/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 …]
|
/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
|
/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
|
/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
|
/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()
|
/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()
|
/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()
|
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
|
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
|
/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
|
/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
|
/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
|
/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
|
/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
|
H A D | graph_algo_lis.cpp | 15 typedef Position<String<unsigned int> >::Type TPosition; in main() typedef
|
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
|
H A D | graph_algo_his.cpp | 12 typedef Position<String<unsigned int> >::Type TPosition; in main() typedef
|
/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
|
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
|