From: <tho...@us...> - 2008-03-27 14:12:14
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Revision: 10561 http://cdk.svn.sourceforge.net/cdk/?rev=10561&view=rev Author: thomaskuhn Date: 2008-03-27 07:12:04 -0700 (Thu, 27 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/smiles/SMILESGenerator.java cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESParser.java cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SmilesTools.java Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESGenerator.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESGenerator.java 2008-03-27 14:11:49 UTC (rev 10560) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESGenerator.java 2008-03-27 14:12:04 UTC (rev 10561) @@ -32,6 +32,7 @@ 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.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.smiles.SmilesGenerator; @@ -73,7 +74,7 @@ List<String> smilesList = null; List<String> comment = new ArrayList<String>(); if(inputs.get(inputNames[0]) != null) { - inputList = (List<CMLChemFile>)((DataThing)(inputs.get(inputNames[0]))).getDataObject(); + inputList = CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(inputs.get(inputNames[0])); if (inputList.isEmpty()){ comment.add("no entry in list"); Map<String, DataThing> outputs = new HashMap<String, DataThing>(); Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESParser.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESParser.java 2008-03-27 14:11:49 UTC (rev 10560) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SMILESParser.java 2008-03-27 14:12:04 UTC (rev 10561) @@ -67,31 +67,30 @@ // 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 { + Map<String, DataThing> outputs = new HashMap<String, DataThing>(); + List<String> inputList = null; List<CMLChemFile> cmlChemFileList = null; List<String> comment = new ArrayList<String>(); FileNameGenerator fileNameGenerator = new FileNameGenerator(); SmilesParser smilesParser = null; if(inputs.get(inputNames[0]) != null) { - inputList = (List)((DataThing)(inputs.get(inputNames[0]))).getDataObject(); + inputList = (List<String>)((DataThing)(inputs.get(inputNames[0]))).getDataObject(); if (inputList.isEmpty()){ comment.add("no entry in list"); - Map outputs = new HashMap(); outputs.put(outputNames[0], new DataThing(comment)); return outputs; } } else { comment.add("no entry in map"); - Map outputs = new HashMap(); outputs.put(outputNames[0], new DataThing(comment)); return outputs; } try { smilesParser = new SmilesParser(DefaultChemObjectBuilder.getInstance()); cmlChemFileList = new ArrayList<CMLChemFile>(); - for (Iterator iter = inputList.iterator(); iter.hasNext();) { - String SMILES = (String) iter.next(); + for (Iterator<String> iter = inputList.iterator(); iter.hasNext();) { + String SMILES = iter.next(); Molecule molecule = (Molecule) smilesParser.parseSmiles(SMILES.trim()); StructureDiagramGenerator str = new StructureDiagramGenerator(); @@ -112,7 +111,7 @@ } catch (Exception exception) { throw new TaskExecutionException(exception); } - Map outputs = new HashMap(); + outputs.put(outputNames[0], new DataThing(cmlChemFileList)); outputs.put(outputNames[1], new DataThing(comment)); return outputs; Modified: cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SmilesTools.java =================================================================== --- cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SmilesTools.java 2008-03-27 14:11:49 UTC (rev 10560) +++ cdk-taverna/trunk/src/main/java/org/openscience/cdk/applications/taverna/smiles/SmilesTools.java 2008-03-27 14:12:04 UTC (rev 10561) @@ -100,12 +100,12 @@ public static String[] generateSMILES(CMLChemFile cmlChemFile)throws Exception { SmilesGenerator smilesGenerator; //IAtomContainer[] atomcontainer = ChemFileManipulator.getAllAtomContainers(cmlChemFile); - List moleculeList = ChemFileManipulator.getAllAtomContainers(cmlChemFile); + List<IAtomContainer> moleculeList = ChemFileManipulator.getAllAtomContainers(cmlChemFile); IAtomContainer atomcontainer; String[] resultSmiles = new String[moleculeList.size()]; int p = 0; - for (Iterator iterator = moleculeList.iterator(); iterator.hasNext();){ - atomcontainer = (IAtomContainer)iterator.next(); + for (Iterator<IAtomContainer> iterator = moleculeList.iterator(); iterator.hasNext();){ + atomcontainer = iterator.next(); smilesGenerator = new SmilesGenerator(); resultSmiles[p] = smilesGenerator.createSMILES((IMolecule)atomcontainer); p++; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |