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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/snp__utils_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/snputil/snp_utils.cpp Source File

& dbtag =

.GetTag();

(dbtag.IsStr() && (string::npos != dbtag.GetStr().find(

))) {

NStr::StringToNumeric<NSnp::TRsid>(dbtag.GetStr().substr(2));

dbtag.GetId8();

length = rc +

+ 1;

((*pnt_iter)->CanGetClinical_significance()) {

((*pnt_iter)->GetClinical_significance(), LetterCase);

sResult =

;

sResult =

;

sResult =

;

sResult =

;

sResult =

;

sResult =

;

sResult =

;

isRefAlleleEmpty{

};

isAnyAltAlleleEmpty{

};

Alleles.reserve(feat.

().size());

(qual.

() ==

) {

sQualVal(qual.

());

Alleles.push_back(sQualVal.empty() ?

: sQualVal);

(sQualVal.empty()) {

(it == feat.

().begin()) {

isRefAlleleEmpty =

;

isAnyAltAlleleEmpty =

;

(isPadding && bsh && (isRefAlleleEmpty || isAnyAltAlleleEmpty)) {

(isRefAlleleEmpty ? 0 : -1);

(

& allele: Alleles) {

allele = allele ==

? sPadding : sPadding + allele;

isKnown =

;

(; feat_it && !isKnown; ++feat_it) {

(qual->

() ==

&&

qual->

().find(allele) != string::npos) {

Variation.

().push_back(pExt);

gene_location = 0;

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

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);

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);

ResList.push_back(

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);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

ResList.push_back(

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

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.

size_t GetSize(void) const

CTime AsCTime(CTime::ETimeZone tz=CTime::eLocal) const

@Gb_qual.hpp User-defined methods of the data storage class.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

ESubtype GetSubtype(void) const

namespace ncbi::objects::

CConstRef< CDbtag > GetNamedDbxref(const CTempString &db) const

Return a specified DB xref.

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

bool IsTrue(EProperty prop) const

@ eHasSnp3D

Has 3D structure SNP3D.

@ eHasLinkOut

Has SubmitterLinkOut From SNP->SubSNP->Batch.link_out.

@ eIsMutation

! temp here for backward compatibility; remove once a jump to SC11 is done

CConstRef< CUser_field > GetFieldRef(const string &str, const string &delim=".", NStr::ECase use_case=NStr::eCase) const

CUser_field & SetField(const string &str, const string &delim=".", const string &obj_subtype=kEmptyStr, NStr::ECase use_case=NStr::eCase)

Access a named field in this user object.

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

static const string sResourceLink_RsID

static bool ConvertFeat(CVariation &Variation, const CSeq_feat &SrcFeat)

legacy SNP feature conversion into a variation object

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

@ eSNPPropName_ResourceLinkURL

generate URL templates, with one of sResourceLink_ substrings potentially inside

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

convert SNP bitfield data to respective fields in CVariantProperties

static void VariantPropAsStrings(list< string > &ResList, const CVariantProperties &prop, ESNPPropTypes ePropType)

get lists of strings corresponding to a given property type

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

static int GetLength(const CMappedFeat &)

Return distance of neighbors in flanking sequence.

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 CTime GetCreateTime(const CMappedFeat &mapped_feat)

Get Create Time It will fetch the creation time based on the CAnnotDescr of the feature's parent anno...

static const string sm_dbTag_dbSNP

static bool IsSnpKnown(CScope &scope, const CMappedFeat &private_snp, const string &allele=kEmptyStr)

Check if SNP exists in GenBank database.

static string ClinSigAsString(const CVariation_ref &var, ELetterCase LetterCase=eLetterCase_Mixed)

get a human-readable text for various clinical significance types

static const char * str(char *buf, int n)

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define MSerial_AsnText

I/O stream manipulators –.

TRange GetTotalRange(void) const

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

TSeqPos GetStop(ESeqLocExtremes ext) const

const CSeq_annot_Handle & GetAnnot(void) const

Get handle to seq-annot for this feature.

const CSeq_annot::TDesc & Seq_annot_GetDesc(void) const

bool Seq_annot_CanGetDesc(void) const

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetOverlapTotalRange(void)

Check overlapping only of total ranges.

const CSeq_loc & GetLocation(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

SAnnotSelector & SetExcludeExternal(bool exclude=true)

External annotations for the Object Manger are annotations located in top level Seq-entry different f...

SAnnotSelector & SetAnnotType(TAnnotType type)

Set annotation type (feat, align, graph)

SAnnotSelector & SetMaxSize(TMaxSize max_size)

Set maximum number of annotations to find.

SAnnotSelector & AddNamedAnnots(const CAnnotName &name)

Add named annot to set of annots names to look for.

SAnnotSelector & SetFeatSubtype(TFeatSubtype subtype)

Set feature subtype (also set annotation and feat type)

SAnnotSelector & ExcludeUnnamedAnnots(void)

Add unnamed annots to set of annots names to exclude.

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

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

bool NotEmpty(void) const THROWS_NONE

Check if CConstRef is not empty – pointing to an object and has a non-null value.

position_type GetLength(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

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 & ToLower(string &str)

Convert string to lower case – string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

void SetClass(const TClass &value)

Assign a value to Class data member.

void SetData(TData &value)

Assign a value to Data data member.

const TVal & GetVal(void) const

Get the Val member data.

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

bool CanGetQual(void) const

Check if it is safe to call GetQual method.

bool IsSetExt(void) const

user defined structure extension Check if a value has been assigned to Ext data member.

const TQual & GetQual(void) const

Get the Qual member data.

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

vector< CRef< CGb_qual > > TQual

const TQual & GetQual(void) const

Get the Qual member data.

const TExt & GetExt(void) const

Get the Ext member data.

const TCreate_date & GetCreate_date(void) const

Get the variant data.

const Tdata & Get(void) const

Get the member data.

bool IsCreate_date(void) const

Check if variant Create_date is selected.

bool CanGet(void) const

Check if it is safe to call Get method.

list< CRef< CAnnotdesc > > Tdata

TExt & SetExt(void)

Assign a value to Ext data member.

TPlacements & SetPlacements(void)

Assign a value to Placements data member.

void SetLoc(TLoc &value)

Assign a value to Loc data member.

void SetQuality_check(TQuality_check value)

Assign a value to Quality_check data member.

TFrequency_based_validation GetFrequency_based_validation(void) const

Get the Frequency_based_validation member data.

void SetFrequency_based_validation(TFrequency_based_validation value)

Assign a value to Frequency_based_validation data member.

void SetGenotype(TGenotype value)

Assign a value to Genotype data member.

list< CRef< CPhenotype > > TPhenotype

void SetResource_link(TResource_link value)

Assign a value to Resource_link data member.

TEffect GetEffect(void) const

Get the Effect member data.

bool CanGetGene_location(void) const

Check if it is safe to call GetGene_location method.

void SetVersion(TVersion value)

Assign a value to Version data member.

TMapping GetMapping(void) const

Get the Mapping member data.

bool CanGetQuality_check(void) const

Check if it is safe to call GetQuality_check method.

const TPhenotype & GetPhenotype(void) const

Get the Phenotype member data.

bool CanGetFrequency_based_validation(void) const

Check if it is safe to call GetFrequency_based_validation method.

TResource_link GetResource_link(void) const

Get the Resource_link member data.

int TFrequency_based_validation

void SetGene_location(TGene_location value)

Assign a value to Gene_location data member.

bool CanGetEffect(void) const

Check if it is safe to call GetEffect method.

bool CanGetResource_link(void) const

Check if it is safe to call GetResource_link method.

TQuality_check GetQuality_check(void) const

Get the Quality_check member data.

void SetMapping(TMapping value)

Assign a value to Mapping data member.

void SetEffect(TEffect value)

Assign a value to Effect data member.

bool CanGetMapping(void) const

Check if it is safe to call GetMapping method.

TGene_location GetGene_location(void) const

Get the Gene_location member data.

@ eMapping_has_assembly_conflict

Weight 1 or 2 SNPs that map to different chromosomes on different assemblies (0x02)

@ eMapping_has_other_snp

Another SNP has the same mapped positions on reference assembly (0x01)

@ eMapping_is_assembly_specific

Only maps to 1 assembly (0x04)

@ eGenotype_has_genotypes

SNP has individual genotype (0x02)

@ eGenotype_in_haplotype_set

Exists in a haplotype tagging set (0x01)

@ eFrequency_based_validation_above_5pct_1plus

>5% minor allele freq in 1+ populations (0x04)

@ eFrequency_based_validation_validated

Bit is set if the variant has a minor allele observed in two or more separate chromosomes.

@ eFrequency_based_validation_above_1pct_all

>1% minor allele freq in each and all populations (0x10)

@ eFrequency_based_validation_above_5pct_all

>5% minor allele freq in each and all populations (0x02)

@ eFrequency_based_validation_above_1pct_1plus

>1% minor allele freq in 1+ populations (0x20)

@ eFrequency_based_validation_is_mutation

low frequency variation that is cited in journal or other reputable sources (0x01)

@ eEffect_stop_gain

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

@ eEffect_down_regulator

the variant causes decreased transcription (0x20)

@ 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_up_regulator

the variant causes increased transcription (0x10)

@ eEffect_no_change

known to cause no functional changes since 0 does not combine with any other bit value,...

@ 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)

@ eQuality_check_genotype_conflict

Has Genotype Conflict (0x10)

@ eQuality_check_strain_specific

Straing specific fixed difference (0x08)

@ eQuality_check_non_overlapping_alleles

RS set has 2+ alleles from different submissions and these sets share no alleles in common (0x04)

@ eQuality_check_contig_allele_missing

Reference sequence allele at the mapped position is not present in the SNP allele list,...

@ eQuality_check_withdrawn_by_submitter

One member SS is withdrawn by submitter (0x02)

@ eResource_link_has3D

Has 3D strcture SNP3D table (0x04)

@ eResource_link_provisional

Provisional Third Party Annotations (0x02)

@ eResource_link_genotypeKit

Marker exists on high density genotyping kit (0x20)

@ eResource_link_clinical

Clinical if LSDB, OMIM, TPA, Diagnostic (0x10)

@ eResource_link_submitterLinkout

SNP->SubSNP->Batch link_out (0x08)

@ eResource_link_preserved

Clinical, Pubmed, Cited, (0x01)

@ 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)

@ eClinical_significance_drug_response

@ eClinical_significance_probable_pathogenic

@ eClinical_significance_unknown

@ eClinical_significance_untested

@ eClinical_significance_pathogenic

@ eClinical_significance_probable_non_pathogenic

@ eClinical_significance_other

@ eClinical_significance_histocompatibility

@ eClinical_significance_non_pathogenic

Int4 delta(size_t dimension_, const Int4 *score_)

#define SNP_VAR_EXT_CLASS

#define SNP_VAR_EXT_BITFIELD

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