/**
* sets the model used to generate results
*
* @param manager the model used to generate results
*/
public void setManager(ModelManager manager) {
this.manager = manager;
ctCodingNucleotide = new PredictedActualBinaryContingencyTable();
ctExons = new PredictedActualBinaryContingencyTable();
ctExons.forgetTN();
nStates = manager.getNumStates();
ctStates = new ArrayList<PredictedActualBinaryContingencyTable>();
for (int i = 0; i < nStates; i++) {
ctStates.add(new PredictedActualBinaryContingencyTable());
}
DenseBooleanMatrix2D LT = manager.getLegalTransitions();
fromInd = new ArrayList<Integer>();
toInd = new ArrayList<Integer>();
for (int from = 0; from < nStates; from++) {
for (int to = 0; to < nStates; to++) {
if (LT.getQuick(from, to)) {
fromInd.add(from);
toInd.add(to);
}
}
}
nTransitions = fromInd.size();
ctTransitions = new ArrayList<PredictedActualBinaryContingencyTable>();
for (int i = 0; i < nTransitions; i++) {
ctTransitions.add(new PredictedActualBinaryContingencyTable());
}
}
@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;
}