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// $Id: fromCountTableComponentToDistance2Codon.h 950 2006-10-19 12:12:34Z eyalprivman $
#ifndef ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_2_CODON
#define ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_2_CODON
#include "definitions.h"
#include "countTableComponent.h"
#include "stochasticProcess.h"
static const MDOUBLE startingGuessForTreeBrLen = 0.029;
class fromCountTableComponentToDistance2Codon {
public:
explicit fromCountTableComponentToDistance2Codon(
const countTableComponentGam& ctc,
const vector<stochasticProcess> &spVec,
const MDOUBLE toll,
const MDOUBLE brLenIntialGuess);// =startingGuessForTreeBrLen
void computeDistance();// return the likelihood
MDOUBLE getDistance() { return _distance;} // return the distance.
MDOUBLE getLikeDistance() { return _likeDistance;} // return the distance.
private:
const vector<stochasticProcess> & _spVec;
const countTableComponentGam& _ctc;
MDOUBLE _toll;
MDOUBLE _distance;
MDOUBLE _likeDistance;
int alphabetSize() {return _ctc.alphabetSize();}
};
#endif
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