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/*****************************************************************************\
* Filename : ncmodel.hh
* Author : Mario Stanke
* Description: Model for non-protein-coding genes (nc)
*
*
* Date | Author | Changes
*------------|-----------------|----------------------------------------
* 21.02.2015 | Mario Stanke | creation of the file
\******************************************************************************/
#ifndef _NCMODEL_HH
#define _NCMODEL_HH
#include "statemodel.hh"
/**
* The nc model class.
*
* author Mario Stanke
*/
class NcModel : public StateModel {
public:
NcModel();
~NcModel();
StateType getStateType( ) const {
return nctype;
}
/**
* No training of parameters. Other parameters are reused.
*/
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
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