@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());
}
}
@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 SCWList compute() throws Exception {
ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
final OperationPool op = OperationPool.getInstance();
final Collection<Callable<Void>> threadList = new ArrayList<Callable<Void>>();
final SCWListBuilder resultListBuilder = new SCWListBuilder(scwList);
for (final Chromosome chromosome : projectChromosomes) {
final ListView<ScoredChromosomeWindow> currentList = scwList.get(chromosome);
Callable<Void> currentThread =
new Callable<Void>() {
@Override
public Void call() throws Exception {
if (currentList != null) {
// We log each element
for (int j = 0; (j < currentList.size()) && !stopped; j++) {
int start = currentList.get(j).getStart();
int stop = currentList.get(j).getStop();
float score = currentList.get(j).getScore();
// log is define on R+*
if (score > 0) {
if (logBase == LogBase.BASE_E) {
// the Math.log function return the natural log (no needs to change the base)
score = (float) Math.log(score);
} else {
// change of base: logb(x) = logk(x) / logk(b)
score = (float) (Math.log(score) / Math.log(logBase.getValue()));
}
} else if (score < 0) {
// can't apply a log function on a negative or null numbers
throw new ArithmeticException("Logarithm of a negative value not allowed");
}
resultListBuilder.addElementToBuild(chromosome, start, stop, score);
}
}
// tell the operation pool that a chromosome is done
op.notifyDone();
return null;
}
};
threadList.add(currentThread);
}
op.startPool(threadList);
return resultListBuilder.getSCWList();
}
@Override
public BinList compute()
throws InterruptedException, ExecutionException, CloneNotSupportedException {
final int binSize = binList.getBinSize();
final int halfWidth = movingWindowWidth / 2 / binSize;
// we create an array of coefficients. The index correspond to a distance and for each distance
// we calculate a coefficient
final double[] weights = new double[halfWidth + 1];
for (int i = 0; i <= halfWidth; i++) {
weights[i] = Math.pow(1d - Math.pow(i / (double) halfWidth, 3d), 3d);
}
ProjectChromosomes projectChromosomes = ProjectManager.getInstance().getProjectChromosomes();
final OperationPool op = OperationPool.getInstance();
final Collection<Callable<Void>> threadList = new ArrayList<Callable<Void>>();
final BinListBuilder resultListBuilder = new BinListBuilder(binList.getBinSize());
for (final Chromosome chromosome : projectChromosomes) {
final ListView<ScoredChromosomeWindow> currentList = binList.get(chromosome);
Callable<Void> currentThread =
new Callable<Void>() {
@Override
public Void call() throws Exception {
if (currentList != null) {
for (int j = 0; (j < currentList.size()) && !stopped; j++) {
float score = 0f;
if ((currentList.get(j).getScore() != 0) || (fillNullValues)) {
// apply the array of coefficients centered on the current value to gauss
double sumWts = 0;
double sumWtX = 0;
double sumWtX2 = 0;
double sumWtY = 0;
double sumWtXY = 0;
for (int k = -halfWidth; (k <= halfWidth) && !stopped; k++) {
int movingX = j + k; // x coordinate of the current point in the moving window
if ((movingX >= 0) && (movingX < currentList.size())) {
int distance = Math.abs(k);
if (currentList.get(j + k).getScore() != 0) {
sumWts += weights[distance];
sumWtX += movingX * weights[distance];
sumWtX2 += (movingX ^ 2) * weights[distance];
sumWtY += currentList.get(movingX).getScore() * weights[distance];
sumWtXY +=
movingX * currentList.get(movingX).getScore() * weights[distance];
}
}
}
double denom = (sumWts * sumWtX2) - Math.pow(sumWtX, 2);
if (denom != 0) {
double WLRSlope = ((sumWts * sumWtXY) - (sumWtX * sumWtY)) / denom;
double WLRIntercept = ((sumWtX2 * sumWtY) - (sumWtX * sumWtXY)) / denom;
double yLoess = (WLRSlope * j) + WLRIntercept;
score = (float) yLoess;
}
resultListBuilder.addElementToBuild(chromosome, score);
}
}
}
op.notifyDone();
return null;
}
};
threadList.add(currentThread);
}
op.startPool(threadList);
return (BinList) resultListBuilder.getSCWList();
}