@Override
public long[][] compute() throws Exception {
long[][] result = new long[geneList1.size()][];
final OperationPool op = OperationPool.getInstance();
final Collection<Callable<long[]>> threadList = new ArrayList<Callable<long[]>>();
for (int i = 0; i < geneList1.size(); i++) {
final int chromoindex = i;
Callable<long[]> currentThread =
new Callable<long[]>() {
@Override
public long[] call() throws Exception {
long[] chromoresult = new long[geneList1.get(chromoindex).size()];
if ((geneList1 != null) && (geneList2 != null)) {
chromoresult = handleCases(geneList1.get(chromoindex), geneList2, chromoindex);
}
// tell the operation pool that a chromosome is done
op.notifyDone();
return chromoresult;
}
};
threadList.add(currentThread);
}
if (op.startPool(threadList) == null) {
return null;
}
int i = 0;
for (long[] currentResult : op.startPool(threadList)) {
if (currentResult != null) {
result[i++] = currentResult;
}
}
return result;
}
@Override
public GeneList compute() throws Exception {
final OperationPool op = OperationPool.getInstance();
final Collection<Callable<ListView<Gene>>> threadList =
new ArrayList<Callable<ListView<Gene>>>();
for (int i = 0; i < geneList.size(); i++) {
final ListView<Gene> currentGeneList = geneList.get(i);
Callable<ListView<Gene>> currentThread =
new Callable<ListView<Gene>>() {
@Override
public ListView<Gene> call() throws Exception {
if (currentGeneList == null) {
return null;
}
ListViewBuilder<Gene> resultLVBuilder = new GeneListViewBuilder();
for (int j = 0; (j < currentGeneList.size()) && !stopped; j++) {
Gene currentGene = currentGeneList.get(j);
Gene geneToAdd = createGeneCopyWithConstantScore(currentGene);
resultLVBuilder.addElementToBuild(geneToAdd);
}
// tell the operation pool that a chromosome is done
op.notifyDone();
return resultLVBuilder.getListView();
}
};
threadList.add(currentThread);
}
List<ListView<Gene>> result = op.startPool(threadList);
if (result == null) {
return null;
} else {
return new SimpleGeneList(result, geneList.getGeneScoreType(), geneList.getGeneDBURL());
}
}