modelprob.cc

#include "modelprob.h"

probSegregDInternal::probSegregDInternal()
{
	probs.resize( 1024, 0. ) ; // assuming this is the limit.
}

void probSegregDInternal::load( istream &in ) {
        int max_num_derived = 0;

        //probs.resize( 1024, 0. ) ; // assuming this is the limit.
        string s ;
        while ( in ) {
                getline( in, s ) ;
                stringstream ss( s, stringstream::in ) ;
                int num_derived ;
                ss >> num_derived ;
                double prob_derived ;
                ss >> prob_derived ;
                if ( num_derived > 1023 ) {
                        cerr << "Can't deal with coverage > 1023. (Adjust in code observation.cc)" << endl ;
                        exit( 1 ) ;
                }
                probs[num_derived] = prob_derived ;
                if(num_derived>max_num_derived){
                        max_num_derived = num_derived;
                }
        }
        probs.resize(max_num_derived+1);
}

double probSegregDInternal::getProb( int num_derived )
{
        return probs[num_derived] ;
}

void probSegregDInternal::setProbsAt(int index, double value)
{
        if(index<=probs.size())
        {
                probs[index] = value;
	//	cerr << "probs[index]" << probs[index] << "index:" << index << endl;
        }
        else
        {
                cerr << "Can't setProbsAt index > vector size (observation.cc)   size: " << probs.size() << "   index: " << index << endl;
                exit(1);
        }
}

string probSegregDInternal::printAll(void)
{
        ostringstream oss;
        string myStr;

        for(int i=1;i<probs.size()-1;i++)//elements-1 with '\t'
        {
                oss << probs[i];
                oss << "\t";
        }
        oss << probs[probs.size()-1];//last element without <<'\t'
        myStr = oss.str();
        return myStr;
}



modelProb::modelProb()
{
    mStayInternal = 0.0;
    mStayExternal = 0.0;
    mStayLongExternal = 0.0;
    mLErate = 0.0;
    mProbFixDInternal = 0.0;
    mProbFixDExternal = 0.0;
    mProbSegregDExternal = 0.0;
}

char modelProb::loadProb(const char* fileName)
{
        // Initialize observation_prob using emission probability config file
        ifstream dataStream( fileName, ifstream::in) ;
        if ( ! dataStream ) {
                cerr << "Error: Can't open internal state emission probabilities config file `" << fileName << "'" << endl ;
                return 1;
        }
        obs.load( dataStream );
        //dataStream.clear();
        //dataStream.seekg(0, std::ios::beg);
        //backup.load( dataStream ) ;
}