[Cdk-commits] SF.net SVN: cdk: [10529] cdk-taverna/trunk/src/main/java/org/openscience/ cdk/applications/taverna/filters/Has3DCoordinates.java

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

Revision: 10529
          http://cdk.svn.sourceforge.net/cdk/?rev=10529&view=rev
Author:   thomaskuhn
Date:     2008-03-26 12:42:30 -0700 (Wed, 26 Mar 2008)

Log Message:
-----------
Some clean up and upgrade to Java 5 standards

Modified Paths:
--------------
    cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/filters/Has3DCoordinates.java

Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/filters/Has3DCoordinates.java
===================================================================
--- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/filters/Has3DCoordinates.java	2008-03-26 19:42:20 UTC (rev 10528)
+++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/filters/Has3DCoordinates.java	2008-03-26 19:42:30 UTC (rev 10529)
@@ -22,13 +22,13 @@
 
 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.geometry.GeometryTools;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.tools.manipulator.ChemFileManipulator;
@@ -41,7 +41,7 @@
  * @author Egon Willighagen
  */
 public class Has3DCoordinates implements LocalWorkerCDK {
-	//	 Region: input and outpout definition	
+	//	 Region: input and output definition	
 	private String[] inputNames  = new String[] { "inputStructures" };
 	private String[] outputNames = new String[] { "matchingStructures", "otherStructures" };
 
@@ -63,22 +63,18 @@
 	// End of region
 
 	// Region: local worker execution
-	public Map execute(Map inputs) throws TaskExecutionException {
-		List inputList = null;
+	public Map<String, DataThing> execute(Map<String, DataThing> inputs) throws TaskExecutionException {
+		List<CMLChemFile> inputList = null;
 		if(inputs.get("inputStructures") != null){
-			inputList = (List)((DataThing)(inputs.get("inputStructures"))).getDataObject();
+			inputList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0]));
 		}
-		inputList = (List)((DataThing)(inputs.get("inputStructures"))).getDataObject();
-		List matchedList = new ArrayList();
-		List unmatchedList= new ArrayList();
+		List<CMLChemFile> matchedList = new ArrayList<CMLChemFile>();
+		List<CMLChemFile> unmatchedList= new ArrayList<CMLChemFile>();
 
 		try {
-			for (Iterator iter = inputList.iterator(); iter.hasNext(); ) {
-				CMLChemFile file = (CMLChemFile)iter.next();
-				List structures = ChemFileManipulator.getAllAtomContainers(file);
-				IAtomContainer molecule;
-				for (Iterator iterator = structures.iterator(); iterator.hasNext();) {
-					molecule = (IAtomContainer) iterator.next();
+			for (CMLChemFile file : inputList) {
+				List<IAtomContainer> structures = ChemFileManipulator.getAllAtomContainers(file);
+				for (IAtomContainer molecule : structures) {
 					if (GeometryTools.has3DCoordinates(molecule)) {
 						matchedList.add(file);
 					} else {
@@ -89,7 +85,7 @@
 		} catch (Exception exception) {
 			throw new TaskExecutionException(exception);
 		}
-		Map outputs = new HashMap();
+		Map<String, DataThing> outputs = new HashMap<String, DataThing>();
 		outputs.put("matchingStructures",new DataThing(matchedList));
 		outputs.put("otherStructures",new DataThing(unmatchedList));
 		return outputs;


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