Class Hierarchy

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

[detail level 1234]

▼Cymir::AbstractInsertionModel	Class for representing VJ / VD / DJ insertions models - either a mono-nucleotide or a di-nucleotide model
Cymir::DiNucInsertionModel
Cymir::MonoNucInsertionModel
▼Cymir::AbstractTDContainer
Cymir::TDMatrix
Cymir::TDMatrixList
Cymir::TDVector	Vector of gene segments
Cymir::TDVectorList	List of std::vectors for deletions and insertions
Cymir::StatisticalInferenceAlgorithm::AlgorithmParameters
▼Cymir::AlignmentBase
Cymir::GappedAlignment
Cymir::NoGapAlignment
Cymir::AlignmentColumnOptions
Cymir::AlignmentEventScore
Cymir::AlignmentMatrixBase< AlignmentType >
Cymir::AlignmentMatrixBase< GappedAlignmentVector >
▼Cymir::AlignmentVectorBase
Cymir::GappedAlignmentVector
Cymir::NoGapAlignmentVector
CBlockEMAlgorithm	Implementation of the online EM-algorithm for statistical inference of assembling model parameters
Cymir::CDR3AlignerFunctor_D
Cymir::CDR3AlignerFunctor_J
Cymir::CDR3AlignerFunctor_V
▼CCharReader
CJson::OurCharReader
▼Cymir::ClonesetView
Cymir::Cloneset
Cymir::ClonotypeAssembler
Cymir::CodonTable::Codons
Cymir::CodonTable	A struct for representing nucleotide codons for amino acids
CJson::CommentStyle	Scoped enums are not available until C++11
CEventIndMatrixChain	Class for storing chain of matrices of indices of scenario events
▼Cexception
▼CJson::Exception
CJson::LogicError
CJson::RuntimeError
▼Cymir::ForwardBackwardAlgorithm
Cymir::VD2JForwardBackward
Cymir::VDJForwardBackward
Cymir::VJForwardBackward
Cymir::GeneSegmentAlphabet::GeneSegment
Cymir::GeneSegmentAlphabet
Cymir::MAAGForwardBackwardAlgorithm
Cymir::Matrix< _Scalar, _Dim >	Simple matrix class
Cymir::ModelParameterVector	Class for storing parameters of assembling statistical model. Note: event with index 0 (zero) is "null" event and always has zero probability. Vector is ordered so for VJ or VDJ recombination specific family events stored in specific order
▼Cymir::ModelParser
Cymir::VDJModelParser
Cymir::VJModelParser
▼Cymir::MultiMatrixChain< _Scalar >	Class for storing lists of matrices, where one node in the list (called "chain") could contain more than one matrix
▼Cymir::MAAG	Multi-Alignment Assembly Graph - basic class for representing all possible generation scenarios of a nucleotide or amino acid sequence of an immune receptor
Cymir::MAAGBuilder
Cymir::NaiveCDR3AlignerFunctor_D
Cymir::NaiveCDR3AlignerFunctor_J
Cymir::NaiveCDR3AlignerFunctor_V
Cymir::MultiMatrixChain< _Scalar >::Node	Node in the chain. Stores one or more matrices with equal size
CNumErrorsMMC	Class for storing a number of errors for each scenario event
CJson::OurFeatures
CJson::OurReader
Cymir::ProbabilisticAssemblingModel
CProbMatrixChain	Class for storing chain of matrices of scenario event probabilities
Cymir::RepertoireParser< Aligner >	Parser for text files with repertoire data. By default it's MiTCR parser. To make new parsers inherit from this class and rewrite virtual private method "parseRepertoire"
Cymir::RepertoireParserStatistics
Cymir::RepertoireWriter
▼Cymir::StatisticalInferenceAlgorithm	Interface for algorithms for statistical inference of assembling model parameters
▼Cymir::EMAlgorithm	Implementation of the EM-algorithm for statistical inference of assembling model parameters. Classic version described in (Murugan et al 2012)
Cymir::SGAlgorithm
▼CStreamWriter
CJson::BuiltStyledStreamWriter
CJson::OurReader::StructuredError
Cymir::SWAlignerFunctor_D
Cymir::SWAlignerFunctor_VJ
Cymir::SWNGAlignerFunctor_D
Cymir::SWNGAlignerFunctor_J
Cymir::SWNGAlignerFunctor_V
Cymir::TestInfo
Cymir::VDJAlignerParameters
▼Cymir::VDJAlignment
▼Cymir::Clonotype
▼Cymir::ClonotypeBuilder
Cymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >
▼Cymir::VDJAlignmentBuilder
Cymir::ClonotypeBuilder
Cymir::VDJAlignmentEventScore
Cymir::VDJAlignmentScoreThreshold
Cymir::VDJRecombinationGenes