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NCBI C++ ToolKit: include/objtools/snputil/snp_utils.hpp Source File

IsSnp(

&feat);

ClinSigAsString(

& var, ELetterCase LetterCase = eLetterCase_Mixed);

ClinSigAsString(TClinSigID ClinSigID, ELetterCase LetterCase = eLetterCase_Mixed);

eSNPPropName_ResourceLinkURL

VariantPropAsStrings(list<string>& ResList,

& prop, ESNPPropTypes ePropType);

<

TVariation>

GetDeltas(list<string>& Alleles,

TVariation* pVariation);

<

TPVariation>

x_CommonConvertFeat(TPVariation pVariation,

& SrcFeat);

(!pVariation || !pVariation->CanGetData())

TVariation::TData& Data(pVariation->GetData());

TVariation::TData::TSet& Set(Data.GetSet());

(Set.CanGetVariations()) {

(

TVariation::TData::TSet::TVariations, iVariations, Set.GetVariations()) {

(Alleles, iVariations->GetPointer());

(Data.IsInstance()) {

VarInst(Data.GetInstance());

(VarInst.CanGetDelta()) {

((*iDelta)->CanGetSeq()) {

(DeltaSeq.

()) {

(!sAllele.empty())

Alleles.push_back(sAllele);

vector<string> alleles;

sAllelesTogether(

(alleles,

));

pVariation->SetDescription(

);

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.

namespace ncbi::objects::

CSnpBitfield is a facade for representing any version of the SNP bitfield.

EVariationClass GetVariationClass() const

void SetDeletionInsertion(const string &sequence, ESeqType seq_type)

Make this variant an insertion.

void SetSNV(const CSeq_data &nucleotide, CRef< CDelta_item > offset=null)

void SetMNP(const CSeq_data &nucleotide, TSeqPos length, CRef< CDelta_item > offset=null)

set of functions for dealing with SNP represented as variation objects

static void GetDeltas(list< string > &Alleles, const TVariation *pVariation)

add alleles to a list of strings from deltas in variation data

static bool x_CommonConvertFeat(TPVariation pVariation, const CSeq_feat &SrcFeat)

static const string sResourceLink_RsID

ESNPPropTypes

enums to control getting a string list representation of various CVariantProperties

@ eSNPPropName_GeneLocation

prop.gene-location

@ eSNPPropName_ResourceLink

prop.resource-link

@ eSNPPropName_QualityCheck

prop.quality-check

@ eSNPPropName_Mapping

prop.mapping

@ eSNPPropName_FreqValidation

prop.frequence-based-validation

@ eSNPPropName_Effect

prop.effect

static void DecodeBitfield(CVariantProperties &prop, const CSnpBitfield &bf)

convert SNP bitfield data to respective fields in CVariantProperties

static TRsid GetRsid(const CMappedFeat &mapped_feat)

Return rsid of SNP.

ELetterCase

controls the case of strings returned from ClinSigAsString()

@ eLetterCase_ForceLower

always use lower case only

CPhenotype::EClinical_significance EClinSigID

static CConstRef< CDbtag > GetTag(const CSeq_feat &SrcFeat)

find a SNP tag in the feature returns NULL if no such tag (sm_dbTag_dbSNP)

vector< string > TAlleles

list of alleles belonging to particular SNP a deletion is represented by a "-"

static bool IsSnp(const CMappedFeat &mapped_feat)

Determine if feature is a SNP.

static void GetAlleles(const CMappedFeat &mapped_feat, TAlleles &Alleles)

Return list of alleles encoded in qual.

static CSnpBitfield GetBitfield(const CMappedFeat &)

Return bitfield information stored in the feature.

static const string sm_dbTag_dbSNP

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

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const TPrim & Get(void) const

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

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

#define NCBI_SNPUTIL_EXPORT

const TIupacaa & GetIupacaa(void) const

Get the variant data.

bool IsIupacaa(void) const

Check if variant Iupacaa is selected.

const TIupacna & GetIupacna(void) const

Get the variant data.

bool CanGetSeq_data(void) const

Check if it is safe to call GetSeq_data method.

bool IsIupacna(void) const

Check if variant Iupacna is selected.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

const TInstance & GetInstance(void) const

Get the variant data.

E_Choice Which(void) const

Which variant is currently selected.

void SetData(TData &value)

Assign a value to Data data member.

const TData & GetData(void) const

Get the Data member data.

bool IsInstance(void) const

Check if variant Instance is selected.

const TLiteral & GetLiteral(void) const

Get the variant data.

EClinical_significance

does this variant have known clinical significance?

@ e_This

same location as variation-ref itself

AutoArray< int > TDelta

container for mass deltas

Defines: CTimeFormat - storage class for time format.

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