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@ -27,6 +27,7 @@ |
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namespace dna |
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namespace dna |
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{ |
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{ |
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/// Standard genetic code translation table.
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constexpr char* standard_code = |
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constexpr char* standard_code = |
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"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" // Amino acid
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"FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" // Amino acid
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"---M------**--*----M---------------M----------------------------" // Start/stop
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"---M------**--*----M---------------M----------------------------" // Start/stop
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@ -42,6 +43,116 @@ constexpr char* standard_code = |
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* @param d_first Beginning of the destination range. |
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* @param d_first Beginning of the destination range. |
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* @return Output iterator to the amino acid in the destination range, one past the last amino acid translated. |
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* @return Output iterator to the amino acid in the destination range, one past the last amino acid translated. |
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*/ |
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*/ |
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template <class InputIt1, class InputIt2, class OutputIt> |
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OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_first); |
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/**
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* Finds the first start codon in a sequence of bases. |
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* |
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* @param first,last Range of bases to search. |
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* @param t_first Beginning of the translation table. |
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* @return Iterator to the first base of the first start codon in the sequence, or @p last if no start codon is found. |
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*/ |
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template <class ForwardIt1, class ForwardIt2> |
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ForwardIt1 find_start(ForwardIt1 first, ForwardIt1 last, ForwardIt2 t_first); |
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/**
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* Finds the first stop codon in a sequence of codons. |
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* |
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* @param first,last Range of codons to search. |
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* @param t_first Beginning of the translation table. |
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* @return Iterator to the first base of the first stop codon in the sequence, or @p last if no stop codon is found. |
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*/ |
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template <class ForwardIt1, class ForwardIt2> |
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ForwardIt1 find_stop(ForwardIt1 first, ForwardIt1 last, ForwardIt2 t_first); |
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template <class ForwardIt1, class ForwardIt2> |
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ForwardIt1 find_start(ForwardIt1 first, ForwardIt1 last, ForwardIt2 t_first) |
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{ |
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ForwardIt1 second = first; |
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++second; |
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ForwardIt1 third = second; |
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++third; |
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ForwardIt2 start_first = t_first; |
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std::advance(start_first, 64); |
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ForwardIt2 base1_first = start_first; |
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std::advance(base1_first, 64); |
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ForwardIt2 base2_first = base1_first; |
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std::advance(base2_first, 64); |
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ForwardIt2 base3_first = base2_first; |
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std::advance(base3_first, 64); |
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if (first != last && second != last) |
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{ |
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while (third != last) |
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{ |
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ForwardIt2 start = start_first; |
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ForwardIt2 base1 = base1_first; |
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ForwardIt2 base2 = base2_first; |
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ForwardIt2 base3 = base3_first; |
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for (std::uint_fast8_t i = 64; i; --i) |
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{ |
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if (*start != '-' && *start != '*' && *first == *base1 && *second == *base2 && *third == *base3) |
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return first; |
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++start; |
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++base1; |
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++base2; |
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++base3; |
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} |
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first = second; |
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second = third; |
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++third; |
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} |
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} |
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return last; |
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} |
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template <class ForwardIt1, class ForwardIt2> |
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ForwardIt1 find_stop(ForwardIt1 first, ForwardIt1 last, ForwardIt2 t_first) |
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{ |
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ForwardIt1 second = first; |
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++second; |
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ForwardIt1 third = second; |
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++third; |
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ForwardIt2 base1_first = t_first; |
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std::advance(base1_first, 128); |
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ForwardIt2 base2_first = base1_first; |
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std::advance(base2_first, 64); |
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ForwardIt2 base3_first = base2_first; |
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std::advance(base3_first, 64); |
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while (first != last && second != last && third != last) |
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{ |
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ForwardIt2 aa = t_first; |
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ForwardIt2 base1 = base1_first; |
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ForwardIt2 base2 = base2_first; |
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ForwardIt2 base3 = base3_first; |
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for (std::uint_fast8_t i = 64; i; --i) |
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{ |
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if (*aa == '*' && *first == *base1 && *second == *base2 && *third == *base3) |
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return first; |
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++aa; |
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++base1; |
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++base2; |
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++base3; |
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} |
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first = ++third; |
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second = ++third; |
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++third; |
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} |
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return last; |
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} |
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template <class InputIt1, class InputIt2, class OutputIt> |
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template <class InputIt1, class InputIt2, class OutputIt> |
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OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_first) |
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OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_first) |
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{ |
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{ |
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@ -64,7 +175,7 @@ OutputIt translate(InputIt1 first, InputIt1 last, InputIt2 t_first, OutputIt d_f |
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InputIt2 base2 = base2_first; |
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InputIt2 base2 = base2_first; |
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InputIt2 base3 = base3_first; |
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InputIt2 base3 = base3_first; |
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for (std::uint_fast8_t i = 0; i < 64; ++i) |
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for (std::uint_fast8_t i = 64; i; --i) |
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{ |
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{ |
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if (*first == *base1 && *second == *base2 && *third == *base3) |
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if (*first == *base1 && *second == *base2 && *third == *base3) |
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{ |
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{ |
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