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

(sequence.size() > 1) {

sequence = sequence.front() +

+ sequence.back();

->SetSeq_data().SetNcbieaa().Set(sequence);

->SetSeq_data().SetIupacna().Set(sequence);

->SetLength(sequence.size());

);

((*it)->IsSetAction() &&

normalized_feat->Assign(identity_feat);

(!normalized_feat->IsSetData() ||

!normalized_feat->GetData().IsVariation() ||

!normalized_feat->GetData().GetVariation().IsSetData() ||

!normalized_feat->GetData().GetVariation().GetData().IsInstance() ||

!normalized_feat->GetData().GetVariation().GetData().GetInstance().IsSetType() ||

normalized_feat;

& var_inst = normalized_feat->SetData().SetVariation().SetData().SetInstance();

normalized_feat;

(!identity_inst.

()) {

message =

(

<<

);

& delta_item = *identity_inst.

().back();

(!delta_item.IsSetSeq()) {

(delta_item.IsSetSeq() &&

(!delta_item.GetSeq().IsLiteral() ||

!delta_item.GetSeq().GetLiteral().IsSetSeq_data())) {

delta_item.SetSeq().SetLiteral(*new_literal);

literal_length =

.GetLength();

(literal_length != interval_length) {

+

+

(interval_length) +

;

eSeqliteralIntervalError,

message =

;

message +=

;

message +=

message +=

;

);

& delta_item = *identity_inst.

().back();

(!delta_item.IsSetSeq()) {

(!delta_item.GetSeq().IsLiteral()) {

);

&

= delta_item.GetSeq().GetLiteral();

message =

;

message +=

;

);

& delta_item = *ms_inst.

().back();

(!delta_item.IsSetSeq()) {

(delta_item.GetSeq().IsLiteral()) {

);

(!data_set.IsSetType() ||

!data_set.IsSetVariations()) {

(variation_list.size() < 2) {

err_msg =

&& assertion = variation_list.front();

&& reference = variation_list.back();

(!assertion->IsSetData() ||

!reference->IsSetData()) {

);

(!reference->GetData().IsInstance()) {

);

& reference_inst = reference->GetData().GetInstance();

(!reference_inst.IsSetType()) {

);

(assertion->GetData().IsUnknown()) {

(!assertion->GetData().IsInstance()) {

);

& assertion_inst = assertion->GetData().GetInstance();

(!assertion_inst.IsSetType()) {

);

= assertion_inst.GetType();

User-defined methods of the data storage class.

CRef< CSeq_feat > GetNormalizedIdentity(const CSeq_feat &seaq_feat) const

void NormalizeIdentityInstance(CVariation_inst &identity_inst, const CSeq_loc &location) const

bool HasIntronOffset(const CVariation_inst &var_inst) const

CRef< CSeq_literal > GetLiteralAtLoc(const CSeq_loc &loc, CScope &scope) const

namespace ncbi::objects::

void ValidateIdentityInst(const CVariation_inst &identity_inst, const CSeq_loc &location, bool IsCDS=false)

void ValidateMicrosatelliteInst(const CVariation_inst &identity_inst, const CSeq_loc &location, bool IsCDS=false)

static const char location[]

#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.

#define NCBI_THROW(exception_class, err_code, message)

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

void Warning(CExceptionArgs_Base &args)

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

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

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

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

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

bool IsProtein(void) const

const_iterator begin(void) const

const_iterator end(void) const

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.

CTempString literal(const char(&str)[Size])

Templatized initialization from a string literal.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

bool IsSetData(void) const

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

const TLocation & GetLocation(void) const

Get the Location member data.

const TData & GetData(void) const

Get the Data member data.

bool IsVariation(void) const

Check if variant Variation is selected.

const TVariation & GetVariation(void) const

Get the variant data.

TType GetType(void) const

Get the Type member data.

const TInstance & GetInstance(void) const

Get the variant data.

const TSet & GetSet(void) const

Get the variant data.

bool IsSetDelta(void) const

Sequence that replaces the location, in biological order.

void SetObservation(TObservation value)

Assign a value to Observation data member.

const TDelta & GetDelta(void) const

Get the Delta member data.

const TData & GetData(void) const

Get the Data member data.

bool IsInstance(void) const

Check if variant Instance is selected.

bool IsSet(void) const

Check if variant Set is selected.

void SetType(TType value)

Assign a value to Type data member.

list< CRef< CDelta_item > > TDelta

bool IsSetType(void) const

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

TDelta & SetDelta(void)

Assign a value to Delta data member.

const TVariations & GetVariations(void) const

Get the Variations member data.

bool IsSetData(void) const

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

@ eType_inv

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

@ eType_microsatellite

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

@ eType_delins

delta=[del, ins]

@ eType_identity

delta=[]

@ eAction_offset

go downstream by distance specified by multiplier (upstream if < 0), in genomic context.

@ eData_set_type_package

set represents a package of observations at a given location, generally containing asserted + referen...

@ eObservation_asserted

inst represents the asserted base at a position

Defines NCBI C++ diagnostic APIs, classes, and macros.

void s_ValidateSeqLiteral(const CSeq_literal &literal, const CSeq_loc &location, CScope *scope, bool IsCDS=false)

void g_ValidateVariationSeqfeat(const CSeq_feat &feat, CScope *scope, bool IsCDS)

CRef< CSeq_feat > g_NormalizeVariationSeqfeat(const CSeq_feat &feat, CScope *scope)

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