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#include "muscle.h"
#include <ctype.h>
/***
Nucleotide alphabet is AGCUTRYN
T and U are equivalent in scoring etc.
R = purine (G or A)
Y = pyrimidine (C or T/U)
N = any
***/
unsigned g_CharToLetter[MAX_CHAR];
unsigned g_CharToLetterEx[MAX_CHAR];
char g_LetterToChar[MAX_ALPHA];
char g_LetterExToChar[MAX_ALPHA_EX];
char g_UnalignChar[MAX_CHAR];
char g_AlignChar[MAX_CHAR];
bool g_IsWildcardChar[MAX_CHAR];
bool g_IsResidueChar[MAX_CHAR];
ALPHA g_Alpha = ALPHA_Undefined;
unsigned g_AlphaSize = 0;
#define Res(c, Letter) \
{ \
const unsigned char Upper = (unsigned char) toupper(c); \
const unsigned char Lower = (unsigned char) tolower(c); \
g_CharToLetter[Upper] = Letter; \
g_CharToLetter[Lower] = Letter; \
g_CharToLetterEx[Upper] = Letter; \
g_CharToLetterEx[Lower] = Letter; \
g_LetterToChar[Letter] = Upper; \
g_LetterExToChar[Letter] = Upper; \
g_IsResidueChar[Upper] = true; \
g_IsResidueChar[Lower] = true; \
g_AlignChar[Upper] = Upper; \
g_AlignChar[Lower] = Upper; \
g_UnalignChar[Upper] = Lower; \
g_UnalignChar[Lower] = Lower; \
}
#define Wild(c, Letter) \
{ \
const unsigned char Upper = (unsigned char) toupper(c); \
const unsigned char Lower = (unsigned char) tolower(c); \
g_CharToLetterEx[Upper] = Letter; \
g_CharToLetterEx[Lower] = Letter; \
g_LetterExToChar[Letter] = Upper; \
g_IsResidueChar[Upper] = true; \
g_IsResidueChar[Lower] = true; \
g_AlignChar[Upper] = Upper; \
g_AlignChar[Lower] = Upper; \
g_UnalignChar[Upper] = Lower; \
g_UnalignChar[Lower] = Lower; \
g_IsWildcardChar[Lower] = true; \
g_IsWildcardChar[Upper] = true; \
}
static unsigned GetAlphaSize(ALPHA Alpha)
{
switch (Alpha)
{
case ALPHA_Amino:
return 20;
case ALPHA_Nucleo:
return 4;
}
Quit("Invalid Alpha=%d", Alpha);
return 0;
}
static void InitArrays()
{
memset(g_CharToLetter, 0xff, sizeof(g_CharToLetter));
memset(g_CharToLetterEx, 0xff, sizeof(g_CharToLetterEx));
memset(g_LetterToChar, '?', sizeof(g_LetterToChar));
memset(g_LetterExToChar, '?', sizeof(g_LetterExToChar));
memset(g_AlignChar, '?', sizeof(g_UnalignChar));
memset(g_UnalignChar, '?', sizeof(g_UnalignChar));
memset(g_IsWildcardChar, 0, sizeof(g_IsWildcardChar));
}
static void SetGapChar(char c)
{
unsigned char u = (unsigned char) c;
g_CharToLetterEx[u] = AX_GAP;
g_LetterExToChar[AX_GAP] = u;
g_AlignChar[u] = u;
g_UnalignChar[u] = u;
}
static void SetAlphaNucleo()
{
Res('A', NX_A)
Res('C', NX_C)
Res('G', NX_G)
Res('U', NX_U)
Res('T', NX_T)
Wild('N', NX_N)
Wild('R', NX_R)
Wild('Y', NX_Y)
}
static void SetAlphaAmino()
{
Res('A', AX_A)
Res('C', AX_C)
Res('D', AX_D)
Res('E', AX_E)
Res('F', AX_F)
Res('G', AX_G)
Res('H', AX_H)
Res('I', AX_I)
Res('K', AX_K)
Res('L', AX_L)
Res('M', AX_M)
Res('N', AX_N)
Res('P', AX_P)
Res('Q', AX_Q)
Res('R', AX_R)
Res('S', AX_S)
Res('T', AX_T)
Res('V', AX_V)
Res('W', AX_W)
Res('Y', AX_Y)
Wild('B', AX_B)
Wild('X', AX_X)
Wild('Z', AX_Z)
}
void SetAlpha(ALPHA Alpha)
{
InitArrays();
SetGapChar('.');
SetGapChar('-');
switch (Alpha)
{
case ALPHA_Amino:
SetAlphaAmino();
break;
case ALPHA_Nucleo:
SetAlphaNucleo();
break;
default:
Quit("Invalid Alpha=%d", Alpha);
}
g_AlphaSize = GetAlphaSize(Alpha);
g_Alpha = Alpha;
}
char GetWildcardChar()
{
switch (g_Alpha)
{
case ALPHA_Amino:
return 'X';
case ALPHA_Nucleo:
return 'N';
default:
Quit("Invalid Alpha=%d", g_Alpha);
}
return '?';
}
bool IsNucleo(char c)
{
return strchr("ACGTURYNacgturyn", c) != 0;
}
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