1 //uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.
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11 const unsigned INVALID_LETTER = 0;
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12 const unsigned char INVALID_CHAR = '?';
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14 extern unsigned g_CharToLetterAmino[];
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15 extern unsigned g_CharToLetterAminoStop[];
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16 extern unsigned char g_LetterToCharAmino[];
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17 extern unsigned g_CharToLetterNucleo[];
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18 extern unsigned char g_LetterToCharNucleo[];
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19 extern unsigned g_CodonWordToAminoLetter[];
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20 extern char g_CodonWordToAminoChar[];
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21 extern unsigned char g_CharToCompChar[];
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22 extern unsigned g_CharToCompLetter[];
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23 extern bool g_IsAminoChar[];
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24 extern bool g_IsNucleoChar[];
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25 extern bool g_IsACGTU[];
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26 extern float g_AminoFreqs[];
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28 extern unsigned g_CharToLetterRed[];
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29 extern unsigned char g_LetterToCharRed[];
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30 extern unsigned g_RedAlphaSize;
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32 void LogRedAlphaRed();
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33 void ReadRedAlphaFromFile(const string &FileName);
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34 unsigned char GetAminoCharFrom3NucChars(unsigned char c1, unsigned char c2,
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37 static inline bool AminoLetterIsStartCodon(unsigned char Letter)
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39 return Letter == 10;
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42 static inline bool AminoLetterIsStopCodon(unsigned char Letter)
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44 return Letter == 20;
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47 const char *WordToStr(unsigned Word, unsigned WordLength, bool Nucleo);
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48 const char *WordToStrNucleo(unsigned Word, unsigned WordLength);
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49 const char *WordToStrAmino(unsigned Word, unsigned WordLength);
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50 const char *WordToStrAmino2(unsigned Word, unsigned WordLength, char *Str);
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