/usr/include/libphylo/replacementModel.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 | // $Id: replacementModel.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___REPLACEMENT_MODEL
#define ___REPLACEMENT_MODEL
#include "definitions.h"
class replacementModel{
public:
virtual const MDOUBLE Pij_t(const int i, const int j, const MDOUBLE t) const = 0;
virtual const MDOUBLE freq(const int i) const = 0;
virtual const MDOUBLE dPij_dt(const int i, const int j, const MDOUBLE t) const =0;
virtual const MDOUBLE d2Pij_dt2(const int i, const int j, const MDOUBLE t) const =0;
virtual replacementModel* clone() const = 0;
virtual ~replacementModel()=0;
virtual const int alphabetSize() const =0;
//virtual const MDOUBLE Q(const int i, const int j, const MDOUBLE r = 1.0) const = 0;
//note that we ask that sigma over i sigma over j!=i of p(i)Qij = 1;
//this is beacuse we ask the [sigma over i sigma over j!=i p(i)*pij(d)]/d approaches
//1 as d -> 0. (and l'hopital from here).
};
#endif
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