ncmodel.hh

/*
 * ncmodel.hh
 *
 * License: Artistic License, see file LICENSE.TXT or 
 *          https://opensource.org/licenses/artistic-license-1.0
 */
 
#ifndef _NCMODEL_HH
#define _NCMODEL_HH
 
#include "statemodel.hh"
 
 
 class NcModel : public StateModel {
public:
    NcModel();
    ~NcModel();
 
    StateType getStateType( ) const {
    return nctype;
    }
 
    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;
    Double endPartEmiProb     (int begin, int end, int endOfBioExon) const;
    Double notEndPartEmiProb  (int begin, int end, int endOfBioExon, Feature *exonparts) const;
    void getEndPositions      ( int end, int &beginOfEndPart, int &endOfBioExon) const;
    void precomputeTxEndProbs    ( );
    static void init();
    static void resetPars(){
    if (nccount == 0)
        return;
    initSnippetProbs();
    initAlgorithmsCalled = false;
    }
    static void updateToLocalGC(int from = -1, int to = -1);
    static void readAllParameters();
    static void resetModelCount(){nccount = 0;};
    
private:
   //    Double seqProb            ( int left, int right) const;
    void computeLengthDistributions( );
    Double longIntronProb(int internalBegin, int internalEnd) const;
    static void initSnippetProbs();
 
private:
    StateType              nctype;
    Strand                 strand;
    Integer                gweight;
    double                 pIntron; // geometric intron probability for states ncintron, rncintron
    EOPList                eop;
    static Integer         nccount;
    static vector<Double>  lenDistInternal;       // length distribution of internal, initial and terminal
    static vector<Double>  lenDistSingle;         // length distribution of nc genes with a single exon
    static Boolean         hasLenDist;
    static bool            initAlgorithmsCalled;
    static bool            haveSnippetProbs;
    static SnippetProbs    *snippetProbs;
    static SegProbs        *segProbs;
    static int             boundSpacing; // without hints 5' and 3' transcript end only every ttsSpacing bases, for speed
    static vector<Double>  ttsProbPlus, ttsProbMinus;
    static vector<Double>  tssProbPlus, tssProbMinus;
};
 
 
class NcModelError : public ProjectError {
public:
    NcModelError(string msg) : ProjectError(msg) {}
};
 
#endif    //  _NCMODEL_HH