private void incrementCTFromRangeMaps(
PredictedActualBinaryContingencyTable ct, RangeMap pred, RangeMap real) {
// By looping through the predictions, can get at TP and FP
Set<IntervalRangeMapValue> pv = pred.values();
Iterator<IntervalRangeMapValue> pvi = pv.iterator();
while (pvi.hasNext()) {
IntervalRangeMapValue irmv = pvi.next();
Set<IntervalRangeMapValue> vals = real.find(irmv.start, irmv.end);
if (vals.size() == 0) {
ct.incrementFP();
} else {
IntervalRangeMapValue val = vals.iterator().next();
if (val.start == irmv.start && val.end == irmv.end) {
ct.incrementTP();
} else {
ct.incrementFP();
}
}
}
Set<IntervalRangeMapValue> rv = real.values();
Iterator<IntervalRangeMapValue> rvi = rv.iterator();
while (rvi.hasNext()) {
IntervalRangeMapValue irmv = rvi.next();
if (!pred.hasEntry(irmv.start, irmv.end)) {
ct.incrementFN();
}
Set<IntervalRangeMapValue> vals = pred.find(irmv.start, irmv.end);
if (vals.size() == 0) {
ct.incrementFN();
} else {
IntervalRangeMapValue val = vals.iterator().next();
if (val.start == irmv.start && val.end == irmv.end) {
} else {
ct.incrementFN();
}
}
}
}
private void makeExonRangeMapFrom13SV(int[] hidden, RangeMap exonsPlus, RangeMap exonsMinus) {
int len = hidden.length;
for (int i = 1; i < len; i++) {
if ((!isCodingPlus(hidden[i - 1]) && (isCodingPlus(hidden[i])))) {
int j = i;
while ((isCodingPlus(hidden[j])) && (j < (len - 1))) {
j++;
}
exonsPlus.add(i, j, new IntervalRangeMapValue(i, j, 1.0));
// log.info("Add + "+i+" "+j);
}
if ((!isCodingMinus(hidden[i - 1]) && (isCodingMinus(hidden[i])))) {
int j = i;
while ((isCodingMinus(hidden[j])) && (j < len - 1)) {
j++;
}
exonsMinus.add(i, j, new IntervalRangeMapValue(i, j, 1.0));
// log.info("Add - "+i+" "+j);
}
}
}