| /dports/audio/py-mutagen/mutagen-1.42.0/tests/ |
| H A D | test__id3specs.py | 157 class TStringSpec(TestCase): class
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | dp_traceback_adaptor.h | 58 typename TGapsSpecVertical, typename TPosition, typename TSize, typename TStringSpec>
62 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
69 typedef typename Iterator<String<TTraceSegment, TStringSpec> const>::Type TTraceIterator; in _adaptTraceSegmentsTo()
124 typename TPosition, typename TSize, typename TStringSpec>
129 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
183 typename TStringSpec>
188 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
225 template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequenceH, typena…
228 _adaptTraceSegmentsTo(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & matches, in _adaptTraceSegmentsTo()
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| H A D | global_alignment_banded.h | 314 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
319 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
327 typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments; in globalAlignment()
346 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
350 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
362 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
366 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
380 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
383 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
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| H A D | global_alignment_unbanded.h | 381 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
386 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
392 typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments; in globalAlignment()
410 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
414 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
424 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
428 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
440 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
443 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
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| H A D | local_alignment_banded.h | 188 template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequence, typenam…
190 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in localAlignment()
197 typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments; in localAlignment()
210 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
213 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in localAlignment()
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| H A D | local_alignment_unbanded.h | 278 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
281 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in localAlignment()
286 typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments; in localAlignment()
300 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
303 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in localAlignment()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/consensus/ |
| H A D | consensus_base.h | 154 template<typename TValue, typename TStrSpec, typename TPosPair, typename TStringSpec, typename TSpe…
157 String<TPosPair, TStringSpec> & startEndPos, in _loadContigReads()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_guidetree.h | 80 template<typename TValue, typename TStringSpec, typename TCargo, typename TSpec>
82 njTree(String<TValue, TStringSpec> const & matIn, in njTree()
85 typedef String<TValue, TStringSpec> TMatrix; in njTree()
607 template<typename TStringValue, typename TStringSpec, typename TCargo, typename TSpec, typename TTa…
609 upgmaTree(String<TStringValue, TStringSpec>& mat, in upgmaTree()
617 typedef String<TStringValue, TStringSpec> TMatrix; in upgmaTree()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/index/ |
| H A D | index_skew7.h | 226 template <typename T, typename TStringSpec>
227 struct Skew7StringSpec_<String<T, TStringSpec> >
229 typedef TStringSpec Type;
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/journaled_set/ |
| H A D | journal_alignment_traceback_adaptor.h | 64 typename TSource, typename TPosition, typename TSize, typename TStringSpec>
69 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
80 typedef typename Iterator<String<TTraceSegment, TStringSpec> const>::Type TTraceIterator; in _adaptTraceSegmentsTo()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/pipe/ |
| H A D | pipe_base.h | 635 typename TStringSpec,
638 inline void assign(String<TValue, TStringSpec> &dest, Pipe<TInput, TSpec> &src)
640 typedef typename Iterator<String<TValue, TStringSpec>, Standard >::Type TDestIter;
663 typename TStringSpec,
666 inline void operator << (String<TValue, TStringSpec> &dest, Pipe<TInput, TSpec> &src)
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| H A D | pool_base.h | 1342 typename TStringSpec >
1343 inline bool append(Pool<TValue, TSpec> &dest, String<TValue, TStringSpec> &src) {
1344 typedef typename Iterator< String<TValue, TStringSpec> const, Standard >::Type TIter;
1385 typename TStringSpec,
1388 inline bool assign(String<TValue1, TStringSpec> &dest, Pool<TValue2, TSpec> &src) {
1389 typedef typename Iterator< String<TValue1, TStringSpec>, Standard >::Type TIter;
1390 typename Size< String<TValue1, TStringSpec> >::Type _size = length(src);
1405 typename TStringSpec,
1408 inline bool operator<<(String<TValue1, TStringSpec> &dest, Pool<TValue2, TSpec> &src) {
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
| H A D | banded_chain_alignment.h | 402 template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequence, typenam…
406 bandedChainAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
429 template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequence, typenam…
433 bandedChainAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
444 template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequence, typenam…
447 bandedChainAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
459 template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequence, typenam…
462 bandedChainAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString,
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| H A D | banded_chain_alignment_traceback.h | 99 template <typename TTraceSegment, typename TStringSpec, typename TSize>
101 _smoothGluePoint(String<TTraceSegment, TStringSpec> & tracePath, TSize referenceSize)
103 typedef typename Iterator<String<TTraceSegment, TStringSpec> >::Type TTraceSegmentsIterator;
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/sequence/ |
| H A D | string_base.h | 1989 template <typename TValue, typename TStringSpec, typename TSpec, typename TSize>
1990 inline void advanceChunk(Iter<String<TValue, TStringSpec>, TSpec> &iter, TSize size)
1992 typedef String<TValue, TStringSpec> TContainer;
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | dp_traceback_adaptor.h | 58 typename TGapsSpecVertical, typename TPosition, typename TSize, typename TStringSpec>
62 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
69 typedef typename Iterator<String<TTraceSegment, TStringSpec> const>::Type TTraceIterator; in _adaptTraceSegmentsTo()
124 typename TPosition, typename TSize, typename TStringSpec>
129 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
183 typename TStringSpec>
188 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
225 template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequenceH, typena…
228 _adaptTraceSegmentsTo(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & matches, in _adaptTraceSegmentsTo()
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| H A D | global_alignment_banded.h | 314 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
319 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
327 typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments; in globalAlignment()
346 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
350 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
362 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
366 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
380 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
383 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
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| H A D | global_alignment_unbanded.h | 381 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
386 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
392 typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments; in globalAlignment()
410 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
414 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
424 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
428 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
440 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
443 TScoreValue globalAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in globalAlignment()
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| H A D | local_alignment_banded.h | 188 template <typename TSize, typename TFragmentSpec, typename TStringSpec, typename TSequence, typenam…
190 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in localAlignment()
197 typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments; in localAlignment()
210 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
213 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in localAlignment()
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| H A D | local_alignment_unbanded.h | 278 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
281 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in localAlignment()
286 typedef String<Fragment<TSize, TFragmentSpec>, TStringSpec> TFragments; in localAlignment()
300 template <typename TSize, typename TFragmentSpec, typename TStringSpec,
303 TScoreValue localAlignment(String<Fragment<TSize, TFragmentSpec>, TStringSpec> & fragmentString, in localAlignment()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/consensus/ |
| H A D | consensus_base.h | 154 template<typename TValue, typename TStrSpec, typename TPosPair, typename TStringSpec, typename TSpe…
157 String<TPosPair, TStringSpec> & startEndPos, in _loadContigReads()
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/graph_msa/ |
| H A D | graph_align_tcoffee_guidetree.h | 80 template<typename TValue, typename TStringSpec, typename TCargo, typename TSpec>
82 njTree(String<TValue, TStringSpec> const & matIn, in njTree()
85 typedef String<TValue, TStringSpec> TMatrix; in njTree()
603 template<typename TStringValue, typename TStringSpec, typename TCargo, typename TSpec, typename TTa…
605 upgmaTree(String<TStringValue, TStringSpec>& mat, in upgmaTree()
612 typedef String<TStringValue, TStringSpec> TMatrix; in upgmaTree()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/index/ |
| H A D | find2_index_approx.h | 581 typename TChar, typename TStringSpec,
586 String<TChar, TStringSpec> const & needle,
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| H A D | index_skew7.h | 226 template <typename T, typename TStringSpec>
227 struct Skew7StringSpec_<String<T, TStringSpec> >
229 typedef TStringSpec Type;
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/journaled_set/ |
| H A D | journal_alignment_traceback_adaptor.h | 64 typename TSource, typename TPosition, typename TSize, typename TStringSpec>
69 String<TraceSegment_<TPosition, TSize>, TStringSpec> const & traceSegments) in _adaptTraceSegmentsTo()
80 typedef typename Iterator<String<TTraceSegment, TStringSpec> const>::Type TTraceIterator; in _adaptTraceSegmentsTo()
|