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#ifndef alpha_h
#define alpha_h
namespace muscle {
bool StrHasAmino(const char *Str);
bool StrHasGap(const char *Str);
void ClearInvalidLetterWarning();
void InvalidLetterWarning(char c, char w);
void ReportInvalidLetters();
// AX=Amino alphabet with eXtensions (B, Z and X)
enum AX
{
AX_A,
AX_C,
AX_D,
AX_E,
AX_F,
AX_G,
AX_H,
AX_I,
AX_K,
AX_L,
AX_M,
AX_N,
AX_P,
AX_Q,
AX_R,
AX_S,
AX_T,
AX_V,
AX_W,
AX_Y,
AX_X, // Any
AX_B, // D or N
AX_Z, // E or Q
AX_GAP,
};
const unsigned AX_COUNT = AX_GAP + 1;
// NX=Nucleotide alphabet with extensions
enum NX
{
NX_A,
NX_C,
NX_G,
NX_T,
NX_U = NX_T,
NX_M, // AC
NX_R, // AG
NX_W, // AT
NX_S, // CG
NX_Y, // CT
NX_K, // GT
NX_V, // ACG
NX_H, // ACT
NX_D, // AGT
NX_B, // CGT
NX_X, // GATC
NX_N, // GATC
NX_GAP
};
const unsigned NX_COUNT = NX_GAP + 1;
const unsigned MAX_ALPHA = 20;
const unsigned MAX_ALPHA_EX = AX_COUNT;
const unsigned MAX_CHAR = 256;
extern TLS<ALPHA> g_Alpha;
extern TLS<unsigned> g_AlphaSize;
void SetAlpha(ALPHA Alpha);
char GetWildcardChar();
bool IsNucleo(char c);
bool IsDNA(char c);
bool IsRNA(char c);
extern TLS<unsigned[MAX_CHAR]> g_CharToLetter;
extern TLS<unsigned[MAX_CHAR]> g_CharToLetterEx;
extern TLS<char[MAX_ALPHA]> g_LetterToChar;
extern TLS<char[MAX_ALPHA_EX]> g_LetterExToChar;
extern TLS<char[MAX_CHAR]> g_UnalignChar;
extern TLS<char[MAX_CHAR]> g_AlignChar;
extern TLS<bool[MAX_CHAR]> g_IsWildcardChar;
extern TLS<bool[MAX_CHAR]> g_IsResidueChar;
#define CharToLetter(c) (g_CharToLetter.get()[(unsigned char) (c)])
#define CharToLetterEx(c) (g_CharToLetterEx.get()[(unsigned char) (c)])
#define LetterToChar(u) (g_LetterToChar.get()[u])
#define LetterExToChar(u) (g_LetterExToChar.get()[u])
#define IsResidueChar(c) (g_IsResidueChar.get()[(unsigned char) (c)])
#define IsGapChar(c) ('-' == (c) || '.' == (c))
#define IsWildcardChar(c) (g_IsWildcardChar.get()[(unsigned char) (c)])
#define AlignChar(c) (g_AlignChar.get()[(unsigned char) (c)])
#define UnalignChar(c) (g_UnalignChar.get()[(unsigned char) (c)])
} // namespace muscle
#endif // alpha_h
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