protected void getInputList() throws Exception {
List<byte[]> dataList = new ArrayList<byte[]>();
inputList = new ArrayList<CMLChemFile>();
if (testDataWith3DCoordinates) {
originalData = CDKTavernaTestData.getCMLChemFileWith3DCoordinates();
} else if (testDataWithAtomTypePerception) {
originalData = CDKTavernaTestData.getCMLChemFile();
// AtomTypeTools att =new AtomTypeTools();
} else {
originalData = CDKTavernaTestData.getCMLChemFile();
}
for (int i = 0; i < originalData.length; i++) {
inputList.add(originalData[i]);
}
for (CMLChemFile c : inputList) {
dataList.add(CDKObjectHandler.getBytes(c));
}
inputMap = new HashMap<String, Object>();
inputMap.put(activityInputNames[0], dataList);
}
@SuppressWarnings("unchecked")
protected void checkResults() throws Exception {
resultListCalculatedStructures = new ArrayList<CMLChemFile>();
List<byte[]> dataListCalculatedStructures =
(List<byte[]>) resultMap.get(activityOutputNames[0]);
for (byte[] data : dataListCalculatedStructures) {
resultListCalculatedStructures.add((CMLChemFile) CDKObjectHandler.getObject(data));
}
resultListNOTCalculatedStructures = new ArrayList<CMLChemFile>();
List<byte[]> dataListNOTCalculatedStructures =
(List<byte[]>) resultMap.get(activityOutputNames[1]);
for (byte[] data : dataListNOTCalculatedStructures) {
resultListNOTCalculatedStructures.add((CMLChemFile) CDKObjectHandler.getObject(data));
}
boolean notCalculatedResults = false;
if (resultListNOTCalculatedStructures.size() != 0) {
notCalculatedResults = true;
CDKIOFileWriter.writeListOfCMLChemFilesToFile(
resultListNOTCalculatedStructures,
activityName + "Problem.txt",
CDKTavernaTestData.getPathForWritingFilesOfUnitTests(false));
}
assertEquals(false, notCalculatedResults);
}