/** calculates statstics and output for results on a given test sequence */
public void calcResultIncrement(TrainingSequence training, int[] predictedHiddenSequence) {
labeled.add(
new TrainingSequence(
training.getInputSequence(),
predictedHiddenSequence)); // This is only place that labelled gets added to???
// So I guess the results just get built up incrementally, both the actuall hidden sequences and
// the stats?
Assert.a(training.length() == predictedHiddenSequence.length);
int[] actualHiddenSequence = new int[training.length()];
for (int i = 0; i < training.length(); i++) {
actualHiddenSequence[i] = training.getY(i);
}
boolean thisperfect = true;
for (int i = 0; i < predictedHiddenSequence.length; ++i) {
int predY = predictedHiddenSequence[i];
int realY = actualHiddenSequence[i];
if (realY == predY) {
correct += 1;
} else {
incorrect += 1;
thisperfect = false;
}
ctCodingNucleotide.increment(isCodingPlus(predY), isCodingPlus(realY));
ctCodingNucleotide.increment(isCodingMinus(predY), isCodingMinus(realY));
for (int s = 0; s < nStates; s++) {
ctStates.get(s).increment((predY == s), (realY == s));
}
}
if (thisperfect) {
perfect++;
} else {
imperfect++;
}
for (int i = 1; i < predictedHiddenSequence.length; ++i) {
int predY = predictedHiddenSequence[i];
int realY = actualHiddenSequence[i];
int predYp = predictedHiddenSequence[i - 1];
int realYp = actualHiddenSequence[i - 1];
for (int t = 0; t < nTransitions; t++) {
boolean bPred = ((predYp == fromInd.get(t)) && (predY == toInd.get(t)));
boolean bReal = ((realYp == fromInd.get(t)) && (realY == toInd.get(t)));
ctTransitions.get(t).increment(bPred, bReal);
}
}
// Now let's increment the contingency table for exons; note that here not counting TN's
RangeMap predExonsPlus = new RangeMap();
RangeMap predExonsMinus = new RangeMap();
RangeMap realExonsPlus = new RangeMap();
RangeMap realExonsMinus = new RangeMap();
makeExonRangeMapFrom13SV(predictedHiddenSequence, predExonsPlus, predExonsMinus);
makeExonRangeMapFrom13SV(actualHiddenSequence, realExonsPlus, realExonsMinus);
incrementCTFromRangeMaps(ctExons, predExonsPlus, realExonsPlus);
incrementCTFromRangeMaps(ctExons, predExonsMinus, realExonsMinus);
}
@Override
public String toString() {
String ret = "";
for (int s = 0; s < nStates; s++) {
ret += "[State=" + manager.getStateName(s) + "] ";
ctStates.get(s).freeze();
ret += "Predicted: " + ctStates.get(s).pp();
ret += "\n";
}
for (int t = 0; t < nTransitions; t++) {
ret +=
"[Transition "
+ manager.getStateName(fromInd.get(t))
+ " --> "
+ manager.getStateName(toInd.get(t))
+ " ] ";
ctTransitions.get(t).freeze();
ret += "Predicted: " + ctTransitions.get(t).pp();
ret += "\n";
}
ctCodingNucleotide.freeze();
ret += "[Coding nucleotides] Predicted: " + ctCodingNucleotide.pp() + "\n";
ctExons.freeze();
ret += "[Coding exons] Predicted: " + ctExons.pp() + "\n";
if (lla > 0) {
ret += "LLA:" + lla + " LLV:" + llv + " " + "\n";
}
// ret += String.format("Perfectly predicted hidden sequences: %d/%d %.2f
// %%",perfect,perfect+imperfect,perfect*100.0/(float) (perfect+imperfect))+ "\n";
// ret += String.format("Nucleotide Hidden State Agreement: %d/%d %.2f %%",correct, correct +
// incorrect, correct * 100.0 / (float) (correct + incorrect)) + "\n";
return ret;
}
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();
}
}
}
}
