NSnp –. More...

#include <objtools/snputil/snp_utils.hpp>

Public Types
enum	ELetterCase { eLetterCase_ForceLower , eLetterCase_Mixed }
	controls the case of strings returned from ClinSigAsString() More...

typedef CObject_id::TId8	TRsid

typedef CPhenotype::EClinical_significance	EClinSigID

typedef int	TClinSigID

typedef vector< string >	TAlleles
	list of alleles belonging to particular SNP a deletion is represented by a "-" More...

Static Public Member Functions
static bool	IsSnp (const CMappedFeat &mapped_feat)
	Determine if feature is a SNP. More...

static bool	IsSnp (const CSeq_feat &feat)

static bool	IsSnp (const CDbtag &tag)

static CConstRef< CDbtag >	GetTag (const CSeq_feat &SrcFeat)
	find a SNP tag in the feature returns NULL if no such tag (sm_dbTag_dbSNP) More...

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

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 annotation object. More...

static TRsid	GetRsid (const CMappedFeat &mapped_feat)
	Return rsid of SNP. More...

static TRsid	GetRsid (const CSeq_feat &feat)
	Return rsid of SNP. More...

static TRsid	GetRsid (const CDbtag &tag)

static int	GetLength (const CMappedFeat &)
	Return distance of neighbors in flanking sequence. More...

static int	GetLength (const CSeq_feat &)
	Return distance of neighbors in flanking sequence. More...

static CSnpBitfield	GetBitfield (const CMappedFeat &)
	Return bitfield information stored in the feature. More...

static CSnpBitfield	GetBitfield (const CSeq_feat &feat)
	Return bitfield information stored in the feature. More...

static bool	IsSnpKnown (CScope &scope, const CMappedFeat &private_snp, const string &allele=kEmptyStr)
	Check if SNP exists in GenBank database. More...

static bool	IsSnpKnown (CScope &scope, const CSeq_loc &loc, const string &allele=kEmptyStr)
	Check if SNP exists in GenBank database. More...

static void	GetAlleles (const CMappedFeat &mapped_feat, TAlleles &Alleles)
	Return list of alleles encoded in qual. More...

static void	GetAlleles (const CSeq_feat &feat, TAlleles &Alleles, bool isPadding=false, CBioseq_Handle *bsh=NULL)
	Return list of alleles encoded in qual. More...

static string	ClinSigAsString (const CVariation_ref &var, ELetterCase LetterCase=eLetterCase_Mixed)
	get a human-readable text for various clinical significance types More...

static string	ClinSigAsString (TClinSigID ClinSigID, ELetterCase LetterCase=eLetterCase_Mixed)
	get a human-readable text for various clinical significance types More...

Static Public Attributes
static const string	sm_dbTag_dbSNP

Detailed Description

NSnp –.

Helper functions for SNP features

Definition at line 62 of file snp_utils.hpp.

Member Typedef Documentation

◆ EClinSigID

typedef CPhenotype::EClinical_significance NSnp::EClinSigID

Definition at line 75 of file snp_utils.hpp.

◆ TAlleles

typedef vector<string> NSnp::TAlleles

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

Definition at line 188 of file snp_utils.hpp.

◆ TClinSigID

typedef int NSnp::TClinSigID

Definition at line 76 of file snp_utils.hpp.

◆ TRsid

typedef CObject_id::TId8 NSnp::TRsid

Definition at line 70 of file snp_utils.hpp.

Member Enumeration Documentation

◆ ELetterCase

enum NSnp::ELetterCase

controls the case of strings returned from ClinSigAsString()

Enumerator
eLetterCase_ForceLower	always use lower case only
eLetterCase_Mixed	return strings in mixes case

Definition at line 211 of file snp_utils.hpp.

Member Function Documentation

◆ ClinSigAsString() [1/2]

string NSnp::ClinSigAsString	(	const CVariation_ref &	var,
		ELetterCase	LetterCase = `eLetterCase_Mixed`
	)

static

get a human-readable text for various clinical significance types

Parameters

var	the clinical significance will be taken from var.phenotype.clinical-significance if it is defined
LetterCase	controls the letter case of the result

Returns

string describing the first clinical significance in the first phenotype

will be empty if clinical-significance is not present

Definition at line 172 of file snp_utils.cpp.

References CVariation_ref_Base::GetPhenotype(), and ITERATE.

Referenced by NSnpGui::GetBinTooltip(), CSeq_featHandler::GetLabel(), and CGuiObjectInfoVariant::GetToolTip().

◆ ClinSigAsString() [2/2]

string NSnp::ClinSigAsString	(	TClinSigID	ClinSigID,
		ELetterCase	LetterCase = `eLetterCase_Mixed`
	)

static

get a human-readable text for various clinical significance types

Parameters

ClinSigID	clinical significance ID
LetterCase	controls the letter case of the result

Returns: string describing the given clinical significance ID

Definition at line 182 of file snp_utils.cpp.

◆ GetAlleles() [1/2]

void NSnp::GetAlleles	(	const CMappedFeat &	mapped_feat,
		TAlleles &	Alleles
	)

static

Return list of alleles encoded in qual.

"replace"

Parameters

mapped_feat CMappedFeat object representing snp feature

Returns

list of alleles found in the feature (if any)

Definition at line 237 of file snp_utils.cpp.

References CMappedFeat::GetOriginalFeature().

Referenced by CFeatGlyph::GetAdditionalInfo(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariation::GetToolTip(), and NSNPVariationHelper::x_CommonConvertFeat().

◆ GetAlleles() [2/2]

void NSnp::GetAlleles	(	const CSeq_feat &	feat,
		TAlleles &	Alleles,
		bool	isPadding = `false`,
		CBioseq_Handle *	bsh = `NULL`
	)

static

Return list of alleles encoded in qual.

"replace"

Parameters

feat	CSeq_feat object representing snp feature
isPadding	if true, add allele padding according to VCF spec
bsh	must be not NULL if isPadding == true

Returns

list of alleles found in the feature (if any)

Definition at line 242 of file snp_utils.cpp.

References CSeq_feat_Base::CanGetQual(), delta(), CBioseq_Handle::eCoding_Iupac, eExtreme_Positional, CSeq_feat_Base::GetLocation(), CGb_qual_Base::GetQual(), CSeq_feat_Base::GetQual(), CSeqVector::GetSeqData(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), CGb_qual_Base::GetVal(), and ITERATE.

◆ GetBitfield() [1/2]

CSnpBitfield NSnp::GetBitfield ( const CMappedFeat & mapped_feat )

static

Return bitfield information stored in the feature.

Parameters

mapped_feat CMappedFeat object representing snp feature

Returns

CSnpBitfield.isGood() is false if no bitfield is found

Definition at line 220 of file snp_utils.cpp.

References CMappedFeat::GetOriginalFeature().

Referenced by NSNPVariationHelper::ConvertFeat(), GetLength(), CGuiObjectInfoVariation::GetToolTip(), and NSNPVariationHelper::x_CommonConvertFeat().

◆ GetBitfield() [2/2]

CSnpBitfield NSnp::GetBitfield ( const CSeq_feat & feat )

static

Return bitfield information stored in the feature.

Parameters

mapped_feat CSeq_feat object representing snp feature

Returns

bitfield created from octect sequence of QualityCodes
CSnpBitfield is empty if no "QualityCodes" are found

Definition at line 225 of file snp_utils.cpp.

References b, and IsSnp().

◆ GetCreateTime()

CTime NSnp::GetCreateTime ( const CMappedFeat & mapped_feat )

static

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

Parameters

mapped_feat CMappedFeat object representing feature

Returns

CTime object representing Creation time. A default constructed CTime object will be returned if no Create-time was found.

Definition at line 88 of file snp_utils.cpp.

References CDate::AsCTime(), CAnnot_descr_Base::CanGet(), CAnnot_descr_Base::Get(), CSeq_feat_Handle::GetAnnot(), CAnnotdesc_Base::GetCreate_date(), CAnnotdesc_Base::IsCreate_date(), ITERATE, CSeq_annot_Handle::Seq_annot_CanGetDesc(), and CSeq_annot_Handle::Seq_annot_GetDesc().

◆ GetLength() [1/2]

int NSnp::GetLength ( const CMappedFeat & mapped_feat )

static

Return distance of neighbors in flanking sequence.

Parameters

mapped_feat CMappedFeat object representing feature

Returns

length of neighbors on flanking sequencer
0 if no length information found

Definition at line 133 of file snp_utils.cpp.

References CMappedFeat::GetOriginalFeature().

Referenced by CSeq_featHandler::GetLabel().

◆ GetLength() [2/2]

int NSnp::GetLength ( const CSeq_feat & feat )

static

Return distance of neighbors in flanking sequence.

Parameters

mapped_feat CSeq_feat object representing feature

Returns

length of neighbors on flanking sequencer
0 if no length information found

Definition at line 138 of file snp_utils.cpp.

References CSeq_feat_Base::CanGetLocation(), NStr::fConvErr_NoThrow, GetBitfield(), CUser_field_Base::GetData(), CSeq_feat_Base::GetExt(), CUser_object::GetFieldRef(), COpenRange< Position >::GetLength(), CSeq_feat_Base::GetLocation(), CUser_field_Base::C_Data::GetStr(), CSeq_loc::GetTotalRange(), CSeq_feat_Base::IsSetExt(), lc, NStr::Split(), NStr::SplitInTwo(), str(), and NStr::StringToInt().

◆ GetRsid() [1/3]

NSnp::TRsid NSnp::GetRsid ( const CDbtag & tag )

static

Definition at line 122 of file snp_utils.cpp.

References tag.

◆ GetRsid() [2/3]

NSnp::TRsid NSnp::GetRsid ( const CMappedFeat & mapped_feat )

static

Return rsid of SNP.

Parameters

mapped_feat CMappedFeat object representing SNP feature

Returns

rsid of SNP as set in its Tag data
0 if no rsid found

Definition at line 109 of file snp_utils.cpp.

References CMappedFeat::GetOriginalFeature().

Referenced by CLinkUtils::AddDbxrefLinksForSNP(), CSeq_featHandler::GetLabel(), CGuiObjectInfoVariation::GetLinks(), GetRsid(), CGuiObjectInfoVariation::GetToolTip(), NSearchFeatPanel::s_GetFeatureLabel(), and NSNPVariationHelper::x_CommonConvertFeat().

◆ GetRsid() [3/3]

NSnp::TRsid NSnp::GetRsid ( const CSeq_feat & feat )

static

Return rsid of SNP.

Parameters

feat	CSeq_feat object representing SNP feature

Returns

rsid of SNP as set in its Tag data
0 if no rsid found

Definition at line 114 of file snp_utils.cpp.

References GetRsid(), and GetTag().

◆ GetTag() [1/2]

CConstRef< CDbtag > NSnp::GetTag ( const CMappedFeat & SrcFeat )

static

Definition at line 82 of file snp_utils.cpp.

References CMappedFeat::GetOriginalFeature(), and GetTag().

◆ GetTag() [2/2]

CConstRef< CDbtag > NSnp::GetTag ( const CSeq_feat & SrcFeat )

static

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

Definition at line 77 of file snp_utils.cpp.

References CSeq_feat::GetNamedDbxref(), and sm_dbTag_dbSNP.

Referenced by CFeatGlyph::GetHTMLActiveAreas(), GetRsid(), GetTag(), IsSnp(), and NSNPVariationHelper::x_CommonConvertFeat().

◆ IsSnp() [1/3]

bool NSnp::IsSnp ( const CDbtag & tag )

static

Definition at line 72 of file snp_utils.cpp.

References CDbtag::eDbtagType_dbSNP, and tag.

◆ IsSnp() [2/3]

bool NSnp::IsSnp ( const CMappedFeat & mapped_feat )

static

Determine if feature is a SNP.

Parameters

mapped_feat CMappedFeat object representing feature

Returns

true if Subtype is variation
false otherwise

Definition at line 62 of file snp_utils.cpp.

References CMappedFeat::GetOriginalFeature().

Referenced by GetBitfield(), CGuiObjectInfoVariation::GetLinks(), CGuiObjectInfoVariation::GetToolTip(), IsSnp(), and NSNPVariationHelper::x_CommonConvertFeat().

◆ IsSnp() [3/3]

bool NSnp::IsSnp ( const CSeq_feat & feat )

static

Definition at line 67 of file snp_utils.cpp.

References CSeqFeatData::eSubtype_variation, CSeq_feat_Base::GetData(), CSeqFeatData::GetSubtype(), GetTag(), CSeq_feat_Base::IsSetData(), IsSnp(), and CConstRef< C, Locker >::NotEmpty().

◆ IsSnpKnown() [1/2]

bool NSnp::IsSnpKnown	(	CScope &	scope,
		const CMappedFeat &	private_snp,
		const string &	allele = `kEmptyStr`
	)

static

Check if SNP exists in GenBank database.

Parameters

scope	CScope object representing scope of data
mapped_feat	CMappedFeat object representing snp feature
allele	string object representing allele of SNP (e.g. A or GG or -)

Returns

true if SNP was found
false otherwise

Definition at line 282 of file snp_utils.cpp.

References CMappedFeat::GetLocation().

◆ IsSnpKnown() [2/2]

bool NSnp::IsSnpKnown	(	CScope &	scope,
		const CSeq_loc &	loc,
		const string &	allele = `kEmptyStr`
	)

static

Check if SNP exists in GenBank database.

Parameters

scope	CScope object representing scope of data
loc	CSeq_loc representing location of SNP
allele	string object representing allele of SNP (e.g. A or GG or -)

Returns

true if SNP was found
false otherwise

Definition at line 288 of file snp_utils.cpp.

References SAnnotSelector::AddNamedAnnots(), CSeq_feat_Base::CanGetQual(), CSeq_annot_Base::C_Data::e_Ftable, CSeqFeatData::eSubtype_variation, SAnnotSelector::ExcludeUnnamedAnnots(), CMappedFeat::GetOriginalFeature(), CGb_qual_Base::GetQual(), CSeq_feat_Base::GetQual(), CAnnotTypes_CI::GetSize(), CGb_qual_Base::GetVal(), ITERATE, kEmptyStr, SAnnotSelector::SetAnnotType(), SAnnotSelector::SetExcludeExternal(), SAnnotSelector::SetFeatSubtype(), SAnnotSelector::SetMaxSize(), SAnnotSelector::SetOverlapTotalRange(), and SAnnotSelector::SetResolveAll().

Member Data Documentation

◆ sm_dbTag_dbSNP

const string NSnp::sm_dbTag_dbSNP

static

Definition at line 67 of file snp_utils.hpp.

Referenced by GetTag().

The documentation for this class was generated from the following files:

include/objtools/snputil/snp_utils.hpp
src/objtools/snputil/snp_utils.cpp

Public Types

Static Public Member Functions

Static Public Attributes

Detailed Description

Member Typedef Documentation

◆ EClinSigID

◆ TAlleles

◆ TClinSigID

◆ TRsid

Member Enumeration Documentation

◆ ELetterCase

Member Function Documentation

◆ ClinSigAsString() [1/2]

◆ ClinSigAsString() [2/2]

◆ GetAlleles() [1/2]

◆ GetAlleles() [2/2]

◆ GetBitfield() [1/2]

◆ GetBitfield() [2/2]

◆ GetCreateTime()

◆ GetLength() [1/2]

◆ GetLength() [2/2]

◆ GetRsid() [1/3]

◆ GetRsid() [2/3]

◆ GetRsid() [3/3]

◆ GetTag() [1/2]

◆ GetTag() [2/2]

◆ IsSnp() [1/3]

◆ IsSnp() [2/3]

◆ IsSnp() [3/3]

◆ IsSnpKnown() [1/2]

◆ IsSnpKnown() [2/2]

Member Data Documentation

◆ sm_dbTag_dbSNP