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[Cdk-commits] SF.net SVN: cdk:[12091] cdk-taverna/trunk/src/main/java/org/openscience/cdk /applications/taverna/qsar/model/ART2AClassificator/tools
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From: <tho...@us...> - 2008-08-26 12:22:31
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Revision: 12091
http://cdk.svn.sourceforge.net/cdk/?rev=12091&view=rev
Author: thomaskuhn
Date: 2008-08-26 12:22:27 +0000 (Tue, 26 Aug 2008)
Log Message:
-----------
Add a new worker and the corresponding actions. This worker extracts the molecule id's from a selected cluster or class from an ART2A classification result
Added Paths:
-----------
cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/ART2AClassificator/tools/GetMoleculeIDsForGivenClasses.java
cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/ART2AClassificator/tools/action/GetMoleculeIDsForGivenClassesAction.java
Added: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/ART2AClassificator/tools/GetMoleculeIDsForGivenClasses.java
===================================================================
--- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/ART2AClassificator/tools/GetMoleculeIDsForGivenClasses.java (rev 0)
+++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/ART2AClassificator/tools/GetMoleculeIDsForGivenClasses.java 2008-08-26 12:22:27 UTC (rev 12091)
@@ -0,0 +1,235 @@
+/* $RCSfile$
+ * $Author: $
+ * $Date: $
+ * $Revision: $
+ *
+ * Copyright (C) 2008 by Thomas Kuhn <tho...@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.ART2AClassificator.tools;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.stream.XMLStreamReader;
+
+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.Element;
+import org.openscience.cdk.applications.art2aClassification.Art2aClassificator;
+import org.openscience.cdk.applications.taverna.LocalWorkerCDK;
+import org.openscience.cdk.applications.taverna.io.XMLFileIO;
+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;
+
+import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException;
+
+/**
+ * Class which implements a local worker for the cdk-taverna project.
+ * This worker extracts the molecule id's from the corresponding object of vectors which are within a given class number of an ART2A classification result.
+ * @author Thomas Kuhn
+ *
+ */
+public class GetMoleculeIDsForGivenClasses implements LocalWorkerCDK, CDKLocalWorkerWithPorts, XMLExtensible{
+
+// Region: class variables
+
+ private static final String[] inputNames = new String[] { "clasNnumber", "fileName" };
+ private static final String[] outputNames = new String[] { "moleculeIDs", "Comment" };
+ private List<String> fileNames = new ArrayList<String>();
+
+ // Region: XML tags/attributes
+
+ private static final String EXTENSIONS = "extensions";
+ private static final String GETMOLECULEIDSFORGIVENCLASSES = "GetMoleculeIDsForGivenClasses";
+ private static final String FILENAMES = "filenames";
+ private static final String FILENAMELIST = "filenamelist";
+ private static final String FILENAME = "filename";
+
+ // End of region
+
+ // End of region
+
+ // Region: public methods
+
+ // Region: get / set properties
+
+ /**
+ * Returns the current file names
+ * @return filenames
+ */
+ public List<String> getFileNames() {
+ return this.fileNames;
+ }
+ /**
+ * Add the file name to the file name list
+ * @param fileName file name of the file which should be loaded1
+ */
+ public void addFileName(String fileName){
+ this.fileNames.add(fileName);
+ }
+
+ // End of region
+
+ // Region: input and output definition
+
+ public String[] inputNames() {
+ return inputNames;
+ }
+ public String[] inputTypes() {
+ return new String[] { LocalWorkerCDK.STRING, LocalWorkerCDK.STRING_ARRAY };
+ }
+
+ public String[] outputNames() {
+ return outputNames;
+ }
+ public String[] outputTypes() {
+ return new String[] {LocalWorkerCDK.STRING_ARRAY, LocalWorkerCDK.STRING_ARRAY};
+ }
+
+ 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;
+ }
+
+ // End of region
+
+ // Region: local worker execution
+ /**
+ * This worker extracts the molecule id's from the corresponding object of vectors which are within a given class number of an ART2A classification result.
+ */
+ @SuppressWarnings("unchecked")
+ public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException {
+ List<String> fileNamesList = new ArrayList<String>();
+ String classNumbers = null;
+ List<String> comment = new ArrayList<String>();
+ List<String> moleculeIDs = new ArrayList<String>(1000);
+ Map<String, DataThing> outputs = new HashMap<String, DataThing>();
+ if(inputs.get(inputNames[0]) != null) {
+ classNumbers = (String)((DataThing)(inputs.get(inputNames[0]))).getDataObject();
+ }
+ else {
+ comment.add("no class number in list");
+ outputs.put(outputNames[0], new DataThing(comment));
+ return outputs;
+ }
+ if(inputs.get(inputNames[1]) != null) {
+ fileNamesList = (List<String>)((DataThing)(inputs.get(inputNames[1]))).getDataObject();
+ }
+ if (this.fileNames != null && this.fileNames.size() != 0) {
+ fileNamesList.addAll(this.fileNames);
+ }
+ if (fileNamesList == null || fileNamesList.isEmpty()){
+ comment.add("no entry in list");
+ outputs.put(outputNames[0], new DataThing(comment));
+ return outputs;
+ }
+ try {
+ XMLStreamReader xmlReader;
+ Art2aClassificator classificator;
+ XMLFileIO xmlFileIO = new XMLFileIO();
+ List<Object> correspontingObjects;
+ for (String fileName : fileNamesList) {
+ xmlReader = xmlFileIO.getXMLStreamReaderWithCompression(fileName);
+ xmlReader.next();
+ classificator = new Art2aClassificator(xmlReader, true);
+ xmlReader.close();
+ xmlFileIO.closeXMLStreamReader();
+
+ correspontingObjects = classificator.getCorrespondingObjectsOfClass(Integer.valueOf(classNumbers));
+ for (Object correspondingObject : correspontingObjects) {
+ if (correspondingObject instanceof Integer) {
+ Integer moleculeID = (Integer) correspondingObject;
+ moleculeIDs.add(String.valueOf(moleculeID));
+ }
+ }
+ }
+ outputs.put(outputNames[0],new DataThing(moleculeIDs));
+ } catch (Exception exception) {
+ throw new TaskExecutionException(exception);
+ }
+ outputs.put(outputNames[1], new DataThing(comment));
+ return outputs;
+ }
+
+ // End of region
+
+ // Region: XML processing methods
+ @SuppressWarnings("unchecked")
+ public void consumeXML(Element element) {
+ Element ele = element.getChild(GETMOLECULEIDSFORGIVENCLASSES, XScufl.XScuflNS);
+ if (ele == null) {
+ return;
+ }
+ Element fileNames = ele.getChild(FILENAMELIST, XScufl.XScuflNS);
+ for (Iterator<Element> iterator = fileNames.getChildren(FILENAMES, XScufl.XScuflNS).iterator(); iterator.hasNext();) {
+ Element elem = (Element) iterator.next();
+ if (elem.getAttribute(FILENAME, XScufl.XScuflNS) != null) {
+ this.addFileName(elem.getAttribute(FILENAME, XScufl.XScuflNS).getValue());
+ }
+ }
+
+ }
+ public Element provideXML() {
+ Element extensions = new Element(EXTENSIONS, XScufl.XScuflNS);
+ Element insertElement = new Element(GETMOLECULEIDSFORGIVENCLASSES, XScufl.XScuflNS);
+ Element fileNames = new Element(FILENAMELIST, XScufl.XScuflNS);
+ Element fileName;
+ for (Iterator<String> iterator = this.fileNames.iterator(); iterator.hasNext();) {
+ String name = iterator.next();
+ fileName = new Element(FILENAMES, XScufl.XScuflNS);
+ fileName.setAttribute(FILENAME, name, XScufl.XScuflNS);
+ fileNames.addContent(fileName);
+ }
+ insertElement.addContent(fileNames);
+ extensions.addContent(insertElement);
+ return extensions;
+ }
+
+
+
+ // End of region
+
+ // End of region
+}
\ No newline at end of file
Added: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/ART2AClassificator/tools/action/GetMoleculeIDsForGivenClassesAction.java
===================================================================
--- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/ART2AClassificator/tools/action/GetMoleculeIDsForGivenClassesAction.java (rev 0)
+++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/qsar/model/ART2AClassificator/tools/action/GetMoleculeIDsForGivenClassesAction.java 2008-08-26 12:22:27 UTC (rev 12091)
@@ -0,0 +1,155 @@
+/* $RCSfile$
+ * $Author: egonw $
+ * $Date: 2008-05-05 12:58:11 +0200 (Mo, 05 Mai 2008) $
+ * $Revision: 10819 $
+ *
+ * Copyright (C) 2008 by Thomas Kuhn <tho...@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.ART2AClassificator.tools.action;
+
+import java.awt.Dimension;
+import java.io.File;
+import java.util.Iterator;
+
+import javax.swing.ImageIcon;
+import javax.swing.JComponent;
+import javax.swing.JFileChooser;
+import javax.swing.JFrame;
+
+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.ART2AClassificator.tools.GetMoleculeIDsForGivenClasses;
+import org.openscience.cdk.applications.taverna.scuflworkers.cdk.CDKProcessor;
+/**
+ * This class handles the action of the Get Molecule IDs for given classes. It provides a filechooser dialog to choose the classification result file
+ * @author Thomas Kuhn
+ */
+public class GetMoleculeIDsForGivenClassesAction extends AbstractCDKProcessorAction {
+ private String descriptionAdder = "";
+
+ /* (non-Javadoc)
+ * @see org.embl.ebi.escience.scuflui.actions.AbstractProcessorAction#getComponent(org.embl.ebi.escience.scufl.Processor)
+ */
+ @Override
+ public JComponent getComponent(Processor processor) {
+ if (!(processor instanceof CDKProcessor)) {
+ return null;
+ }
+ JFileChooser fileChooser = new JFileChooser();
+ CDKProcessor proc = (CDKProcessor) processor;
+ final GetMoleculeIDsForGivenClasses worker = (GetMoleculeIDsForGivenClasses) proc.getWorker();
+ boolean fileSearch = true;
+ try {
+ String fileName = null;
+ fileChooser.setMultiSelectionEnabled(true);
+ while (fileSearch) {
+ if (worker.getFileNames() != null && worker.getFileNames().size() != 0) {
+ fileName = worker.getFileNames().get(0);
+ }
+ if (fileName != null && fileName.length() > 0) {
+ fileChooser.setCurrentDirectory(new java.io.File(fileName));
+ }
+ // Is true if the user selects a file within the filechooser
+ fileChooser.setMultiSelectionEnabled(true);
+ if (fileChooser.showOpenDialog(null) == JFileChooser.APPROVE_OPTION) {
+ File[] files = fileChooser.getSelectedFiles();
+ for (int i = 0; i < files.length; i++) {
+ worker.addFileName(files[i].getAbsolutePath());
+ }
+ fileName = fileChooser.getSelectedFiles()[0].getAbsolutePath();
+ fileSearch = false;
+ // Is true if the is in an format which is supported by the cdk-taverna project
+ } else {
+ fileSearch = false;
+ }
+ }
+ } catch (Exception e) {
+ return null;
+ }
+ // TODO Don't give null back!! Change this!
+ return null;
+ }
+
+ /* (non-Javadoc)
+ * @see org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI#canHandle(org.embl.ebi.escience.scufl.Processor)
+ */
+ public boolean canHandle(Processor processor) {
+ if (!(processor instanceof CDKProcessor)) {
+ return false;
+ }
+ CDKProcessor proc = (CDKProcessor) processor;
+ if (proc.getWorker() instanceof GetMoleculeIDsForGivenClasses) {
+ GetMoleculeIDsForGivenClasses reader = (GetMoleculeIDsForGivenClasses)proc.getWorker();
+ File file;
+ String temp = "";
+ if (reader.getFileNames().size() != 0) {
+ for (Iterator<String> iterator = reader.getFileNames().iterator(); iterator
+ .hasNext();) {
+ String fileName = iterator.next();
+ file = new File(fileName);
+ if (file.isFile()) {
+ temp += file.getName() + "; ";
+ }
+ }
+
+ if (temp.length() != 0) {
+ this.descriptionAdder = " - selected file: " + temp;
+ }
+ }
+ else {
+ this.descriptionAdder = "";
+ }
+ return true;
+ }
+ else {
+ return false;
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI#getDescription()
+ */
+ public String getDescription() {
+ return "Choose File" + this.descriptionAdder;
+ }
+
+ /* (non-Javadoc)
+ * @see org.embl.ebi.escience.scuflui.actions.AbstractProcessorAction#getFrameSize()
+ */
+ public Dimension getFrameSize() {
+ // should be small enought due to using a file dialog
+ return new Dimension(1, 1);
+ }
+
+
+ /* (non-Javadoc)
+ * @see org.embl.ebi.escience.scuflui.spi.ProcessorActionSPI#getIcon()
+ */
+ public ImageIcon getIcon() {
+ return TavernaIcons.openIcon;
+ }
+
+ @Override
+ public JFrame getFrame(Processor processor) {
+ return null;
+ }
+}
\ No newline at end of file
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