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// $Id: fromCountTableComponentToDistanceProp.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_PROP
#define ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_PROP
#include "definitions.h"
#include "countTableComponent.h"
#include "stochasticProcess.h"
class fromCountTableComponentToDistanceProp {
public:
explicit fromCountTableComponentToDistanceProp(
const vector<countTableComponentGam>& ctc,
const vector<stochasticProcess> &sp,
const MDOUBLE toll,
const MDOUBLE brLenIntialGuess = 0.029);// =startingGuessForTreeBrLen
void computeDistance();// return the likelihood
MDOUBLE getDistance() { return _distance;} // return the distance.
MDOUBLE getLikeDistance() { return _likeDistance;} // return the distance.
private:
const vector<stochasticProcess> & _sp;
const vector<countTableComponentGam>& _ctc;
MDOUBLE _toll;
MDOUBLE _distance;
MDOUBLE _likeDistance;
int alphabetSize() {return (_ctc.empty()?0:_ctc[0].alphabetSize());}
};
#endif
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