[Cdk-commits] SF.net SVN: cdk: [7266] trunk/cdk-taverna/src/org/openscience/cdk/ applications/taverna/structgen/StructureDiagramGenerator.java

[<tho...@us...>]

Revision: 7266
          http://svn.sourceforge.net/cdk/?rev=7266&view=rev
Author:   thomaskuhn
Date:     2006-11-07 04:19:05 -0800 (Tue, 07 Nov 2006)

Log Message:
-----------
Add a structure diagramm generator as local worker

Added Paths:
-----------
    trunk/cdk-taverna/src/org/openscience/cdk/applications/taverna/structgen/StructureDiagramGenerator.java

Added: trunk/cdk-taverna/src/org/openscience/cdk/applications/taverna/structgen/StructureDiagramGenerator.java
===================================================================
--- trunk/cdk-taverna/src/org/openscience/cdk/applications/taverna/structgen/StructureDiagramGenerator.java	                        (rev 0)
+++ trunk/cdk-taverna/src/org/openscience/cdk/applications/taverna/structgen/StructureDiagramGenerator.java	2006-11-07 12:19:05 UTC (rev 7266)
@@ -0,0 +1,125 @@
+/* $RCSfile$
+ * $Author: thomaskuhn $
+ * $Date: 2006-01-20 08:21:14 +0100 (Fr, 20 Jan 2006) $
+ * $Revision: 5602 $
+ * 
+ * Copyright (C) 2006 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.structgen;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+
+import org.embl.ebi.escience.baclava.DataThing;
+import org.openscience.cdk.applications.taverna.CMLChemFile;
+import org.openscience.cdk.applications.taverna.LocalWorkerCDK;
+import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper;
+import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
+
+import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException;
+
+/**
+ * This class provides a local worker for the cdk-taverna project. 
+ * This local worker creates a structured diagram for a given list of molecules in form of CMLChemfiles
+ * @author Thomas Kuhn
+ *
+ */
+public class StructureDiagramGenerator implements LocalWorkerCDK {
+	private String[] inputNames  = new String[] { "inputStructures" };
+	private String[] outputNames = new String[] { "resultStructures", "ErrorStructures", "Comment" };
+
+	// Region: input and outpout definition
+
+	public String[] inputNames() {
+		return inputNames;
+	}
+	public String[] inputTypes() {
+		return new String[] {LocalWorkerCDK.CMLChemFileList};
+	}
+
+	public String[] outputNames() {
+		return outputNames;
+	}
+	public String[] outputTypes() {
+		return new String[] {LocalWorkerCDK.CMLChemFileList, LocalWorkerCDK.CMLChemFileList, 
+				LocalWorkerCDK.STRING_ARRAY};
+	}
+
+	// End of region
+
+	// Region: local worker execution
+
+	public Map execute(Map inputs) throws TaskExecutionException {
+		FileNameGenerator fileNameGenerator = new FileNameGenerator();
+		List<CMLChemFile> inputList = null;
+		List<CMLChemFile> resultList = new ArrayList<CMLChemFile>();
+		List<CMLChemFile> errorResultList = new ArrayList<CMLChemFile>();
+		List comment = new ArrayList();
+		org.openscience.cdk.layout.StructureDiagramGenerator str;
+		String fileNameResultStructures = "StructureDiagramGenerator";
+		String fileNameErrorStructures = "StructureDiagramGenerator_ErrorStructures";
+		CMLChemFile resultFile = null;
+		if (inputs.get(inputNames[0]) != null) {
+			inputList = (List<CMLChemFile>) ((DataThing) (inputs.get(inputNames[0]))).getDataObject();
+		} else {
+			// FIXME Do not return null!! Could be a problem!
+			return null;
+		}
+		try {
+			for (Iterator iter = inputList.iterator(); iter.hasNext();) {
+				CMLChemFile file = (CMLChemFile) iter.next();
+				List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(file);
+				for (Iterator iterator = moleculeList.iterator(); iterator.hasNext();) {
+					IAtomContainer molecule = (IAtomContainer)iterator.next();
+					try {
+						// Tries to create the structured diagram, if it fails it will put the failed molecule into the errorResultList
+						str = new org.openscience.cdk.layout.StructureDiagramGenerator();
+						str.setMolecule((IMolecule)molecule);
+						str.generateCoordinates();
+						resultFile = CMLChemFileWrapper.wrapAtomContainerInChemModel(str.getMolecule());
+						resultFile.setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(fileNameResultStructures, (List<String>)file.getProperty(FileNameGenerator.FILENAME)));
+						resultList.add(resultFile);
+					} catch (Exception e) {
+						resultFile = CMLChemFileWrapper.wrapAtomContainerInChemModel(molecule);
+						resultFile.setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(fileNameErrorStructures, (List<String>)file.getProperty(FileNameGenerator.FILENAME)));
+						errorResultList.add(resultFile);
+						comment.add("An error occured during the creation of the structured diagram" + e);
+					}
+				}
+			}
+		} catch (Exception exception) {
+			throw new TaskExecutionException(exception);
+		}
+		Map outputs = new HashMap();
+		outputs.put(outputNames[0], new DataThing(resultList));
+		outputs.put(outputNames[1], new DataThing(errorResultList));
+		outputs.put(outputNames[2], new DataThing(comment));
+
+		return outputs;
+	}
+	// End of region
+}


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