+++ /dev/null
-/*
- *
- * Beta.hpp
- *
- */
-#ifndef BETA_HPP
-#define BETA_HPP
-using namespace std;
-
-struct Beta {
- static const int NBASE = 4;// A, C, G, U
- static const int NBASEG = (NBASE + 1); // A, C, G, U, Gap
- static const int NBASENG = (NBASE + 2); // A, C, G, U, N, Gap
- static const int NPBASE = (NBASE * NBASE);
- static const int NPBASEG = (NBASEG * NBASEG);
- static const int NPBASENG = (NBASENG * NBASENG);
- static const int NCODE = 7;
- static const int BASEBIT = 2;
- static const int BASEMSK = ~(~0 << BASEBIT);
- enum BaseCode {
- A_CODE = 0,
- C_CODE = 1,
- G_CODE = 2,
- U_CODE = 3,
- N_CODE = 4,
- GAP_CODE = 5,
- INVALID_CODE = 16
- };
- enum PairCode {
- AA_CODE = 0, AC_CODE = 1, AG_CODE = 2, AU_CODE = 3,
- CA_CODE = 4, CC_CODE = 5, CG_CODE = 6, CU_CODE = 7,
- GA_CODE = 8, GC_CODE = 9, GG_CODE = 10, GU_CODE = 11,
- UA_CODE = 12, UC_CODE = 13, UG_CODE = 14, UU_CODE = 15,
- INVALID_PAIR_CODE = 16
- };
- enum ReducedPairCode {
- REDUCED_NPBASE = 7,
- REDUCED_AU_CODE = 0,
- REDUCED_CG_CODE = 1,
- REDUCED_GC_CODE = 2,
- REDUCED_GU_CODE = 3,
- REDUCED_UA_CODE = 4,
- REDUCED_UG_CODE = 5,
- REDUCED_MM_CODE = 6,
- REDUCED_INVALID_PAIR_CODE = 16
- };
-
- static const int N_CANONICAL = 6;
- static const int canonicalPairs[N_CANONICAL];
- static const int N_NON_CANONICAL = 10;
- static const int nonCanonicalPairs[N_NON_CANONICAL];
- static const int i2nt[NCODE];
- static const int nt2i[256];
- static const bool isCanonicalBasePair[NPBASE];
-
- static bool IsValidCode(const int& c) {return A_CODE <= c && c <= GAP_CODE;}
- static bool IsBaseCode(const int& c) {return (A_CODE <= c && c <= U_CODE);}
- static bool IsBasePairCode(const int& c){return (AA_CODE <= c && c <= UU_CODE);}
- static bool IsReducedBasePairCode(const int& c) {
- return (REDUCED_AU_CODE <= c && c <= REDUCED_MM_CODE);
- }
- static bool IsAmbiguousCode(const int& c) {return c == N_CODE;}
- static bool IsGapCode(const int& c) {return c == GAP_CODE;}
- static bool IsValidChar(const unsigned char& c) {
- return IsValidCode(nt2i[c]);
- }
- static bool IsBaseChar(const int& c) {return IsBaseCode(nt2i[c]);}
- static bool IsAmbiguousChar(const int& c) {return IsAmbiguousCode(nt2i[c]);}
- static bool IsGapChar(const int& c) {return IsGapCode(nt2i[c]);}
- static int nt2code(const int& nt) {
- if (0 <= nt && nt < 256) {
- return nt2i[nt];
- } else {
- return INVALID_CODE;
- }
- }
- static int getPairCode(const int& c, const int& c1) {
- return (IsBaseCode(c) && IsBaseCode(c1)
- ? ((c << BASEBIT) | c1)
- : INVALID_PAIR_CODE);
- }
- static bool isValidPairCode(const int& pairCode) {
- return (0 <= pairCode && pairCode < NPBASE);
- }
- static void pair2Bases(const int& pairCode, int& c, int& c1) {
- //Assert(IsBasePairCode(pairCode));
- c1 = pairCode & BASEMSK;
- c = (pairCode >> BASEBIT) & BASEMSK;
- }
- static int getReducedPairCode(const int& c, const int& c1) {
- return reducePairCode(getPairCode(c, c1));
- }
- static int reducePairCode(const int& pairCode) {
- static const int table[NPBASE] = {
- REDUCED_MM_CODE, REDUCED_MM_CODE, REDUCED_MM_CODE, REDUCED_AU_CODE,
- REDUCED_MM_CODE, REDUCED_MM_CODE, REDUCED_CG_CODE, REDUCED_MM_CODE,
- REDUCED_MM_CODE, REDUCED_GC_CODE, REDUCED_MM_CODE, REDUCED_GU_CODE,
- REDUCED_UA_CODE, REDUCED_MM_CODE, REDUCED_UG_CODE, REDUCED_MM_CODE,
- };
- return (IsBasePairCode(pairCode)
- ? table[pairCode]
- : REDUCED_INVALID_PAIR_CODE);
- }
- static bool isValidReducedPairCode(const int& pairCode) {
- return (0 <= pairCode && pairCode < REDUCED_NPBASE);
- }
- static bool isCanonicalReducedPairCode(const int& pairCode) {
- return (REDUCED_AU_CODE <= pairCode
- && pairCode <= REDUCED_UG_CODE);
- }
- static int flipReducedPairCode(const int& reducedPairCode) {
- static const int table[REDUCED_NPBASE + 1] = {
- REDUCED_UA_CODE,
- REDUCED_GC_CODE,
- REDUCED_CG_CODE,
- REDUCED_UG_CODE,
- REDUCED_AU_CODE,
- REDUCED_GU_CODE,
- REDUCED_MM_CODE,
- REDUCED_INVALID_PAIR_CODE
- };
- return (IsReducedBasePairCode(reducedPairCode)
- ? table[reducedPairCode] : table[REDUCED_NPBASE]);
- }
- static void seq2i(char* s, const char* t, int len) {
- const char* const s_end = s + len;
- while (s < s_end) *s++ = nt2i[(unsigned) (*t++)];
- }
- static void i2seq(char* s, const char* t, int len) {
- const char* const s_end = s + len;
- while (s < s_end) *s++ = i2nt[(unsigned) (*t++)];
- }
- static void i2seq(ostream& fo, const char* t, int len) {
- const char* const t_end = t + len;
- while (t < t_end) fo << (char) i2nt[(unsigned) (*t++)];
- }
- static char* wd2str(unsigned int wdSize, unsigned int wd) {
- const unsigned int MAX_WD_SIZE = (sizeof(unsigned int) * 8 / BASEBIT);
- static char buf[MAX_WD_SIZE + 1] = {};
- //Assert(wdSize <= MAX_WD_SIZE);
-
- char* s = buf + wdSize;
- *s = '\0';
- do {
- *(--s) = Beta::i2nt[wd & BASEMSK];
- wd >>= BASEBIT;
- } while (s > buf);
- return buf;
- }
- static void printWd(ostream& fo, unsigned int wdSize, unsigned int wd) {
- fo << wd2str(wdSize, wd);
- }
- static const char* code2str(const int& code) {
- static const char table[NBASENG+1][2] = {
- "A", "C", "G", "U", "N", ".", "?"
- };
- return ((A_CODE <= code && code <= GAP_CODE)
- ? table[code] : table[NBASENG]);
- }
- static const char* pairCode2str(const int& pairCode) {
- static const char table[NPBASE+1][3] = {
- "AA", "AC", "AG", "AU",
- "CA", "CC", "CG", "CU",
- "GA", "GC", "GG", "GU",
- "UA", "UC", "UG", "UU",
- "??"
- };
- return (IsBasePairCode(pairCode) ? table[pairCode] : table[NPBASE]);
- }
- static const char* reducedPairCode2str(const int& reducedPairCode) {
- static const char table[REDUCED_NPBASE+1][3] = {
- "AU", "CG", "GC", "GU", "UA", "UG", "MM", "??"
- };
- return (IsReducedBasePairCode(reducedPairCode)
- ? table[reducedPairCode] : table[REDUCED_NPBASE]);
- }
- static char nt2Code(const char& c){
- if (!IsValidChar(c)) { cerr << "character " << c << " is not valid"; }
-
- return (char) nt2i[(int) c];
- }
- static char code2char(const int& c) {
- static const char table[NBASENG+1] = {
- 'A', 'C', 'G', 'U', 'N', '.', '?'
- };
- return ((A_CODE <= c && c <= GAP_CODE)
- ? table[(int) c] : table[NBASENG]);
- }
- /*
- static string generateRandomRNA(const int& len) {
- static const char nt[5] = "ACGU";
- string rna(len, '\0');
- for (int i = 0; i < len; i++) {
- rna[i] = nt[Rand(4)];
- }
- return rna;
- }
- */
-};
-
-#endif
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