[Cdk-commits] SF.net SVN: cdk: [10526] cdk-taverna/trunk/src/main/java/org/openscience/ cdk/applications/taverna/atomtype/PerceiveMMFF94AtomTypes.java

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

Revision: 10526
          http://cdk.svn.sourceforge.net/cdk/?rev=10526&view=rev
Author:   thomaskuhn
Date:     2008-03-26 12:41:39 -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/atomtype/PerceiveMMFF94AtomTypes.java

Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/atomtype/PerceiveMMFF94AtomTypes.java
===================================================================
--- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/atomtype/PerceiveMMFF94AtomTypes.java	2008-03-26 19:41:27 UTC (rev 10525)
+++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/atomtype/PerceiveMMFF94AtomTypes.java	2008-03-26 19:41:39 UTC (rev 10526)
@@ -34,6 +34,7 @@
 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.atomtype.MMFF94AtomTypeMatcher;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
@@ -42,52 +43,63 @@
 
 import uk.ac.soton.itinnovation.taverna.enactor.entities.TaskExecutionException;
 
-public class PerceiveMMFF94AtomTypes implements LocalWorkerCDK{
+public class PerceiveMMFF94AtomTypes implements LocalWorkerCDK {
 
 	private static MMFF94AtomTypeMatcher matcher;
-	private String[] inputNames  = new String[] { "inputStructures" };
-	private String[] outputNames = new String[] { "outputStructure" , "otherStructures"};
+	private String[] inputNames = new String[] { "inputStructures" };
+	private String[] outputNames = new String[] { "outputStructure",
+			"otherStructures" };
 
-	// Region: input and outpout definition
+	// Region: input and output definition
 
 	public String[] inputNames() {
 		return inputNames;
 	}
+
 	public String[] inputTypes() {
-		return new String[] {LocalWorkerCDK.CMLChemFileList};
+		return new String[] { LocalWorkerCDK.CMLChemFileList };
 	}
 
 	public String[] outputNames() {
 		return outputNames;
 	}
+
 	public String[] outputTypes() {
-		return new String[] {LocalWorkerCDK.CMLChemFileList , LocalWorkerCDK.CMLChemFileList};
+		return new String[] { LocalWorkerCDK.CMLChemFileList,
+				LocalWorkerCDK.CMLChemFileList };
 	}
 
-	public Map execute(Map inputs) throws TaskExecutionException {
-		if (matcher == null) matcher = new MMFF94AtomTypeMatcher();
-		List calculatedList = new ArrayList();
-		List notCalculatedList = new ArrayList();
-		List inputList = null;
+	public Map<String, DataThing> execute(Map<String, DataThing> inputs)
+			throws TaskExecutionException {
+		if (matcher == null)
+			matcher = new MMFF94AtomTypeMatcher();
+		List<CMLChemFile> calculatedList = new ArrayList<CMLChemFile>();
+		List<CMLChemFile> notCalculatedList = new ArrayList<CMLChemFile>();
+		List<CMLChemFile> inputList = null;
 		if (inputs.get(inputNames[0]) != null) {
-			inputList = (List) ((DataThing) (inputs.get(inputNames[0]))).getDataObject();
+			inputList = CMLChemFileWrapper
+					.getListOfCMLChemfileFromDataThing(inputs
+							.get(inputNames[0]));
 		} else {
 			return null;
 		}
-		Map outputs = new HashMap();
+		Map<String, DataThing> outputs = new HashMap<String, DataThing>();
 		try {
-			for (Iterator iter = inputList.iterator(); iter.hasNext();) {
-				CMLChemFile file = (CMLChemFile) iter.next();
-				List moleculeList = ChemFileManipulator.getAllAtomContainers(file);
-				List allAtoms = new ArrayList();
-				for (Iterator iterator = moleculeList.iterator(); iterator.hasNext();){
-					IAtomContainer[] molecules = {(IAtomContainer)iterator.next()};
+			for (CMLChemFile file : inputList) {
+				List<IAtomContainer> moleculeList = ChemFileManipulator
+						.getAllAtomContainers(file);
+				List<IAtom> allAtoms = new ArrayList<IAtom>();
+				for (IAtomContainer molecule : moleculeList) {
 					try {
-						for (Iterator atoms = molecules[0].atoms(); atoms.hasNext();){
-							allAtoms.add(0 , atoms.next());    
-							IAtomType type = matcher.findMatchingAtomType(molecules[0], ((IAtom)allAtoms.get(0)));
-							((IAtom)(allAtoms.get(0))).setAtomTypeName(type.getAtomTypeName());
-							// FIXME: maybe should do a full atom type configuration??
+						for (Iterator<IAtom> atoms = molecule.atoms(); atoms
+								.hasNext();) {
+							allAtoms.add(0, atoms.next());
+							IAtomType type = matcher.findMatchingAtomType(
+									molecule, ((IAtom) allAtoms.get(0)));
+							((IAtom) (allAtoms.get(0))).setAtomTypeName(type
+									.getAtomTypeName());
+							// FIXME: maybe should do a full atom type
+							// configuration??
 						}
 						calculatedList.add(file);
 						allAtoms.clear();


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