[Cdk-commits] CVS: cdk-taverna/src/org/openscience/cdk/applications/taverna ParseSmiles.java,NONE,1.1

[Egon W. <eg...@us...>]

Update of /cvsroot/cdk/cdk-taverna/src/org/openscience/cdk/applications/taverna
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10652/src/org/openscience/cdk/applications/taverna

Added Files:
	ParseSmiles.java 
Log Message:
Added example local worker used for presentation at CUBIC 2005-03-29

--- NEW FILE: ParseSmiles.java ---
/**
 * This file is licensed under the GNU GPL.
 * Copyright Egon Willighagen
 */
package org.openscience.cdk.applications.taverna;

import org.embl.ebi.escience.scuflworkers.java.LocalWorker;
import org.embl.ebi.escience.baclava.DataThing;
import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException;
import java.util.*;
import java.io.*;

import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.io.MDLWriter;

/**
 * @author Egon Willighagen
 */
public class ParseSmiles implements LocalWorker {

    public String[] inputNames() {
        return new String[]{"smilesList"};
    }
    public String[] inputTypes() {
        return new String[]{"l('text/plain')"};
    }
    
    public String[] outputNames() {
        return new String[]{"connectionTables"};
    }
    public String[] outputTypes() {
        return new String[]{"l('text/plain')"};
    }
    
    public Map execute(Map inputs) throws TaskExecutionException {
        List inputList = (List)((DataThing)(inputs.get("smilesList"))).getDataObject();
        SmilesParser parser = new SmilesParser();
        List outputList = new ArrayList();
        for (Iterator i = inputList.iterator(); i.hasNext(); ) {
            Object nextObj = i.next();
            System.out.println("Class of i.next(): " + nextObj.getClass()); 
            String item = (String)nextObj;
            try {
                StringWriter outputString = new StringWriter();
                MDLWriter writer = new MDLWriter(outputString);
                writer.write(parser.parseSmiles(item));
                outputList.add(outputString.toString());
            } catch (Exception exception) {
                throw new TaskExecutionException("Error while parsing SMILES (" + item + "): " + exception.getMessage());
            }
        }
        Map outputs = new HashMap();
        outputs.put("connectionTables",new DataThing(outputList));
        return outputs;
    }

}