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NCBI C++ ToolKit: src/misc/hgvs/variation_util.cpp Source File

* asserted_out,

have_asserted_seq =

;

(

.GetSeq_data().IsIupacna()) {

asserted_seq =

.GetSeq_data().GetIupacna();

have_asserted_seq =

;

}

(

.GetSeq_data().IsNcbieaa()) {

asserted_seq =

.GetSeq_data().GetNcbieaa();

have_asserted_seq =

;

prefix, suffix;

v.GetSeqData(v.begin(), v.end(), actual_seq);

*asserted_out = asserted_seq;

*actual_out = actual_seq;

is_intronic =

;

v.

().SetInstance().SetDelta().pop_front();

v.

().SetInstance().SetDelta().pop_front();

v.

().SetInstance().SetDelta().pop_back();

(

, eInvalidArg,

);

closest_start = 0;

closest_stop = 0;

closest_start = start;

(start != closest_start || stop != closest_stop) {

loc->

().SetFrom(closest_start);

loc->

().SetTo(closest_stop);

(start != closest_start) {

= start - closest_start;

->SetMultiplier(-1);

v.

().SetInstance().SetDelta().push_back(

);

v.

().SetInstance().SetDelta().push_front(

);

(stop != closest_stop && start != stop) {

= stop - closest_stop;

->SetMultiplier(-1);

v.

().SetInstance().SetDelta().push_front(

);

v.

().SetInstance().SetDelta().push_back(

);

(**it, mapper, variation_loc);

di.

().SetLoc().Assign(*merged_mapped_loc);

feat->

(variation_feat);

(

= 0;

< 2;

++) {

(target_row == -1) {

TExtLoc ext_loc(

TExtLoc::TObjectType);

ext_loc->SetId().SetStr(

);

feat->

().SetVariation().ResetLocation();

.SetInt().SetTo(start - 1);

(stop == max_pos) {

second.

().SetFrom(stop + 1);

(prot_str.size() != 1) {

* alphabet =

;

codon =

;

(

i0 = 0; i0 < 4; i0++) {

codon[0] = alphabet[i0];

(

i1 = 0; i1 < 4; i1++) {

codon[1] = alphabet[i1];

(

i2 = 0; i2 < 4; i2++) {

codon[2] = alphabet[i2];

(

== prot_str) {

(

= 0;

<

(

.size(),

.size());

++ ) {

(

[

] ==

[

]) {

& codon_from,

& prot_to,

vector<string>& codons_to)

vector<string> candidates1;

max_matches(0);

(vector<string>, it1, candidates1) {

(matches >= max_matches) {

(matches > max_matches) {

codons_to.push_back(*it1);

max_matches = matches;

collapsed_seq;

vector<string> TConstStrs;

(TConstStrs, it, seqs) {

& seq = *it;

(seq.size() > bits.size()) {

bits.resize(seq.size());

(

= 0;

< seq.size();

++) {

m = (nt ==

? 1

: nt ==

? 8 : 0);

* iupac_bases =

;

collapsed_seq.resize(bits.size());

(

= 0;

< collapsed_seq.size();

++) {

collapsed_seq[

] = iupac_bases[bits[

]];

collapsed_seq;

(!

.IsSetSeq() || !

.GetSeq().IsLiteral() ||

.GetSeq().GetLiteral().GetLength() != 1) {

(!prot2precursor_mapper) {

original_allele_codon;

vector<string> variant_codons;

(variant_codon.length() > 1 && variant_codon.at(0) == original_allele_codon.at(0)) {

variant_codon = variant_codon.substr(1);

original_allele_codon = variant_codon.substr(1);

nuc_loc->

().SetTo()--;

nuc_loc->

().SetFrom()++;

(variant_codon.length() > 1 &&

variant_codon.at(variant_codon.length() - 1) == original_allele_codon.at(original_allele_codon.length() - 1))

variant_codon.resize(variant_codon.length() - 1);

original_allele_codon.resize(variant_codon.length() - 1);

nuc_loc->

().SetFrom()++;

nuc_loc->

().SetTo()--;

delta2->SetSeq().SetLiteral().SetLength(variant_codon.length());

delta2->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(variant_codon);

inst2.

().push_back(delta2);

->SetLength(seq.length());

->SetSeq_data().SetNcbieaa().Set(seq);

->SetSeq_data().SetIupacna().Set(seq);

(

.GetLength() == 0) {

}

(

.GetLength() == 0) {

.GetSeq_data(), 0,

.GetLength(),

.GetSeq_data(), 0,

.GetLength());

(

.IsSetFuzz() ||

.IsSetFuzz()) {

(inst.

().size() == 0) {

di->SetSeq().SetLiteral().SetLength(0);

di->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(

);

}

(inst.

().size() > 1) {

di.

().SetLiteral().SetLength(0);

di.

().SetLiteral().SetSeq_data().SetIupacna().Set(

);

str_kernel =

.GetSeq_data().GetIupacna().Get();

.SetSeq_data().SetIupacna().Set(

);

.SetSeq_data().SetIupacna().Set() += str_kernel;

di.

().SetLiteral(*cat_literal);

(!loc.

()) {

(!inst.

().size() == 1) {

(!

.IsSetSeq() || !

.GetSeq().IsLiteral()) {

(prefix_loc, suffix_loc);

.SetSeq().SetLiteral(*tmp_literal2);

(!prot2nuc_mapper) {

(!v->IsSetLocation()) {

v->SetLocation().Assign(nuc_variation_feat.

());

(!v->GetLocation().GetId()) {

&

= *v->GetData().GetInstance().GetDelta().front();

have_frameshift = ((long)

(v->GetLocation(),

) - (

)

.GetSeq().GetLiteral().GetLength()) % 3 != 0;

codons_loc->

(*v->GetLocation().GetId());

&

= v->SetData().SetInstance().SetDelta().front()->SetSeq().SetLiteral();

prot_literal_len =

.GetLength() / 3;

.SetLength(prot_literal_len * 3);

.SetSeq_data().SetIupacna().Set().resize(

.GetLength());

prot_delta_str(

);

.GetSeq().GetLiteral().GetSeq_data().GetIupacna(),

prot_delta_str.resize(

.GetSeq().GetLiteral().GetLength() / 3);

.SetLength(prot_delta_str.size());

.SetSeq_data().SetNcbieaa().Set(prot_delta_str);

prot_ref_str(

);

v->SetVariant_prop().SetEffect(0);

(

.GetLength() == 0) {

v->SetData().SetInstance().SetDelta().clear();

}

(prot_delta_str.size() != prot_ref_str.size()) {

(prot_ref_str == prot_delta_str) {

(

= 0;

< prot_ref_str.size() &&

< prot_delta_str.size();

++) {

(prot_ref_str[

] == prot_delta_str[

]) {

}

(prot_ref_str[

] ==

) {

}

(prot_delta_str[

] ==

) {

prot_variation_feat->

().SetVariation(*v);

(have_frameshift) {

uo->

().SetStr(

);

uo->

(

, prot_ref_str);

(!v->IsSetVariant_prop() || !v->GetVariant_prop().IsSetVersion()) {

(v->IsSetVariant_prop() && v->GetVariant_prop().GetEffect() == 0) {

v->SetVariant_prop().ResetEffect();

prot_variation_feat;

have_offsets =

;

observation_vr.

(&vr2);

(!have_offsets) {

(!observation_vr) {

v.

().SetSet().SetVariations().push_back(observation_vr);

di->SetSeq().SetLiteral(*

);

observation_vr->SetData().SetInstance().SetDelta().clear();

observation_vr->SetData().SetInstance().SetDelta().push_back(di);

;

;

;

;

;

;

;

;

;

;

;

;

;

;

;

overlaps_gene_range =

;

overlaps_rna_range =

;

overlaps_cds_range =

;

(ci->GetData().IsGene()) {

overlaps_gene_range =

;

}

(ci->GetData().IsRna()) {

overlaps_rna_range =

;

}

(ci->GetData().IsCdregion()) {

overlaps_cds_range =

;

((ci->GetData().IsRna() || ci->GetData().IsCdregion()) && !have_overlap)

(ci->GetData().IsCdregion()) {

found_any_cds =

;

(

ci(bsh, sel); ci; ++ci) {

(ci->GetData().IsCdregion()) {

found_any_cds =

;

(!found_any_cds) {

&& !overlaps_rna_range

&& !overlaps_cds_range

&& overlaps_gene_range)

cds.

(&ci->GetMappedFeature());

}

(ci->GetData().IsRna()) {

(!overlaps_rna_range

&& !overlaps_cds_range

&& !overlaps_gene_range

found_in_neighborhood =

;

(

ci(*

, *neighborhood_loc, gene_sel); ci; ++ci) {

& gene_loc = ci->GetLocation();

found_in_neighborhood =

;

found_in_neighborhood =

;

(!found_in_neighborhood) {

(offset < 0 && offset >= -2) {

}

(vi.

().size() <= 1) {

nuc_vf->

().SetVariation().SetData().SetInstance().Assign(vi);

found_inst =

;

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.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

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.

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.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

namespace ncbi::objects::

static TSeqPos Convert(const CSeq_data &in_seq, CSeq_data *out_seq, CSeq_data::E_Choice to_code, TSeqPos uBeginIdx=0, TSeqPos uLength=0, bool bAmbig=false, Uint4 seed=17734276)

static TSeqPos Append(CSeq_data *out_seq, const CSeq_data &in_seq1, TSeqPos uBeginIdx1, TSeqPos uLength1, const CSeq_data &in_seq2, TSeqPos uBeginIdx2, TSeqPos uLength2)

Template class for iteration on objects of class C.

CUser_object & AddField(const string &label, const string &value, EParseField parse=eParse_String)

add a data field to the user object that holds a given value

const TLocation & GetLocation(void) const

void SetLocation(TLocation &value)

bool IsSetLocation(void) const

NOTE: THESE ARE GOING AWAY SOON!!

TExt_locs & SetExt_locs(void)

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

void ChangeToDelins(CVariation_ref &v)

static const int m_variant_properties_schema_version

static void s_AddIntronicOffsets(CVariation_ref &v, const CSpliced_seg &ss, const CSeq_loc &parent_variation_loc)

void AdjustDelinsToInterval(CVariation_ref &delins_variation, const CSeq_loc &int_loc)

CRef< CSeq_literal > x_GetLiteralAtLoc(const CSeq_loc &loc)

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

vector< ESOTerm > TSOTerms

static void s_FactorOutLocsInPlace(CVariation_ref &v)

CRef< CSeq_feat > ProtToPrecursor(const CSeq_feat &prot_variation_feat)

Convert protein-variation (single-AA missense/nonsense) to nuc-variation on the parent.

CRef< CSeq_feat > PrecursorToProt(const CSeq_feat &prot_variation_feat)

Convert to nuc-variation on the parent to protein-variation (single-AA missense/nonsense) Only a subs...

static void s_PropagateLocsInPlace(CVariation_ref &v)

Propagate parent variation location to the members of set, unles they have their own location set.

CRef< CSeq_feat > Remap(const CSeq_feat &variation_feat, const CSeq_align &aln)

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

static void s_Remap(CVariation_ref &vr, CSeq_loc_Mapper &mapper, const CSeq_loc &parent_variation_loc)

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

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

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

ETestStatus CheckExonBoundary(const CSeq_feat &variation_feat, const CSeq_align &aln)

bool SetReferenceSequence(CVariation_ref &vr, const CSeq_loc &location)

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

ESOTerm

Supported SO-terms.

@ eSO_5_prime_UTR_variant

@ eSO_coding_sequence_variant

@ eSO_splice_acceptor_variant

@ eSO_nc_transcript_variant

@ eSO_splice_donor_variant

@ eSO_2KB_upstream_variant

@ eSO_3_prime_UTR_variant

@ eSO_non_synonymous_codon

@ eSO_500B_downstream_variant

void SetVariantProperties(CVariantProperties &prop, const CSeq_loc &orig_loc)

Set location-specific variant-properties.

static string AsString(ESOTerm term)

static void s_ResolveIntronicOffsets(CVariation_ref &v, const CSeq_loc &parent_variation_loc)

SFlankLocs CreateFlankLocs(const CSeq_loc &loc, TSeqPos len)

void x_ProtToPrecursor(CVariation_ref &v)

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

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

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

const TResidue codons[4][4]

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

#define MSerial_AsnText

I/O stream manipulators –.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

const string AsFastaString(void) const

ENa_strand GetStrand(void) const

Get the location's strand.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Override Assign() to incorporate cache invalidation.

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CRef< CSeq_loc > Merge(TOpFlags flags, ISynonymMapper *syn_mapper) const

All functions create and return a new seq-loc object.

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

CRef< CSeq_loc > Subtract(const CSeq_loc &other, TOpFlags flags, ISynonymMapper *syn_mapper, ILengthGetter *len_getter) const

Subtract seq-loc from this, merge/sort resulting ranges depending on flags.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

void SetStrand(ENa_strand strand)

Set the strand for all of the location's ranges.

void SetNull(void)

Override all setters to incorporate cache invalidation.

TSeqPos GetStop(ESeqLocExtremes ext) const

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

CMappedFeat GetBestCdsForMrna(const CMappedFeat &mrna_feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0)

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

sequence::ECompare Compare(const CSeq_loc &loc1, const CSeq_loc &loc2, CScope *scope)

Returns the sequence::ECompare containment relationship between CSeq_locs.

CRef< CSeq_loc > Seq_loc_Subtract(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Subtract the second seq-loc from the first one.

CRef< CSeq_loc > Seq_loc_Merge(const CSeq_loc &loc, CSeq_loc::TOpFlags flags, CScope *scope)

Merge ranges in the seq-loc.

CRef< CSeq_loc > Seq_loc_Add(const CSeq_loc &loc1, const CSeq_loc &loc2, CSeq_loc::TOpFlags flags, CScope *scope)

Add two seq-locs.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

@ eNoOverlap

CSeq_locs do not overlap or abut.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

@ fIs5PrimePartial

= 0x4 Translate first codon even if not start codon (because sequence is 5' partial)

CRef< CSeq_loc > Map(const CSeq_loc &src_loc)

Map seq-loc.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

@ eProductToLocation

Map from the feature's product to location.

@ eLocationToProduct

Map from the feature's location to product.

TInst_Length GetInst_Length(void) const

TMol GetBioseqMolType(void) const

Get some values from core:

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & SetOverlapTotalRange(void)

Check overlapping only of total ranges.

SAnnotSelector & IncludeFeatType(TFeatType type)

Include feature type in the search.

SAnnotSelector & SetIgnoreStrand(bool value=true)

Ignore strand when testing for range overlap.

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

bool IsProtein(void) const

const_iterator begin(void) const

bool IsNucleotide(void) const

const_iterator end(void) const

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CTempString literal(const char(&str)[Size])

Templatized initialization from a string literal.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

size_type size(void) const

Return the length of the represented array.

void SetType(TType &value)

Assign a value to Type data member.

const TProtpos & GetProtpos(void) const

Get the variant data.

const TGenomic_id & GetGenomic_id(void) const

Get the Genomic_id member data.

TGenomic_start GetGenomic_start(void) const

Get the Genomic_start member data.

TAmin GetAmin(void) const

Get the Amin member data.

const TProduct_start & GetProduct_start(void) const

Get the Product_start member data.

const TProduct_end & GetProduct_end(void) const

Get the Product_end member data.

const TSpliced & GetSpliced(void) const

Get the variant data.

list< CRef< CSpliced_exon > > TExons

const TExons & GetExons(void) const

Get the Exons member data.

TGenomic_end GetGenomic_end(void) const

Get the Genomic_end member data.

bool IsSpliced(void) const

Check if variant Spliced is selected.

bool IsNucpos(void) const

Check if variant Nucpos is selected.

TNucpos GetNucpos(void) const

Get the variant data.

const TSegs & GetSegs(void) const

Get the Segs member data.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

bool IsVariation(void) const

Check if variant Variation is selected.

const TVariation & GetVariation(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

bool IsInt(void) const

Check if variant Int is selected.

bool IsPnt(void) const

Check if variant Pnt is selected.

@ eNa_strand_both

in forward orientation

const TIupacaa & GetIupacaa(void) const

Get the variant data.

void SetLength(TLength value)

Assign a value to Length data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

TLength GetLength(void) const

Get the Length member data.

void SetFuzz(TFuzz &value)

Assign a value to Fuzz data member.

@ e_Iupacaa

IUPAC 1 letter amino acid code.

const TInstance & GetInstance(void) const

Get the variant data.

const TVariant_prop & GetVariant_prop(void) const

Get the Variant_prop member data.

TAction GetAction(void) const

Get the Action member data.

void ResetGene_location(void)

Reset Gene_location data member.

list< CRef< CVariation_ref > > TVariations

TObservation GetObservation(void) const

Get the Observation member data.

const TSet & GetSet(void) const

Get the variant data.

TType GetType(void) const

Get the Type member data.

bool IsSetSeq(void) const

Check if a value has been assigned to Seq data member.

bool IsSetAction(void) const

Check if a value has been assigned to Action data member.

const TLoc & GetLoc(void) const

Get the variant data.

TEffect GetEffect(void) const

Get the Effect member data.

void SetObservation(TObservation value)

Assign a value to Observation data member.

bool IsSetVersion(void) const

Check if a value has been assigned to Version data member.

const TDelta & GetDelta(void) const

Get the Delta member data.

void SetVersion(TVersion value)

Assign a value to Version data member.

void SetMultiplier_fuzz(TMultiplier_fuzz &value)

Assign a value to Multiplier_fuzz data member.

void SetData(TData &value)

Assign a value to Data data member.

const TData & GetData(void) const

Get the Data member data.

const TSeq & GetSeq(void) const

Get the Seq member data.

bool IsInstance(void) const

Check if variant Instance is selected.

const TLiteral & GetLiteral(void) const

Get the variant data.

void SetVariant_prop(TVariant_prop &value)

Assign a value to Variant_prop data member.

void ResetAction(void)

Reset Action data member.

bool IsSet(void) const

Check if variant Set is selected.

void SetType(TType value)

Assign a value to Type data member.

void SetSeq(TSeq &value)

Assign a value to Seq data member.

TMultiplier GetMultiplier(void) const

Get the Multiplier member data.

bool IsSetMultiplier_fuzz(void) const

Check if a value has been assigned to Multiplier_fuzz data member.

list< CRef< CDelta_item > > TDelta

bool IsLiteral(void) const

Check if variant Literal is selected.

void SetGene_location(TGene_location value)

Assign a value to Gene_location data member.

bool IsSetMultiplier(void) const

Multiplier allows representing a tandem, e.g.

void ResetMultiplier(void)

Reset Multiplier data member.

bool IsSetObservation(void) const

Check if a value has been assigned to Observation data member.

bool IsSetEffect(void) const

Check if a value has been assigned to Effect data member.

TDelta & SetDelta(void)

Assign a value to Delta data member.

void SetEffect(TEffect value)

Assign a value to Effect data member.

bool IsThis(void) const

Check if variant This is selected.

TGene_location GetGene_location(void) const

Get the Gene_location member data.

bool IsSetGene_location(void) const

Check if a value has been assigned to Gene_location data member.

bool IsLoc(void) const

Check if variant Loc is selected.

@ eType_snv

delta=[morph of length 1] NOTE: this is snV not snP; the latter requires frequency-based validation t...

@ eType_mnp

delta=[morph of length >1]

@ eType_delins

delta=[del, ins]

@ eType_prot_nonsense

delta=[del]; variation-location is the tail of the protein being truncated

@ eType_prot_other

delta=any

@ eType_prot_silent

delta=[morph of length 1, same AA as at variation-location]

@ eType_identity

delta=[]

@ eType_prot_missense

delta=[morph of length 1]

@ eEffect_stop_gain

reference codon is not stop codon, but the snp variant allele changes the codon to a terminating codo...

@ eEffect_missense

one allele in the set changes protein peptide (0x4)

@ eEffect_nonsense

one allele in the set changes to STOP codon (TER). (0x2)

@ eEffect_stop_loss

reverse of STOP-GAIN: reference codon is a stop codon, but a snp variant allele changes the codon to ...

@ eEffect_synonymous

one allele in the set does not change the encoded amino acid (0x1)

@ eEffect_frameshift

one allele in the set changes all downstream amino acids (0x8)

@ eGene_location_in_start_codon

the variant is observed in a start codon (0x100)

@ eGene_location_acceptor

In acceptor splice-site (0x20)

@ eGene_location_near_gene_5

Within 2kb of the 5' end of a gene feature.

@ eGene_location_near_gene_3

Within 0.5kb of the 3' end of a gene feature.

@ eGene_location_utr_3

In 3' UTR (0x80)

@ eGene_location_in_gene

Sequence intervals covered by a gene ID but not having an aligned transcript (0x01)

@ eGene_location_utr_5

In 5' UTR (0x40)

@ eGene_location_intron

In Intron (0x08)

@ eGene_location_intergenic

variant located between genes (0x400)

@ eGene_location_donor

In donor splice-site (0x10)

@ eGene_location_in_stop_codon

the variant is observed in a stop codon (0x200)

@ eGene_location_conserved_noncoding

variant is located in a conserved non-coding region (0x800)

@ eAction_offset

go downstream by distance specified by multiplier (upstream if < 0), in genomic context.

@ eAction_morph

replace len(seq) positions starting with location.start with seq

@ eAction_del_at

excise sequence at location if multiplier is specified, delete len(location)*multiplier positions dow...

@ eAction_ins_before

insert seq before the location.start

@ eData_set_type_package

set represents a package of observations at a given location, generally containing asserted + referen...

@ eObservation_variant

inst represent the observed variant at a given position

@ eObservation_asserted

inst represents the asserted base at a position

@ eObservation_reference

inst represents the reference base at the position

double value_type

The numeric datatype used by the parser.

bool IsFirstSubsetOfSecond(const CSeq_loc &aa, const CSeq_loc &bb)

Defines command line argument related classes.

Int4 delta(size_t dimension_, const Int4 *score_)

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

CRef< CSeq_loc > downstream

CRef< CSeq_loc > upstream

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