| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seeds/ |
| H A D | test_align_banded_chain_impl.cpp | 54 CharString seqV = "ACGATCGATCGACTGACT"; in testBandedChainAlignmentEmptyChain() local
87 DnaString seqV = "AAAAAAAAAAA"; in testBandedChainAlignmentOneSeed() local
112 DnaString seqV = "GGGGGAAAAAAAAAAAGGGGG"; in testBandedChainAlignmentOneSeed() local
147 DnaString seqV = "GGGGGCGTGCAAAAAAAAAAAGTAGCGGGGG"; in testBandedChainAlignmentOneSeed() local
217 DnaString seqV = "CGTGCAAAAAAAAAAAGTAGCGGGGG"; in testBandedChainAlignmentOneSeed() local
252 DnaString seqV = "CGTGCAAAAAAAAAAAGTAGCGGGGG"; in testBandedChainAlignmentOneSeed() local
287 DnaString seqV = "CGTGCAAAAAAAAAAAGTAGCGGGGG"; in testBandedChainAlignmentOneSeed() local
322 DnaString seqV = "CGTGCAAAAAAAAAAAGTAGCGGGGG"; in testBandedChainAlignmentOneSeed() local
357 DnaString seqV = "CCCCCGTGTGAAAAAAAAAAATCGAT"; in testBandedChainAlignmentOneSeed() local
402 DnaString seqV = "AAAAAAAAAAAGGGGGGGGGGCCCCCCCC"; in testBandedChainAlignmentTwoSeeds() local
[all …]
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
| H A D | test_align_alignment_operations.h | 49 Dna5String seqV = "CGAT" "CGAT"; in SEQAN_DEFINE_TEST() local
87 Dna5String seqV = "CGATT" "CGAT"; in SEQAN_DEFINE_TEST() local
126 Dna5String seqV = "CGAT" "CGAT"; in SEQAN_DEFINE_TEST() local
164 Dna5String seqV = "CGATCGATT"; in SEQAN_DEFINE_TEST() local
206 Dna5String seqV = "NNNGGNNAACGATCGATT"; in SEQAN_DEFINE_TEST() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align_parallel/ |
| H A D | test_align_parallel_wavefront_alignment.h | 58 DnaString seqV = "ACAGAGCGCGTACTGTCTGACGACGTATCCGCGCGGACTAGAAGGCTGGTGCCTCGTCCAACAAATAGAT" in SEQAN_DEFINE_TEST() local
100 DnaString seqV = "ACAGAGCGCGTACTGTCTGACGACGTATCCGCGCGGACTAGAAGGCTGGTGCCTCGTCCAACAAATAGAT" in SEQAN_DEFINE_TEST() local
148 DnaString seqV = "ACAGAGCGCGTACTGTCTGACGACGTATCCGCGCGGACTAGAAGGCTGGTGCCTCGTCCAACAAATAGAT" in SEQAN_DEFINE_TEST() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/seed_and_extend/ |
| H A D | example1.cpp | 14 CharString seqV = "thick BROWNIES for me!"; in main() local
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| H A D | solution1.cpp | 11 CharString seqV = "thick BROWNIES for me!"; in main() local
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| H A D | example2.cpp | 15 CharString seqV = "thick BROWN boxes of brownies!"; in main() local
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| H A D | solution2.cpp | 12 CharString seqV = "thick BROWN boxes of brownies!"; in main() local
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| H A D | example3.cpp | 16 CharString seqV = "thick BROWN boxes of brownies!"; in main() local
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| H A D | solution3.cpp | 13 CharString seqV = "thick BROWN boxes of brownies!"; in main() local
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| H A D | example5.cpp | 17 Dna5String seqV; in main() local
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| H A D | solution4.cpp | 14 Dna5String seqV; in main() local
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
| H A D | global_alignment_specialized.h | 136 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
162 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
185 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
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| H A D | local_alignment_banded_waterman_eggert_impl.h | 71 TSequenceV const & seqV, in _alignBandedSmithWaterman()
205 TSequenceV const & seqV, in _alignBandedSmithWatermanDeclump()
371 TSequenceV const & seqV, in _alignBandedSmithWatermanTrace()
477 TSequenceV const & seqV, in _initLocalAlignmentFinder()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | global_alignment_specialized.h | 136 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
162 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
185 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
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| H A D | local_alignment_banded_waterman_eggert_impl.h | 71 TSequenceV const & seqV, in _alignBandedSmithWaterman()
205 TSequenceV const & seqV, in _alignBandedSmithWatermanDeclump()
371 TSequenceV const & seqV, in _alignBandedSmithWatermanTrace()
477 TSequenceV const & seqV, in _initLocalAlignmentFinder()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | global_alignment_specialized.h | 134 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
160 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
183 String<TAlphabetV, TSpecV> const & seqV, in globalAlignmentScore()
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| H A D | dp_algorithm_impl.h | 170 TSequenceV const & seqV, in _checkBandProperties()
221 TSequenceV const & seqV, in _isValidDPSettings()
454 TSequenceV const & seqV, in _computeUnbandedAlignment()
530 TSequenceV const & seqV, in _computeBandedAlignment()
1190 TSequenceV const & seqV, in _computeHammingDistance()
1384 TSequenceV const & seqV, in _computeAlignment()
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| /dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/align/ |
| H A D | global_alignment_unbanded.cpp | 12 Dna5String seqV = "CGAAATT"; in main() local
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| H A D | global_alignment_banded.cpp | 13 Dna5String seqV = "CGAAATT"; in main() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/align/ |
| H A D | global_alignment_unbanded.cpp | 12 Dna5String seqV = "CGAAATT"; in main() local
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| H A D | global_alignment_banded.cpp | 13 Dna5String seqV = "CGAAATT"; in main() local
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align_parallel/ |
| H A D | async_wave_execution_interface.h | 102 TSeqV const & seqV, in submit()
188 TSeqV const & seqV, in submit()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align_parallel/ |
| H A D | async_wave_execution_interface.h | 102 TSeqV const & seqV, in submit()
188 TSeqV const & seqV, in submit()
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| /dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/seeds/ |
| H A D | seeds_add_seed.cpp | 13 DnaString seqV = "ttccgACGTgTTCGAgACtgaGGTca"; in main() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/seeds/ |
| H A D | seeds_add_seed.cpp | 13 DnaString seqV = "ttccgACGTgTTCGAgACtgaGGTca"; in main() local
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