+++ /dev/null
-#include "muscle.h"
-#include <ctype.h>
-
-/***
-From Bioperl docs:
-Extended DNA / RNA alphabet
-------------------------------------------
-Symbol Meaning Nucleic Acid
-------------------------------------------
- A A Adenine
- C C Cytosine
- G G Guanine
- T T Thymine
- U U Uracil
- M A or C
- R A or G
- W A or T
- S C or G
- Y C or T
- K G or T
- V A or C or G
- H A or C or T
- D A or G or T
- B C or G or T
- X G or A or T or C
- N G or A or T or C
-
-IUPAC-IUB SYMBOLS FOR NUCLEOTIDE NOMENCLATURE:
- Cornish-Bowden (1985) Nucl. Acids Res. 13: 3021-3030.
-***/
-
-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_RNA:
- case ALPHA_DNA:
- 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 SetAlphaDNA()
- {
- Res('A', NX_A)
- Res('C', NX_C)
- Res('G', NX_G)
- Res('T', NX_T)
- Wild('M', NX_M)
- Wild('R', NX_R)
- Wild('W', NX_W)
- Wild('S', NX_S)
- Wild('Y', NX_Y)
- Wild('K', NX_K)
- Wild('V', NX_V)
- Wild('H', NX_H)
- Wild('D', NX_D)
- Wild('B', NX_B)
- Wild('X', NX_X)
- Wild('N', NX_N)
- }
-
-static void SetAlphaRNA()
- {
- Res('A', NX_A)
- Res('C', NX_C)
- Res('G', NX_G)
- Res('U', NX_U)
- Res('T', NX_T)
- Wild('M', NX_M)
- Wild('R', NX_R)
- Wild('W', NX_W)
- Wild('S', NX_S)
- Wild('Y', NX_Y)
- Wild('K', NX_K)
- Wild('V', NX_V)
- Wild('H', NX_H)
- Wild('D', NX_D)
- Wild('B', NX_B)
- Wild('X', NX_X)
- Wild('N', NX_N)
- }
-
-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_DNA:
- SetAlphaDNA();
-
- case ALPHA_RNA:
- SetAlphaRNA();
- break;
-
- default:
- Quit("Invalid Alpha=%d", Alpha);
- }
-
- g_AlphaSize = GetAlphaSize(Alpha);
- g_Alpha = Alpha;
-
- if (g_bVerbose)
- Log("Alphabet %s\n", ALPHAToStr(g_Alpha));
- }
-
-char GetWildcardChar()
- {
- switch (g_Alpha)
- {
- case ALPHA_Amino:
- return 'X';
-
- case ALPHA_DNA:
- case ALPHA_RNA:
- return 'N';
-
- default:
- Quit("Invalid Alpha=%d", g_Alpha);
- }
- return '?';
- }
-
-bool IsNucleo(char c)
- {
- return strchr("ACGTURYNacgturyn", c) != 0;
- }
-
-bool IsDNA(char c)
- {
- return strchr("AGCTNagctn", c) != 0;
- }
-
-bool IsRNA(char c)
- {
- return strchr("AGCUNagcun", c) != 0;
- }
-
-static char InvalidLetters[256];
-static int InvalidLetterCount = 0;
-
-void ClearInvalidLetterWarning()
- {
- memset(InvalidLetters, 0, 256);
- }
-
-void InvalidLetterWarning(char c, char w)
- {
- InvalidLetters[(unsigned char) c] = 1;
- ++InvalidLetterCount;
- }
-
-void ReportInvalidLetters()
- {
- if (0 == InvalidLetterCount)
- return;
-
- char Str[257];
- memset(Str, 0, 257);
-
- int n = 0;
- for (int i = 0; i < 256; ++i)
- {
- if (InvalidLetters[i])
- Str[n++] = (char) i;
- }
- Warning("Assuming %s (see -seqtype option), invalid letters found: %s",
- ALPHAToStr(g_Alpha), Str);
- }
git://source.jalview.org / jabaws.git / blobdiff