1 #ifndef alpha_h 2 #define alpha_h 3 4 #include <limits.h> 5 #include <string> 6 7 using namespace std; 8 9 const unsigned INVALID_LETTER = 0; 10 const unsigned char INVALID_CHAR = '?'; 11 12 extern unsigned g_CharToLetterAmino[]; 13 extern unsigned g_CharToLetterAminoStop[]; 14 extern unsigned char g_LetterToCharAmino[]; 15 extern unsigned g_CharToLetterNucleo[]; 16 extern unsigned char g_LetterToCharNucleo[]; 17 extern unsigned g_CodonWordToAminoLetter[]; 18 extern char g_CodonWordToAminoChar[]; 19 extern unsigned char g_CharToCompChar[]; 20 extern unsigned g_CharToCompLetter[]; 21 extern bool g_IsAminoChar[]; 22 extern bool g_IsNucleoChar[]; 23 extern bool g_IsACGTU[]; 24 extern float g_AminoFreqs[]; 25 26 extern unsigned g_CharToLetterRed[]; 27 extern unsigned char g_LetterToCharRed[]; 28 extern unsigned g_RedAlphaSize; 29 30 void LogRedAlphaRed(); 31 void ReadRedAlphaFromFile(const string &FileName); 32 unsigned char GetAminoCharFrom3NucChars(unsigned char c1, unsigned char c2, 33 unsigned char c3); 34 AminoLetterIsStartCodon(unsigned char Letter)35static inline bool AminoLetterIsStartCodon(unsigned char Letter) 36 { 37 return Letter == 10; 38 } 39 AminoLetterIsStopCodon(unsigned char Letter)40static inline bool AminoLetterIsStopCodon(unsigned char Letter) 41 { 42 return Letter == 20; 43 } 44 45 const char *WordToStr(unsigned Word, unsigned WordLength, bool Nucleo); 46 const char *WordToStrNucleo(unsigned Word, unsigned WordLength); 47 const char *WordToStrAmino(unsigned Word, unsigned WordLength); 48 const char *WordToStrAmino2(unsigned Word, unsigned WordLength, char *Str); 49 50 #endif // alpha_h 51