/usr/include/libphylo/unObservableData.h is in rate4site 3.0.0-5.
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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 | #ifndef ___unObservableData___GL
#define ___unObservableData___GL
#include "definitions.h"
#include "tree.h"
#include "stochasticProcess.h"
#include "sequenceContainer.h"
#include "gainLossAlphabet.h"
#include "computePijComponent.h"
/********************************************************************************************
unObservableData
*********************************************************************************************/
class unObservableData{
public:
explicit unObservableData(const sequenceContainer& sc,const stochasticProcess* sp ,const gainLossAlphabet alph, const int minNumOfOnes, const int minNumOfZeros);
unObservableData(const unObservableData& other); //const
virtual ~unObservableData(){};
virtual unObservableData* clone() const {return new unObservableData(*this);}
Vdouble* getpLforMissingDataPerCat();
Vdouble getLforMissingDataPerCat();
MDOUBLE getlogLforMissingData();
int getNumOfUnObservablePatterns();
void setLforMissingData(const tree& _tr, const stochasticProcess* _sp);
//void setLforMissingData(const tree& _tr, const stochasticProcess* _sp);
void setLforMissingData(const tree& _tr, const vector<vector<stochasticProcess*> >& spVVec, const distribution * distGain, const distribution* distLoss);
//MDOUBLE getCorrectedLikelihood(MDOUBLE likePre){return }
protected:
//func
protected:
//members
sequenceContainer _scZero;
Vdouble _LforMissingDataPerCat; // used foreach rate category
MDOUBLE _logLforMissingData;
computePijGam _pi;
};
#endif
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