/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/modifier/ |
H A D | test_modifier_alphabet.h | 73 SEQAN_ASSERT_EQ(Dna5('A'), convert<Dna5>(TDna5QWithGap('A'))); in SEQAN_DEFINE_TEST() 74 SEQAN_ASSERT_EQ(Dna5('C'), convert<Dna5>(TDna5QWithGap('C'))); in SEQAN_DEFINE_TEST() 75 SEQAN_ASSERT_EQ(Dna5('G'), convert<Dna5>(TDna5QWithGap('G'))); in SEQAN_DEFINE_TEST() 76 SEQAN_ASSERT_EQ(Dna5('T'), convert<Dna5>(TDna5QWithGap('T'))); in SEQAN_DEFINE_TEST() 77 SEQAN_ASSERT_EQ(Dna5('N'), convert<Dna5>(Dna5Q('N'))); in SEQAN_DEFINE_TEST() 78 SEQAN_ASSERT_EQ(Dna5('N'), convert<Dna5>(TDna5QWithGap('N'))); in SEQAN_DEFINE_TEST() 86 SEQAN_ASSERT_EQ(Dna5('T'), convert<Dna5>(TDnaQWithX('T'))); in SEQAN_DEFINE_TEST() 208 SEQAN_ASSERT(TDnaWithX('A') == Dna5('A')); in SEQAN_DEFINE_TEST() 336 SEQAN_ASSERT(TDnaWithX('A') < Dna5('C')); in SEQAN_DEFINE_TEST() 337 SEQAN_ASSERT(Dna5('A') < TDnaWithX('C')); in SEQAN_DEFINE_TEST() [all …]
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H A D | test_modifier_functors.h | 71 seqan::FunctorComplement<seqan::Dna5> func; in SEQAN_DEFINE_TEST() 73 SEQAN_ASSERT_EQ(seqan::Dna5('C'), func(seqan::Dna5('G'))); in SEQAN_DEFINE_TEST() 74 SEQAN_ASSERT_EQ(seqan::Dna5('G'), func(seqan::Dna5('C'))); in SEQAN_DEFINE_TEST() 75 SEQAN_ASSERT_EQ(seqan::Dna5('A'), func(seqan::Dna5('T'))); in SEQAN_DEFINE_TEST() 76 SEQAN_ASSERT_EQ(seqan::Dna5('T'), func(seqan::Dna5('A'))); in SEQAN_DEFINE_TEST() 77 SEQAN_ASSERT_EQ(seqan::Dna5('N'), func(seqan::Dna5('N'))); in SEQAN_DEFINE_TEST()
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H A D | test_modifier_view.h | 264 typedef FunctorConvert<char, Dna5> TFunctor; in SEQAN_DEFINE_TEST() 313 ModifiedString< Dna5String, ModView< FunctorComplement<Dna5> > >, in SEQAN_DEFINE_TEST() 319 ModView< FunctorComplement<Dna5> > in SEQAN_DEFINE_TEST() 332 ModifiedString< Dna5String const, ModView< FunctorComplement<Dna5> > >, in SEQAN_DEFINE_TEST() 338 ModView< FunctorComplement<Dna5> > in SEQAN_DEFINE_TEST() 342 ModifiedString< Dna5String const, ModView< FunctorComplement<Dna5> > > const, in SEQAN_DEFINE_TEST() 348 ModView< FunctorComplement<Dna5> > in SEQAN_DEFINE_TEST() 353 ModView< FunctorComplement<Dna5> > in SEQAN_DEFINE_TEST() 358 ModView< FunctorComplement<Dna5> > in SEQAN_DEFINE_TEST()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/ |
H A D | basic_alphabet.h | 55 inline bool operator==(Dna5 const & left_, Dna5Q const & right_) 61 inline bool operator==(Dna5Q const & left_, Dna5 const & right_) 67 inline bool operator!=(Dna5 const & left_, Dna5Q const & right_) 73 inline bool operator!=(Dna5Q const & left_, Dna5 const & right_) 79 inline bool operator<(Dna5 const & left_, Dna5Q const & right_) 85 inline bool operator<(Dna5Q const & left_, Dna5 const & right_) 91 inline bool operator>(Dna5 const & left_, Dna5Q const & right_) 97 inline bool operator>(Dna5Q const & left_, Dna5 const & right_) 135 inline bool ordLess(Dna5 const & left_, Dna5 const & right_) in ordLess() 141 inline bool ordEqual(Dna5 const & left_, Dna5 const & right_) in ordEqual() [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/basic/ |
H A D | alphabet_residue.h | 137 struct ValueSize<Dna5> 150 inline Dna5 151 unknownValueImpl(Dna5 *) 153 static const Dna5 _result = Dna5('N'); 315 typedef Dna5 Type; 703 typedef Dna5 Type; 714 typedef Dna5 Type; 725 typedef Dna5 Type; 1165 typedef Dna5 Type; 1217 typedef Dna5 Type; [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/basic/ |
H A D | alphabet_residue.h | 137 struct ValueSize<Dna5> 150 inline Dna5 151 unknownValueImpl(Dna5 *) 153 static const Dna5 _result = Dna5('N'); 315 typedef Dna5 Type; 703 typedef Dna5 Type; 714 typedef Dna5 Type; 725 typedef Dna5 Type; 1165 typedef Dna5 Type; 1217 typedef Dna5 Type; [all …]
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/basic/ |
H A D | alphabet_residue.h | 137 struct ValueSize<Dna5> 150 inline Dna5 151 unknownValueImpl(Dna5 *) 153 static const Dna5 _result = Dna5('N'); 315 typedef Dna5 Type; 707 typedef Dna5 Type; 718 typedef Dna5 Type; 733 typedef Dna5 Type; 1162 typedef Dna5 Type; 1214 typedef Dna5 Type; [all …]
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/basic/ |
H A D | test_basic_alphabet_residue.h | 131 SEQAN_ASSERT_EQ(std::numeric_limits<Dna5>::max(), Dna5('N')); in SEQAN_DEFINE_TEST() 132 SEQAN_ASSERT_EQ(std::numeric_limits<Dna5>::min(), Dna5('A')); in SEQAN_DEFINE_TEST() 148 SEQAN_ASSERT_EQ(unknownValue<Dna5>(), Dna5('N')); in SEQAN_DEFINE_TEST() 293 char x = Dna5(i); in SEQAN_DEFINE_TEST() 500 Dna5 a = 'A', n = 'N'; in SEQAN_DEFINE_TEST() 502 SEQAN_ASSERT_EQ(++a, Dna5('C')); in SEQAN_DEFINE_TEST() 503 SEQAN_ASSERT_EQ(a, Dna5('C')); in SEQAN_DEFINE_TEST() 505 SEQAN_ASSERT_EQ(a, Dna5('G')); in SEQAN_DEFINE_TEST() 508 SEQAN_ASSERT_EQ(n, Dna5('T')); in SEQAN_DEFINE_TEST() 510 SEQAN_ASSERT_EQ(n, Dna5('G')); in SEQAN_DEFINE_TEST() [all …]
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H A D | test_basic_iterator_concepts.h | 62 SEQAN_CONCEPT_ASSERT((AlphabetConcept<Dna5>)); in testAlphabetConcepts() 89 SEQAN_CONCEPT_ASSERT((OrderedAlphabetConcept<Dna5>)); in testOrderedAlphabetConcepts() 112 SEQAN_CONCEPT_ASSERT((FiniteOrderedAlphabetConcept<Dna5>)); in testFiniteOrderedAlphabetConcepts() 141 SEQAN_CONCEPT_ASSERT((AlphabetWithUnknownValueConcept<Dna5>)); in testAlphabetWithUnknownValueConcept()
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H A D | test_basic_alphabet.h | 394 TestConversion<char, Dna5>(); in SEQAN_DEFINE_TEST() 404 TestConversion<Dna, Dna5>(); in SEQAN_DEFINE_TEST() 407 TestConversion<Dna5, char>(); in SEQAN_DEFINE_TEST() 408 TestConversion<Dna5, uint8_t>(); in SEQAN_DEFINE_TEST() 409 TestConversion<Dna5, Unicode>(); in SEQAN_DEFINE_TEST() 410 TestConversion<Dna5, Dna>(); in SEQAN_DEFINE_TEST() 411 TestConversion<Dna5, Iupac>(); in SEQAN_DEFINE_TEST() 428 TestConversion<Iupac, Dna5>(); in SEQAN_DEFINE_TEST() 510 TestSimpleType<Dna5>(); in SEQAN_DEFINE_TEST()
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/dports/biology/seqan1/seqan-1.3.1/seqan/modifier/ |
H A D | modifier_functors.h | 153 struct FunctorComplement<char> : public ::std::unary_function<Dna5,Dna5> 155 inline Dna5 operator()(Dna5 x) const { 172 struct FunctorComplement<Dna5> : public ::std::unary_function<Dna5,Dna5> 174 inline Dna5 operator()(Dna5 x) const { 194 inline Dna5 operator()(Rna5 x) const { 220 x = TranslateTableDna5ToDna5Complement_<>::VALUE[ordValue((Dna5)x)];
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/modifier/ |
H A D | modifier_functors.h | 219 struct FunctorComplement<char> : public std::unary_function<Dna5,Dna5> 221 inline Dna5 operator()(Dna5 x) const 237 struct FunctorComplement<Dna5> : public std::unary_function<Dna5,Dna5> 239 inline Dna5 operator()(Dna5 x) const 257 inline Dna5 operator()(Rna5 x) const 280 x = TranslateTableDna5ToDna5Complement_<>::VALUE[ordValue((Dna5)x)];
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/modifier/ |
H A D | modifier_functors.h | 219 struct FunctorComplement<char> : public std::unary_function<Dna5,Dna5> 221 inline Dna5 operator()(Dna5 x) const 237 struct FunctorComplement<Dna5> : public std::unary_function<Dna5,Dna5> 239 inline Dna5 operator()(Dna5 x) const 257 inline Dna5 operator()(Rna5 x) const 280 x = TranslateTableDna5ToDna5Complement_<>::VALUE[ordValue((Dna5)x)];
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/modifier/ |
H A D | modifier_functors.h | 219 struct FunctorComplement<char> : public std::unary_function<Dna5,Dna5> 221 inline Dna5 operator()(Dna5 x) const 237 struct FunctorComplement<Dna5> : public std::unary_function<Dna5,Dna5> 239 inline Dna5 operator()(Dna5 x) const 257 inline Dna5 operator()(Rna5 x) const 280 x = TranslateTableDna5ToDna5Complement_<>::VALUE[ordValue((Dna5)x)];
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/index/ |
H A D | test_index_fm_right_array_binary_tree_iterator.h | 596 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 606 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 616 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 626 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 636 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 646 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 656 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 666 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 676 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() 686 RightArrayBinaryTree<Dna5, void> waveletTreeStructure; in SEQAN_DEFINE_TEST() [all …]
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H A D | test_index_fm_rank_dictionary.cpp | 81 TagList<RankDictionary<Dna5, Prefix1Level>, 87 TagList<RankDictionary<Dna5, Prefix2Level>, 93 TagList<RankDictionary<Dna5, Prefix3Level>, 99 TagList<RankDictionary<Dna5, WaveletTree<> >, 110 TagList<RankDictionary<Dna5, Default1Level>, 116 TagList<RankDictionary<Dna5, Default2Level>, 117 TagList<RankDictionary<Dna5, Default2Level>, 122 TagList<RankDictionary<Dna5, Default3Level>,
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/howto/scores/ |
H A D | init_score.cpp | 47 struct ScoringMatrixData_<int, Dna5, UserDefinedMatrix> 51 VALUE_SIZE = ValueSize<Dna5>::VALUE, 102 typedef Score<TValue, ScoreMatrix<Dna5, Default> > TScoringScheme; in main() 121 for (unsigned i = 0; i < ValueSize<Dna5>::VALUE; ++i) in main() 123 for (unsigned j = 0; j < ValueSize<Dna5>::VALUE; ++j) in main() 125 setScore(scoringScheme, Dna5(i), Dna5(j), i * j); in main() 137 Score<TValue, ScoreMatrix<Dna5, UserDefinedMatrix> > userScoringSchemeDna; in main()
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/dports/biology/seqan1/seqan-1.3.1/seqan/basic/ |
H A D | basic_alphabet_simple.h | 1332 struct CompareType<Dna5, __uint8> { typedef Dna5 Type; }; 1341 struct CompareType<Dna5, Ascii> { typedef Dna5 Type; }; 1350 struct CompareType<Dna5, Unicode> { typedef Dna5 Type; }; 1359 struct CompareType<Dna5, Iupac> { typedef Dna5 Type; }; 1592 typedef Dna5 Type; 1699 struct CompareType<Dna5, Dna5Q> { typedef Dna5 Type; }; 1731 struct CompareType<Dna5Q, Dna5> { typedef Dna5 Type; }; 1845 struct CompareType<Dna5, DnaQ> { typedef Dna5 Type; }; 2080 c_target = Dna5(source); 2088 c_target = Dna5(source); [all …]
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/find/ |
H A D | find_hamming_simple.h | 149 inline bool _findHammingSimpleCharsEqual(Dna5 const & ndlChar, Dna5 const & hstckChar, Pattern<TNee… in _findHammingSimpleCharsEqual() 150 if (ndlChar == Dna5('N') && pattern.matchNFlags & 1) { in _findHammingSimpleCharsEqual() 152 } else if (hstckChar == Dna5('N') && pattern.matchNFlags & 2) { in _findHammingSimpleCharsEqual() 161 inline bool _findHammingSimpleCharsEqual(Dna5Q const & a, Dna5 const & b, Pattern<TNeedle, HammingS… in _findHammingSimpleCharsEqual() 162 return _findHammingSimpleCharsEqual(convert<Dna5>(a), b, pattern); in _findHammingSimpleCharsEqual() 167 inline bool _findHammingSimpleCharsEqual(Dna5 const & a, Dna5Q const & b, Pattern<TNeedle, HammingS… in _findHammingSimpleCharsEqual() 168 return _findHammingSimpleCharsEqual(a, convert<Dna5>(b), pattern); in _findHammingSimpleCharsEqual() 174 return _findHammingSimpleCharsEqual(convert<Dna5>(a), convert<Dna5>(b), pattern); in _findHammingSimpleCharsEqual()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/find/ |
H A D | find_hamming_simple.h | 149 inline bool _findHammingSimpleCharsEqual(Dna5 const & ndlChar, Dna5 const & hstckChar, Pattern<TNee… in _findHammingSimpleCharsEqual() 150 if (ndlChar == Dna5('N') && pattern.matchNFlags & 1) { in _findHammingSimpleCharsEqual() 152 } else if (hstckChar == Dna5('N') && pattern.matchNFlags & 2) { in _findHammingSimpleCharsEqual() 161 inline bool _findHammingSimpleCharsEqual(Dna5Q const & a, Dna5 const & b, Pattern<TNeedle, HammingS… in _findHammingSimpleCharsEqual() 162 return _findHammingSimpleCharsEqual(convert<Dna5>(a), b, pattern); in _findHammingSimpleCharsEqual() 167 inline bool _findHammingSimpleCharsEqual(Dna5 const & a, Dna5Q const & b, Pattern<TNeedle, HammingS… in _findHammingSimpleCharsEqual() 168 return _findHammingSimpleCharsEqual(a, convert<Dna5>(b), pattern); in _findHammingSimpleCharsEqual() 174 return _findHammingSimpleCharsEqual(convert<Dna5>(a), convert<Dna5>(b), pattern); in _findHammingSimpleCharsEqual()
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/dports/biology/seqan1/seqan-1.3.1/seqan/find/ |
H A D | find_hamming_simple.h | 168 inline bool _findHammingSimpleCharsEqual(Dna5 const & ndlChar, Dna5 const & hstckChar, Pattern<TNee… in _findHammingSimpleCharsEqual() 169 if (ndlChar == Dna5('N') && pattern.matchNFlags & 1) { in _findHammingSimpleCharsEqual() 171 } else if (hstckChar == Dna5('N') && pattern.matchNFlags & 2) { in _findHammingSimpleCharsEqual() 180 inline bool _findHammingSimpleCharsEqual(Dna5Q const & a, Dna5 const & b, Pattern<TNeedle, HammingS… in _findHammingSimpleCharsEqual() 181 return _findHammingSimpleCharsEqual(convert<Dna5>(a), b, pattern); in _findHammingSimpleCharsEqual() 186 inline bool _findHammingSimpleCharsEqual(Dna5 const & a, Dna5Q const & b, Pattern<TNeedle, HammingS… in _findHammingSimpleCharsEqual() 187 return _findHammingSimpleCharsEqual(a, convert<Dna5>(b), pattern); in _findHammingSimpleCharsEqual() 193 return _findHammingSimpleCharsEqual(convert<Dna5>(a), convert<Dna5>(b), pattern); in _findHammingSimpleCharsEqual()
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/find/ |
H A D | find_hamming_simple.h | 168 inline bool _findHammingSimpleCharsEqual(Dna5 const & ndlChar, Dna5 const & hstckChar, Pattern<TNee… in _findHammingSimpleCharsEqual() 169 if (ndlChar == Dna5('N') && pattern.matchNFlags & 1) { in _findHammingSimpleCharsEqual() 171 } else if (hstckChar == Dna5('N') && pattern.matchNFlags & 2) { in _findHammingSimpleCharsEqual() 180 inline bool _findHammingSimpleCharsEqual(Dna5Q const & a, Dna5 const & b, Pattern<TNeedle, HammingS… in _findHammingSimpleCharsEqual() 181 return _findHammingSimpleCharsEqual(convert<Dna5>(a), b, pattern); in _findHammingSimpleCharsEqual() 186 inline bool _findHammingSimpleCharsEqual(Dna5 const & a, Dna5Q const & b, Pattern<TNeedle, HammingS… in _findHammingSimpleCharsEqual() 187 return _findHammingSimpleCharsEqual(a, convert<Dna5>(b), pattern); in _findHammingSimpleCharsEqual() 193 return _findHammingSimpleCharsEqual(convert<Dna5>(a), convert<Dna5>(b), pattern); in _findHammingSimpleCharsEqual()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/ |
H A D | casbar_score_data.h | 18 VALUE_SIZE = ValueSize<Dna5>::VALUE, 42 VALUE_SIZE = ValueSize<Dna5>::VALUE, 69 VALUE_SIZE = ValueSize<Dna5>::VALUE, 84 VALUE_SIZE = ValueSize<Dna5>::VALUE, 103 VALUE_SIZE = ValueSize<Dna5>::VALUE, 118 VALUE_SIZE = ValueSize<Dna5>::VALUE,
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/indices/ |
H A D | assignment_2.cpp | 8 String<Dna5> genome = "TTATTAAGCGTATAGCCCTATAAATATAA"; in main() 9 Index<String<Dna5>, IndexEsa<> > esaIndex(genome); in main() 10 Finder<Index<String<Dna5>, IndexEsa<> > > esaFinder(esaIndex); in main()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/sequences/ |
H A D | assignment_3_solution.cpp | 9 String<Dna5> nucleotides = "AGTCGTGNNANCT"; in main() 10 String<Dna5> lesser; in main() 11 String<Dna5> greater; in main()
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