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/*
* igenicmodel.hh
*
* License: Artistic License, see file LICENSE.TXT or
* https://opensource.org/licenses/artistic-license-1.0
*/
#ifndef __IGENICMODEL_HH
#define __IGENICMODEL_HH
#include "statemodel.hh"
/**
* @author Mario Stanke
*
*/
class IGenicModelError : public ProjectError {
public:
IGenicModelError(string msg) : ProjectError(msg) {}
};
/**
* @brief intergenic region
*
* @author Mario Stanke
*
*/
class IGenicModel : public StateModel {
public:
IGenicModel() : gweight(1) {
init();
}
~IGenicModel() {}
StateType getStateType() const {
return igenic;
}
void buildModel ( const AnnoSequence* annoseq, int parIndex );
void registerPars ( Parameters* parameters);
void printProbabilities ( int zusNumber, BaseCount *bc, const char* suffix = NULL );
void initAlgorithms ( Matrix<Double>&, int);
void viterbiForwardAndSampling(ViterbiMatrixType&, ViterbiMatrixType&, int, int,
AlgorithmVariant, OptionListItem&);
Double emiProbUnderModel(int begin, int end) const;
static void init();
static void setSFC(SequenceFeatureCollection *sfc) {
seqFeatColl = sfc;
}
static void resetPars() {}
static void updateToLocalGC(int from, int to);
static void readProbabilities(int zusNumber);
static void readAllParameters();
static void storeGCPars(int idx);
static double getGeoProb(){return geoProb;}
static vector<double> getNucleotideProbs(){return nucProbs[0];}
private:
void processSequence( const char* start, const char* end );
public:
static Integer k; // UTR intron and intron
static PatMMGroup emiprobs; // can use this data.
static PatMMGroup *GCemiprobs; // array for each GC content class
private:
Integer gweight;
static Double patpseudocount;
static Integer gesbasen;
static vector<Integer> emicount;
static vector<vector<Double> > Pls;
static vector<vector<Double> >* GCPls;
static vector<vector<double> > nucProbs;
static int lastParIndex; // GC-index of current parameter set
static int verbosity;
static double geoProb;
};
#endif // __IGENICMODEL_HH
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