[Cdk-commits] CVS: cdk-taverna/src/org/openscience/cdk/applications/taverna/filters Has3DCoordinates.java,NONE,1.1 Has2DCoordinates.java,NONE,1.1

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

Update of /cvsroot/cdk/cdk-taverna/src/org/openscience/cdk/applications/taverna/filters
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv6121/src/org/openscience/cdk/applications/taverna/filters

Added Files:
	Has3DCoordinates.java Has2DCoordinates.java 
Log Message:
Added two filters that check certain data features.

--- NEW FILE: Has3DCoordinates.java ---
/* $RCSfile: Has3DCoordinates.java,v $
 * $Author: egonw $
 * $Date: 2005/10/17 19:42:21 $
 * $Revision: 1.1 $
 * 
 * Copyright (C) 2005 by Egon Willighagen <eg...@us...>
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; version 2 of the License.
 *
 * 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the
 * Free Software Foundation, Inc.,
 * 51 Franklin Steet, Fifth Floor, Boston, MA 02110-1301, USA.
 */
package org.openscience.cdk.applications.taverna.filters;

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 org.openscience.cdk.applications.taverna.CMLChemFile;
import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.interfaces.AtomContainer;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * Determines if the structure has a 3D coordinates.
 * 
 * @author Egon Willighagen
 */
public class Has3DCoordinates implements LocalWorker {

    public String[] inputNames() {
        return new String[] {"inputStructures"};
    }
    public String[] inputTypes() {
        return new String[] {"l('text/plain')"};
    }
    
    public String[] outputNames() {
        return new String[] {"matchingStructures", "otherStructures"};
    }
    public String[] outputTypes() {
        return new String[] {"l('text/plain')", "l('text/plain')"};
    }
    
    public Map execute(Map inputs) throws TaskExecutionException {
        List inputList = (List)((DataThing)(inputs.get("inputStructures"))).getDataObject();
        List matchedList = new ArrayList();
        List unmatchedList= new ArrayList();

    	try {
    		for (Iterator iter = inputList.iterator(); iter.hasNext(); ) {
                String item = (String)iter.next();

                CMLChemFile file = new CMLChemFile(item);
                AtomContainer structure = ChemFileManipulator.getAllInOneContainer(file);

                if (GeometryTools.has3DCoordinates(structure)) {
                	matchedList.add(item);
                } else { // not a substructure
                	unmatchedList.add(item);
                }
    		}
    	} catch (Exception exception) {
    		throw new TaskExecutionException(exception);
    	}
        Map outputs = new HashMap();
        outputs.put("matchingStructures",new DataThing(matchedList));
        outputs.put("otherStructures",new DataThing(unmatchedList));
        return outputs;
    }

}

--- NEW FILE: Has2DCoordinates.java ---
/* $RCSfile: Has2DCoordinates.java,v $
 * $Author: egonw $
 * $Date: 2005/10/17 19:42:21 $
 * $Revision: 1.1 $
 * 
 * Copyright (C) 2005 by Egon Willighagen <eg...@us...>
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; version 2 of the License.
 *
 * 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 General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the
 * Free Software Foundation, Inc.,
 * 51 Franklin Steet, Fifth Floor, Boston, MA 02110-1301, USA.
 */
package org.openscience.cdk.applications.taverna.filters;

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 org.openscience.cdk.applications.taverna.CMLChemFile;
import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.interfaces.AtomContainer;
import org.openscience.cdk.tools.manipulator.ChemFileManipulator;

/**
 * Determines if the structure has a 2D coordinates.
 * 
 * @author Egon Willighagen
 */
public class Has2DCoordinates implements LocalWorker {

    public String[] inputNames() {
        return new String[] {"inputStructures"};
    }
    public String[] inputTypes() {
        return new String[] {"l('text/plain')"};
    }
    
    public String[] outputNames() {
        return new String[] {"matchingStructures", "otherStructures"};
    }
    public String[] outputTypes() {
        return new String[] {"l('text/plain')", "l('text/plain')"};
    }
    
    public Map execute(Map inputs) throws TaskExecutionException {
        List inputList = (List)((DataThing)(inputs.get("inputStructures"))).getDataObject();
        List matchedList = new ArrayList();
        List unmatchedList= new ArrayList();

    	try {
    		for (Iterator iter = inputList.iterator(); iter.hasNext(); ) {
                String item = (String)iter.next();

                CMLChemFile file = new CMLChemFile(item);
                AtomContainer structure = ChemFileManipulator.getAllInOneContainer(file);

                if (GeometryTools.has2DCoordinates(structure)) {
                	matchedList.add(item);
                } else { // not a substructure
                	unmatchedList.add(item);
                }
    		}
    	} catch (Exception exception) {
    		throw new TaskExecutionException(exception);
    	}
        Map outputs = new HashMap();
        outputs.put("matchingStructures",new DataThing(matchedList));
        outputs.put("otherStructures",new DataThing(unmatchedList));
        return outputs;
    }

}