1 //uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
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11 const byte *AminoSeq;
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19 unsigned GetNucPosFirstBase() const;
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20 unsigned GetAAPos(unsigned NucPos) const;
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21 unsigned GetCodex(unsigned NucPos) const;
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22 unsigned GetNucLo(unsigned AALo, unsigned AAHi) const;
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23 unsigned GetNucHi(unsigned AALo, unsigned AAHi) const;
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24 unsigned GetAALo(unsigned NucLo, unsigned NucHi) const;
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25 unsigned GetAAHi(unsigned NucLo, unsigned NucHi) const;
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26 unsigned GetNucPosFirstBaseInCodon(unsigned AAPos) const;
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27 unsigned GetNucPosLastBaseInCodon(unsigned AAPos) const;
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28 unsigned RoundToCodonLo(unsigned NucPos) const;
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29 unsigned RoundToCodonHi(unsigned NucPos) const;
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31 void LogMe2() const;
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34 const byte ORFEND = '.';
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36 void GetORFs(const byte *NucSeq, unsigned NucL, vector<ORFData> &ORFs,
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37 unsigned ORFStyle, int FindFrame, int Sign);
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