/usr/include/libphylo/computePijComponent.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 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 | // $Id: computePijComponent.h 9253 2011-01-31 01:37:21Z rubi $
#ifndef ___COMPUTE_PIJ_COMPONENT
#define ___COMPUTE_PIJ_COMPONENT
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "multipleStochasticProcess.h"
#include "gammaDistribution.h"
class computePijHomSpec {//specific node, no rate variation
public:
virtual ~computePijHomSpec(){};
void fillPij(const MDOUBLE dis, const stochasticProcess& sp, int derivationOrder = 0, bool isReversible =true);
void resize(const int alphabetSize) {
_V.resize(alphabetSize);
for (int z=0;z<alphabetSize;++z) _V[z].resize(alphabetSize);
}
int alphabetSize() const {return _V.size();}
MDOUBLE getPij(const int let1,const int let2)const{
return _V[let1][let2];
}
VVdouble _V; // let, let
};
class computePijHom {//all nodes, no rate variation
public:
virtual ~computePijHom(){};
void fillPij(const tree& et, const stochasticProcess& sp, int derivationOrder = 0, bool isReversible =true);
int alphabetSize() const {return _V[0].alphabetSize();}
int getNodesNum() const {return _V.size();}
MDOUBLE getPij(const int nodeId,const int let1,const int let2)const{
return _V[nodeId].getPij(let1,let2);
}
vector<computePijHomSpec> _V; // let, let
};
class computePijGam {//
public:
virtual ~computePijGam(){};
void fillPij(const tree& et, const stochasticProcess& sp, int derivationOrder = 0, bool isReversible =true);
int categories() const {return _V.size();}
int alphabetSize() const {return _V[0].alphabetSize();}
int getNodesNum() const {return _V[0].getNodesNum();}
MDOUBLE getPij(const int rateCategor,const int nodeId,const int let1,const int let2)const{
return _V[rateCategor].getPij(nodeId,let1,let2);
}
computePijHom& operator[] (int i) {return _V[i];}
const computePijHom& operator[] (int i) const {return _V[i];}
vector<computePijHom> _V; // each rate category
};
#endif
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