| /dports/biology/seqan1/seqan-1.3.1/seqan/seeds/ |
| H A D | seed_multi.h | 108 leftDim0(Seed<TPosition, ChainedSeed> const &seed) in leftDim0()
139 length(Seed<TPosition, ChainedSeed> const & seed) in length()
149 setLeftDim0(Seed<TPosition, ChainedSeed> &seed, in setLeftDim0()
162 setRightDim0(Seed<TPosition,ChainedSeed> & seed, in setRightDim0()
172 setLeftDim1(Seed<TPosition, ChainedSeed> &seed, in setLeftDim1()
185 setRightDim1(Seed<TPosition,ChainedSeed> & seed, in setRightDim1()
211 _getDiagSet(Seed<TPosition,ChainedSeed> & seed){ in _getDiagSet()
230 appendDiag(Seed<TPosition,ChainedSeed> & seed, in appendDiag()
324 _mergeTwoSeeds(Seed<TPosition, ChainedSeed> &firstSeed, in _mergeTwoSeeds()
456 _mergeTwoSeedsScore(Seed<TPosition, ChainedSeed> &firstSeed, in _mergeTwoSeedsScore()
[all …]
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
| H A D | banded_chain_alignment.h | 195 typedef typename Position<TSequence>::Type TPosition; typedef
264 typedef typename Position<TSequenceH>::Type TPosition; typedef
340 typedef typename Position<TStringSet>::Type TPosition; typedef
414 typedef typename Position<TSequence>::Type TPosition; typedef
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
| H A D | banded_chain_alignment.h | 195 typedef typename Position<TSequence>::Type TPosition; typedef
264 typedef typename Position<TSequenceH>::Type TPosition; typedef
340 typedef typename Position<TStringSet>::Type TPosition; typedef
414 typedef typename Position<TSequence>::Type TPosition; typedef
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
| H A D | banded_chain_alignment.h | 195 typedef typename Position<TSequence>::Type TPosition; typedef
264 typedef typename Position<TSequenceH>::Type TPosition; typedef
340 typedef typename Position<TStringSet>::Type TPosition; typedef
414 typedef typename Position<TSequence>::Type TPosition; typedef
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
| H A D | dp_traceback_adaptor.h | 62 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
129 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
188 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
231 String<TraceSegment_<TPosition, TSize2>, TStringSpec2> const & traceSegments) in _adaptTraceSegmentsTo()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | dp_traceback_adaptor.h | 62 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
129 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
188 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
231 String<TraceSegment_<TPosition, TSize2>, TStringSpec2> const & traceSegments) in _adaptTraceSegmentsTo()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | dp_traceback_adaptor.h | 62 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
129 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
188 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
231 String<TraceSegment_<TPosition, TSize2>, TStringSpec2> const & traceSegments) in _adaptTraceSegmentsTo()
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| H A D | local_alignment_unbanded.h | 169 typedef typename Position<TAlign>::Type TPosition; in localAlignment() typedef
206 typedef typename Position<TSequenceH>::Type TPosition; in localAlignment() typedef
245 typedef typename Position<TGraph>::Type TPosition; in localAlignment() typedef
287 typedef typename Position<TFragments>::Type TPosition; in localAlignment() typedef
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| H A D | local_alignment_banded.h | 71 typedef typename Position<TAlign>::Type TPosition; in localAlignment() typedef
113 typedef typename Position<TSequenceH>::Type TPosition; in localAlignment() typedef
153 typedef typename Position<TGraph>::Type TPosition; in localAlignment() typedef
198 typedef typename Position<TFragments>::Type TPosition; in localAlignment() typedef
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seeds/ |
| H A D | test_seeds_seed_diagonal.cpp | 75 typedef Position<TSeedDiagonal>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
85 typedef Position<TSeedDiagonal>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/basic/ |
| H A D | basic_stream.h | 187 typedef typename Position<TStream>::Type TPosition; typedef
213 typedef typename Position<TStream>::Type TPosition; typedef
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/basic/ |
| H A D | basic_stream.h | 187 typedef typename Position<TStream>::Type TPosition; typedef
213 typedef typename Position<TStream>::Type TPosition; typedef
|
| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/basic/ |
| H A D | basic_stream.h | 187 typedef typename Position<TStream>::Type TPosition; typedef
213 typedef typename Position<TStream>::Type TPosition; typedef
|
| /dports/biology/seqan1/seqan-1.3.1/apps/mason/ |
| H A D | util.h | 38 typedef typename Position<TStringSet>::Type TPosition; in write() typedef
58 typedef typename Position<TStringSet>::Type TPosition; in write() typedef
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/graph_types/ |
| H A D | test_graph_types_derived.cpp | 57 typedef Position<String<char> >::Type TPosition; in SEQAN_DEFINE_TEST() typedef
133 typedef Position<String<char> >::Type TPosition; in SEQAN_DEFINE_TEST() typedef
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| /dports/biology/seqan1/seqan-1.3.1/seqan/seeds2/ |
| H A D | seeds_seed_base.h | 67 typedef size_t TPosition; typedef
78 typedef size_t TPosition; typedef
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/sequence/ |
| H A D | test_sequence_std_adaptions.h | 110 typedef Position<TVector>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
119 typedef Size<TVector>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
340 typedef Position<TString>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
349 typedef Size<TString>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
526 typedef Position<TList>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
535 typedef Size<TList>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
815 typedef Position<TArray>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
824 typedef Size<TArray>::Type TPosition; in SEQAN_DEFINE_TEST() typedef
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| /dports/biology/seqan1/seqan-1.3.1/demos/ |
| H A D | lagan.cpp | 28 typedef typename Value<TSeed>::Type TPosition; in laganChaining() typedef
47 typedef typename Position<TFinder>::Type TPosition; in laganChaining() typedef
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| H A D | graph_algo_lis.cpp | 15 typedef Position<String<unsigned int> >::Type TPosition; in main() typedef
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| H A D | graph_algo_his.cpp | 15 typedef Position<String<unsigned int> >::Type TPosition; in main() typedef
|
| /dports/biology/seqan1/seqan-1.3.1/docs/ |
| H A D | graph_algo_lis.cpp | 12 typedef Position<String<unsigned int> >::Type TPosition; in main() typedef
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| H A D | graph_algo_his.cpp | 12 typedef Position<String<unsigned int> >::Type TPosition; in main() typedef
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| /dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/graph_algorithms/ |
| H A D | longest_increasing_subsequence.cpp | 22 typedef Position<String<unsigned> >::Type TPosition; in main() typedef
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| H A D | heaviest_increasing_subsequence.cpp | 16 typedef Position<String<unsigned int> >::Type TPosition; in main() typedef
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/graph_algorithms/ |
| H A D | longest_increasing_subsequence.cpp | 22 typedef Position<String<unsigned> >::Type TPosition; in main() typedef
|