/** 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);
}
