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NCBI C++ ToolKit: include/misc/hgvs/variation_util2.hpp Source File

& codon_from,

& prot_to,

vector<string>& codons_to);

!this->cdregion_feat ?

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

namespace ncbi::objects::

Cache seq-data in the CDS regions and the cds features by location.

void Get(const CSeq_loc &loc, TCdregions &cdregions)

map< CSeq_id_Handle, SSeqData > TSeqDataMap

vector< SCdregion > TCdregions

TSeqDataMap m_seq_data_map

map< CSeq_id_Handle, TRangeMap > TIdRangeMap

CCdregionIndex(CScope &scope, TOptions options)

CRangeMap< TCdregions, TSeqPos > TRangeMap

void x_Index(const CSeq_id_Handle &idh)

CRef< CSeq_literal > GetCachedLiteralAtLoc(const CSeq_loc &loc)

void x_CacheSeqData(const CSeq_loc &loc, const CSeq_id_Handle &idh)

Given a seq-loc, compute CVariantProperties::TGene_location from annotation.

static TLocsPair s_GetIntronsAndSpliceSiteLocs(const CSeq_loc &rna_loc)

pair< CRef< CSeq_loc >, CRef< CSeq_loc > > TLocsPair

static int s_GetGeneIdForProduct(CBioseq_Handle bsh)

void GetLocationProperties(const CSeq_loc &loc, TGeneIDAndPropVector &v)

CRangeMap< TGeneIDAndPropVector, TSeqPos > TRangeMap

pair< int, CVariantProperties::TGene_location > TGeneIDAndProp

CVariantPropertiesIndex(CScope &scope)

static TLocsPair s_GetNeighborhoodLocs(const CSeq_loc &gene_loc, TSeqPos max_pos)

static TLocsPair s_GetUTRLocs(const CSeq_loc &cds_loc, const CSeq_loc &parent_loc)

static TLocsPair s_GetStartAndStopCodonsLocs(const CSeq_loc &cds_loc)

static int s_GetGeneID(const CMappedFeat &mf, feature::CFeatTree &ft)

void x_Add(const CSeq_loc &loc, int gene_id, CVariantProperties::TGene_location prop)

map< CSeq_id_Handle, TRangeMap > TIdRangeMap

void x_Index(const CSeq_id_Handle &idh)

vector< TGeneIDAndProp > TGeneIDAndPropVector

CRef< CVariantPlacement > RemapToAnnotatedTarget(const CVariation &v, const CSeq_id &target)

Remap variation from product coordinates onto a nucleotide sequence on which this product is annotate...

static void s_AddInstOffsetsFromPlacementOffsets(CVariation_inst &vi, const CVariantPlacement &p)

static const CVariation::TPlacements * s_GetPlacements(const CVariation &v)

@ fAA2NA_truncate_common_prefix_and_suffix

void FindLocationProperties(const CSeq_align &transcript_aln, const CSeq_loc &query_loc, TSOTerms &terms)

Find location properties based on alignment.

CRef< CSeq_literal > GetLiteralAtLoc(const CSeq_loc &loc)

CRef< CVariation > x_AsVariation(const CVariation_ref &vr)

SFlankLocs CreateFlankLocs(const CSeq_loc &loc, TSeqPos len)

vector< ESOTerm > TSOTerms

CRef< CVariation > x_CreateUnknownVariation(const CSeq_id &id, CVariantPlacement::TMol mol)

bool CheckAmbiguitiesInLiterals(CVariation &v)

if variation.data contains a seq-literal with non-ACGT residues, attach VariationException to the fir...

static size_t s_CountMatches(const string &a, const string &b)

void x_AdjustDelinsToInterval(CVariation &v, const CSeq_loc &loc)

ETestStatus CheckExonBoundary(const CVariantPlacement &p, const CSeq_align &aln)

static void s_FactorOutPlacements(CVariation &v)

If at any level in variation-set all variations have all same placements, move them to the parent lev...

static CConstRef< CVariation > s_FindConsequenceForPlacement(const CVariation &v, const CVariantPlacement &p)

Find attached consequence variation in v that corresponds to p (has same seq-id).

CRef< CVariation > TranslateNAtoAA(const CVariation_inst &nuc_inst, const CVariantPlacement &p, const CSeq_feat &cds_feat)

Evaluate protein effect of a single-inst @ single-placement.

static string AsString(ESOTerm term)

static CRef< CSeq_literal > s_SpliceLiterals(const CSeq_literal &payload, const CSeq_literal &ref, TSeqPos pos)

insert seq-literal payload into ref before pos (pos=0 -> prepend; pos=ref.len -> append)

void x_SetVariantPropertiesForIntronic(CVariantPlacement &p, int offset, const CSeq_loc &loc, CBioseq_Handle &bsh)

bool AttachSeq(CVariantPlacement &p, TSeqPos max_len=kMaxAttachSeqLen)

If have offsets (intronic) or too long, return false; else set seq field on the placement and return ...

CRef< CVariation > AsVariation(const CSeq_feat &variation_ref)

@ fOpt_cache_exon_sequence

Use when there will be many calls to calculate protein consequnece per sequence.

void x_ChangeToDelins(CVariation &v)

void x_SetVariantProperties(CVariantProperties &p, const CVariation_inst &vi, const CSeq_loc &loc)

CVariationUtil(CScope &scope, TOptions options=fOpt_default)

bool CheckPlacement(CVariantPlacement &p)

if placement is invalid SeqLocCheck fails, or offsets out of order, attach VariationException and ret...

static void s_AddIntronicOffsets(CVariantPlacement &p, const CSpliced_seg &ss, CScope *scope)

CVariantPlacement::TMol GetMolType(const CSeq_id &id)

void x_InferNAfromAA(CVariation &v, TAA2NAFlags flags)

static string s_CollapseAmbiguities(const vector< string > &seqs)

static void s_FindLocationProperties(CConstRef< CSeq_loc > rna_loc, CConstRef< CSeq_loc > cds_loc, const CSeq_loc &query_loc, TSOTerms &terms)

void ChangeToDelins(CVariation &v)

static void s_ResolveIntronicOffsets(CVariantPlacement &p)

static void s_UntranslateProt(const string &prot_str, vector< string > &codons)

void AsSOTerms(const CVariantProperties &p, TSOTerms &terms)

static void s_AttachGeneIDdbxref(CVariantPlacement &p, int gene_id)

static const CConstRef< CSeq_literal > s_FindFirstLiteral(const CVariation &v)

CRef< CSeq_literal > x_GetLiteralAtLoc(const CSeq_loc &loc)

CRef< CVariation > InferNAfromAA(const CVariation &prot_variation, TAA2NAFlags flags=fAA2NA_default)

void FlipStrand(CVariation &v) const

Other utility methods:

void SetPlacementProperties(CVariantPlacement &placement)

Methods to compute properties.

CVariantPropertiesIndex m_variant_properties_index

CRef< CVariation_ref > x_AsVariation_ref(const CVariation &v, const CVariantPlacement &p)

CRef< CVariantPlacement > Remap(const CVariantPlacement &p, const CSeq_align &aln, bool check_placements=true)

Methods to remap a VariantPlacement.

static bool s_IsInstStrandFlippable(const CVariation &v, const CVariation_inst &inst)

CCdregionIndex m_cdregion_index

static TSeqPos s_GetLength(const CVariantPlacement &p, CScope *scope)

ESOTerm

Supported SO-terms.

@ eSO_splice_acceptor_variant

@ eSO_nc_transcript_variant

@ eSO_initiator_codon_variant

@ eSO_coding_sequence_variant

@ eSO_2KB_upstream_variant

@ eSO_splice_donor_variant

@ eSO_3_prime_UTR_variant

@ eSO_5_prime_UTR_variant

@ eSO_500B_downstream_variant

@ eSO_terminator_codon_variant

TSeqPos GetEffectiveTranscriptLength(const CBioseq_Handle &bsh)

Length up to last position of the last exon (i.e.

void AttachProteinConsequences(CVariation &nuc_variation, const CSeq_id *=NULL, bool ignore_genomic=false)

Find the CDSes for the first placement; Compute prot consequence using TranslateNAtoAA for each and a...

void x_TranslateNAtoAA(CVariation &prot_variation)

CConstRef< CSeq_literal > x_FindOrCreateLiteral(const CVariation &v)

static void s_ConvertInstOffsetsToPlacementOffsets(CVariation &v, CVariantPlacement &p)

static const CConstRef< CSeq_literal > s_FindAssertedLiteral(const CVariation &v)

void AsVariation_feats(const CVariation &v, CSeq_annot::TData::TFtable &feats)

void SetVariantProperties(CVariation &v)

static CRef< CSeq_literal > s_CatLiterals(const CSeq_literal &a, const CSeq_literal &b)

join two seq-literals

int TAA2NAFlags

Methods to convert between nucleotide and protein.

void s_CalcPrecursorVariationCodon(const string &codon_from, const string &prot_to, vector< string > &codons_to)

CRef< CVariantPlacement > x_Remap(const CVariantPlacement &p, CSeq_loc_Mapper &mapper)

Include a standard set of the NCBI C++ Toolkit most basic headers.

const TResidue codons[4][4]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

list< CRef< CSeq_feat > > TFtable

list< CRef< CVariantPlacement > > TPlacements

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

bool operator<(const SCdregion &other) const

CConstRef< CSeq_feat > cdregion_feat

CRef< CSeq_loc_Mapper > mapper

Calculate upstream (first) and downstream(second) flanks for loc.

CRef< CSeq_loc > upstream

CRef< CSeq_loc > downstream

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