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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/variation__ref__utils_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/readers/hgvs/variation_ref_utils.cpp Source File

var_ref->SetMethod().push_back(method);

& inst = var_ref->SetData().SetInstance();

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 = var_ref->SetData().SetInstance();

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 = var_ref->SetData().SetInstance();

inst.SetDelta().clear();

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

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

inst.SetDelta().push_back(delta_item);

(start_offset.

()) {

inst.

().push_back(start_offset);

delta_item->SetSeq().SetThis();

inst.

().push_back(delta_item);

inst.

().push_back(stop_offset);

& inst = var_ref->SetData().SetInstance();

inst.SetDelta().clear();

(start_offset.

()) {

inst.SetDelta().push_back(start_offset);

delta_item->SetSeq().SetThis();

delta_item->SetMultiplier() = 2;

inst.SetDelta().push_back(delta_item);

inst.SetDelta().push_back(stop_offset);

enforce_assert)

& inst = var_ref->SetData().SetInstance();

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);

enforce_assert)

& inst = var_ref->SetData().SetInstance();

inst.SetType(

);

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);

& inst = var_ref->SetData().SetInstance();

inst.SetDelta().clear();

(start_offset.

()) {

inst.SetDelta().push_back(start_offset);

delta_item->SetSeq().SetLiteral(insertion);

inst.SetDelta().push_back(delta_item);

inst.SetDelta().push_back(stop_offset);

& inst = var_ref->SetData().SetInstance();

inst.SetDelta().clear();

(start_offset.

()) {

inst.SetDelta().push_back(start_offset);

delta_item->SetSeq().SetLiteral(insertion);

inst.SetDelta().push_back(delta_item);

inst.SetDelta().push_back(stop_offset);

& inst = var_ref->SetData().SetInstance();

inst.SetDelta().clear();

(start_offset.

()) {

inst.SetDelta().push_back(start_offset);

inst.SetDelta().push_back(stop_offset);

& inst = var_ref->SetData().SetInstance();

inst.SetDelta().clear();

(start_offset.

()) {

inst.SetDelta().push_back(start_offset);

inst.SetDelta().push_back(repeat_info);

inst.SetDelta().push_back(stop_offset);

& inst = var_ref->SetData().SetInstance();

inst.SetDelta().clear();

(start_offset.

()) {

inst.SetDelta().push_back(start_offset);

delta_item->SetSeq().SetLoc().Assign(interval);

inst.SetDelta().push_back(delta_item);

inst.SetDelta().push_back(stop_offset);

delta_item->SetSeq().SetLiteral().SetSeq_data().SetNcbieaa().Set(

(

));

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

var_ref->SetData().SetInstance().SetDelta().push_back(delta_item);

cons =

(

CVariation_ref::TConsequence::value_type::TObjectType());

cons->SetFrameshift();

var_ref->SetConsequence().push_back(cons);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

unsigned int TSeqPos

Type for sequence locations and lengths.

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.

#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.

bool IsSetSeq_data(void) const

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

void SetType(TType value)

Assign a value to Type data member.

TDelta & SetDelta(void)

Assign a value to Delta data member.

@ eType_snv

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

@ eType_inv

delta=[del, ins.seq= RevComp(variation-location)]

@ 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_transposon

delta=[del, ins.seq= known donor or 'this'] variation-location is equiv of transposon locs.

@ eType_prot_other

delta=any

@ eType_identity

delta=[]

@ eType_prot_missense

delta=[morph of length 1]

@ 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

@ eObservation_asserted

inst represents the asserted base at a position

CRef< CVariation_ref > g_CreateDuplication(const CVariation_ref::EMethod_E method, CRef< CDelta_item > start_offset, CRef< CDelta_item > stop_offset)

CRef< CVariation_ref > g_CreateIdentity(CRef< CSeq_literal > seq_literal, const CVariation_ref::EMethod_E method, const CRef< CDelta_item > start_offset, const CRef< CDelta_item > stop_offset, const bool enforce_assert)

CRef< CVariation_ref > g_CreateMNP(const CSeq_data &nucleotide, const TSeqPos length, const CVariation_ref::EMethod_E method, const CRef< CDelta_item > offset)

CRef< CVariation_ref > g_CreateInversion(const CVariation_ref::EMethod_E method, const CRef< CDelta_item > start_offset, const CRef< CDelta_item > stop_offset)

void s_SetVariationMethod(CRef< CVariation_ref > var_ref, const CVariation_ref::EMethod_E method)

CRef< CVariation_ref > g_CreateFrameshift(const CVariation_ref::EMethod_E method)

CRef< CVariation_ref > g_CreateConversion(const CSeq_loc &interval, const CVariation_ref::EMethod_E method, const CRef< CDelta_item > start_offset, const CRef< CDelta_item > stop_offset)

CRef< CVariation_ref > g_CreateDelins(CSeq_literal &insertion, const CVariation_ref::EMethod_E method, const CRef< CDelta_item > start_offset, const CRef< CDelta_item > stop_offset)

CRef< CVariation_ref > g_CreateVarref(CRef< CSeq_literal > seq_literal, const CVariation_inst::EType type, const CVariation_ref::EMethod_E method, const CRef< CDelta_item > start_offset, const CRef< CDelta_item > stop_offset, const bool enforce_assert)

CRef< CVariation_ref > g_CreateMissense(const CSeq_data &amino_acid, const CVariation_ref::EMethod_E method)

CRef< CVariation_ref > g_CreateDeletion(const CVariation_ref::EMethod_E method, CRef< CDelta_item > start_offset, CRef< CDelta_item > stop_offset)

CRef< CVariation_ref > g_CreateMicrosatellite(const CRef< CDelta_item > repeat_info, const CVariation_ref::EMethod_E method, const CRef< CDelta_item > start_offset, const CRef< CDelta_item > stop_offset)

CRef< CVariation_ref > g_CreateSNV(const CSeq_data &nucleotide, const CVariation_ref::EMethod_E method, const CRef< CDelta_item > offset)

CRef< CVariation_ref > g_CreateInsertion(CSeq_literal &insertion, const CVariation_ref::EMethod_E method, const CRef< CDelta_item > start_offset, const CRef< CDelta_item > stop_offset)

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