/**
* 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());
}
}
