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Searched defs:TGaps (Results 1 – 25 of 50) sorted by relevance

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/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Dgaps_iterator_anchor.h54 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 …]
H A Dgaps_iterator_array.h156 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 …]
H A Dgaps_array.h439 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
H A Dalign_base.h90 typedef Gaps<TSource, TSpec> TGaps; typedef
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Dgaps_iterator_anchor.h54 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 …]
H A Dgaps_iterator_array.h156 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 …]
H A Dgaps_array.h439 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
H A Dalign_base.h90 typedef Gaps<TSource, TSpec> TGaps; typedef
/dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/
H A Dgaps_iterator_anchor.h54 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 …]
H A Dgaps_iterator_array.h156 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 …]
H A Dalign_base.h90 typedef Gaps<TSource, TSpec> TGaps; typedef
H A Dgaps_array.h431 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
H A Devaluate_alignment.h207 typedef typename Row<TAlign>::Type TGaps; in computeAlignmentStats() typedef
289 TScoreVal computeAlignmentStats(Align<TGaps, TAlignSpec> const & align, in computeAlignmentStats()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/align/
H A Dtest_align_gaps.h58 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
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H A Dtest_align_gaps_iterator.h52 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 …]
/dports/biology/seqan1/seqan-1.3.1/seqan/align/
H A Dgaps_array.h398 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 …]
H A Dgaps_sumlist.h263 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
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/tests/blast/
H A Dtest_blast_statistics.h186 typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps; in SEQAN_DEFINE_TEST() typedef
223 typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps; in SEQAN_DEFINE_TEST() typedef
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/blast_io/
H A Dread_assignment.cpp16 typedef Gaps<String<AminoAcid>, ArrayGaps> TGaps; in main() typedef
H A Dwrite_assignment.cpp18 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/pairwise_sequence_alignment/
H A Dassignment5_step2.cpp10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
H A Dassignment5_step3.cpp10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
H A Dassignment5_step4.cpp10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
H A Dassignment5_step5.cpp10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef
H A Dassignment5.cpp10 typedef Gaps<TSequence, ArrayGaps> TGaps; in main() typedef

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