Following code run into concurrent modification exception when ran in more than
1 thread. Any ideas??
ExecutorService eservice = Executors.newFixedThreadPool(threads);
CompletionService <List<String>> cservice = new
ExecutorCompletionService <List<String>> (eservice);
int k=0;
for (IAtomContainer mol : mols3D)
{
DescCalculator dc = new DescCalculator(mol);
cservice.submit(dc);
k=k+1;
}
---------------------------------------------------------------------------------
public class DescCalculator implements Callable<List<String>>{
private IAtomContainer mol;
DescCalculator(IAtomContainer mol_)
{
this.mol = mol_;
}
@Override
public List<String> call() {
List<String> dataItems = new ArrayList<String>();
try
{
DescriptorEngine engine = new
DescriptorEngine(DescriptorEngine.MOLECULAR);
List<String> classNames = engine.getDescriptorClassNames();
List<String> removeList = new ArrayList();
removeList.add("org.openscience.cdk.qsar.descriptors.molecular.IPMolecularLearningDescriptor");
classNames.removeAll(removeList);
List<IDescriptor> instances = engine.instantiateDescriptors(classNames);
engine.setDescriptorInstances(instances);
ArrayList<IMolecularDescriptor> descriptors = new ArrayList();
for (Object object : instances)
{
IMolecularDescriptor descriptor = (IMolecularDescriptor) object;
descriptors.add(descriptor);
}
String title = (String) mol.getProperty("PUBCHEM_COMPOUND_CID");
dataItems.add(title);
int ndesc = 0;
for (IMolecularDescriptor descriptor : descriptors) {
DescriptorValue value = descriptor.calculate(mol);
if (value.getException() != null) {
for (int i = 0; i < value.getNames().length; i++) {
dataItems.add("NA");
}
continue;
}
IDescriptorResult result = value.getValue();
if (result instanceof DoubleResult) {
dataItems.add(String.valueOf(((DoubleResult)
result).doubleValue()));
} else if (result instanceof IntegerResult) {
dataItems.add(String.valueOf(((IntegerResult)
result).intValue()));
} else if (result instanceof DoubleArrayResult) {
for (int i = 0; i < ((DoubleArrayResult) result).length();
i++) {
dataItems.add(String.valueOf(((DoubleArrayResult)
result).get(i)));
}
} else if (result instanceof IntegerArrayResult) {
for (int i = 0; i < ((IntegerArrayResult) result).length();
i++) {
dataItems.add(String.valueOf(((IntegerArrayResult)
result).get(i)));
}
}
ndesc++;
}
}
catch(Exception e)
{
e.printStackTrace();
}
return dataItems;
}
}------------------------------------------------------------------------------
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