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NCBI C++ ToolKit: src/objects/seqfeat/Variation_ref.cpp Source File

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inst.SetDelta().clear();

inst.SetDelta().push_back(

);

& seq_literal = delta_item->SetSeq().SetLiteral();

seq_literal.SetSeq_data().Assign(nucleotide);

seq_literal.SetLength(1);

inst.SetDelta().push_back(delta_item);

inst.SetDelta().clear();

inst.SetDelta().push_back(

);

& seq_literal = delta_item->SetSeq().SetLiteral();

seq_literal.SetSeq_data().Assign(nucleotide);

seq_literal.SetLength(length);

inst.SetDelta().push_back(delta_item);

inst.SetDelta().clear();

delta_item->SetSeq().SetLiteral().SetSeq_data().Assign(amino_acid);

delta_item->SetSeq().SetLiteral().SetLength() = 1;

inst.SetDelta().push_back(delta_item);

inst.SetDelta().clear();

(start_offset.

()) {

inst.SetDelta().push_back(start_offset);

delta_item->SetDuplication();

inst.SetDelta().push_back(delta_item);

inst.SetDelta().push_back(stop_offset);

inst.SetDelta().clear();

(start_offset.

()) {

inst.SetDelta().push_back(start_offset);

delta_item->SetSeq().SetLiteral(*seq_literal);

inst.SetDelta().push_back(delta_item);

inst.SetDelta().push_back(stop_offset);

vector<string>& replaces,

list< CRef<CDelta_item> > items;

has_del =

;

(vector<string>, it, replaces) {

(rep.empty() || rep ==

) {

item->SetSeq().SetLiteral().SetLength(

(rep.size()));

item->SetSeq().SetLiteral().SetSeq_data().SetIupacna().Set(rep);

item->SetSeq().SetLiteral().SetSeq_data().SetIupacaa().Set(rep);

items.push_back(item);

(has_del && items.size()) {

ref.

().SetSet().SetType

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

ref.

().SetSet().SetVariations().push_back(sub);

sub->SetData().SetInstance().SetType(var_type);

sub->SetData().SetInstance().SetDelta()

.insert(sub->SetData().SetInstance().SetDelta().end(),

items.begin(), items.end());

ref.

().SetSet().SetVariations().push_back(sub);

ref.

().SetInstance().SetDelta().clear();

(items.size()) {

ref.

().SetInstance().SetType(var_type);

ref.

().SetInstance().SetDelta()

.insert(ref.

().SetInstance().SetDelta().end(),

items.begin(), items.end());

(

().IsInstance() &&

().GetInstance().IsSetType() &&

item->SetSeq().SetThis();

vector<string> replaces;

replaces.push_back(sequence);

vector<string> replaces;

replaces.push_back(sequence);

vector<string> replaces;

replaces.push_back(nucleotide_seq);

inst.

().front()->SetMultiplier(min_repeats);

->SetMultiplier_fuzz().SetRange().SetMin(min_repeats);

->SetMultiplier_fuzz().SetRange().SetMax(max_repeats);

vector<TSeqPos>& observed_repeats)

vector<string> replaces;

replaces.push_back(nucleotide_seq);

inst.

().front()->SetMultiplier(observed_repeats.front());

(observed_repeats.size() > 1) {

observed_repeats.end(),

back_inserter(inst.

().front()

->SetMultiplier_fuzz().SetAlt()));

item->SetSeq().SetThis();

item->SetSeq().SetThis();

item->SetSeq().SetThis();

item->SetSeq().SetThis();

item->SetMultiplier_fuzz().SetRange().SetMin(min_copy);

item->SetMultiplier_fuzz().SetRange().SetMax(max_copy);

item->SetSeq().SetThis();

(observed_copies.begin(), observed_copies.end(),

back_inserter(item->SetMultiplier_fuzz().SetAlt()));

item->SetSeq().SetLoc().Assign(other_loc);

item->SetSeq().SetLoc().Assign(other_loc);

item->SetSeq().SetLoc().Assign(other_loc);

User-defined methods of the data storage class.

static void s_SetReplaces(CVariation_ref &ref, const vector< string > &replaces, CVariation_ref::ESeqType seq_type, CVariation_inst::EType var_type)

User-defined methods of the data storage class.

bool CanGetExt_locs(void) const

void SetCNV()

Make this variant a copy number variant.

TValidated GetValidated(void) const

TAllele_state & SetAllele_state(void)

TLocation & SetLocation(void)

const TPub & GetPub(void) const

bool CanGetAllele_state(void) const

void SetEversion(const CSeq_loc &other_loc)

The feature represents an eversion at the specified location The provided location should be downstre...

void ResetPopulation_data(void)

bool IsSetIs_ancestral_allele(void) const

TIs_ancestral_allele GetIs_ancestral_allele(void) const

const TExt & GetExt(void) const

const TClinical_test & GetClinical_test(void) const

void SetInsertion()

Make this variant an insertion of unknown sequence.

TAllele_origin & SetAllele_origin(void)

void SetDeletionInsertion(const string &sequence, ESeqType seq_type)

Make this variant an insertion.

const TExt_locs & GetExt_locs(void) const

bool IsSetAllele_origin(void) const

bool IsSetPopulation_data(void) const

Prohibited deprecated functions Due to limitations in ASN spec-land, we cannot officially remove thes...

void PostRead()

PostRead() hooks to establish correct, non-deprecated data layout.

TPopulation_data & SetPopulation_data(void)

void ResetAllele_frequency(void)

const TLocation & GetLocation(void) const

TAllele_frequency & SetAllele_frequency(void)

bool IsSetExt(void) const

void SetOther()

Create a variant of type 'other'.

bool IsMicrosatellite() const

TAllele_origin GetAllele_origin(void) const

void SetUnknown()

Create a variant of unknown type.

void ResetAllele_origin(void)

TValidated & SetValidated(void)

bool CanGetAllele_frequency(void) const

void SetDeletion()

Make this variant a deletion.

bool CanGetPub(void) const

bool IsUniparentalDisomy() const

TAllele_state GetAllele_state(void) const

bool IsSetClinical_test(void) const

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

void ResetAllele_state(void)

bool IsDeletionInsertion() const

ESeqType

Enum governing sequence types for supplied sequence strings.

void SetUniparentalDisomy()

Establish a uniparental disomy mark-up.

bool IsSetLocation(void) const

NOTE: THESE ARE GOING AWAY SOON!!

bool IsSetValidated(void) const

bool IsTranslocation() const

bool CanGetValidated(void) const

void ResetValidated(void)

void SetGain()

Special subtype of CNV: 'gain' - an unspecified increase in copy number.

TClinical_test & SetClinical_test(void)

bool CanGetAllele_origin(void) const

void SetIdentity(CRef< CSeq_literal > seq_literal, CRef< CDelta_item > start_offset=null, CRef< CDelta_item > stop_offset=null)

TExt_locs & SetExt_locs(void)

bool IsSetAllele_frequency(void) const

TAllele_frequency GetAllele_frequency(void) const

bool CanGetPopulation_data(void) const

bool CanGetClinical_test(void) const

bool CanGetLocation(void) const

bool IsSetExt_locs(void) const

void ResetIs_ancestral_allele(void)

void SetLoss()

Special subtype of CNV: 'loss' - an unspecified decrease in copy number.

void SetMissense(const CSeq_data &amino_acid)

const TPopulation_data & GetPopulation_data(void) const

void SetMicrosatellite(const string &nucleotide_seq, TSeqPos min_repeats, TSeqPos max_repeats)

Set the standard fields for a microsatellite.

bool IsSetPub(void) const

void SetTranslocation(const CSeq_loc &other_loc)

The feature represents a translocation event The provided location can be anywhere; a special case ex...

bool CanGetExt(void) const

bool IsSetAllele_state(void) const

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

void SetInversion(const CSeq_loc &other_loc)

The feature represents an inversion at the specified location The provided location should be upstrea...

TIs_ancestral_allele & SetIs_ancestral_allele(void)

void SetComplex()

Create a complex undescribed variant.

bool CanGetIs_ancestral_allele(void) const

void SetDuplication(CRef< CDelta_item > start_offset=null, CRef< CDelta_item > stop_offset=null)

void Validate()

Validate that all semantic fields are correct.

void ResetClinical_test(void)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string & ToUpper(string &str)

Convert string to upper case – string& version.

bool IsSetSeq_data(void) const

may have the data Check if a value has been assigned to Seq_data data member.

void ResetClinical_test(void)

Reset Clinical_test data member.

TType GetType(void) const

Get the Type member data.

TAllele_origin GetAllele_origin(void) const

Get the Allele_origin member data.

const TInstance & GetInstance(void) const

Get the variant data.

const TVariant_prop & GetVariant_prop(void) const

Get the Variant_prop member data.

void ResetPopulation_data(void)

Reset Population_data data member.

void SetComplex(void)

Select the variant.

bool CanGetIs_ancestral_allele(void) const

Check if it is safe to call GetIs_ancestral_allele method.

list< CRef< CVariation_ref > > TVariations

bool CanGetAllele_frequency(void) const

Check if it is safe to call GetAllele_frequency method.

void ResetOther_validation(void)

Reset Other_validation data member.

void ResetValidated(void)

Reset Validated data member.

TAllele_state GetAllele_state(void) const

Get the Allele_state member data.

void SetAllele_state(TAllele_state value)

Assign a value to Allele_state data member.

bool IsSetAllele_state(void) const

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

const TSet & GetSet(void) const

Get the variant data.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

bool CanGetExt_locs(void) const

Check if it is safe to call GetExt_locs method.

void ResetAllele_frequency(void)

Reset Allele_frequency data member.

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

bool IsSetVariant_prop(void) const

variant properties bit fields Check if a value has been assigned to Variant_prop data member.

bool IsSetAllele_origin(void) const

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

void ResetAllele_state(void)

Reset Allele_state data member.

bool CanGetLocation(void) const

Check if it is safe to call GetLocation method.

TType GetType(void) const

Get the Type member data.

void ResetAllele_frequency(void)

Reset Allele_frequency data member.

void ResetAllele_origin(void)

Reset Allele_origin data member.

void SetType(TType value)

Assign a value to Type data member.

bool CanGetAllele_state(void) const

Check if it is safe to call GetAllele_state method.

bool CanGetValidated(void) const

Check if it is safe to call GetValidated method.

bool IsSetAllele_origin(void) const

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

bool IsSetPopulation_data(void) const

Note about SNP representation and pretinent fields: allele-frequency, population, quality-codes: The ...

TIs_ancestral_allele GetIs_ancestral_allele(void) const

Get the Is_ancestral_allele member data.

bool CanGetVariant_prop(void) const

Check if it is safe to call GetVariant_prop method.

bool CanGetAllele_origin(void) const

Check if it is safe to call GetAllele_origin method.

const TDelta & GetDelta(void) const

Get the Delta member data.

TLocation & SetLocation(void)

Assign a value to Location data member.

void SetUnknown(void)

Select the variant.

bool IsSetPub(void) const

publication support.

void ResetLocation(void)

Reset Location data member.

void ResetExt(void)

Reset Ext data member.

void SetData(TData &value)

Assign a value to Data data member.

void ResetAllele_state(void)

Reset Allele_state data member.

bool IsSetAllele_frequency(void) const

NOTE: 'allele-frequency' here refers to the minor allele frequency of the default population DEPRECAT...

const TData & GetData(void) const

Get the Data member data.

TData & SetData(void)

Assign a value to Data data member.

bool CanGetOther_validation(void) const

Check if it is safe to call GetOther_validation method.

const TLocation & GetLocation(void) const

Get the Location member data.

TValidated GetValidated(void) const

Get the Validated member data.

TVariant_prop & SetVariant_prop(void)

Assign a value to Variant_prop data member.

TExt_locs & SetExt_locs(void)

Assign a value to Ext_locs data member.

bool CanGetAllele_origin(void) const

Check if it is safe to call GetAllele_origin method.

bool CanGetAllele_state(void) const

Check if it is safe to call GetAllele_state method.

void ResetExt_locs(void)

Reset Ext_locs data member.

void SetAllele_origin(TAllele_origin value)

Assign a value to Allele_origin data member.

bool IsInstance(void) const

Check if variant Instance is selected.

TOther_validation GetOther_validation(void) const

Get the Other_validation member data.

bool IsSetAllele_state(void) const

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

list< CRef< CPopulation_data > > TPopulation_data

bool CanGetAllele_frequency(void) const

Check if it is safe to call GetAllele_frequency method.

bool TIs_ancestral_allele

bool IsSetIs_ancestral_allele(void) const

is this variant the ancestral allele? DEPRECATED: new field = VariantProperties.is-ancestral-allele C...

bool IsUniparental_disomy(void) const

Check if variant Uniparental_disomy is selected.

bool IsSet(void) const

Check if variant Set is selected.

void SetType(TType value)

Assign a value to Type data member.

bool IsSetClinical_test(void) const

link-outs to GeneTests database DEPRECATED - do not use Check if a value has been assigned to Clinica...

TAllele_frequency GetAllele_frequency(void) const

Get the Allele_frequency member data.

void SetIs_ancestral_allele(TIs_ancestral_allele value)

Assign a value to Is_ancestral_allele data member.

void ResetAllele_origin(void)

Reset Allele_origin data member.

TSet & SetSet(void)

Select the variant.

void ResetPub(void)

Reset Pub data member.

bool IsUnknown(void) const

Check if variant Unknown is selected.

TVariations & SetVariations(void)

Assign a value to Variations data member.

void ResetIs_ancestral_allele(void)

Reset Is_ancestral_allele data member.

bool IsSetLocation(void) const

Observed location, if different from the parent set or feature.location.

bool IsSetType(void) const

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

bool IsSetIs_ancestral_allele(void) const

is this variant the ancestral allele? Check if a value has been assigned to Is_ancestral_allele data ...

bool IsSetOther_validation(void) const

has this variant been validated? While a boolean flag offers no subtle distinctions of validation met...

bool IsSetValidated(void) const

has this variant been validated? DEPRECATED: new field = VariantProperties.other-validation Check if ...

void SetUniparental_disomy(void)

Select the variant.

TIs_ancestral_allele GetIs_ancestral_allele(void) const

Get the Is_ancestral_allele member data.

void SetOther_validation(TOther_validation value)

Assign a value to Other_validation data member.

list< CRef< CExt_loc > > TExt_locs

TAllele_frequency GetAllele_frequency(void) const

Get the Allele_frequency member data.

void ResetIs_ancestral_allele(void)

Reset Is_ancestral_allele data member.

TInstance & SetInstance(void)

Select the variant.

const TExt_locs & GetExt_locs(void) const

Get the Ext_locs member data.

bool IsSetExt_locs(void) const

reference other locs, e.g.

bool CanGetIs_ancestral_allele(void) const

Check if it is safe to call GetIs_ancestral_allele method.

void SetAllele_frequency(TAllele_frequency value)

Assign a value to Allele_frequency data member.

TDelta & SetDelta(void)

Assign a value to Delta data member.

const TExt & GetExt(void) const

Get the Ext member data.

TExt & SetExt(void)

Assign a value to Ext data member.

list< CRef< CDbtag > > TClinical_test

bool IsSetAllele_frequency(void) const

NOTE: 'allele-frequency' here refers to the minor allele frequency of the default population Check if...

bool IsSetExt(void) const

DEPRECATED - do not use; use Seq-feat.exts instead Check if a value has been assigned to Ext data mem...

TAllele_origin GetAllele_origin(void) const

Get the Allele_origin member data.

bool IsComplex(void) const

Check if variant Complex is selected.

TAllele_state GetAllele_state(void) const

Get the Allele_state member data.

@ eType_snv

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

@ eType_inverted_copy

delta=[ins.seq= upstream location on the opposite strand]

@ eType_mnp

delta=[morph of length >1]

@ eType_microsatellite

delta=[del, ins.seq= repeat-unit with fuzzy multiplier] variation-location is the microsat expansion ...

@ eType_delins

delta=[del, ins]

@ eType_everted_copy

delta=[ins.seq= downstream location on the opposite strand]

@ eType_cnv

delta=[del, ins= 'this' with fuzzy multiplier]

@ eType_identity

delta=[]

@ eType_prot_missense

delta=[morph of length 1]

@ eType_translocation

delta=like delins

@ 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_compound

complex change at the same location on the same molecule

@ eObservation_asserted

inst represents the asserted base at a position

const GenericPointer< typename T::ValueType > T2 value

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

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