Home
last modified time | relevance | path

Searched refs:SeedSet (Results 1 – 25 of 44) sorted by relevance

12

/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/
H A Dseeds_seed_set_unordered.h59 class SeedSet<TSeed, Unordered>
72 SeedSet() : _minScore(0), _minSeedSize(0) in SeedSet() function
85 struct Position<SeedSet<TSeed, Unordered> >
93 struct Position<SeedSet<TSeed, Unordered> const> : Position<SeedSet<TSeed, Unordered> >
101 struct Size<SeedSet<TSeed, Unordered> >
109 struct Size<SeedSet<TSeed, Unordered> const> : Size<SeedSet<TSeed, Unordered> >
117 struct Value<SeedSet<TSeed, Unordered> >
133 struct Reference<SeedSet<TSeed, Unordered> >
170 length(SeedSet<TSeed, Unordered> & seedSet)
224 front(SeedSet<TSeed, Unordered> & seedSet)
[all …]
H A Dseeds_seed_set_base.h79 class SeedSet; variable
175 typename SeedScore<typename Value<SeedSet<TSeed, TSeedSetSpec> >::Type >::Type
176 minScore(SeedSet<TSeed, TSeedSetSpec> const & seedSet) in minScore()
201 void setMinScore(SeedSet<TSeed, TSeedSetSpec> & seedSet, TScoreValue val) in setMinScore()
211 typename Size<typename Value<SeedSet<TSeed, TSeedSetSpec> >::Type >::Type
212 minSeedSize(SeedSet<TSeed, TSeedSetSpec> const & seedSet) in minSeedSize()
222 void setMinSeedSize(SeedSet<TSeed, TSeedSetSpec> & seedSet, TSize siz) in setMinSeedSize()
233 inline bool _qualityReached(SeedSet<TSeed, TSeedSetSpec> const & seedSet, in _qualityReached()
255 inline void clear(SeedSet<TSeed, TSeedSetSpec> & seedSet) in clear()
270 SeedSet<TSeed, TSeedSetSpec> const & seedSet, in __write()
[all …]
/dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/
H A Dseeds_seed_set_unordered.h59 class SeedSet<TSeed, Unordered>
72 SeedSet() : _minScore(0), _minSeedSize(0) in SeedSet() function
85 struct Position<SeedSet<TSeed, Unordered> >
93 struct Position<SeedSet<TSeed, Unordered> const> : Position<SeedSet<TSeed, Unordered> >
101 struct Size<SeedSet<TSeed, Unordered> >
109 struct Size<SeedSet<TSeed, Unordered> const> : Size<SeedSet<TSeed, Unordered> >
117 struct Value<SeedSet<TSeed, Unordered> >
133 struct Reference<SeedSet<TSeed, Unordered> >
170 length(SeedSet<TSeed, Unordered> & seedSet)
224 front(SeedSet<TSeed, Unordered> & seedSet)
[all …]
H A Dseeds_seed_set_base.h79 class SeedSet; variable
175 typename SeedScore<typename Value<SeedSet<TSeed, TSeedSetSpec> >::Type >::Type
176 minScore(SeedSet<TSeed, TSeedSetSpec> const & seedSet) in minScore()
201 void setMinScore(SeedSet<TSeed, TSeedSetSpec> & seedSet, TScoreValue val) in setMinScore()
211 typename Size<typename Value<SeedSet<TSeed, TSeedSetSpec> >::Type >::Type
212 minSeedSize(SeedSet<TSeed, TSeedSetSpec> const & seedSet) in minSeedSize()
222 void setMinSeedSize(SeedSet<TSeed, TSeedSetSpec> & seedSet, TSize siz) in setMinSeedSize()
233 inline bool _qualityReached(SeedSet<TSeed, TSeedSetSpec> const & seedSet, in _qualityReached()
255 inline void clear(SeedSet<TSeed, TSeedSetSpec> & seedSet) in clear()
270 SeedSet<TSeed, TSeedSetSpec> const & seedSet, in __write()
[all …]
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/
H A Dseeds_seed_set_unordered.h59 class SeedSet<TSeed, Unordered>
72 SeedSet() : _minScore(0), _minSeedSize(0) in SeedSet() function
85 struct Position<SeedSet<TSeed, Unordered> >
93 struct Position<SeedSet<TSeed, Unordered> const> : Position<SeedSet<TSeed, Unordered> >
101 struct Size<SeedSet<TSeed, Unordered> >
109 struct Size<SeedSet<TSeed, Unordered> const> : Size<SeedSet<TSeed, Unordered> >
117 struct Value<SeedSet<TSeed, Unordered> >
133 struct Reference<SeedSet<TSeed, Unordered> >
170 length(SeedSet<TSeed, Unordered> & seedSet)
224 front(SeedSet<TSeed, Unordered> & seedSet)
[all …]
H A Dseeds_seed_set_base.h79 class SeedSet; variable
175 typename SeedScore<typename Value<SeedSet<TSeed, TSeedSetSpec> >::Type >::Type
176 minScore(SeedSet<TSeed, TSeedSetSpec> const & seedSet) in minScore()
201 void setMinScore(SeedSet<TSeed, TSeedSetSpec> & seedSet, TScoreValue val) in setMinScore()
211 typename Size<typename Value<SeedSet<TSeed, TSeedSetSpec> >::Type >::Type
212 minSeedSize(SeedSet<TSeed, TSeedSetSpec> const & seedSet) in minSeedSize()
222 void setMinSeedSize(SeedSet<TSeed, TSeedSetSpec> & seedSet, TSize siz) in setMinSeedSize()
233 inline bool _qualityReached(SeedSet<TSeed, TSeedSetSpec> const & seedSet, in _qualityReached()
255 inline void clear(SeedSet<TSeed, TSeedSetSpec> & seedSet) in clear()
270 SeedSet<TSeed, TSeedSetSpec> const & seedSet, in __write()
[all …]
/dports/biology/seqan1/seqan-1.3.1/seqan/seeds2/
H A Dseeds_seed_set_unordered.h55 class SeedSet<TSeedSpec, Unordered, TSeedSetConfig>
73 SeedSet() in SeedSet() function
83 struct Position<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >
95 struct Size<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >
103 struct Size<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> const>
107 struct Value<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >
115 struct Value<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> const>
123 struct Reference<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >
170 length(SeedSet<TSeedSpec, Unordered, TSeedSetConfig> & seedSet)
228 front(SeedSet<TSeedSpec, Unordered, TSeedSetConfig> & seedSet)
[all …]
H A Dseeds2_generated_forwards.h501 … TSeedSetConfig> inline void addSeed(SeedSet<TSeedSpec, Unordered, TSeedSetConfig> & seedSet, type…
519 …name TSeedSetConfig> inline typename Value<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >::Type b…
520 …me TSeedSetConfig> inline typename Value<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> const>::Typ…
532 …e TSeedSetConfig> inline typename Iterator<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >::Type b…
533 …SeedSetConfig> inline typename Iterator<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> const>::Type…
545 …me TSeedSetConfig> inline typename Iterator<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >::Type …
546 …TSeedSetConfig> inline typename Iterator<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> const>::Typ…
563 …name TSeedSetConfig> inline typename Value<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >::Type f…
564 …e TSeedSetConfig> inline typename Value<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> const>::Type…
636 …name TSeedSetConfig> inline typename Size<SeedSet<TSeedSpec, Unordered, TSeedSetConfig> >::Type le…
[all …]
H A Dseeds_seed_set_base.h158 class SeedSet; variable
253 SeedSet<TSeedSpec, TSeedSetSpec, TSeedConfig> const & seedSet, in _write()
256 typedef SeedSet<TSeedSpec, TSeedSetSpec, TSeedConfig> TSeedSet; in _write()
H A Dseeds_global_chaining.h77 SeedSet<TSeedSpec, TSeedSetSpec, TSeedConfig> const & seedSet, in chainSeedsGlobally()
82 typedef SeedSet<TSeedSpec, TSeedSetSpec, TSeedConfig> TSeedSet; in chainSeedsGlobally()
/dports/biology/seqan1/seqan-1.3.1/seqan/seeds/
H A DseedSet_base.h114 class SeedSet; variable
155 SeedSet(){ in SeedSet() function
165 ~SeedSet(){ in ~SeedSet()
187 SeedSet(){ in SeedSet() function
197 ~SeedSet() in ~SeedSet()
264 struct Size<SeedSet<TValue,TSeedSpec, TSpecScoring, TSpec> >
279 append(SeedSet<TValue, TSeedSpec,
291 appendValue(SeedSet<TValue,
302 begin(SeedSet<TValue,TSeedSpec, TSpecScoring, TSpec> &set)
311 end(SeedSet<TValue,TSeedSpec, TSpecScoring, TSpec> &set)
[all …]
H A Dseeds_generated_forwards.h97 …Value, typename TSeedSpec, typename TSpecScoring, typename TSpec > class SeedSet; // "seqan… variable
441 …PropertyMap<TValue, Block<BLOCK_SIZE<SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec> >::Value> >* …
493 …pec, typename TScoringSpec> bool addSeedSet(SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec> &targe…
494 …pec, typename TScoringSpec> bool addSeedSet(SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec> &targe…
495 …ngSpec, typename TAlgoSpec> bool addSeedSet(SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec> &targe…
565 …name TSpec> inline typename Iterator<SeedSet<TValue,TSeedSpec, TSpecScoring, TSpec>, Standard >::T…
566 …me TSpec> inline typename Iterator<SeedSet<TValue,TSeedSpec, TSpecScoring, TSpec> const, Standard>…
578 …e, typename TSeedSpec, typename TSpec, typename TScoringSpec> void clear(SeedSet<TValue, TSeedSpec…
592 …ename TSpec> inline typename Iterator<SeedSet<TValue,TSeedSpec, TSpecScoring, TSpec>, Standard >::…
593 …me TSpec> inline typename Iterator<SeedSet<TValue, TSeedSpec, TSpecScoring, TSpec> const, Standard…
[all …]
H A DseedSet_score.h158 class SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec>
175 SeedSet(){
191 ~SeedSet(){
200 class SeedSet<TValue, ChainedSeed, TScoringSpec, TSpec>
215 SeedSet(){
224 ~SeedSet()
311 clear(SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec> &set)
350 addSeed(SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec> &set,
380 addSeed(SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec> &set,
486 addSeed(SeedSet<TValue, TSeedSpec, TScoringSpec, TSpec> &set,
[all …]
H A Dglobal_seed_chain.h102 globalChaining(SeedSet<TValue, TSeedSpec, TScoreSpec, TSpec> const &source, //Seedset containing th… in globalChaining()
107 typedef SeedSet<TValue, TSeedSpec, TScoreSpec, TSpec> TSeedSet; in globalChaining()
173 globalChaining(SeedSet<TValue, TSeedSpec, TScoreSpec, TSpec> const &source, //Seedset containing th… in globalChaining()
181 typedef SeedSet<TValue, TSeedSpec, TScoreSpec, TSpec> TSeedSet; in globalChaining()
247 globalChaining(SeedSet<TValue, TSeedSpec, TScoreSpec, TSpec> const &source, //Seedset containing th… in globalChaining()
251 typedef SeedSet<TValue, TSeedSpec, TScoreSpec, TSpec> TSeedSet; in globalChaining()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/seeds/
H A Dtest_seeds_seed_set_base.cpp50 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetContainerFunctions()
100 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedSingleNoThreshold()
121 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedSingleThresholdReachedLength()
143 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedSingleThresholdNotReachedLength()
165 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedSingleThresholdReachedScore()
189 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedSingleThresholdNotReachedScore()
211 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedMergeLeftMergingPossibleNoThreshold()
237 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedMergeRightMergingPossibleNoThreshold()
262 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedMergeLeftMergingImpossibleNoThreshold()
298 typedef SeedSet<Seed<TSeedSpec>, TSeedSetSpec> TSeedSet; in testSeedsSeedSetAddSeedMergeLeftMergingPossibleThresholdNotReachedLength()
[all …]
/dports/biology/diamond/diamond-2.0.13/src/data/
H A Dqueries.h40 struct SeedSet;
42 extern std::unique_ptr<SeedSet> query_seeds_bitset;
H A Dseed_set.h37 struct SeedSet struct
39 …SeedSet(Block &seqs, double max_coverage, const std::vector<bool>* skip, const double seed_cut, co…
H A Dseed_set.cpp64 SeedSet::SeedSet(Block &seqs, double max_coverage, const std::vector<bool>* skip, const double seed… in SeedSet() function in SeedSet
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/seed_and_extend/
H A Dexample6.cpp13 typedef SeedSet<TSeed> TSeedSet; in main()
H A Dsolution5.cpp10 typedef SeedSet<TSeed> TSeedSet; in main()
H A Dexample4.cpp13 typedef SeedSet<TSeed> TSeedSet; in main()
H A Dexample5.cpp14 typedef SeedSet<TSeed> TSeedSet; in main()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/manual/source/Tutorial/Algorithms/
H A DSeedExtension.rst128 SeqAn provides the :dox:`SeedSet` class as a data structure to efficiently store seeds and combine …
129 The following example creates a :dox:`SeedSet` object ``seeds``, adds four seeds to it and then pri…
141 By using different overloads of the :dox:`SeedSet#addSeed`, we can use various local chaining strat…
152 The :dox:`SeedSet#addSeed` function returns a boolean value indicating success in finding a suitabl…
196 …of :dox:`Seed` objects for the result as its first parameter and a :dox:`SeedSet` as its second pa…
197 A subset of the seeds from the :dox:`SeedSet` are then selected and stored in the result sequence.
/dports/biology/seqan/seqan-library-2.4.0/share/doc/seqan/html/demos/dox/seeds/
H A Dseeds_chaining.cpp9 SeedSet<Seed<Simple>, Unordered> seedSet; in main()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/dox/seeds/
H A Dseeds_chaining.cpp9 SeedSet<Seed<Simple>, Unordered> seedSet; in main()

12