9 const byte *AminoSeq;
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17 unsigned GetNucPosFirstBase() const;
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18 unsigned GetAAPos(unsigned NucPos) const;
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19 unsigned GetCodex(unsigned NucPos) const;
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20 unsigned GetNucLo(unsigned AALo, unsigned AAHi) const;
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21 unsigned GetNucHi(unsigned AALo, unsigned AAHi) const;
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22 unsigned GetAALo(unsigned NucLo, unsigned NucHi) const;
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23 unsigned GetAAHi(unsigned NucLo, unsigned NucHi) const;
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24 unsigned GetNucPosFirstBaseInCodon(unsigned AAPos) const;
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25 unsigned GetNucPosLastBaseInCodon(unsigned AAPos) const;
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26 unsigned RoundToCodonLo(unsigned NucPos) const;
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27 unsigned RoundToCodonHi(unsigned NucPos) const;
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29 void LogMe2() const;
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32 const byte ORFEND = '.';
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34 void GetORFs(const byte *NucSeq, unsigned NucL, vector<ORFData> &ORFs,
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35 unsigned ORFStyle, int FindFrame, int Sign);
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