| LocARNA::MultipleAlignment::AliColumn | Read only proxy class representing a column of the alignment |
| LocARNA::Aligner | Implements locarna alignment algorithm |
| LocARNA::AlignerImpl | Implementation of Aligner |
| LocARNA::AlignerN | Implements SPARSE, next generation alignment algorithm for locarna |
| LocARNA::AlignerNParams | Parameters for AlignerN |
| LocARNA::AlignerP | Computes partition function of alignment, arc match and base match probabilities |
| LocARNA::AlignerParams | Parameter for alignment by Aligner |
| LocARNA::AlignerPParams | Parameters for AlignerP |
| LocARNA::AlignerRestriction | Restricts range of an alignment in Aligner |
| LocARNA::Alignment | Represents a structure-annotated sequence alignment |
| LocARNA::AlignmentEdges | Pair of vector of alignment edges |
| LocARNA::AlignmentImpl | Implementation of Alignment |
| LocARNA::Alphabet< T > | Specifies an alphabet |
| LocARNA::AnchorConstraints | Represents anchor constraints between two sequences |
| LocARNA::MultipleAlignment::AnnoType | Type of sequence annotation. enumerates legal annotation types |
| LocARNA::ArcMatch | Represents a match of two base pairs (arc match) |
| LocARNA::ArcMatches | Maintains the relevant arc matches and their scores |
| LocARNA::ArcMatchesIndexed | Class ArcMatches with additional mapping |
| LocARNA::BasePairs | Describes sequence and structure ensemble of an RNA |
| LocARNA::BasePairs__Arc | Represents a base pair |
| LocARNA::BasePairFilter::BPMinLoopSize | Loop size base pair filter |
| LocARNA::BasePairFilter::Canonical | Base pair filter to allow only canonical base pairs |
| LocARNA::BasePairFilter::Combined | |
| LocARNA::ConfusionMatrix | Compare RNA secondary structure by their confusion matrix |
| LocARNA::DiscreteDistribution | |
| LocARNA::EdgeEnd | End of an alignment edge |
| LocARNA::SparseMatrix< T >::element | Element of sparse matrix |
| LocARNA::SparseVector< T >::element | Element of sparse vector |
| LocARNA::EPM | Class for the representation of exact pattern matches (EPM) |
| LocARNA::ExactMatcher | Computes exact pattern matchings (EPM) between two RNA sequences |
| LocARNA::ExtRnaData | Represent sparsified data of RNA ensemble extended by in loop probabilities |
| LocARNA::ExtRnaDataImpl | Implementation of ExtRnaData |
| LocARNA::failure | Simple exception class that supports a text message |
| LocARNA::BasePairFilter::Filter | Basic class for base pair filters (no filtering) |
| LocARNA::FiniteInt | |
| LocARNA::FitOnOff | Implements fitting of a two-step function to a number sequence |
| LocARNA::MultipleAlignment::FormatType | File format type for multiple alignments |
| LocARNA::FreeEndgapsDescription | Description of free end gaps |
| LocARNA::Gap | "enum class" of gaps in alignment edges |
| LocARNA::greater_second< T > | Implements comparison by member second |
| LocARNA::SparsificationMapper::info_for_pos | |
| LocARNA::InftyInt | |
| LocARNA::RnaDataImpl::keyvec< KEY > | |
| LocARNA::LCSEPM | Computes the best chain of EPMs, the LCS-EPM |
| LocARNA::BasePairs::LeftAdjEntry | Entry in a left adjacency list |
| LocARNA::ArcMatches::lex_greater_left_ends | |
| LocARNA::MatchController | Abstract class that declares the method is_valid_match() |
| LocARNA::MatchProbs | Provides probabilities for each match |
| LocARNA::Matrix< T > | Simple 2D matrix class, provides access via operator (int,int) |
| LocARNA::McC_ali_matrices_t | Alifold-McCaskill matrices |
| LocARNA::McC_matrices_base | |
| LocARNA::McC_matrices_t | McCaskill matrices |
| LocARNA::AlignerImpl::ModifiedScoringView | Provides a modified view on the scoring |
| LocARNA::AlignerN::ModifiedScoringViewN | Provides a modified view on the scoring |
| LocARNA::MultipleAlignment | Represents a multiple alignment |
| LocARNA::OMatrix< elem_t > | Simple matrix class with offset |
| LocARNA::option_def | Definition structure of an option |
| LocARNA::pair_of_size_t_hash | Function class definining hash function for pairs of size_t |
| LocARNA::PatternPair | Able to manage an EPM, consists of 2 singlepatterns, one in each RNA |
| LocARNA::PatternPairMap | Manage a set of EPMs (PatternPair) |
| LocARNA::PFoldParams | Parameters 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::Ribofit | Family of Ribofit matrices |
| LocARNA::Ribofit_will2014 | |
| LocARNA::Ribosum | Represents ribosum similarity matrices |
| LocARNA::RibosumFreq | Represents ribosum similarity matrices including raw frequencies |
| LocARNA::BasePairs::RightAdjEntry | Entry in a right adjacency list |
| LocARNA::RMatrix< elem_t > | Simple matrix class with restriction to a range |
| LocARNA::RnaData | Represent sparsified data of RNA ensemble |
| LocARNA::RnaDataImpl | Implementation of RnaData |
| LocARNA::RnaEnsemble | Represents the raw structure ensemble data for an RNA |
| LocARNA::RnaEnsembleImpl | Implementation of RnaEnsemble |
| LocARNA::RnaStructure | An RNA secondary structure |
| LocARNA::RotMatrix< elem_t > | A matrix class with rotation |
| LocARNA::Scoring | Provides methods for the scoring of alignments |
| LocARNA::ScoringParams | Parameters for scoring |
| LocARNA::MultipleAlignment::SeqEntry | A row in a multiple alignment |
| LocARNA::Sequence | "Sequence View" of multiple alignment as array of column vectors |
| LocARNA::SequenceAnnotation | Annotation of a sequence |
| LocARNA::SinglePattern | Stores a Pattern in one sequence |
| LocARNA::BasePairFilter::SpanRange | Base pair range filter |
| LocARNA::SparseMatrix< T > | Represents a sparse 2D matrix |
| LocARNA::SparseTraceController | Combines the TraceController with the Mapper for both sequences |
| LocARNA::SparseVector< T > | Represents a sparse vector |
| LocARNA::SparsificationMapper | Represents the mapping for sparsification |
| LocARNA::StopWatch | Control a set of named stop watch like timers |
| LocARNA::StralScore | Implements the stral-like scoring function |
| LocARNA::string1 | A simple 1-based string |
| LocARNA::syntax_error_failure | Thrown, when the format is recognized but syntax is incorrect |
| LocARNA::TaintedInftyInt | |
| LocARNA::TraceController | Controls the matrix cells valid for traces |
| LocARNA::TraceRange | Represents a range of traces |
| LocARNA::triple< T1, T2, T3 > | Represents a 3-tuple |
| LocARNA::ArcMatches::tuple5 | |
| LocARNA::type_wrapper< T > | Generic type_wrapper class |
| LocARNA::AlignerImpl::UnmodifiedScoringView | Provides the standard view on the scoring |
| LocARNA::AlignerN::UnmodifiedScoringViewN | Provides the standard view on the scoring |
| LocARNA::unordered_map< Key, T, Hash, Pred, Alloc > | |
| LocARNA::unordered_set< Key, Hash, Pred, Alloc > | |
| LocARNA::wrong_format_failure | Thrown, when reading data that is not in the supposed format |
1.7.6.1
