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#ifndef orf_h
#define orf_h
#include "alpha.h"
struct ORFData
{
const byte *NucSeq;
const byte *AminoSeq;
int Frame;
unsigned NucL;
unsigned AminoL;
unsigned NucLo;
unsigned NucHi;
ORFData *Next;
unsigned GetNucPosFirstBase() const;
unsigned GetAAPos(unsigned NucPos) const;
unsigned GetCodex(unsigned NucPos) const;
unsigned GetNucLo(unsigned AALo, unsigned AAHi) const;
unsigned GetNucHi(unsigned AALo, unsigned AAHi) const;
unsigned GetAALo(unsigned NucLo, unsigned NucHi) const;
unsigned GetAAHi(unsigned NucLo, unsigned NucHi) const;
unsigned GetNucPosFirstBaseInCodon(unsigned AAPos) const;
unsigned GetNucPosLastBaseInCodon(unsigned AAPos) const;
unsigned RoundToCodonLo(unsigned NucPos) const;
unsigned RoundToCodonHi(unsigned NucPos) const;
void LogMe() const;
void LogMe2() const;
};
const byte ORFEND = '.';
void GetORFs(const byte *NucSeq, unsigned NucL, vector<ORFData> &ORFs,
unsigned ORFStyle, int FindFrame, int Sign);
#endif // orf_h
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