--- /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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