| 1 | #ifndef alpha_h |
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| 2 | #define alpha_h |
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| 3 | |
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| 4 | bool StrHasAmino(const char *Str); |
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| 5 | bool StrHasGap(const char *Str); |
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| 6 | void ClearInvalidLetterWarning(); |
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| 7 | void InvalidLetterWarning(char c, char w); |
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| 8 | void ReportInvalidLetters(); |
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| 9 | |
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| 10 | extern unsigned g_CharToLetter[]; |
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| 11 | extern unsigned g_CharToLetterEx[]; |
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| 12 | |
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| 13 | extern char g_LetterToChar[]; |
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| 14 | extern char g_LetterExToChar[]; |
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| 15 | |
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| 16 | extern char g_UnalignChar[]; |
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| 17 | extern char g_AlignChar[]; |
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| 18 | |
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| 19 | extern bool g_IsWildcardChar[]; |
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| 20 | extern bool g_IsResidueChar[]; |
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| 21 | |
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| 22 | #define CharToLetter(c) (g_CharToLetter[(unsigned char) (c)]) |
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| 23 | #define CharToLetterEx(c) (g_CharToLetterEx[(unsigned char) (c)]) |
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| 24 | |
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| 25 | #define LetterToChar(u) (g_LetterToChar[u]) |
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| 26 | #define LetterExToChar(u) (g_LetterExToChar[u]) |
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| 27 | |
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| 28 | #define IsResidueChar(c) (g_IsResidueChar[(unsigned char) (c)]) |
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| 29 | #define IsGapChar(c) ('-' == (c) || '.' == (c)) |
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| 30 | #define IsWildcardChar(c) (g_IsWildcardChar[(unsigned char) (c)]) |
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| 31 | |
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| 32 | #define AlignChar(c) (g_AlignChar[(unsigned char) (c)]) |
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| 33 | #define UnalignChar(c) (g_UnalignChar[(unsigned char) (c)]) |
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| 34 | |
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| 35 | // AX=Amino alphabet with eXtensions (B, Z and X) |
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| 36 | enum AX |
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| 37 | { |
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| 38 | AX_A, |
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| 39 | AX_C, |
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| 40 | AX_D, |
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| 41 | AX_E, |
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| 42 | AX_F, |
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| 43 | AX_G, |
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| 44 | AX_H, |
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| 45 | AX_I, |
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| 46 | AX_K, |
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| 47 | AX_L, |
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| 48 | AX_M, |
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| 49 | AX_N, |
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| 50 | AX_P, |
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| 51 | AX_Q, |
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| 52 | AX_R, |
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| 53 | AX_S, |
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| 54 | AX_T, |
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| 55 | AX_V, |
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| 56 | AX_W, |
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| 57 | AX_Y, |
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| 58 | |
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| 59 | AX_X, // Any |
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| 60 | |
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| 61 | AX_B, // D or N |
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| 62 | AX_Z, // E or Q |
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| 63 | |
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| 64 | AX_GAP, |
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| 65 | }; |
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| 66 | const unsigned AX_COUNT = AX_GAP + 1; |
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| 67 | |
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| 68 | // NX=Nucleotide alphabet with extensions |
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| 69 | enum NX |
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| 70 | { |
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| 71 | NX_A, |
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| 72 | NX_C, |
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| 73 | NX_G, |
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| 74 | NX_T, |
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| 75 | NX_U = NX_T, |
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| 76 | |
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| 77 | NX_M, // AC |
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| 78 | NX_R, // AG |
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| 79 | NX_W, // AT |
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| 80 | NX_S, // CG |
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| 81 | NX_Y, // CT |
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| 82 | NX_K, // GT |
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| 83 | NX_V, // ACG |
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| 84 | NX_H, // ACT |
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| 85 | NX_D, // AGT |
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| 86 | NX_B, // CGT |
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| 87 | NX_X, // GATC |
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| 88 | NX_N, // GATC |
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| 89 | NX_GAP |
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| 90 | }; |
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| 91 | const unsigned NX_COUNT = NX_GAP + 1; |
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| 92 | |
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| 93 | const unsigned MAX_ALPHA = 20; |
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| 94 | const unsigned MAX_ALPHA_EX = AX_COUNT; |
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| 95 | const unsigned MAX_CHAR = 256; |
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| 96 | |
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| 97 | extern ALPHA g_Alpha; |
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| 98 | extern unsigned g_AlphaSize; |
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| 99 | |
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| 100 | void SetAlpha(ALPHA Alpha); |
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| 101 | char GetWildcardChar(); |
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| 102 | bool IsNucleo(char c); |
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| 103 | bool IsDNA(char c); |
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| 104 | bool IsRNA(char c); |
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| 105 | |
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| 106 | #endif // alpha_h |
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