Class Index

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A	Combined (LocARNA::BasePairFilter)	InftyInt (LocARNA)	PatternPairMap (LocARNA)	SinglePattern (LocARNA)
	ConfusionMatrix (LocARNA)	K	PFoldParams (LocARNA)	SpanRange (LocARNA::BasePairFilter)
MultipleAlignment::AliColumn (LocARNA)	D		plusvector (LocARNA)	SparseMatrix (LocARNA)
Aligner (LocARNA)		RnaDataImpl::keyvec (LocARNA)	Q	SparseTraceController (LocARNA)
AlignerImpl (LocARNA)	DiscreteDistribution (LocARNA)	L		SparseVector (LocARNA)
AlignerN (LocARNA)	E		quadruple (LocARNA)	SparsificationMapper (LocARNA)
AlignerNParams (LocARNA)		LCSEPM (LocARNA)	quintuple (LocARNA)	StopWatch (LocARNA)
AlignerP (LocARNA)	EdgeEnd (LocARNA)	BasePairs::LeftAdjEntry (LocARNA)	R	StralScore (LocARNA)
AlignerParams (LocARNA)	SparseVector::element (LocARNA)	ArcMatches::lex_greater_left_ends (LocARNA)		string1 (LocARNA)
AlignerPParams (LocARNA)	SparseMatrix::element (LocARNA)	M	Ribofit (LocARNA)	syntax_error_failure (LocARNA)
AlignerRestriction (LocARNA)	EPM (LocARNA)		Ribofit_will2014 (LocARNA)	T
Alignment (LocARNA)	ExactMatcher (LocARNA)	MatchController (LocARNA)	Ribosum (LocARNA)
AlignmentEdges (LocARNA)	ExtRnaData (LocARNA)	MatchProbs (LocARNA)	RibosumFreq (LocARNA)	TaintedInftyInt (LocARNA)
AlignmentImpl (LocARNA)	ExtRnaDataImpl (LocARNA)	Matrix (LocARNA)	BasePairs::RightAdjEntry (LocARNA)	TraceController (LocARNA)
Alphabet (LocARNA)	F	McC_ali_matrices_t (LocARNA)	RMatrix (LocARNA)	TraceRange (LocARNA)
AnchorConstraints (LocARNA)		McC_matrices_base (LocARNA)	RnaData (LocARNA)	triple (LocARNA)
MultipleAlignment::AnnoType (LocARNA)	failure (LocARNA)	McC_matrices_t (LocARNA)	RnaDataImpl (LocARNA)	ArcMatches::tuple5 (LocARNA)
ArcMatch (LocARNA)	Filter (LocARNA::BasePairFilter)	AlignerImpl::ModifiedScoringView (LocARNA)	RnaEnsemble (LocARNA)	type_wrapper (LocARNA)
ArcMatches (LocARNA)	FiniteInt (LocARNA)	AlignerN::ModifiedScoringViewN (LocARNA)	RnaEnsembleImpl (LocARNA)	U
ArcMatchesIndexed (LocARNA)	FitOnOff (LocARNA)	MultipleAlignment (LocARNA)	RnaStructure (LocARNA)
B	MultipleAlignment::FormatType (LocARNA)	O	RotMatrix (LocARNA)	AlignerImpl::UnmodifiedScoringView (LocARNA)
	FreeEndgapsDescription (LocARNA)		S	AlignerN::UnmodifiedScoringViewN (LocARNA)
BasePairs (LocARNA)	G	OMatrix (LocARNA)		unordered_map (LocARNA)
BasePairs__Arc (LocARNA)		option_def (LocARNA)	Scoring (LocARNA)	unordered_set (LocARNA)
BPMinLoopSize (LocARNA::BasePairFilter)	Gap (LocARNA)	P	ScoringParams (LocARNA)	W
C	greater_second (LocARNA)		MultipleAlignment::SeqEntry (LocARNA)
	I	pair_of_size_t_hash (LocARNA)	Sequence (LocARNA)	wrong_format_failure (LocARNA)
Canonical (LocARNA::BasePairFilter)		PatternPair (LocARNA)	SequenceAnnotation (LocARNA)
	SparsificationMapper::info_for_pos (LocARNA)

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