[Cdk-commits] SF.net SVN: cdk: [10567] cdk-taverna/trunk/src/test/java/org/openscience/ cdk/applications/taverna

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

Revision: 10567
          http://cdk.svn.sourceforge.net/cdk/?rev=10567&view=rev
Author:   thomaskuhn
Date:     2008-03-27 08:03:23 -0700 (Thu, 27 Mar 2008)

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

Modified Paths:
--------------
    cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/CDKTavernaTestData.java
    cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/CMLChemfileTest.java

Modified: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/CDKTavernaTestData.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/CDKTavernaTestData.java	2008-03-27 15:02:42 UTC (rev 10566)
+++ cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/CDKTavernaTestData.java	2008-03-27 15:03:23 UTC (rev 10567)
@@ -33,7 +33,6 @@
 import org.openscience.cdk.Reaction;
 import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper;
 import org.openscience.cdk.applications.taverna.basicutilities.FileNameGenerator;
-import org.openscience.cdk.applications.taverna.io.CDKIOFileWriter;
 import org.openscience.cdk.applications.taverna.io.CDKIOReader;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.smiles.SmilesParser;
@@ -104,7 +103,7 @@
 		}
 		else {
 			for (int i = 0; i < cmlChemFile.length; i++) {
-				cmlChemFile[i].setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
+				cmlChemFile[i].setProperty(FileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
 			}
 		}
 		return cmlChemFile;
@@ -152,7 +151,7 @@
 		if (file.exists()) {
 			cmlChemFileWith3DCoordinates = CDKIOReader.readFromMDLFile(path);
 			for (int i = 0; i < cmlChemFileWith3DCoordinates.length; i++) {
-				cmlChemFileWith3DCoordinates[i].setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
+				cmlChemFileWith3DCoordinates[i].setProperty(FileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
 			}
 		}
 		path = "." + File.separator + "target" + File.separator + "test-classes"
@@ -167,7 +166,7 @@
 		if (file.exists()) {
 			reactionEvaluationEductOne = CDKIOReader.readFromSDV2000File(path);
 			for (int i = 0; i < reactionEvaluationEductOne.length; i++) {
-				reactionEvaluationEductOne[i].setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
+				reactionEvaluationEductOne[i].setProperty(FileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
 			}
 		}
 		path = "." + File.separator + "target" + File.separator + "test-classes"
@@ -176,7 +175,7 @@
 		if (file.exists()) {
 			reactionEvaluationEductTwo = CDKIOReader.readFromSDV2000File(path);
 			for (int i = 0; i < reactionEvaluationEductTwo.length; i++) {
-				reactionEvaluationEductTwo[i].setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
+				reactionEvaluationEductTwo[i].setProperty(FileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
 			}
 		}
 		path = "." + File.separator + "target" + File.separator + "test-classes"
@@ -185,7 +184,7 @@
 		if (file.exists()) {
 			reactionEvaluationResult = CDKIOReader.readFromSDV2000File(path);
 			for (int i = 0; i < reactionEvaluationResult.length; i++) {
-				reactionEvaluationResult[i].setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
+				reactionEvaluationResult[i].setProperty(FileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList(JUNITTESTINGFILENAME, fileNameGenerator.getNewFileNameList()));
 			}
 		}
 		pathToWriteInUnitTestFiles = pathToWriteInUnitTestFiles + File.separator + "original_Data.txt";
@@ -261,7 +260,7 @@
 			loadDefaultDataForTests();
 		}
 		for (int i = 0; i < cmlChemFileWith3DCoordinates.length; i++) {
-			cmlChemFileWith3DCoordinates[i].setProperty(fileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList("JunitTesting", fileNameGenerator.getNewFileNameList()));
+			cmlChemFileWith3DCoordinates[i].setProperty(FileNameGenerator.FILENAME, fileNameGenerator.addFileNameToFileNameList("JunitTesting", fileNameGenerator.getNewFileNameList()));
 		}
 		return cmlChemFileWith3DCoordinates;
 	}

Modified: cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/CMLChemfileTest.java
===================================================================
--- cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/CMLChemfileTest.java	2008-03-27 15:02:42 UTC (rev 10566)
+++ cdk-taverna/trunk/src/test/java/org/openscience/cdk/applications/taverna/CMLChemfileTest.java	2008-03-27 15:03:23 UTC (rev 10567)
@@ -35,6 +35,7 @@
 import junit.framework.TestSuite;
 
 import org.embl.ebi.escience.baclava.DataThing;
+import org.openscience.cdk.applications.taverna.basicutilities.CMLChemFileWrapper;
 import org.openscience.cdk.applications.taverna.qsar.descriptors.molecular.XLogP;
 import org.openscience.cdk.qsar.DescriptorValue;
 import org.openscience.cdk.qsar.result.DoubleResult;
@@ -54,7 +55,7 @@
 		inputList.add(cmlChemfile);
 		inputMap.put(xlopP.inputNames()[0], new DataThing(inputList));
 		Map<String, DataThing> resultMap = xlopP.execute(inputMap);
-		List<CMLChemFile> result =(List<CMLChemFile>)((DataThing)resultMap.get(xlopP.outputNames()[0])).getDataObject();
+		List<CMLChemFile> result =CMLChemFileWrapper.getListOfCMLChemfileFromDataThing(resultMap.get(xlopP.outputNames()[0]));
 		CMLChemFile res = result.get(0);
 		DescriptorValue[] test = new DescriptorValue[1];
 		DescriptorValue[] values = (DescriptorValue[])res.getChemSequence(0).getChemModel(0).getMoleculeSet().getAtomContainer(0).getProperties().values().toArray(test);


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