LocARNA-1.8.11
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▼NLocARNA | |
CAligner | Implements locarna alignment algorithm |
►CAlignerImpl | Implementation of Aligner |
►CAlignerN | Implements SPARSE, next generation alignment algorithm for locarna |
CAlignerNParams | Parameters for AlignerN |
CAlignerP | Computes partition function of alignment, arc match and base match probabilities |
CAlignerParams | Parameter for alignment by Aligner |
CAlignerPParams | Parameters for AlignerP |
CAlignerRestriction | Restricts range of an alignment in Aligner |
CAlignment | Represents a structure-annotated sequence alignment |
CAlignmentEdges | Pair of vector of alignment edges |
CAlignmentImpl | Implementation of Alignment |
CAlphabet | Specifies an alphabet |
CAnchorConstraints | Represents anchor constraints between two sequences |
CArcMatch | Represents a match of two base pairs (arc match) |
►CArcMatches | Maintains the relevant arc matches and their scores |
CArcMatchesIndexed | Class ArcMatches with additional mapping |
►CBasePairs | Describes sequence and structure ensemble of an RNA |
CBasePairs__Arc | Represents a base pair |
►CConfusionMatrix | Compare RNA secondary structure by their confusion matrix |
CDiscreteDistribution | |
CEdgeEnd | End of an alignment edge |
CEPM | Class for the representation of exact pattern matches (EPM) |
CExactMatcher | Computes exact pattern matchings (EPM) between two RNA sequences |
CExtRnaData | Represent sparsified data of RNA ensemble extended by in loop probabilities |
CExtRnaDataImpl | Implementation of ExtRnaData |
Cfailure | Simple exception class that supports a text message |
CFiniteInt | |
CFitOnOff | Implements fitting of a two-step function to a number sequence |
CFreeEndgapsDescription | Description of free end gaps |
CGap | "enum class" of gaps in alignment edges |
Cgreater_second | Implements comparison by member second |
CInftyInt | |
CLCSEPM | Computes the best chain of EPMs, the LCS-EPM |
CMatchController | Abstract class that declares the method is_valid_match() |
CMatchProbs | Provides probabilities for each match |
CMatrix | Simple 2D matrix class, provides access via operator (int,int) |
CMcC_ali_matrices_t | Alifold-McCaskill matrices |
CMcC_matrices_base | |
CMcC_matrices_t | McCaskill matrices |
►CMultipleAlignment | Represents a multiple alignment |
COMatrix | Simple matrix class with offset |
Coption_def | Definition structure of an option |
Cpair_of_size_t_hash | Function class definining hash function for pairs of size_t |
CPatternPair | Able to manage an EPM, consists of 2 singlepatterns, one in each RNA |
CPatternPairMap | Manage a set of EPMs (PatternPair) |
CPFoldParams | Parameters for partition folding |
Cplusvector | Implements a vector with += operator |
Cquadruple | Represents a 4-tuple |
Cquintuple | Represents a 5-tuple |
CRibofit | Family of Ribofit matrices |
CRibofit_will2014 | |
CRibosum | Represents ribosum similarity matrices |
CRibosumFreq | Represents ribosum similarity matrices including raw frequencies |
CRMatrix | Simple matrix class with restriction to a range |
CRnaData | Represent sparsified data of RNA ensemble |
►CRnaDataImpl | Implementation of RnaData |
CRnaEnsemble | Represents the raw structure ensemble data for an RNA |
CRnaEnsembleImpl | Implementation of RnaEnsemble |
CRnaStructure | An RNA secondary structure |
CRotMatrix | A matrix class with rotation |
CScoring | Provides methods for the scoring of alignments |
CScoringParams | Parameters for scoring |
CSequence | "Sequence View" of multiple alignment as array of column vectors |
CSequenceAnnotation | Annotation of a sequence |
CSinglePattern | Stores a Pattern in one sequence |
►CSparseMatrix | Represents a sparse 2D matrix |
CSparseTraceController | Combines the TraceController with the Mapper for both sequences |
►CSparseVector | Represents a sparse vector |
►CSparsificationMapper | Represents the mapping for sparsification |
CStopWatch | Control a set of named stop watch like timers |
CStralScore | Implements the stral-like scoring function |
Cstring1 | A simple 1-based string |
Csyntax_error_failure | Thrown, when the format is recognized but syntax is incorrect |
CTaintedInftyInt | |
CTraceController | Controls the matrix cells valid for traces |
CTraceRange | Represents a range of traces |
Ctriple | Represents a 3-tuple |
Ctype_wrapper | Generic type_wrapper class |
Cunordered_map | |
Cunordered_set | |
Cwrong_format_failure | Thrown, when reading data that is not in the supposed format |