/usr/include/libphylo/fromCountTableComponentToDistancePropEB.h is in rate4site 3.0.0-2.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | // $Id: fromCountTableComponentToDistanceProp.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_PROP_EB
#define ___FROM_COUNT_TABLE_COMPONENT_TO_DISTANCE_PROP_EB
#include "definitions.h"
#include "countTableComponent.h"
#include "multipleStochasticProcess.h"
#include "gammaDistribution.h"
class fromCountTableComponentToDistancePropEB {
public:
explicit fromCountTableComponentToDistancePropEB(
const vector< vector<countTableComponentGamProportional> >& ctc,
const int nodeID,
multipleStochasticProcess* msp,
const gammaDistribution* pProportionDist,
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:
multipleStochasticProcess * _msp;
const vector< vector<countTableComponentGamProportional> >& _ctc;
const gammaDistribution* _pProportionDist;
const int _nodeID;
MDOUBLE _toll;
MDOUBLE _distance;
MDOUBLE _likeDistance;
int alphabetSize() {return (_ctc.empty()?0:_ctc[0][_nodeID].alphabetSize());}
};
#endif
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