|
Ymir
.9
Fast\C++toolforcomputationofassemblingprobabilities,statisticalinferenceofassemblingstatisticalmodelandgenerationofartificialsequencesofT-cellreceptorsdata.
|
|
Ymir
.9
Fast\C++toolforcomputationofassemblingprobabilities,statisticalinferenceofassemblingstatisticalmodelandgenerationofartificialsequencesofT-cellreceptorsdata.
|
This is the complete list of members for ymir::MAAGBuilder, including all inherited members.
| _chain (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | protected |
| _err_prob (defined in ymir::MAAG) | ymir::MAAG | protected |
| _errors | ymir::MAAG | protected |
| _events | ymir::MAAG | protected |
| _genes (defined in ymir::MAAGBuilder) | ymir::MAAGBuilder | protected |
| _n_poses (defined in ymir::MAAG) | ymir::MAAG | protected |
| _param_vec (defined in ymir::MAAGBuilder) | ymir::MAAGBuilder | protected |
| _recomb (defined in ymir::MAAG) | ymir::MAAG | protected |
| _seq_poses | ymir::MAAG | protected |
| _seq_type | ymir::MAAG | protected |
| _sequence | ymir::MAAG | protected |
| _values (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | protected |
| addNode() | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| addNode(matrix_ind_t n_matrices, dim_t rows, dim_t cols) (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| at(node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| at(node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| build(const Clonotype &clonotype, MetadataMode metadata_mode, ErrorMode error_mode, SequenceType seq_type=NUCLEOTIDE) const | ymir::MAAGBuilder | inline |
| build(const ClonesetView &cloneset, MetadataMode metadata_mode, ErrorMode error_mode, SequenceType seq_type=NUCLEOTIDE, bool verbose=true) const (defined in ymir::MAAGBuilder) | ymir::MAAGBuilder | inline |
| buildAndCompute(const Clonotype &clonotype, ErrorMode error_mode, SequenceType seq_type=NUCLEOTIDE, MAAGComputeProbAction action=SUM_PROBABILITY) const | ymir::MAAGBuilder | inline |
| buildAndCompute(const ClonesetView &cloneset, ErrorMode error_mode, SequenceType seq_type=NUCLEOTIDE, MAAGComputeProbAction action=SUM_PROBABILITY, bool verbose=true) const (defined in ymir::MAAGBuilder) | ymir::MAAGBuilder | inline |
| buildDiversity(const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, ErrMMC &errors, vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const | ymir::MAAGBuilder | inlineprotected |
| buildDJinsertions(const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, const vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const | ymir::MAAGBuilder | inlineprotected |
| buildInsertions(const string &sequence, ProbMMC &probs, EventIndMMC &events, const vector< seq_len_t > &seq_poses, ProbMMC::node_ind_t ins_node_index, event_ind_t null_insertion, seq_len_t max_size, MetadataMode metadata_mode, bool error_mode, seq_len_t left_vertices_start, seq_len_t left_vertices_end, seq_len_t right_vertices_start, seq_len_t right_vertices_end, const AbstractInsertionModel &mc, bool reversed=false) const | ymir::MAAGBuilder | inlineprotected |
| buildJoining(const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, ErrMMC &errors, vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const | ymir::MAAGBuilder | inlineprotected |
| buildVariable(const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, ErrMMC &errors, vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const | ymir::MAAGBuilder | inlineprotected |
| buildVDinsertions(const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, const vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const | ymir::MAAGBuilder | inlineprotected |
| buildVJinsertions(const Clonotype &clonotype, ProbMMC &probs, EventIndMMC &events, const vector< seq_len_t > &seq_poses, MetadataMode metadata_mode, ErrorMode error_mode) const | ymir::MAAGBuilder | inlineprotected |
| chainSize() const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| cols(node_ind_t node_i) const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| dim_t typedef | ymir::MultiMatrixChain< _Scalar > | protected |
| error_prob() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| errors(node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| event_index(node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| event_probability(node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const | ymir::MAAG | inlineprotected |
| fill(node_ind_t node, matrix_ind_t mat, _Scalar val=0) (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| finish() (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| fullProbability(event_ind_t v_index, event_ind_t j_index) const | ymir::MAAG | inlineprotected |
| fullProbability(event_ind_t v_index, event_ind_t d_index, event_ind_t j_index) const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| fullProbability(MAAGComputeProbAction action=SUM_PROBABILITY) const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| has_errors() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| has_events() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| initNode(node_ind_t node_i, matrix_ind_t n_matrices, dim_t rows, dim_t cols) (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| is_vdj() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| is_vj() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| load(const std::string &filepath) (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| load(std::istream &stream) (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| MAAG() | ymir::MAAG | inlineprotected |
| MAAG(const MAAG &other) (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| MAAG(MAAG &&other) (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| MAAGBuilder(const ModelParameterVector ¶m_vec, const VDJRecombinationGenes &genes) | ymir::MAAGBuilder | inline |
| MAAGBuilder() | ymir::MAAGBuilder | inlineprotected |
| matrix(node_ind_t node, matrix_ind_t mat) const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| matrix_ind_t typedef | ymir::MultiMatrixChain< _Scalar > | protected |
| matrix_t typedef | ymir::MultiMatrixChain< _Scalar > | protected |
| MultiMatrixChain() (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| n_poses() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| nDiv() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| nJoi() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| node_ind_t typedef | ymir::MultiMatrixChain< _Scalar > | protected |
| nodeColumns(node_ind_t node_i) const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| nodeRows(node_ind_t node_i) const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| nodeSize(node_ind_t node_i) const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| nVar() const | ymir::MAAG | inlineprotected |
| operator()(node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| operator()(node_ind_t node_i, matrix_ind_t mat_i, dim_t row, dim_t col) const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| operator=(const MAAG &other) (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| operator=(MAAG &&other) (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| operator[](size_t index) const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| position(seq_len_t i) const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| recombination() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| resize(node_ind_t n_nodes) (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| rows(node_ind_t node_i) const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| save(const std::string &filepath) const | ymir::MAAG | inlineprotected |
| save(std::ostream &stream) const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| sequence() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| sequence_type() const (defined in ymir::MAAG) | ymir::MAAG | inlineprotected |
| swap(MultiMatrixChain &other) (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| updateEventProbabilities(MAAG *maag) const | ymir::MAAGBuilder | inline |
| updateEventProbabilities(MAAGRepertoire *repertoire, bool verbose=true) const (defined in ymir::MAAGBuilder) | ymir::MAAGBuilder | inline |
| updateModelParameterVector(const ModelParameterVector ¶m_vec) (defined in ymir::MAAGBuilder) | ymir::MAAGBuilder | inline |
| values_size() const (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotected |
| ~MAAG() | ymir::MAAG | inlineprotectedvirtual |
| ~MAAGBuilder() (defined in ymir::MAAGBuilder) | ymir::MAAGBuilder | inlinevirtual |
| ~MultiMatrixChain() (defined in ymir::MultiMatrixChain< _Scalar >) | ymir::MultiMatrixChain< _Scalar > | inlineprotectedvirtual |
1.8.11
