private int getRightBound(int i, Region w) {
int right =
i >= data.getCount() - 1
? w.getEnd()
: Math.min(data.getPos(i) + maxJump, (data.getPos(i) + data.getPos(i + 1)) / 2);
return right;
}
private int getLeftBound(int i, Region w) {
int left =
i == 0
? w.getStart()
: Math.max(
Math.max(1, data.getPos(i) - maxJump), (data.getPos(i) + data.getPos(i - 1)) / 2);
return left;
}
private double getRatio(int i) {
double sum = 0.0;
int c = 0;
for (int j = 0; j < data.getReplicates(i); j++) {
sum += data.getRatio(i, j);
c += 1;
}
return c > 0 ? sum / (double) c : 0.0;
}
private int findNextDomainIndex(int pi, Region w) {
double sum = getRatio(pi);
int farthest = pi;
int start = data.getPos(pi);
int lastHighProbe = pi;
int probeCount = 1;
if (sum >= meanThreshold) {
boolean searching = true;
int ppos = start;
for (int j = pi + 1; searching && j < data.getCount(); j++) {
double r = getRatio(j);
int jpos = data.getPos(j);
if (jpos - ppos <= maxJump) {
sum += r;
if (r >= meanThreshold) {
// lastHighProbe = j;
probeCount += 1;
double mean = sum / (double) (j - pi + 1);
int numProbes = j - pi + 1;
double probeThreshFrac = (double) probeCount / (double) numProbes;
if (mean >= meanThreshold && probeThreshFrac >= probeThreshold) {
farthest = j;
}
}
} else {
searching = false;
}
ppos = jpos;
}
// farthest = lastHighProbe;
} else {
return -1;
}
if (farthest > pi && data.getPos(farthest) - data.getPos(pi) > minSize) {
return farthest;
} else {
return -1;
}
}
public Iterator<SimpleDomain> execute(Region a) {
try {
LinkedList<SimpleDomain> doms = new LinkedList<SimpleDomain>();
data.window(a.getChrom(), a.getStart(), a.getEnd());
int np = data.getCount();
for (int pi = 0; pi < np - 1; pi++) {
int f = findNextDomainIndex(pi, a);
if (f != -1) {
SimpleDomain dom = buildDomain(pi, f, a);
doms.addLast(dom);
pi = f;
}
}
return doms.iterator();
} catch (NotFoundException e) {
e.printStackTrace();
return new EmptyIterator<SimpleDomain>();
}
}