exoncand.hh

/*
 * exoncand.hh
 *
 * License: Artistic License, see file LICENSE.TXT or 
 *          https://opensource.org/licenses/artistic-license-1.0
 */
 
#ifndef _EXONCAND_HH
#define _EXONCAND_HH
 
#include <stdint.h>
 
#include "types.hh"
#include "exonmodel.hh" // for OpenReadingFrame
#define EXON_TYPES 17
 
enum ExonType {UNKNOWN_EXON = -1,
    // forward strand
    singleGene, initial_0, initial_1, initial_2, internal_0, internal_1, internal_2, terminal_exon,
    // reverse strand
    rsingleGene, rinitial_exon, rinternal_0, rinternal_1, rinternal_2, rterminal_0, rterminal_1, rterminal_2
};
 
bool isPlusExon(ExonType t);
bool hasStopCodon(ExonType t);
 
extern const int exonTypeReadingFrames[EXON_TYPES-1];
extern const char* stateExonTypeIdentifiers[EXON_TYPES-1];
 
// converts a stateTypeIdentifier to the ExonType
ExonType toExonType(const char* str);
 
class ExonCandidate {
public:
    ExonCandidate(ExonType s=UNKNOWN_EXON, long int b=0, long int e=0, double sc=0.0, Double up_sc=1.0, Double down_sc=1.0):
        type(s),
        begin(b),
        end(e),
        score(sc),
        upScore(up_sc),
        downScore(down_sc)
    {}
    ExonCandidate(ExonCandidate* other){
        begin = other->begin;
        end = other->end;
        type = other->type;
        score = other->score;
        upScore = other->upScore;
        downScore = other->downScore;
    }
    ~ExonCandidate(){}
    ExonType type;
    int begin, end;
    double score;
 
    int getStart();
    int getEnd();
    int frame() const { return exonTypeReadingFrames[type]; }  // frame of the exon
    int frame(int p) const { return isPlusExon(type) ?         // frame at position p within the exon
        mod3(frame() - (end + 1) + p) :
        mod3(frame() +  end + 1  - p);
    }
    Double getUpScore() const {return upScore;}
    Double getDownScore() const {return downScore;}
    double getScore() const {return score;}
    void setUpScore(Double s) {upScore = s;}
    void setDownScore(Double s) {downScore = s;}
    void setScore(double s) {score = s;}
 
    int getFirstCodingBase();
    int getLastCodingBase();
    int gff3Frame();
    int len() {return end-begin+1;}
    ExonType getExonType();
    int complementType();
    StateType getStateType();
    string key();
    int_fast64_t getKey(); // keys encodes all of: chrStart chrEnd type lenMod3
    bool correctType(const char* dna, int dnalen); // verify ExonType on sequence
    friend ostream& operator<<(ostream& strm, const ExonCandidate &ec);
private:
    Double upScore, downScore;
};
 
/*
 * assqthresh, dssqthresh are between 0 and 1 and thresholds for the inclusion of
 * acceptor/donor splice sites based on the pattern probability
 * assqthresh=0.05 means that only acceptor ss are considered
 * that have a pattern, such that 5% of true splice site patterns have lower probability.
 * The default threshold of 0 means that all splice site patterns are considered.
 */
 
void findExonCands(map<int_fast64_t, ExonCandidate*> &ecs, map<int_fast64_t, ExonCandidate*> &addECs, const char *dna, int minLen=1, double assmotifqthresh=0.15, double assqthresh=0.3, double dssqthresh=0.7);
 
//computes the score for the splice sites of an exon candidate
Double computeSpliceSiteScore(Double exonScore, Double minProb, Double maxProb); 
 
// create new EC from a key encoding all of: chrStart chrEnd type lenMod3
// verification of type, noInFrameStop, etc.
ExonCandidate* create(int_fast64_t key, const char* dna, int dnalen); 
 
#endif  //  _EXONCAND_HH