LocARNA-1.8.11
Class List
Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123]
 NLocARNA
 CAlignerImplements locarna alignment algorithm
 CAlignerImplImplementation of Aligner
 CAlignerNImplements SPARSE, next generation alignment algorithm for locarna
 CAlignerNParamsParameters for AlignerN
 CAlignerPComputes partition function of alignment, arc match and base match probabilities
 CAlignerParamsParameter for alignment by Aligner
 CAlignerPParamsParameters for AlignerP
 CAlignerRestrictionRestricts range of an alignment in Aligner
 CAlignmentRepresents a structure-annotated sequence alignment
 CAlignmentEdgesPair of vector of alignment edges
 CAlignmentImplImplementation of Alignment
 CAlphabetSpecifies an alphabet
 CAnchorConstraintsRepresents anchor constraints between two sequences
 CArcMatchRepresents a match of two base pairs (arc match)
 CArcMatchesMaintains the relevant arc matches and their scores
 CArcMatchesIndexedClass ArcMatches with additional mapping
 CBasePairsDescribes sequence and structure ensemble of an RNA
 CBasePairs__ArcRepresents a base pair
 CConfusionMatrixCompare RNA secondary structure by their confusion matrix
 CDiscreteDistribution
 CEdgeEndEnd of an alignment edge
 CEPMClass for the representation of exact pattern matches (EPM)
 CExactMatcherComputes exact pattern matchings (EPM) between two RNA sequences
 CExtRnaDataRepresent sparsified data of RNA ensemble extended by in loop probabilities
 CExtRnaDataImplImplementation of ExtRnaData
 CfailureSimple exception class that supports a text message
 CFiniteInt
 CFitOnOffImplements fitting of a two-step function to a number sequence
 CFreeEndgapsDescriptionDescription of free end gaps
 CGap"enum class" of gaps in alignment edges
 Cgreater_secondImplements comparison by member second
 CInftyInt
 CLCSEPMComputes the best chain of EPMs, the LCS-EPM
 CMatchControllerAbstract class that declares the method is_valid_match()
 CMatchProbsProvides probabilities for each match
 CMatrixSimple 2D matrix class, provides access via operator (int,int)
 CMcC_ali_matrices_tAlifold-McCaskill matrices
 CMcC_matrices_base
 CMcC_matrices_tMcCaskill matrices
 CMultipleAlignmentRepresents a multiple alignment
 COMatrixSimple matrix class with offset
 Coption_defDefinition structure of an option
 Cpair_of_size_t_hashFunction class definining hash function for pairs of size_t
 CPatternPairAble to manage an EPM, consists of 2 singlepatterns, one in each RNA
 CPatternPairMapManage a set of EPMs (PatternPair)
 CPFoldParamsParameters for partition folding
 CplusvectorImplements a vector with += operator
 CquadrupleRepresents a 4-tuple
 CquintupleRepresents a 5-tuple
 CRibofitFamily of Ribofit matrices
 CRibofit_will2014
 CRibosumRepresents ribosum similarity matrices
 CRibosumFreqRepresents ribosum similarity matrices including raw frequencies
 CRMatrixSimple matrix class with restriction to a range
 CRnaDataRepresent sparsified data of RNA ensemble
 CRnaDataImplImplementation of RnaData
 CRnaEnsembleRepresents the raw structure ensemble data for an RNA
 CRnaEnsembleImplImplementation of RnaEnsemble
 CRnaStructureAn RNA secondary structure
 CRotMatrixA matrix class with rotation
 CScoringProvides methods for the scoring of alignments
 CScoringParamsParameters for scoring
 CSequence"Sequence View" of multiple alignment as array of column vectors
 CSequenceAnnotationAnnotation of a sequence
 CSinglePatternStores a Pattern in one sequence
 CSparseMatrixRepresents a sparse 2D matrix
 CSparseTraceControllerCombines the TraceController with the Mapper for both sequences
 CSparseVectorRepresents a sparse vector
 CSparsificationMapperRepresents the mapping for sparsification
 CStopWatchControl a set of named stop watch like timers
 CStralScoreImplements the stral-like scoring function
 Cstring1A simple 1-based string
 Csyntax_error_failureThrown, when the format is recognized but syntax is incorrect
 CTaintedInftyInt
 CTraceControllerControls the matrix cells valid for traces
 CTraceRangeRepresents a range of traces
 CtripleRepresents a 3-tuple
 Ctype_wrapperGeneric type_wrapper class
 Cunordered_map
 Cunordered_set
 Cwrong_format_failureThrown, when reading data that is not in the supposed format