the Quinlan's model C4.5 known as J48
@@ -58,9 +68,9 @@
* as the pruning set.(Deafult:3)</p>
* <p>-B: Use binary splits for nominal attributes</p>
* <p>-S: Don't perform subtree raising</p>
- * <p>-L: Do not clean up alfter the tree has been built</p>
+ * <p>-L: Do not clean up after the tree has been built</p>
* <p>-A: If set, Laplace smoothing is used for predicted probabilities</p>
- * <p>-Q:The seed for reduced-error pruning</p>
+ * <p>-Q: The seed for reduced-error pruning</p>
*
* @author Mario Baseda
* @cdk.require cdk-svn.jar
@@ -71,7 +81,7 @@
* @cdk.keyword decision and regression trees
* @cdk.keyword J48
*/
-public class GenerateJ48WModel implements LocalWorkerCDK{
+public class GenerateJ48WModel implements LocalWorkerCDK, CDKLocalWorkerWithPorts, XMLExtensible{
// new instance of k mean cluster
private J48WModel j48;
// Contains the dacriptor titles to select the descriptor values, which was chosen before
@@ -100,13 +110,40 @@
public String[] outputTypes() {
return new String[] {LocalWorkerCDK.StringList};
}
+
+// Region: XML tags/attributes
+ private static final String EXTENSIONS = "extensions";
+ private static final String GenerateJ48WModel = "generatej48wmodel";
+ private static final String OPTIONS = "options";
+
/**
* Constructor of the GenerateKMeanCluster object
*
*/
public GenerateJ48WModel(){}
-
+
+ public List<InputPort> inputPorts(CDKProcessor processor) throws DuplicatePortNameException, PortCreationException {
+ List<InputPort> input = new ArrayList<InputPort>();
+ InputPort inPort;
+ for (int i = 0; i < inputNames.length; i++) {
+ inPort = new InputPort(processor, inputNames[i]);
+ inPort.setSyntacticType(inputTypes()[i]);
+ input.add(inPort);
+ }
+ return input;
+ }
+ public List<OutputPort> outputPorts(CDKProcessor processor) throws DuplicatePortNameException, PortCreationException {
+ List<OutputPort> output = new ArrayList<OutputPort>();
+ OutputPort outPort;
+ for (int i = 0; i < outputNames.length; i++) {
+ outPort = new OutputPort(processor, outputNames[i]);
+ outPort.setSyntacticType(outputTypes()[i]);
+ output.add(outPort);
+ }
+ return output;
+ }
+
/**
* This method gets a Map with CMLChemfiles. The molecules in this Chemfile should be classified about their
* specific descriptor values.
@@ -183,7 +220,7 @@
/**
* Set the specific model options.
- * Valid options are (according weka library):
+ * Valid options are (according weka library):
* <p>Valid options are (according weka library):</p>
* <p>-U: Use unpruned tree.</p>
* <p>-C confidence: Set confidence threshold for pruning. (Defalult:0.25)</p>
@@ -202,7 +239,14 @@
public void setOptions(String[] options) throws Exception{
this.options = options;
}
-
+
+ /**Returns the specific model options.
+ * @return A string[] which contains the the specific model options
+ */
+ public String[] getOptions(){
+ return this.options;
+ }
+
/**Set the class attributs. That are the possible dependent values
* @param classAttributs A String[] contains the class attributs
*/
@@ -228,4 +272,40 @@
}
return prediction;
}
+
+// Region: XML processing methods
+
+ public void consumeXML(Element element) {
+ List list = element.getChildren(GenerateJ48WModel, XScufl.XScuflNS);
+ String[] temp = new String[list.size()];
+ Attribute attribute;
+ int i = 0;
+ for (Iterator iter = list.iterator(); iter.hasNext();) {
+ Element elements = (Element) iter.next();
+ attribute = elements.getAttribute(OPTIONS + (i + 1), XScufl.XScuflNS);
+ temp[i] = attribute.getValue();
+ i++;
+ }
+ try {
+ setOptions(temp);
+ } catch (Exception ex) {
+ System.out.println("consumeXML_Exeption" + ex.toString());
+ // TODO: handle exception
+ }
+ }
+
+ public Element provideXML() {
+ Element extensions = new Element(EXTENSIONS, XScufl.XScuflNS);
+ String[] temp = getOptions();
+ if (temp == null) return extensions;
+ Element options;
+ for (int i = 0; i < temp.length; i++){
+ options = new Element(GenerateJ48WModel, XScufl.XScuflNS);
+ options.setAttribute(OPTIONS + (i + 1), temp[i], XScufl.XScuflNS);
+ extensions.addContent(options);
+ }
+ return extensions;
+ }
+
+ // End of region
}
Modified: trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateKMeanCluster.java
===================================================================
--- trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateKMeanCluster.java 2007-08-07 15:20:11 UTC (rev 8671)
+++ trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/GenerateKMeanCluster.java 2007-08-08 19:19:30 UTC (rev 8672)
@@ -328,7 +328,6 @@
*/
public void setOptions(String[] options) throws Exception{
kMean.setOptions(options);
- this.options = new String[2];
this.options = options;
}
Added: trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateEMClusterAction.java
===================================================================
--- trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateEMClusterAction.java (rev 0)
+++ trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateEMClusterAction.java 2007-08-08 19:19:30 UTC (rev 8672)
@@ -0,0 +1,302 @@
+/*
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Copyright (C) 2007 by Mario Baseda <mar...@us...>
+ *
+ * This program 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 (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program 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 Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+package org.openscience.cdk.applications.taverna.qsar.model.weka.action;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemListener;
+import java.awt.Container;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.JFrame;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.JSpinner;
+import javax.swing.WindowConstants;
+import javax.swing.SpringLayout.Constraints;
+import javax.swing.SpringLayout;
+import javax.swing.Spring;
+
+import org.embl.ebi.escience.scuflui.shared.UIUtils;
+import org.embl.ebi.escience.scufl.Processor;
+import org.embl.ebi.escience.scuflui.TavernaIcons;
+import org.openscience.cdk.applications.taverna.actions.AbstractCDKProcessorAction;
+import org.openscience.cdk.applications.taverna.qsar.model.weka.GenerateEMCluster;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.CDKProcessor;
+
+public class GenerateEMClusterAction extends AbstractCDKProcessorAction {
+ private static JFrame frame;
+
+ @Override
+ public JComponent getComponent(Processor processor) {
+ return null;
+ }
+
+ public boolean canHandle(Processor processor) {
+ if (!(processor instanceof CDKProcessor)) {
+ return false;
+ }
+ CDKProcessor proc = (CDKProcessor) processor;
+ if (proc.getWorker() instanceof GenerateEMCluster) {
+ return true;
+ }
+ else {
+ return false;
+ }
+ }
+
+ public String getDescription() {
+ return "Set Options";
+ }
+
+ public Dimension getFrameSize() {
+ // should be small enought due to using a file dialog
+ return new Dimension(1, 1);
+ }
+
+ public ImageIcon getIcon() {
+ return TavernaIcons.editIcon;
+ }
+
+ @Override
+ public JFrame getFrame(Processor processor) {
+ if (!(processor instanceof CDKProcessor)) {
+ return null;
+ }
+ CDKProcessor proc = (CDKProcessor) processor;
+ final List<String> options = new ArrayList<String>();
+ final GenerateEMCluster generator = (GenerateEMCluster) proc.getWorker();
+ String[] pastOptions = generator.getOptions();
+ frame = new JFrame("Set option for the EMCluster");
+ Container contentPane = frame.getContentPane();
+ SpringLayout layout = new SpringLayout();
+ contentPane.setLayout(layout);
+ Spring x = Spring.constant(5);
+ Spring y = Spring.constant(5);
+ Spring xGes = x;
+ final JCheckBox cb1 = new JCheckBox("Specify the number of clusters to generate", false);
+ final JCheckBox cb2 = new JCheckBox("Specify the random number seed ", false);
+ final JCheckBox cb3 = new JCheckBox("Verbose", false);
+ final JCheckBox cb4 = new JCheckBox("Set the minimum allowable standard deviation for normal density calculation", false);
+ final JCheckBox cb5 = new JCheckBox("Terminate after this many iterations if EM has not converged ", false);
+ SpinnerNumberModel model1 = new SpinnerNumberModel(1, 1, null, 1);
+ SpinnerNumberModel model2 = new SpinnerNumberModel(1, 1, null, 1);
+ SpinnerNumberModel model3 = new SpinnerNumberModel(0.001, 0.001, null, 0.001);
+ SpinnerNumberModel model4 = new SpinnerNumberModel(1, 1, null, 1);
+ final JSpinner spin1 = new JSpinner(model1);
+ final JSpinner spin2 = new JSpinner(model2);
+ final JSpinner spin3 = new JSpinner(model3);
+ final JSpinner spin4 = new JSpinner(model4);
+ final JButton button2 = new JButton(" OK ");
+ final JButton button1 = new JButton("Cancel");
+ Constraints c = layout.getConstraints(cb1);
+ c.setX(xGes);
+ xGes = Spring.sum(xGes, c.getConstraint("East"));
+ c.setY(y);
+ contentPane.add(cb1);
+ c = layout.getConstraints(spin1);
+ c.setX(xGes);
+ c.setWidth(Spring.constant(80));
+ c.setY(y);
+ contentPane.add(spin1);
+ c = layout.getConstraints(cb2);
+ c.setX(x);
+ c.setY(Spring.sum(y, layout.getConstraints(cb1).getConstraint("South")));
+ contentPane.add(cb2);
+ c = layout.getConstraints(spin2);
+ c.setX(xGes);
+ c.setWidth(Spring.constant(80));
+ c.setY(Spring.sum(y, layout.getConstraints(cb1).getConstraint("South")));
+ contentPane.add(spin2);
+ c = layout.getConstraints(cb3);
+ c.setX(x);
+ c.setY(Spring.sum(Spring.constant(30), layout.getConstraints(cb2).getConstraint("South")));
+ contentPane.add(cb3);
+ c = layout.getConstraints(cb4);
+ c.setX(x);
+ c.setY(Spring.sum(y, layout.getConstraints(cb3).getConstraint("South")));
+ xGes = Spring.sum(x, c.getConstraint("East"));
+ contentPane.add(cb4);
+ c = layout.getConstraints(spin3);
+ c.setX(xGes);
+ c.setWidth(Spring.constant(80));
+ c.setY(Spring.sum(y, layout.getConstraints(cb3).getConstraint("South")));
+ contentPane.add(spin3);
+ c = layout.getConstraints(cb5);
+ c.setX(x);
+ c.setY(Spring.sum(y, layout.getConstraints(cb4).getConstraint("South")));
+ contentPane.add(cb5);
+ c = layout.getConstraints(spin4);
+ c.setX(xGes);
+ c.setWidth(Spring.constant(80));
+ c.setY(Spring.sum(y, layout.getConstraints(cb4).getConstraint("South")));
+ contentPane.add(spin4);
+ c = layout.getConstraints(button1);
+ Spring s1 = Spring.constant(480);
+ Spring s2 = c.getWidth();
+ s2 = Spring.minus(s2);
+ x = Spring.sum(s1, s2);
+ c.setX(x);
+ c.setY(Spring.sum(Spring.constant(20), layout.getConstraints(cb5).getConstraint("South")));
+ contentPane.add(button1);
+ c = layout.getConstraints(button2);
+ s1 = layout.getConstraints(button1).getConstraint("West");
+ s2 = Spring.sum(Spring.constant(10), c.getWidth());
+ s2 = Spring.minus(s2);
+ x = Spring.sum(s1, s2);
+ c.setX(x);
+ c.setY(Spring.sum(Spring.constant(20), layout.getConstraints(cb5).getConstraint("South")));
+ contentPane.add(button2);
+ spin1.setVisible(false);
+ spin2.setVisible(false);
+ spin3.setVisible(false);
+ spin4.setVisible(false);
+ if (pastOptions != null && pastOptions.length != 0){
+ for (int i = 0; i < pastOptions.length; i++) {
+ if (pastOptions[i].startsWith("-")){
+ if (pastOptions[i].equals("-N")){
+ cb1.setSelected(true);
+ model1.setValue(Integer.parseInt(pastOptions[i+1]));
+ spin1.setVisible(true);
+ }
+ if (pastOptions[i].equals("-S")){
+ cb2.setSelected(true);
+ model2.setValue(Integer.parseInt(pastOptions[i+1]));
+ spin2.setVisible(true);
+ }
+ if (pastOptions[i].equals("-V")) cb3.setSelected(true);
+ if (pastOptions[i].equals("-M")){
+ cb4.setSelected(true);
+ model3.setValue(Double.parseDouble(pastOptions[i+1]));
+ spin3.setVisible(true);
+ }
+ if (pastOptions[i].equals("-I")){
+ cb5.setSelected(true);
+ model4.setValue(Integer.parseInt(pastOptions[i+1]));
+ spin4.setVisible(true);
+ }
+ }
+ }
+ }
+ ItemListener il1 = new ItemListener() {
+ public void itemStateChanged(ItemEvent e){
+ if (cb2.isSelected()){
+ cb2.setSelected(false);
+ }
+ if ((!(cb1.isSelected())) && (!(cb2.isSelected()))){
+ spin1.setVisible(false);
+ spin2.setVisible(false);
+ }
+ if (cb1.isSelected()) {
+ spin1.setVisible(true);
+ spin2.setVisible(false);
+ }
+ }
+ };
+ ItemListener il2 = new ItemListener() {
+ public void itemStateChanged(ItemEvent e2){
+ if (cb1.isSelected()){
+ cb1.setSelected(false);
+ }
+ if ((!(cb1.isSelected())) && (!(cb2.isSelected()))){
+ spin1.setVisible(false);
+ spin2.setVisible(false);
+ }
+ if (cb2.isSelected()){
+ spin1.setVisible(false);
+ spin2.setVisible(true);
+ }
+ }
+ };
+ ItemListener il3 = new ItemListener() {
+ public void itemStateChanged(ItemEvent e3){
+ if (cb4.isSelected()) spin3.setVisible(true);
+ else spin3.setVisible(false);
+ if (cb5.isSelected()) spin4.setVisible(true);
+ else spin4.setVisible(false);
+ }
+ };
+ cb1.addItemListener(il1);
+ cb2.addItemListener(il2);
+ cb3.addItemListener(il3);
+ cb4.addItemListener(il3);
+ cb5.addItemListener(il3);
+ ActionListener ai = new ActionListener() {
+ public void actionPerformed (ActionEvent ae){
+ if (ae.getActionCommand() == " OK "){
+ if (cb1.isSelected()){
+ options.add("-N");
+ options.add(String.valueOf((Integer) spin1.getValue()));
+ }
+ if (cb2.isSelected()){
+ options.add("-S");
+ options.add(String.valueOf((Integer) spin2.getValue()));
+ }
+ if (cb3.isSelected()) options.add("-V");
+ if (cb4.isSelected()) {
+ options.add("-M");
+ options.add(String.valueOf((Double) spin3.getValue()));
+ }
+ if (cb5.isSelected()) {
+ options.add("-I");
+ options.add(String.valueOf((Integer) spin4.getValue()));
+ }
+ String[] option = new String[options.size()];
+ int i = 0;
+ for (Iterator iter = options.iterator(); iter.hasNext();) {
+ String element = (String) iter.next();
+ option[i] = element;
+ i++;
+ }
+ try{
+ generator.setOptions(option);
+ }catch(Exception exception){
+ exception.getStackTrace();
+ }
+ frame.dispose();
+ } else {
+ if (ae.getActionCommand() == "Cancel"){
+ frame.dispose();;
+ }
+ }
+ }
+ };
+ button1.addActionListener(ai);
+ button2.addActionListener(ai);
+ frame.setSize(500, 260);
+ frame.setLocationByPlatform(true);
+ frame.setVisible(true);
+ frame.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ return null;
+ }
+}
\ No newline at end of file
Added: trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateJ48WModelAction.java
===================================================================
--- trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateJ48WModelAction.java (rev 0)
+++ trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateJ48WModelAction.java 2007-08-08 19:19:30 UTC (rev 8672)
@@ -0,0 +1,393 @@
+/*
+ * $Author$
+ * $Date$
+ * $Revision$
+ *
+ * Copyright (C) 2007 by Mario Baseda <mar...@us...>
+ *
+ * This program 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 (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program 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 Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ */
+package org.openscience.cdk.applications.taverna.qsar.model.weka.action;
+
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ItemEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemListener;
+import java.awt.Container;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.JFrame;
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.SpinnerNumberModel;
+import javax.swing.JSpinner;
+import javax.swing.WindowConstants;
+import javax.swing.SpringLayout.Constraints;
+import javax.swing.SpringLayout;
+import javax.swing.Spring;
+
+import org.embl.ebi.escience.scuflui.shared.UIUtils;
+import org.embl.ebi.escience.scufl.Processor;
+import org.embl.ebi.escience.scuflui.TavernaIcons;
+import org.openscience.cdk.applications.taverna.actions.AbstractCDKProcessorAction;
+import org.openscience.cdk.applications.taverna.qsar.model.weka.GenerateJ48WModel;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.CDKProcessor;
+
+public class GenerateJ48WModelAction extends AbstractCDKProcessorAction {
+ private static JFrame frame;
+
+ @Override
+ public JComponent getComponent(Processor processor) {
+ return null;
+ }
+
+ public boolean canHandle(Processor processor) {
+ if (!(processor instanceof CDKProcessor)) {
+ return false;
+ }
+ CDKProcessor proc = (CDKProcessor) processor;
+ if (proc.getWorker() instanceof GenerateJ48WModel) {
+ return true;
+ }
+ else {
+ return false;
+ }
+ }
+
+ public String getDescription() {
+ return "Set Options";
+ }
+
+ public Dimension getFrameSize() {
+ // should be small enought due to using a file dialog
+ return new Dimension(1, 1);
+ }
+
+ public ImageIcon getIcon() {
+ return TavernaIcons.editIcon;
+ }
+
+ @Override
+ public JFrame getFrame(Processor processor) {
+ if (!(processor instanceof CDKProcessor)) {
+ return null;
+ }
+ CDKProcessor proc = (CDKProcessor) processor;
+ final List<String> options = new ArrayList<String>();
+ final GenerateJ48WModel generator = (GenerateJ48WModel) proc.getWorker();
+ String[] pastOptions = generator.getOptions();
+ frame = new JFrame("Set option for the J48WModel");
+ Container contentPane = frame.getContentPane();
+ SpringLayout layout = new SpringLayout();
+ contentPane.setLayout(layout);
+ Spring x = Spring.constant(5);
+ Spring y = Spring.constant(5);
+ Spring xGes = x;
+ final JCheckBox cb1 = new JCheckBox("Use unpruned tree", false);
+ final JCheckBox cb2 = new JCheckBox("Set confidence threshold for pruning ", false);
+ final JCheckBox cb3 = new JCheckBox("Use reduced error pruning. No subte raising is performed", false);
+ final JCheckBox cb4 = new JCheckBox("Don't perform subtree raising", false);
+ final JCheckBox cb5 = new JCheckBox("Set number of folds for reduced error pruning. One fold is used as the pruning set", false);
+ final JCheckBox cb6 = new JCheckBox("Set minimum number of instances per leaf", false);
+ final JCheckBox cb7 = new JCheckBox("The seed for reduced-error pruning ", false);
+ final JCheckBox cb8 = new JCheckBox("Use binary splits for nominal attributes", false);
+ final JCheckBox cb9 = new JCheckBox("Do not clean up after the tree has been built", false);
+ final JCheckBox cb10 = new JCheckBox("If set, Laplace smoothing is used for predicted probabilities", false);
+ SpinnerNumberModel model1 = new SpinnerNumberModel(0.01, 0.01, null, 0.01);
+ SpinnerNumberModel model2 = new SpinnerNumberModel(2, 2, null, 1);
+ SpinnerNumberModel model3 = new SpinnerNumberModel(1, 1, null, 1);
+ SpinnerNumberModel model4 = new SpinnerNumberModel(1, 1, null, 1);
+ final JSpinner spin1 = new JSpinner(model1);
+ final JSpinner spin2 = new JSpinner(model2);
+ final JSpinner spin3 = new JSpinner(model3);
+ final JSpinner spin4 = new JSpinner(model4);
+ final JButton button2 = new JButton(" OK ");
+ final JButton button1 = new JButton("Cancel");
+ Constraints c = layout.getConstraints(cb1);
+ c.setX(xGes);
+ //xGes = Spring.sum(xGes, c.getConstraint("East"));
+ c.setY(y);
+ contentPane.add(cb1);
+ c = layout.getConstraints(cb2);
+ c.setX(xGes);
+ c.setY(Spring.sum(y, layout.getConstraints(cb1).getConstraint("South")));
+ xGes = Spring.sum(Spring.constant(10), layout.getConstraints(cb6).getConstraint("East"));
+ contentPane.add(cb2);
+ c = layout.getConstraints(spin1);
+ c.setX(xGes);
+ c.setWidth(Spring.constant(80));
+ c.setY(Spring.sum(y, layout.getConstraints(cb1).getConstraint("South")));
+ xGes = Spring.sum(x, c.getConstraint("East"));
+ contentPane.add(spin1);
+ c = layout.getConstraints(cb3);
+ c.setX(x);
+ c.setY(Spring.sum(y, layout.getConstraints(cb2).getConstraint("South")));
+ contentPane.add(cb3);
+ c = layout.getConstraints(cb4);
+ c.setX(xGes);
+ Spring xG = xGes;
+ c.setY(Spring.sum(y, layout.getConstraints(cb1).getConstraint("South")));
+ contentPane.add(cb4);
+ c = layout.getConstraints(cb5);
+ c.setX(xGes);
+ c.setY(Spring.sum(y, layout.getConstraints(cb4).getConstraint("South")));
+ xGes = Spring.sum(x, c.getConstraint("East"));
+ contentPane.add(cb5);
+ c = layout.getConstraints(spin2);
+ c.setX(xGes);
+ c.setWidth(Spring.constant(80));
+ c.setY(Spring.sum(y, layout.getConstraints(cb4).getConstraint("South")));
+ contentPane.add(spin2);
+ c = layout.getConstraints(cb6);
+ c.setX(x);
+ c.setY(Spring.sum(Spring.constant(30), layout.getConstraints(cb3).getConstraint("South")));
+ xGes = Spring.sum(x, c.getConstraint("East"));
+ contentPane.add(cb6);
+ c = layout.getConstraints(spin3);
+ c.setX(xGes);
+ c.setWidth(Spring.constant(80));
+ c.setY(Spring.sum(Spring.constant(30), layout.getConstraints(cb3).getConstraint("South")));
+ contentPane.add(spin3);
+ c = layout.getConstraints(cb7);
+ c.setX(x);
+ c.setY(Spring.sum(y, layout.getConstraints(cb6).getConstraint("South")));
+ contentPane.add(cb7);
+ c = layout.getConstraints(spin4);
+ c.setX(xGes);
+ c.setWidth(Spring.constant(80));
+ c.setY(Spring.sum(y, layout.getConstraints(cb6).getConstraint("South")));
+ contentPane.add(spin4);
+ c = layout.getConstraints(cb8);
+ c.setX(x);
+ c.setY(Spring.sum(y, layout.getConstraints(cb7).getConstraint("South")));
+ contentPane.add(cb8);
+ c = layout.getConstraints(cb9);
+ c.setX(xG);
+ c.setY(Spring.sum(Spring.constant(30), layout.getConstraints(cb3).getConstraint("South")));
+ contentPane.add(cb9);
+ c = layout.getConstraints(cb10);
+ c.setX(xG);
+ c.setY(Spring.sum(y, layout.getConstraints(cb9).getConstraint("South")));
+ contentPane.add(cb10);
+ c = layout.getConstraints(button1);
+ Spring s1 = Spring.constant(830);
+ Spring s2 = c.getWidth();
+ s2 = Spring.minus(s2);
+ x = Spring.sum(s1, s2);
+ c.setX(x);
+ c.setY(Spring.sum(Spring.constant(20), layout.getConstraints(cb8).getConstraint("South")));
+ contentPane.add(button1);
+ c = layout.getConstraints(button2);
+ s1 = layout.getConstraints(button1).getConstraint("West");
+ s2 = Spring.sum(Spring.constant(10), c.getWidth());
+ s2 = Spring.minus(s2);
+ x = Spring.sum(s1, s2);
+ c.setX(x);
+ c.setY(Spring.sum(Spring.constant(20), layout.getConstraints(cb8).getConstraint("South")));
+ contentPane.add(button2);
+ spin1.setVisible(false);
+ spin2.setVisible(false);
+ spin3.setVisible(false);
+ spin4.setVisible(false);
+ cb4.setVisible(false);
+ cb5.setVisible(false);
+ if (pastOptions != null && pastOptions.length != 0){
+ for (int i = 0; i < pastOptions.length; i++) {
+ if (pastOptions[i].startsWith("-")){
+ if (pastOptions[i].equals("-C")){
+ cb2.setSelected(true);
+ model1.setValue(Double.parseDouble(pastOptions[i+1]));
+ spin1.setVisible(true);
+ cb4.setVisible(true);
+ }
+ if (pastOptions[i].equals("-N")){
+ cb5.setSelected(true);
+ cb5.setVisible(true);
+ model2.setValue(Integer.parseInt(pastOptions[i+1]));
+ spin2.setVisible(true);
+ }
+ if (pastOptions[i].equals("-M")){
+ cb6.setSelected(true);
+ model3.setValue(Integer.parseInt(pastOptions[i+1]));
+ spin3.setVisible(true);
+ }
+ if (pastOptions[i].equals("-Q")){
+ cb7.setSelected(true);
+ model4.setValue(Integer.parseInt(pastOptions[i+1]));
+ spin4.setVisible(true);
+ }
+ if (pastOptions[i].equals("-U")) cb1.setSelected(true);
+ if (pastOptions[i].equals("-R")) {
+ cb3.setSelected(true);
+ cb4.setVisible(true);
+ cb5.setVisible(true);
+ spin2.setVisible(true);
+ }
+ if (pastOptions[i].equals("-S")) {
+ cb4.setSelected(true);
+ cb4.setVisible(true);
+ }
+ if (pastOptions[i].equals("-B")) cb8.setSelected(true);
+ if (pastOptions[i].equals("-L")) cb9.setSelected(true);
+ if (pastOptions[i].equals("-A")) cb10.setSelected(true);
+ }
+ }
+ }
+ ItemListener il1 = new ItemListener() {
+ public void itemStateChanged(ItemEvent e){
+ if (cb2.isSelected()) cb2.setSelected(false);
+ if (cb3.isSelected()) cb3.setSelected(false);
+ if (cb1.isSelected()){
+ spin1.setVisible(false);
+ cb4.setVisible(false);
+ cb5.setVisible(false);
+ }
+ if (!(cb2.isSelected())){
+ spin1.setVisible(false);
+ cb4.setVisible(false);
+ }
+ if (!(cb3.isSelected())){
+ cb4.setVisible(false);
+ cb5.setVisible(false);
+ cb5.setSelected(false);
+ spin2.setVisible(false);
+ }
+ }
+ };
+ ItemListener il2 = new ItemListener() {
+ public void itemStateChanged(ItemEvent e){
+ if (cb1.isSelected()) cb1.setSelected(false);
+ if (cb3.isSelected()) cb3.setSelected(false);
+ if (cb2.isSelected()){
+ spin1.setVisible(true);
+ cb4.setVisible(true);
+ cb5.setVisible(false);
+ }
+ if (!(cb2.isSelected())){
+ spin1.setVisible(false);
+ cb4.setVisible(false);
+ }
+ if (!(cb3.isSelected())){
+ cb5.setVisible(false);
+ cb5.setSelected(false);
+ spin2.setVisible(false);
+ }
+ }
+ };
+ ItemListener il3 = new ItemListener() {
+ public void itemStateChanged(ItemEvent e){
+ if (cb1.isSelected()) cb1.setSelected(false);
+ if (cb2.isSelected()) cb2.setSelected(false);
+ if (cb3.isSelected()){
+ spin1.setVisible(false);
+ cb4.setVisible(true);
+ cb5.setVisible(true);
+ }
+ if (!(cb2.isSelected())){
+ spin1.setVisible(false);
+ }
+ if (!(cb3.isSelected())){
+ cb4.setVisible(false);
+ cb5.setVisible(false);
+ cb5.setSelected(false);
+ spin2.setVisible(false);
+ }
+ }
+ };
+ ItemListener il4 = new ItemListener() {
+ public void itemStateChanged(ItemEvent e){
+ if (cb5.isSelected()) spin2.setVisible(true);
+ else spin2.setVisible(false);
+ if (cb6.isSelected()) spin3.setVisible(true);
+ else spin3.setVisible(false);
+ if (cb7.isSelected()) spin4.setVisible(true);
+ else spin4.setVisible(false);
+ }
+ };
+ cb1.addItemListener(il1);
+ cb2.addItemListener(il2);
+ cb3.addItemListener(il3);
+ cb4.addItemListener(il4);
+ cb5.addItemListener(il4);
+ cb6.addItemListener(il4);
+ cb7.addItemListener(il4);
+ cb8.addItemListener(il4);
+ cb9.addItemListener(il4);
+ cb10.addItemListener(il4);
+ ActionListener ai = new ActionListener() {
+ public void actionPerformed (ActionEvent ae){
+ if (ae.getActionCommand() == " OK "){
+ if (cb1.isSelected()){
+ options.add("-U");
+ }
+ if (cb2.isSelected()){
+ options.add("-C");
+ options.add(String.valueOf((Double) spin1.getValue()));
+ }
+ if (cb3.isSelected()) options.add("-R");
+ if (cb4.isSelected()) options.add("-S");
+ if (cb5.isSelected()) {
+ options.add("-N");
+ options.add(String.valueOf((Integer) spin2.getValue()));
+ }
+ if (cb6.isSelected()) {
+ options.add("-M");
+ options.add(String.valueOf((Integer) spin3.getValue()));
+ }
+ if (cb7.isSelected()) {
+ options.add("-Q");
+ options.add(String.valueOf((Integer) spin4.getValue()));
+ }
+ if (cb8.isSelected()) options.add("-B");
+ if (cb9.isSelected()) options.add("-L");
+ if (cb10.isSelected()) options.add("-A");
+ String[] option = new String[options.size()];
+ int i = 0;
+ for (Iterator iter = options.iterator(); iter.hasNext();) {
+ String element = (String) iter.next();
+ option[i] = element;
+ i++;
+ }
+ try{
+ generator.setOptions(option);
+ }catch(Exception exception){
+ exception.getStackTrace();
+ }
+ frame.dispose();
+ } else {
+ if (ae.getActionCommand() == "Cancel"){
+ frame.dispose();;
+ }
+ }
+ }
+ };
+ button1.addActionListener(ai);
+ button2.addActionListener(ai);
+ frame.setSize(860, 290);
+ frame.setLocationByPlatform(true);
+ frame.setVisible(true);
+ frame.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
+ return null;
+ }
+}
Modified: trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateKMeanClusterAction.java
===================================================================
--- trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateKMeanClusterAction.java 2007-08-07 15:20:11 UTC (rev 8671)
+++ trunk/cdk-taverna/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/weka/action/GenerateKMeanClusterAction.java 2007-08-08 19:19:30 UTC (rev 8672)
@@ -92,6 +92,7 @@
}
CDKProcessor proc = (CDKProcessor) processor;
final GenerateKMeanCluster generator = (GenerateKMeanCluster) proc.getWorker();
+ String[] pastOptions = generator.getOptions();
frame = new JFrame("Set option for the KMeanCluster");
Container contentPane = frame.getContentPane();
SpringLayout layout = new SpringLayout();
@@ -132,7 +133,7 @@
s2 = Spring.minus(s2);
x = Spring.sum(s1, s2);
c.setX(x);
- c.setY(Spring.sum(y, layout.getConstraints(cb2).getConstraint("South")));
+ c.setY(Spring.sum(Spring.constant(20), layout.getConstraints(cb2).getConstraint("South")));
contentPane.add(button1);
c = layout.getConstraints(button2);
s1 = layout.getConstraints(button1).getConstraint("West");
@@ -140,10 +141,26 @@
s2 = Spring.minus(s2);
x = Spring.sum(s1, s2);
c.setX(x);
- c.setY(Spring.sum(y, layout.getConstraints(cb2).getConstraint("South")));
+ c.setY(Spring.sum(Spring.constant(20), layout.getConstraints(cb2).getConstraint("South")));
contentPane.add(button2);
spin1.setVisible(false);
- spin2.setVisible(false);
+ spin2.setVisible(false);
+ if (pastOptions != null && pastOptions.length != 0){
+ for (int i = 0; i < pastOptions.length; i++) {
+ if (pastOptions[i].startsWith("-")){
+ if (pastOptions[i].equals("-N")){
+ cb1.setSelected(true);
+ model1.setValue(Integer.parseInt(pastOptions[i+1]));
+ spin1.setVisible(true);
+ }
+ if (pastOptions[i].equals("-S")){
+ cb2.setSelected(true);
+ model2.setValue(Integer.parseInt(pastOptions[i+1]));
+ spin2.setVisible(true);
+ }
+ }
+ }
+ }
ItemListener il1 = new ItemListener() {
public void itemStateChanged(ItemEvent e){
if (cb2.isSelected()){
@@ -207,7 +224,7 @@
};
button1.addActionListener(ai);
button2.addActionListener(ai);
- frame.setSize(420, 135);
+ frame.setSize(420, 145);
frame.setLocationByPlatform(true);
frame.setVisible(true);
frame.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
Modified: trunk/cdk-taverna/src/main/resources/META-INF/services/org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI
===================================================================
--- trunk/cdk-taverna/src/main/resources/META-INF/services/org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI 2007-08-07 15:20:11 UTC (rev 8671)
+++ trunk/cdk-taverna/src/main/resources/META-INF/services/org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI 2007-08-08 19:19:30 UTC (rev 8672)
@@ -1,4 +1,6 @@
org.openscience.cdk.applications.taverna.io.action.ReadMDLMolFileAction
org.openscience.cdk.applications.taverna.io.action.FileReaderAction
org.openscience.cdk.applications.taverna.jchempaint.action.JChemPaintEditorAction
-org.openscience.cdk.applications.taverna.qsar.model.weka.action.GenerateKMeanClusterAction
\ No newline at end of file
+org.openscience.cdk.applications.taverna.qsar.model.weka.action.GenerateKMeanClusterAction
+org.openscience.cdk.applications.taverna.qsar.model.weka.action.GenerateEMClusterAction
+org.openscience.cdk.applications.taverna.qsar.model.weka.action.GenerateJ48WModelAction
\ No newline at end of file
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