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// $Id: fromCountTableComponentToDistance.h 4742 2008-08-19 17:40:56Z cohenofi $
#ifndef ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE
#define ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE
#include "definitions.h"
#include "countTableComponent.h"
#include "stochasticProcess.h"
#include "unObservableData.h"
static const MDOUBLE startingGuessForTreeBrLen = 0.029;
class fromCountTableComponentToDistance {
public:
explicit fromCountTableComponentToDistance(
const countTableComponentGam& ctc,
const stochasticProcess &sp,
const MDOUBLE toll,
const MDOUBLE brLenIntialGuess, // =startingGuessForTreeBrLen
unObservableData* unObservableData_p = NULL); // a class used to for presence/absence
void computeDistance();// return the likelihood
MDOUBLE getDistance() { return _distance;} // return the distance.
MDOUBLE getLikeDistance() { return _likeDistance;} // return the distance.
private:
const stochasticProcess & _sp;
const countTableComponentGam& _ctc;
MDOUBLE _toll;
MDOUBLE _distance;
MDOUBLE _likeDistance;
unObservableData* _unObservableData_p;
int alphabetSize() {return _ctc.alphabetSize();}
};
#endif
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