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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/modifier/
H A Dtest_modifier_alphabet.h73 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()
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H A Dtest_modifier_functors.h71 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()
H A Dtest_modifier_view.h264 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/yara/
H A Dbasic_alphabet.h55 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()
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/basic/
H A Dalphabet_residue.h137 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;
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/basic/
H A Dalphabet_residue.h137 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;
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/basic/
H A Dalphabet_residue.h137 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;
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/basic/
H A Dtest_basic_alphabet_residue.h131 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()
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H A Dtest_basic_iterator_concepts.h62 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()
H A Dtest_basic_alphabet.h394 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()
/dports/biology/seqan1/seqan-1.3.1/seqan/modifier/
H A Dmodifier_functors.h153 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)];
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/modifier/
H A Dmodifier_functors.h219 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)];
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/modifier/
H A Dmodifier_functors.h219 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)];
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/modifier/
H A Dmodifier_functors.h219 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)];
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/index/
H A Dtest_index_fm_right_array_binary_tree_iterator.h596 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 …]
H A Dtest_index_fm_rank_dictionary.cpp81 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>,
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/howto/scores/
H A Dinit_score.cpp47 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()
/dports/biology/seqan1/seqan-1.3.1/seqan/basic/
H A Dbasic_alphabet_simple.h1332 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);
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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/find/
H A Dfind_hamming_simple.h149 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/find/
H A Dfind_hamming_simple.h149 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()
/dports/biology/seqan1/seqan-1.3.1/seqan/find/
H A Dfind_hamming_simple.h168 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()
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/find/
H A Dfind_hamming_simple.h168 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/
H A Dcasbar_score_data.h18 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,
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/indices/
H A Dassignment_2.cpp8 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()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/sequences/
H A Dassignment_3_solution.cpp9 String<Dna5> nucleotides = "AGTCGTGNNANCT"; in main()
10 String<Dna5> lesser; in main()
11 String<Dna5> greater; in main()

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