EmissionSequence *HMM::sampleFromState(STATE q,int length) const
{
// Set up roulette wheels
int nD=schema.getNumDiscrete();
Array1D<NmerChain*> chains(nD);
Array1D<HigherOrderAlphabet> HOA(nD);
for(int i=0 ; i<nD ; ++i) {
HOA[i]=HigherOrderAlphabet(schema.getAlphabet(i),order+1);
chains[i]=HOA[i].constructChain();
}
Array2D< Array1D<RouletteWheel> > emitWheels(numStates,nD);
for(STATE q=1 ; q<numStates ; ++q){
for(int i=0 ; i<nD ; ++i) {
NmerChain &chain=*chains[i];
Array1D<RouletteWheel> &wheelArray=emitWheels[q][i];
Alphabet &alphabet=schema.getAlphabet(i);
int radix=alphabet.size();
HigherOrderAlphabet &H=HOA[i];
int numNmers=H.size();
wheelArray.resize(numNmers);
for(int nmer=0 ; nmer<numNmers ; ++nmer) {
RouletteWheel &wheel=wheelArray[nmer];
for(int r=0 ; r<radix ; ++r) { // r iterations thu 0th order symbols
NmerSymbol to=chain.nextNmer(nmer,r); // "to" is a higher order sym
while(int(to)>=discreteEmitProb[q][i].size())
to=chain.getSuffix(to);
wheel.addSector(exp(discreteEmitProb[q][i][to]));
}
wheel.doneAddingSectors();
}
}
}
// Perform sampling
EmissionSequence *seq=new EmissionSequence(schema);
Array1D<Symbol> prevEmissions(nD);
prevEmissions.setAllTo(0); // symbol 0 is always the empty string
int len=0, nC=schema.getNumContinuous();
for(int j=0 ; j<length ; ++j) {
Emission e;
e.resize(nD,nC);
emissionProb[q].sample(e.getContinuous());
for(int i=0 ; i<nD ; ++i) {
NmerSymbol oldNmer=prevEmissions[i];
BaseSymbol s=emitWheels[q][i][oldNmer].spin();
NmerSymbol newNmer=chains[i]->nextNmer(oldNmer,s);
e.getDiscrete(i)=newNmer;
prevEmissions[i]=newNmer;
}
seq->append(e);
++len;
}
for(int i=0 ; i<nD ; ++i) delete chains[i];
// Return sampled sequence
return seq;
}
double HMM::getEmissionProb(int state,const Emission &x,
bool omitContinuous) const
{
double P=omitContinuous || schema.getNumContinuous()==0 ? 0.0 :
emissionProb[state].logDensity(x.getContinuous());
int numDiscrete=schema.getNumDiscrete();
for(int i=0 ; i<numDiscrete ; ++i) {
const NmerChain &chain=chains[i];
NmerSymbol s=x.getDiscrete(i);
const Array1D<double> &d=discreteEmitProb[state][i];
const int dsize=d.size();
while(int(s)>=dsize) s=chain.getSuffix(s);
P+=d[s];
}
return P;
}