modelprob.h

#ifndef MODELPROB_H
#define MODELPROB_H

#include <vector>
#include <map>
#include <string>
#include <cstdlib>
#include <iostream>
#include <sstream>
#include <fstream>

using namespace std ;


class probSegregDInternal
{
        public:
                probSegregDInternal();
                void load( istream &in ) ;
                int getSize(void)	{return probs.size();};
		void resize(int value)  {probs.resize(value);};
                double getProb( int num_derived ) ;
                void setProbsAt(int index, double value);
                string printAll(void);
        private:
                vector<double> probs ; // probabilities: 0 is not used, $1 .. coverage-1$ is for derived alleles 1 to coverage-1.
                size_t fixed_coverage ; // used to check whether input-lines are wrong

} ;


class modelProb
{
public:
    modelProb();

    char loadProb(const char* fileName);

    void setStayInternal(double value)		{mStayInternal = value;};
    void setStayExternal(double value)		{mStayExternal = value;};
    void setStayLongExternal(double value)      {mStayLongExternal = value;};
    void setLErate(double value)                {mLErate = value;};
    void setProbFixDInternal(double value)	{mProbFixDInternal = value;};
    void setProbFixDExternal(double value)	{mProbFixDExternal = value;};
    void setProbSegregDExternal(double value)	{mProbSegregDExternal = value;};
    void setProbSegregDInternalAt(int i, double value) {obs.setProbsAt(i, value);};
    void resizeProbSegregDInternal(int size) {obs.resize(size);};
    int getSizeProbSegregDInternal(void) {return obs.getSize();};
    probSegregDInternal getProbSegregDInternal(void) {return obs;};//read only access

    double getStayInternal(void)		{return mStayInternal;};
    double getStayExternal(void)		{return mStayExternal;};
    double getStayLongExternal(void)            {return mStayLongExternal;};
    double getLErate(void)                      {return mLErate;};
    double getProbFixDInternal(void)		{return mProbFixDInternal;};
    double getProbFixDExternal(void)		{return mProbFixDExternal;};
    double getProbSegregDExternal(void)         {return mProbSegregDExternal;};
    

protected:
    probSegregDInternal obs;
    //probSegregDInternal backup; //used only in the optimization step to get back to old values if the new ones are not better

    double mStayInternal;
    double mStayExternal;
    double mStayLongExternal;
    double mLErate;
    double mProbFixDInternal;
    double mProbFixDExternal;
    double mProbSegregDExternal;
};




#endif // MODELPROB_H