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/*****************************************************************************\
* Filename : exoncand.hh
* Author : Alexander Gebauer
*
* Description: Generation of exon candidates (=possible exons)
*
* An exon candidate is a sequence interval with frame and strand information
* such that
* at the 5' end is either an ASS or a start codon and
* at the 3' end is either a DSS or a stop codon.
*
* Date | Author | Changes
*------------|-----------------------|------------------------------------------
* 3.11.2011 | Mario Stanke | creation of the file
* 06.12.2011 | Alexander Gebauer | definition of the stop codons
* 17.01.2012 | Alexander Gebauer | add class AlignSeq und struct block
* 27.02.2012 | Alexander Gebauer | add class ExonCandidate
* 13.01.2011 | Mario Stanke | revision: general set of stop codons
\******************************************************************************/
#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);
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
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