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Ymir
.9
Fast\C++toolforcomputationofassemblingprobabilities,statisticalinferenceofassemblingstatisticalmodelandgenerationofartificialsequencesofT-cellreceptorsdata.
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Ymir
.9
Fast\C++toolforcomputationofassemblingprobabilities,statisticalinferenceofassemblingstatisticalmodelandgenerationofartificialsequencesofT-cellreceptorsdata.
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This is the complete list of members for ymir::ClonotypeBuilder, including all inherited members.
| ymir::_alignments | ymir::VDJAlignment | protected |
| ymir::VDJAlignmentBuilder::_alignments | ymir::VDJAlignment | protected |
| _Dalign (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | protected |
| _Dseg (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | protected |
| _good (defined in ymir::Clonotype) | ymir::Clonotype | protected |
| _Jalign (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | protected |
| ymir::_n_D_alignments | ymir::VDJAlignment | protected |
| ymir::VDJAlignmentBuilder::_n_D_alignments | ymir::VDJAlignment | protected |
| _n_Dalign (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | protected |
| _recomb (defined in ymir::Clonotype) | ymir::Clonotype | protected |
| _segments (defined in ymir::VDJAlignment) | ymir::VDJAlignment | protected |
| _segments (defined in ymir::VDJAlignment) | ymir::VDJAlignment | protected |
| _seq_type (defined in ymir::Clonotype) | ymir::Clonotype | protected |
| _sequence (defined in ymir::Clonotype) | ymir::Clonotype | protected |
| _Valign (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | protected |
| aa_sequence() const (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| addAlignment(GeneSegments gene, seg_index_t seg_index, seq_len_t genestart, seq_len_t seqstart, seq_len_t alignment_len) (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | inline |
| addDivAlignment(seg_index_t dseg, seq_len_t dstart, seq_len_t seqstart, seq_len_t alignment_len) (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | inline |
| addDivAlignment(const NoGapAlignmentVector &vec) (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | inline |
| addJoiAlignment(seg_index_t jseg, seq_len_t jstart, seq_len_t seqstart, seq_len_t alignment_len) (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | inline |
| addJoiAlignment(const NoGapAlignmentVector &vec) (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | inline |
| addVarAlignment(seg_index_t vseg, seq_len_t vstart, seq_len_t seqstart, seq_len_t alignment_len) | ymir::VDJAlignmentBuilder | inline |
| addVarAlignment(const NoGapAlignmentVector &vec) | ymir::VDJAlignmentBuilder | inline |
| buildAlignment() (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | inline |
| buildClonotype() | ymir::ClonotypeBuilder | inline |
| Clonotype(const sequence_t &sequence, SequenceType seq_type, Recombination recomb, const segments_storage_t &segments, const NoGapAlignmentVector &alignments, const n_D_alignments_storage_t &n_D_alignments) (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| Clonotype(const sequence_t &sequence, SequenceType seq_type, Recombination recomb, VDJAlignment alignment) (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| Clonotype() (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| ClonotypeBuilder() (defined in ymir::ClonotypeBuilder) | ymir::ClonotypeBuilder | inline |
| getDiv(size_t index) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getDiv(size_t index) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getDivGeneEnd(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getDivGeneEnd(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getDivGeneStart(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getDivGeneStart(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getDivLen(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getDivLen(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getDivSeqEnd(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getDivSeqEnd(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getDivSeqStart(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getDivSeqStart(seg_index_t dgene, seg_index_t align_i) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getJoi(size_t index) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getJoi(size_t index) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getJoiGeneEnd(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getJoiGeneEnd(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getJoiGeneStart(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getJoiGeneStart(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getJoiLen(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getJoiLen(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getJoiSeqEnd(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getJoiSeqEnd(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getJoiSeqStart(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getJoiSeqStart(seg_index_t jgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| ymir::getVar(size_t index) const | ymir::VDJAlignment | inlineprotected |
| ymir::VDJAlignmentBuilder::getVar(size_t index) const | ymir::VDJAlignment | inline |
| getVarGeneEnd(seg_index_t vgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getVarGeneEnd(seg_index_t vgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| ymir::getVarGeneStart(seg_index_t vgene) const | ymir::VDJAlignment | inlineprotected |
| ymir::VDJAlignmentBuilder::getVarGeneStart(seg_index_t vgene) const | ymir::VDJAlignment | inline |
| getVarLen(seg_index_t vgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getVarLen(seg_index_t vgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getVarSeqEnd(seg_index_t vgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getVarSeqEnd(seg_index_t vgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| getVarSeqStart(seg_index_t vgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| getVarSeqStart(seg_index_t vgene) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| is_good() const (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| isCoding() const | ymir::Clonotype | inlineprotected |
| isDivMismatch(seg_index_t dgene, seg_index_t align_i, seq_len_t pos) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| isDivMismatch(seg_index_t dgene, seg_index_t align_i, seq_len_t pos) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| isJoiMismatch(seg_index_t jgene, seq_len_t pos) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| isJoiMismatch(seg_index_t jgene, seq_len_t pos) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| isNoncoding() const (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| isOutOfFrame() const (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| isVarMismatch(seg_index_t vgene, seq_len_t pos) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| isVarMismatch(seg_index_t vgene, seq_len_t pos) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| n_D_alignments_storage_t typedef (defined in ymir::VDJAlignment) | ymir::VDJAlignment | protected |
| n_D_alignments_storage_t typedef (defined in ymir::VDJAlignment) | ymir::VDJAlignment | |
| nDiv() const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| nDiv() const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| nJoi() const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| nJoi() const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| nuc_sequence() const (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| ymir::numDivAlignments(seg_index_t index) const | ymir::VDJAlignment | inlineprotected |
| ymir::VDJAlignmentBuilder::numDivAlignments(seg_index_t index) const | ymir::VDJAlignment | inline |
| numDivMismatches(seg_index_t dgene, seg_index_t align_i, seq_len_t start, seq_len_t end) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| numDivMismatches(seg_index_t dgene, seg_index_t align_i, seq_len_t start, seq_len_t end) const (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| ymir::nVar() const | ymir::VDJAlignment | inlineprotected |
| ymir::VDJAlignmentBuilder::nVar() const | ymir::VDJAlignment | inline |
| operator!=(const VDJAlignment &other) (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| operator!=(const VDJAlignment &other) (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| operator==(const VDJAlignment &other) (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| operator==(const VDJAlignment &other) (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| recombination() const (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| segments_storage_t typedef (defined in ymir::VDJAlignment) | ymir::VDJAlignment | protected |
| segments_storage_t typedef (defined in ymir::VDJAlignment) | ymir::VDJAlignment | |
| seq_iterator(seq_len_t pos) const (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| sequence() const | ymir::Clonotype | inlineprotected |
| sequence_type() const (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotected |
| setAminoAcidSeq() (defined in ymir::ClonotypeBuilder) | ymir::ClonotypeBuilder | inline |
| setNucleotideSeq() (defined in ymir::ClonotypeBuilder) | ymir::ClonotypeBuilder | inline |
| setRecombination(Recombination recomb) (defined in ymir::ClonotypeBuilder) | ymir::ClonotypeBuilder | inline |
| setSequence(const std::string &seq) (defined in ymir::ClonotypeBuilder) | ymir::ClonotypeBuilder | inline |
| setSequenceType(SequenceType seq_type) (defined in ymir::ClonotypeBuilder) | ymir::ClonotypeBuilder | inline |
| toString() const | ymir::Clonotype | inlineprotected |
| VDJAlignment(const segments_storage_t &segments, const NoGapAlignmentVector &alignments, const n_D_alignments_storage_t &n_D_alignments) (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inlineprotected |
| ymir::VDJAlignment() | ymir::VDJAlignment | inlineprotected |
| VDJAlignment(const segments_storage_t &segments, const NoGapAlignmentVector &alignments, const n_D_alignments_storage_t &n_D_alignments) (defined in ymir::VDJAlignment) | ymir::VDJAlignment | inline |
| ymir::VDJAlignmentBuilder::VDJAlignment() | ymir::VDJAlignment | inlineprotected |
| VDJAlignmentBuilder() | ymir::VDJAlignmentBuilder | inline |
| ~Clonotype() (defined in ymir::Clonotype) | ymir::Clonotype | inlineprotectedvirtual |
| ~ClonotypeBuilder() (defined in ymir::ClonotypeBuilder) | ymir::ClonotypeBuilder | inlinevirtual |
| ~VDJAlignment() | ymir::VDJAlignment | inlineprotectedvirtual |
| ~VDJAlignmentBuilder() (defined in ymir::VDJAlignmentBuilder) | ymir::VDJAlignmentBuilder | inlinevirtual |
1.8.11
