- _ -

• _alignVar() : ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >

- a -

• addAlignment() : ymir::NoGapAlignmentVector
• addNode() : ymir::MultiMatrixChain< _Scalar >
• addVarAlignment() : ymir::VDJAlignmentBuilder
• alignVar() : ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >
• appendPalindromicNucleotides() : ymir::GeneSegmentAlphabet , ymir::VDJRecombinationGenes

- b -

• build() : ymir::MAAGBuilder
• buildAndCompute() : ymir::MAAGBuilder
• buildClonotype() : ymir::ClonotypeBuilder
• buildDiversity() : ymir::MAAGBuilder
• buildDJinsertions() : ymir::MAAGBuilder
• buildGraphs() : ymir::ProbabilisticAssemblingModel
• buildInsertions() : ymir::MAAGBuilder
• buildJoining() : ymir::MAAGBuilder
• buildVariable() : ymir::MAAGBuilder
• buildVDinsertions() : ymir::MAAGBuilder
• buildVJinsertions() : ymir::MAAGBuilder

- c -

• computeFullProbabilities() : ymir::ProbabilisticAssemblingModel

- e -

• event_index() : ymir::ModelParameterVector
• event_probabilities() : ymir::ProbabilisticAssemblingModel
• event_probability() : ymir::MAAG

- f -

• fill() : ymir::ModelParameterVector
• fullProbability() : ymir::MAAG

- g -

• gene_segments() : ymir::ProbabilisticAssemblingModel
• generateSequences() : ymir::ProbabilisticAssemblingModel
• getVar() : ymir::VDJAlignment
• getVarGeneStart() : ymir::VDJAlignment

- i -

• isCoding() : ymir::Clonotype
• isMatch() : ymir::GappedAlignmentVector

- m -

• MAAG() : ymir::MAAG
• MAAGBuilder() : ymir::MAAGBuilder
• make_assembler() : ymir::ProbabilisticAssemblingModel
• make_builder() : ymir::ProbabilisticAssemblingModel
• ModelParameterVector() : ymir::ModelParameterVector

- n -

• normaliseEventFamilies() : ymir::ModelParameterVector
• nucProbability() : ymir::AbstractInsertionModel , ymir::DiNucInsertionModel , ymir::MonoNucInsertionModel
• numDivAlignments() : ymir::VDJAlignment
• nVar() : ymir::MAAG , ymir::VDJAlignment

- o -

• open() : ymir::RepertoireParser< Aligner >
• operator()() : ymir::MultiMatrixChain< _Scalar >
• operator[]() : ymir::ModelParameterVector

- p -

• parse() : ymir::RepertoireParser< Aligner >
• parseModelConfig() : ymir::ProbabilisticAssemblingModel
• ProbabilisticAssemblingModel() : ymir::ProbabilisticAssemblingModel
• pushEventValue() : ymir::MAAGForwardBackwardAlgorithm

- s -

• save() : ymir::MAAG , ymir::ProbabilisticAssemblingModel
• sequence() : ymir::Clonotype
• status() : ymir::ProbabilisticAssemblingModel

- t -

• toString() : ymir::Clonotype

- u -

• updateEventProbabilities() : ymir::MAAGBuilder , ymir::ProbabilisticAssemblingModel
• updateGeneUsage() : ymir::ProbabilisticAssemblingModel
• updateModelParameterVector() : ymir::ProbabilisticAssemblingModel

- v -

• VDJAlignment() : ymir::VDJAlignment
• VDJAlignmentBuilder() : ymir::VDJAlignmentBuilder

- w -

• write() : ymir::GeneSegmentAlphabet

- ~ -

• ~MAAG() : ymir::MAAG
• ~VDJAlignment() : ymir::VDJAlignment