This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 1234]

CLocARNA::MultipleAlignment::AliColumn	Read only proxy class representing a column of the alignment
CLocARNA::Aligner	Implements locarna alignment algorithm
CLocARNA::AlignerImpl	Implementation of Aligner
CLocARNA::AlignerN	Implements SPARSE, next generation alignment algorithm for locarna
CLocARNA::AlignerP	Computes partition function of alignment, arc match and base match probabilities
►CLocARNA::AlignerParams	Parameter for alignment by Aligner
CLocARNA::AlignerNParams	Parameters for AlignerN
CLocARNA::AlignerPParams	Parameters for AlignerP
CLocARNA::AlignerRestriction	Restricts range of an alignment in Aligner
CLocARNA::Alignment	Represents a structure-annotated sequence alignment
CLocARNA::AlignmentImpl	Implementation of Alignment
CLocARNA::Alphabet< T >	Specifies an alphabet
CLocARNA::Alphabet< char >
CLocARNA::Alphabet< std::string >
CLocARNA::AnchorConstraints	Represents anchor constraints between two sequences
CLocARNA::MultipleAlignment::AnnoType	Type of sequence annotation. enumerates legal annotation types
CLocARNA::ArcMatch	Represents a match of two base pairs (arc match)
►CLocARNA::ArcMatches	Maintains the relevant arc matches and their scores
CLocARNA::ArcMatchesIndexed	Class ArcMatches with additional mapping
CLocARNA::BasePairs	Describes sequence and structure ensemble of an RNA
►CLocARNA::BasePairs__Arc	Represents a base pair
CLocARNA::BasePairs::LeftAdjEntry	Entry in a left adjacency list
CLocARNA::BasePairs::RightAdjEntry	Entry in a right adjacency list
►CLocARNA::ConfusionMatrix::BPFilter	Basic class for base pair filters (no filtering)
CLocARNA::ConfusionMatrix::BPMinLoopSizeFilter	Loop size base pair filter
CLocARNA::ConfusionMatrix::CanonicalBPFilter	Base pair filter to allow only canonical base pairs
CLocARNA::ConfusionMatrix::CombinedBPFilter
CLocARNA::ConfusionMatrix::SpanRangeBPFilter	Base pair range filter
CLocARNA::ConfusionMatrix	Compare RNA secondary structure by their confusion matrix
CLocARNA::DiscreteDistribution
CLocARNA::EdgeEnd	End of an alignment edge
CLocARNA::SparseMatrix< T >::element	Element of sparse matrix
CLocARNA::SparseVector< T >::element	Element of sparse vector
CLocARNA::EPM	Class for the representation of exact pattern matches (EPM)
CLocARNA::ExactMatcher	Computes exact pattern matchings (EPM) between two RNA sequences
►Cstd::exception	STL class
►CLocARNA::failure	Simple exception class that supports a text message
CLocARNA::syntax_error_failure	Thrown, when the format is recognized but syntax is incorrect
CLocARNA::wrong_format_failure	Thrown, when reading data that is not in the supposed format
CLocARNA::ExtRnaDataImpl	Implementation of ExtRnaData
CLocARNA::FitOnOff	Implements fitting of a two-step function to a number sequence
CLocARNA::MultipleAlignment::FormatType	File format type for multiple alignments
CLocARNA::FreeEndgapsDescription	Description of free end gaps
CLocARNA::Gap	"enum class" of gaps in alignment edges
CLocARNA::greater_second< T >	Implements comparison by member second
CLocARNA::SparsificationMapper::info_for_pos	Struct to represent all necessary information for all valid sequence positions
CLocARNA::RnaDataImpl::keyvec< KEY >
CLocARNA::LCSEPM	Computes the best chain of EPMs, the LCS-EPM
CLocARNA::ArcMatches::lex_greater_left_ends	Compare two arc match indices by lexicographically comparing their left ends
►CLocARNA::MatchController	Abstract class that declares the method is_valid_match()
►CLocARNA::TraceController	Controls the matrix cells valid for traces
CLocARNA::SparseTraceController	Combines the TraceController with the Mapper for both sequences
CLocARNA::MatchProbs	Provides probabilities for each match
CLocARNA::Matrix< T >	Simple 2D matrix class, provides access via operator (int,int)
CLocARNA::Matrix< ArcMatchIdxVec >
CLocARNA::Matrix< double >
►CLocARNA::Matrix< elem_t >
CLocARNA::OMatrix< elem_t >	Simple matrix class with offset
CLocARNA::RMatrix< elem_t >	Simple matrix class with restriction to a range
CLocARNA::RotMatrix< elem_t >	A matrix class with rotation
CLocARNA::Matrix< infty_score_t >
CLocARNA::Matrix< pf_score_t >
CLocARNA::Matrix< score_t >
CLocARNA::Matrix< size_t >
►CLocARNA::McC_matrices_base
CLocARNA::McC_ali_matrices_t	Alifold-McCaskill matrices
CLocARNA::McC_matrices_t	McCaskill matrices
CLocARNA::AlignerImpl::ModifiedScoringView	Provides a modified view on the scoring
CLocARNA::AlignerN::ModifiedScoringViewN	Provides a modified view on the scoring
►CLocARNA::MultipleAlignment	Represents a multiple alignment
CLocARNA::Sequence	"Sequence View" of multiple alignment as array of column vectors
CLocARNA::option_def	Definition structure of an option
►Cpair
CLocARNA::AlignmentEdges	Pair of vector of alignment edges
►CLocARNA::triple< T1, T2, T3 >	Represents a 3-tuple
►CLocARNA::quadruple< T1, T2, T3, T4 >	Represents a 4-tuple
CLocARNA::quintuple< T1, T2, T3, T4, T5 >	Represents a 5-tuple
CLocARNA::pair_of_size_t_hash	Function class definining hash function for pairs of size_t
CLocARNA::PatternPair	Able to manage an EPM, consists of 2 singlepatterns, one in each RNA
CLocARNA::PatternPairMap	Manage a set of EPMs (PatternPair)
CLocARNA::PFoldParams	Parameters for partition folding
►CLocARNA::Ribofit	Family of Ribofit matrices
CLocARNA::Ribofit_will2014
►CLocARNA::Ribosum	Represents ribosum similarity matrices
CLocARNA::RibosumFreq	Represents ribosum similarity matrices including raw frequencies
►CLocARNA::RnaData	Represent sparsified data of RNA ensemble
CLocARNA::ExtRnaData	Represent sparsified data of RNA ensemble extended by in loop probabilities
CLocARNA::RnaDataImpl	Implementation of RnaData
CLocARNA::RnaEnsemble	Represents the raw structure ensemble data for an RNA
CLocARNA::RnaEnsembleImpl	Implementation of RnaEnsemble
CLocARNA::RnaStructure	An RNA secondary structure
CLocARNA::Scoring	Provides methods for the scoring of alignments
CLocARNA::ScoringParams	Parameters for scoring
CLocARNA::MultipleAlignment::SeqEntry	A row in a multiple alignment
CLocARNA::SequenceAnnotation	Annotation of a sequence
CLocARNA::SinglePattern	Stores a Pattern in one sequence
CLocARNA::SparseMatrix< T >	Represents a sparse 2D matrix
CLocARNA::SparseMatrix< arc_prob_matrix_t >
CLocARNA::SparseMatrix< arc_prob_vector_t >
CLocARNA::SparseMatrix< double >
CLocARNA::SparseMatrix< int >
CLocARNA::SparseMatrix< pf_score_t >
CLocARNA::SparseVector< T >	Represents a sparse vector
CLocARNA::SparsificationMapper	Represents the mapping for sparsification
CLocARNA::StopWatch	Control a set of named stop watch like timers
CLocARNA::StralScore	Implements the stral-like scoring function
CLocARNA::string1	A simple 1-based string
►CLocARNA::TaintedInftyInt
►CLocARNA::InftyInt
CLocARNA::FiniteInt
►CLocARNA::TraceRange	Represents a range of traces
CLocARNA::TraceController	Controls the matrix cells valid for traces
CLocARNA::ArcMatches::tuple5
CLocARNA::type_wrapper< T >	Generic type_wrapper class
CLocARNA::AlignerImpl::UnmodifiedScoringView	Provides the standard view on the scoring
CLocARNA::AlignerN::UnmodifiedScoringViewN	Provides the standard view on the scoring
CLocARNA::unordered_map< Key, T, Hash, Pred, Alloc >
CLocARNA::unordered_map< idx_pair_t, ArcMatch::idx_type, pair_of_size_t_hash >
CLocARNA::unordered_map< key_t, value_t >
CLocARNA::unordered_map< key_t, value_t, pair_of_size_t_hash >
CLocARNA::unordered_map< std::string, SelfValuePTR >
CLocARNA::unordered_map< std::string, timer_t >
CLocARNA::unordered_set< Key, Hash, Pred, Alloc >
►Cstd::vector< T >	STL class
CLocARNA::plusvector< T >	Implements a vector with += operator