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#ifndef CODE_OutSJ
#define CODE_OutSJ
#include "Parameters.h"
#include "Genome.h"
class Junction {//one junction
public:
const static uint startP=0;
const static uint gapP=startP+sizeof(uint);
const static uint strandP=gapP+sizeof(uint32);
const static uint motifP=strandP+sizeof(char);
const static uint annotP=motifP+sizeof(char);
const static uint countUniqueP=annotP+sizeof(char);
const static uint countMultipleP=countUniqueP+sizeof(uint32);
const static uint overhangLeftP=countMultipleP+sizeof(uint32);
const static uint overhangRightP=overhangLeftP+sizeof(uint16);
uint *start;
uint32 *gap;
char *strand, *motif, *annot;
uint32 *countUnique, *countMultiple;
uint16 *overhangLeft, *overhangRight;
const static uint dataSize=overhangRightP+sizeof(uint16);
Junction(Genome &genomeIn);
void junctionPointer(char* sjPoint, uint isj);
void outputStream(ostream &outStream);
void collapseOneSJ(char* isj1P, char* isjP, Parameters& P);
private:
Genome &genOut;
};
class OutSJ {
public:
//all junctions
char* data; //sj array[Njunctions][dataSize]
uint N; //number of junctions stored
Junction oneSJ;
OutSJ(uint nSJmax, Parameters &Pin, Genome &genomeIn);
void collapseSJ();//collapse the junctions in data
// int compareSJ(void* i1, void* i2);
private:
Parameters &P;
Genome &genOut;
};
int compareSJ(const void* i1, const void* i2); //external functions
#endif
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