ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner > Member List

This is the complete list of members for ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >, including all inherited members.

_alignDiv(seg_index_t id, const sequence_t &sequence, AlignmentType *vec) const (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inlineprotected
_alignJoi(seg_index_t id, const sequence_t &sequence, AlignmentType *vec) const (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inlineprotected
ymir::_alignments	ymir::VDJAlignment	protected
ymir::VDJAlignmentBuilder::_alignments	ymir::VDJAlignment	protected
_alignVar(seg_index_t id, const sequence_t &sequence, AlignmentType *vec) const	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inlineprotected
_D_Aligner (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	protected
_Dalign (defined in ymir::VDJAlignmentBuilder)	ymir::VDJAlignmentBuilder	protected
_Dseg (defined in ymir::VDJAlignmentBuilder)	ymir::VDJAlignmentBuilder	protected
_genes (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	protected
_good (defined in ymir::Clonotype)	ymir::Clonotype	protected
_J_Aligner (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	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
_params (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	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
_V_Aligner (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	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
alignDiv(seg_index_t id, const sequence_t &sequence) const (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
alignDiv() (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
alignJoi(seg_index_t id, const sequence_t &sequence) const (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
alignJoi() (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
alignVar(seg_index_t id, const sequence_t &sequence) const	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
alignVar()	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	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
set_genes(const VDJRecombinationGenes &genes) (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
set_parameters(VDJAlignerParameters params) (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
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
VDJAlignerBase() (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
VDJAlignerBase(const VDJRecombinationGenes &genes, VDJAlignerParameters params) (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inline
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
~VDJAlignerBase() (defined in ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >)	ymir::VDJAlignerBase< AlignmentType, V_Aligner, D_Aligner, J_Aligner >	inlinevirtual
~VDJAlignment()	ymir::VDJAlignment	inlineprotectedvirtual
~VDJAlignmentBuilder() (defined in ymir::VDJAlignmentBuilder)	ymir::VDJAlignmentBuilder	inlinevirtual