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#ifndef ALPHABETS_H_ |
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#define ALPHABETS_H_ |
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|
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#include <stdexcept> |
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#include <string> |
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#include <seqan/sequence.h> |
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#include <sstream> |
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#include "assert_helpers.h" |
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|
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using namespace std; |
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using namespace seqan; |
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|
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/** |
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* Helper function to print a uint32_t as a DNA string where each 2-bit |
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* stretch is a character and more significiant bits appear to the left |
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* of less singificant bits. |
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*/ |
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static inline std::string u32ToDna(uint32_t a, int len) { |
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char buf[17]; // TODO: return a new string; by value I guess |
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assert_leq(len, 16); |
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for(int i = 0; i < len; i++) { |
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buf[len-i-1] = "ACGT"[a & 3]; |
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a >>= 2; |
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} |
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buf[len] = '\0'; |
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return std::string(buf); |
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} |
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|
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/** |
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* Return a new TStr containing the reverse-complement of s. |
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*/ |
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template<typename TStr> |
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static inline TStr reverseComplement(const TStr& s) { |
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typedef typename Value<TStr>::Type TVal; |
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TStr s_rc; |
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size_t slen = length(s); |
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resize(s_rc, slen); |
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for(size_t i = 0; i < slen; i++) { |
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int sv = (int)s[slen-i-1]; |
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if(sv == 4) { |
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s_rc[i] = (TVal)4; |
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} else { |
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s_rc[i] = (TVal)(sv ^ 3); |
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} |
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} |
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return s_rc; |
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} |
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|
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/// Reverse a string in-place |
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template <typename TStr> |
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static inline void reverseInPlace(TStr& s) { |
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typedef typename Value<TStr>::Type TVal; |
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size_t len = length(s); |
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for(size_t i = 0; i < (len>>1); i++) { |
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TVal tmp = s[i]; |
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s[i] = s[len-i-1]; |
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s[len-i-1] = tmp; |
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} |
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} |
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|
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/** |
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* Return the reverse-complement of s. |
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*/ |
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template<typename TStr> |
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static inline TStr reverseCopy(const TStr& s) { |
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typedef typename Value<TStr>::Type TVal; |
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TStr s_rc; |
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size_t slen = length(s); |
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resize(s_rc, slen); |
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for(size_t i = 0; i < slen; i++) { |
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s_rc[i] = (TVal)((int)s[slen-i-1]); |
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} |
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return s_rc; |
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} |
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|
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/** |
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* Return the reverse-complement of s. |
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*/ |
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static inline bool isReverseComplement(const String<Dna5>& s1, |
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const String<Dna5>& s2) |
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{ |
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if(length(s1) != length(s2)) return false; |
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size_t slen = length(s1); |
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for(size_t i = 0; i < slen; i++) { |
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int i1 = (int)s1[i]; |
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int i2 = (int)s2[slen - i - 1]; |
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if(i1 == 4) { |
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if(i2 != 4) return false; |
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} |
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else if(i1 != (i2 ^ 3)) return false; |
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} |
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return true; |
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} |
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|
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/** |
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* Return true iff the first string is dollar-less-than the second. |
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* This means that we pretend that a 'dollar sign' character, |
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* lexicographically larger than all other characters, exists at the |
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* end of both strings. |
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*/ |
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template <typename TStr> |
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static inline bool |
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dollarLt(const TStr& l, const TStr& r) { |
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return isPrefix(r, l) || (l < r && !isPrefix(l, r)); |
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} |
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|
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/** |
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* Return true iff the first string is dollar-greater-than the second. |
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* This means that we pretend that a 'dollar sign' character, |
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* lexicographically larger than all other characters, exists at the |
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* end of both strings. |
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*/ |
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template <typename TStr> |
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static inline bool |
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dollarGt(const TStr& l, const TStr& r) { |
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return !dollarLt(l, r); |
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} |
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|
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|
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extern uint8_t dna4Cat[]; |
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extern uint8_t charToDna5[]; |
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extern uint8_t rcCharToDna5[]; |
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|
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extern uint8_t dna4Cat[]; |
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extern uint8_t charToDna5[]; |
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extern uint8_t rcCharToDna5[]; |
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#endif /*ALPHABETS_H_*/ |
