Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
LocARNA::MultipleAlignment::AliColumnRead only proxy class representing a column of the alignment
LocARNA::AlignerImplements locarna alignment algorithm
LocARNA::AlignerImplImplementation of Aligner
LocARNA::AlignerNImplements SPARSE, next generation alignment algorithm for locarna
LocARNA::AlignerNParamsParameters for AlignerN
LocARNA::AlignerPComputes partition function of alignment, arc match and base match probabilities
LocARNA::AlignerParamsParameter for alignment by Aligner
LocARNA::AlignerPParamsParameters for AlignerP
LocARNA::AlignerRestrictionRestricts range of an alignment in Aligner
LocARNA::AlignmentRepresents a structure-annotated sequence alignment
LocARNA::AlignmentEdgesPair of vector of alignment edges
LocARNA::AlignmentImplImplementation of Alignment
LocARNA::Alphabet< T >Specifies an alphabet
LocARNA::AnchorConstraintsRepresents anchor constraints between two sequences
LocARNA::MultipleAlignment::AnnoTypeType of sequence annotation. enumerates legal annotation types
LocARNA::ArcMatchRepresents a match of two base pairs (arc match)
LocARNA::ArcMatchesMaintains the relevant arc matches and their scores
LocARNA::ArcMatchesIndexedClass ArcMatches with additional mapping
LocARNA::BasePairsDescribes sequence and structure ensemble of an RNA
LocARNA::BasePairs__ArcRepresents a base pair
LocARNA::BasePairFilter::BPMinLoopSizeLoop size base pair filter
LocARNA::BasePairFilter::CanonicalBase pair filter to allow only canonical base pairs
LocARNA::ConfusionMatrixCompare RNA secondary structure by their confusion matrix
LocARNA::EdgeEndEnd of an alignment edge
LocARNA::SparseMatrix< T >::elementElement of sparse matrix
LocARNA::SparseVector< T >::elementElement of sparse vector
LocARNA::EPMClass for the representation of exact pattern matches (EPM)
LocARNA::ExactMatcherComputes exact pattern matchings (EPM) between two RNA sequences
LocARNA::ExtRnaDataRepresent sparsified data of RNA ensemble extended by in loop probabilities
LocARNA::ExtRnaDataImplImplementation of ExtRnaData
LocARNA::failureSimple exception class that supports a text message
LocARNA::BasePairFilter::FilterBasic class for base pair filters (no filtering)
LocARNA::FitOnOffImplements fitting of a two-step function to a number sequence
LocARNA::MultipleAlignment::FormatTypeFile format type for multiple alignments
LocARNA::FreeEndgapsDescriptionDescription of free end gaps
LocARNA::Gap"enum class" of gaps in alignment edges
LocARNA::greater_second< T >Implements comparison by member second
LocARNA::RnaDataImpl::keyvec< KEY >
LocARNA::LCSEPMComputes the best chain of EPMs, the LCS-EPM
LocARNA::BasePairs::LeftAdjEntryEntry in a left adjacency list
LocARNA::MatchControllerAbstract class that declares the method is_valid_match()
LocARNA::MatchProbsProvides probabilities for each match
LocARNA::Matrix< T >Simple 2D matrix class, provides access via operator (int,int)
LocARNA::McC_ali_matrices_tAlifold-McCaskill matrices
LocARNA::McC_matrices_tMcCaskill matrices
LocARNA::AlignerImpl::ModifiedScoringViewProvides a modified view on the scoring
LocARNA::AlignerN::ModifiedScoringViewNProvides a modified view on the scoring
LocARNA::MultipleAlignmentRepresents a multiple alignment
LocARNA::OMatrix< elem_t >Simple matrix class with offset
LocARNA::option_defDefinition structure of an option
LocARNA::pair_of_size_t_hashFunction class definining hash function for pairs of size_t
LocARNA::PatternPairAble to manage an EPM, consists of 2 singlepatterns, one in each RNA
LocARNA::PatternPairMapManage a set of EPMs (PatternPair)
LocARNA::PFoldParamsParameters for partition folding
LocARNA::plusvector< T >Implements a vector with += operator
LocARNA::quadruple< T1, T2, T3, T4 >Represents a 4-tuple
LocARNA::quintuple< T1, T2, T3, T4, T5 >Represents a 5-tuple
LocARNA::RibofitFamily of Ribofit matrices
LocARNA::RibosumRepresents ribosum similarity matrices
LocARNA::RibosumFreqRepresents ribosum similarity matrices including raw frequencies
LocARNA::BasePairs::RightAdjEntryEntry in a right adjacency list
LocARNA::RMatrix< elem_t >Simple matrix class with restriction to a range
LocARNA::RnaDataRepresent sparsified data of RNA ensemble
LocARNA::RnaDataImplImplementation of RnaData
LocARNA::RnaEnsembleRepresents the raw structure ensemble data for an RNA
LocARNA::RnaEnsembleImplImplementation of RnaEnsemble
LocARNA::RnaStructureAn RNA secondary structure
LocARNA::RotMatrix< elem_t >A matrix class with rotation
LocARNA::ScoringProvides methods for the scoring of alignments
LocARNA::ScoringParamsParameters for scoring
LocARNA::MultipleAlignment::SeqEntryA row in a multiple alignment
LocARNA::Sequence"Sequence View" of multiple alignment as array of column vectors
LocARNA::SequenceAnnotationAnnotation of a sequence
LocARNA::SinglePatternStores a Pattern in one sequence
LocARNA::BasePairFilter::SpanRangeBase pair range filter
LocARNA::SparseMatrix< T >Represents a sparse 2D matrix
LocARNA::SparseTraceControllerCombines the TraceController with the Mapper for both sequences
LocARNA::SparseVector< T >Represents a sparse vector
LocARNA::SparsificationMapperRepresents the mapping for sparsification
LocARNA::StopWatchControl a set of named stop watch like timers
LocARNA::StralScoreImplements the stral-like scoring function
LocARNA::string1A simple 1-based string
LocARNA::syntax_error_failureThrown, when the format is recognized but syntax is incorrect
LocARNA::TraceControllerControls the matrix cells valid for traces
LocARNA::TraceRangeRepresents a range of traces
LocARNA::triple< T1, T2, T3 >Represents a 3-tuple
LocARNA::type_wrapper< T >Generic type_wrapper class
LocARNA::AlignerImpl::UnmodifiedScoringViewProvides the standard view on the scoring
LocARNA::AlignerN::UnmodifiedScoringViewNProvides the standard view on the scoring
LocARNA::unordered_map< Key, T, Hash, Pred, Alloc >
LocARNA::unordered_set< Key, Hash, Pred, Alloc >
LocARNA::wrong_format_failureThrown, when reading data that is not in the supposed format
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