/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | gaps_iterator_anchor.h | 54 typedef TGaps_ TGaps; typedef 142 container(Iter<TGaps, GapsIterator<AnchorGaps<TGapsArray> > > & me) in container() 160 source(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in source() 178 getValue(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in getValue() 202 value(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & it) in value() 210 value(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & it) in value() 222 isGap(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me) in isGap() 338 atBegin(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in atBegin() 358 atEnd(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in atEnd() 688 goNext(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in goNext() [all …]
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H A D | gaps_iterator_array.h | 156 isGap(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in isGap() 167 value(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in value() 175 value(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in value() 189 getValue(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in getValue() 323 goPrevious(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in goPrevious() 358 goNext(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in goNext() 405 goFurther(Iter<TGaps, GapsIterator<ArrayGaps> > & it, in goFurther() 497 atBegin(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in atBegin() 509 atEnd(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in atEnd() 516 atEnd(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in atEnd() [all …]
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H A D | gaps_array.h | 439 typedef Gaps<TSequence, ArrayGaps> TGaps; in toSourcePosition() typedef 481 typedef Gaps<TSequence, ArrayGaps> TGaps; in toSourcePosition() typedef 524 typedef Gaps<TSequence, ArrayGaps> TGaps; typedef 576 typedef Gaps<TSequence, ArrayGaps> TGaps; in insertGaps() typedef 649 typedef Gaps<TSequence, ArrayGaps> TGaps; in removeGaps() typedef 751 typedef Gaps<TSequence, ArrayGaps> TGaps; in isGap() typedef 794 typedef Gaps<TSequence, ArrayGaps> TGaps; in clearClipping() typedef
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H A D | align_base.h | 90 typedef Gaps<TSource, TSpec> TGaps; typedef
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | gaps_iterator_anchor.h | 54 typedef TGaps_ TGaps; typedef 142 container(Iter<TGaps, GapsIterator<AnchorGaps<TGapsArray> > > & me) in container() 160 source(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in source() 178 getValue(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in getValue() 202 value(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & it) in value() 210 value(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & it) in value() 222 isGap(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me) in isGap() 338 atBegin(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in atBegin() 358 atEnd(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in atEnd() 688 goNext(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in goNext() [all …]
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H A D | gaps_iterator_array.h | 156 isGap(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in isGap() 167 value(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in value() 175 value(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in value() 189 getValue(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in getValue() 323 goPrevious(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in goPrevious() 358 goNext(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in goNext() 405 goFurther(Iter<TGaps, GapsIterator<ArrayGaps> > & it, in goFurther() 497 atBegin(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in atBegin() 509 atEnd(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in atEnd() 516 atEnd(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in atEnd() [all …]
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H A D | gaps_array.h | 439 typedef Gaps<TSequence, ArrayGaps> TGaps; in toSourcePosition() typedef 481 typedef Gaps<TSequence, ArrayGaps> TGaps; in toSourcePosition() typedef 524 typedef Gaps<TSequence, ArrayGaps> TGaps; typedef 576 typedef Gaps<TSequence, ArrayGaps> TGaps; in insertGaps() typedef 649 typedef Gaps<TSequence, ArrayGaps> TGaps; in removeGaps() typedef 751 typedef Gaps<TSequence, ArrayGaps> TGaps; in isGap() typedef 794 typedef Gaps<TSequence, ArrayGaps> TGaps; in clearClipping() typedef
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H A D | align_base.h | 90 typedef Gaps<TSource, TSpec> TGaps; typedef
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/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
H A D | gaps_iterator_anchor.h | 54 typedef TGaps_ TGaps; typedef 148 container(Iter<TGaps, GapsIterator<AnchorGaps<TGapsArray> > > & me) in container() 166 source(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in source() 184 getValue(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in getValue() 208 value(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & it) in value() 216 value(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & it) in value() 228 isGap(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > const & me) in isGap() 307 atBegin(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in atBegin() 327 atEnd(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in atEnd() 657 goNext(Iter<TGaps, GapsIterator<AnchorGaps<TGapAnchors> > > & me) in goNext() [all …]
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H A D | gaps_iterator_array.h | 156 isGap(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in isGap() 167 value(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in value() 175 value(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in value() 189 getValue(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in getValue() 281 goPrevious(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in goPrevious() 316 goNext(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in goNext() 363 goFurther(Iter<TGaps, GapsIterator<ArrayGaps> > & it, in goFurther() 455 atBegin(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in atBegin() 467 atEnd(Iter<TGaps, GapsIterator<ArrayGaps> > const & it) in atEnd() 474 atEnd(Iter<TGaps, GapsIterator<ArrayGaps> > & it) in atEnd() [all …]
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H A D | align_base.h | 90 typedef Gaps<TSource, TSpec> TGaps; typedef
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H A D | gaps_array.h | 431 typedef Gaps<TSequence, ArrayGaps> TGaps; in toSourcePosition() typedef 475 typedef Gaps<TSequence, ArrayGaps> TGaps; typedef 527 typedef Gaps<TSequence, ArrayGaps> TGaps; in insertGaps() typedef 615 typedef Gaps<TSequence, ArrayGaps> TGaps; in removeGaps() typedef 717 typedef Gaps<TSequence, ArrayGaps> TGaps; in isGap() typedef 760 typedef Gaps<TSequence, ArrayGaps> TGaps; in clearClipping() typedef
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H A D | evaluate_alignment.h | 207 typedef typename Row<TAlign>::Type TGaps; in computeAlignmentStats() typedef 289 TScoreVal computeAlignmentStats(Align<TGaps, TAlignSpec> const & align, in computeAlignmentStats()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/ |
H A D | test_align_gaps.h | 58 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsMetafunctions() typedef 93 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsConstructorAndSource() typedef 125 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsSetSource() typedef 161 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsAssignSource() typedef 188 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsGapOperationsGapCenter() typedef 390 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsGapOperationsGapsLeading() typedef 574 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsGapOperationsGapsTrailing() typedef 793 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsSequenceInterfaceGapsTrailing() typedef 897 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsSourceViewPositionUngapped() typedef 1345 typedef Gaps<Nothing, TGapsSpec> TGaps; in testAlignGapsSourceIsNothing() typedef [all …]
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H A D | test_align_gaps_iterator.h | 52 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorMetafunctions() typedef 75 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorTrivialIteratorFunctions() typedef 94 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorRootedRandomAccessIteratorFunctions() typedef 157 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorMovement() typedef 292 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorRelations() typedef 329 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorPointerArithmetic() typedef 356 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorForwardIteration() typedef 386 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorReverseIteration() typedef 418 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorCountGapsCountCharactersIsGap() typedef 517 typedef Gaps<TString, TGapsSpec> TGaps; in testAlignGapsIteratorClippedCountGapsCountCharactersIsGap() typedef [all …]
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/dports/biology/seqan1/seqan-1.3.1/seqan/align/ |
H A D | gaps_array.h | 398 typedef Gaps<TSource, ArrayGaps> const TGaps; in toViewPosition() typedef 444 typedef Gaps<TSource, ArrayGaps> const TGaps; in toSourcePosition() typedef 602 typedef Gaps<TSource, ArrayGaps> TGaps; in setClippedBeginPosition() typedef 667 typedef Gaps<TSource, ArrayGaps> TGaps; in setClippedEndPosition() typedef 796 getValue(Iter<TGaps, GapsIterator<ArrayGaps> > & me) in getValue() 817 isGap(Iter<TGaps, GapsIterator<ArrayGaps> > const & me) in isGap() 909 goNext(Iter<TGaps, GapsIterator<ArrayGaps> > & me) in goNext() 915 goNext(Iter<TGaps, GapsIterator<ArrayGaps> > const & me) in goNext() 948 goPrevious(Iter<TGaps, GapsIterator<ArrayGaps> > & me) in goPrevious() 962 atBegin(Iter<TGaps, GapsIterator<ArrayGaps> > const & me) in atBegin() [all …]
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H A D | gaps_sumlist.h | 263 typedef Gaps<TSource, SumlistGaps> TGaps; in _initToResize() typedef 315 typedef Gaps<TSource, SumlistGaps> TGaps; in toViewPosition() typedef 342 typedef Gaps<TSource, SumlistGaps> const TGaps; in toSourcePosition() typedef 384 typedef Gaps<TSource, SumlistGaps> TGaps; in iter() typedef 395 typedef Gaps<TSource, SumlistGaps> TGaps; in iter() typedef 410 typedef Gaps<TSource, SumlistGaps> TGaps; in setBeginPosition() typedef 427 typedef Gaps<TSource, SumlistGaps> TGaps; in setClippedBeginPosition() typedef 485 typedef Gaps<TSource, SumlistGaps> TGaps; in setClippedEndPosition() typedef
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/blast/ |
H A D | test_blast_statistics.h | 186 typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps; in SEQAN_DEFINE_TEST() typedef 223 typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps; in SEQAN_DEFINE_TEST() typedef
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/blast_io/ |
H A D | read_assignment.cpp | 16 typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps; in main() typedef
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H A D | write_assignment.cpp | 18 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/pairwise_sequence_alignment/ |
H A D | assignment5_step2.cpp | 10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
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H A D | assignment5_step3.cpp | 10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
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H A D | assignment5_step4.cpp | 10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
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H A D | assignment5_step5.cpp | 10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
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H A D | assignment5.cpp | 10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
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