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// $Id: fromCountTableComponentToDistance2USSRV.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_2_USSRV
#define ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_2_USSRV
#include "definitions.h"
#include "countTableComponent.h"
#include "stochasticProcess.h"
#include "ussrvModel.h"
#include "likeDist2USSRV.h"
static const MDOUBLE startingGuessForTreeBrLen = 0.029;
class fromCountTableComponentToDistance2USSRV {
public:
explicit fromCountTableComponentToDistance2USSRV(
const countTableComponentGam& ctcBase,
const countTableComponentHom& ctcSSRV,
const ussrvModel& model,
MDOUBLE toll,
MDOUBLE brLenIntialGuess);// =startingGuessForTreeBrLen
void computeDistance();// return the likelihood
MDOUBLE getDistance() { return _distance;} // return the distance.
MDOUBLE getLikeDistance() { return _likeDistance;} // return the distance.
private:
const ussrvModel & _model;
const countTableComponentGam& _ctcBase;
const countTableComponentHom& _ctcSSRV;
MDOUBLE _toll;
MDOUBLE _distance;
MDOUBLE _likeDistance;
// int alphabetSize() {return _ctc.alphabetSize();}
};
#endif //___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_2_USSRV
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