Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/hgvs__reader_8cpp_source.html below:

NCBI C++ ToolKit: src/misc/hgvs/hgvs_reader.cpp Source File

(!

.AtEOF()) {

line = *(++

);

( var->IsSetExceptions() ) {

exception_list.insert(exception_list.end(), var->GetExceptions().begin(), var->GetExceptions().end());

( var->IsSetPlacements() ) {

&

=

CVariationException::GetTypeInfo_enum_ECode()->FindName(except.

(),

);

unique_ptr<CObjReaderLineException> err(

unique_ptr<CObjReaderLineException> err(

Ref<CSerialObject>(

(

, pMessageListener).GetPointer());

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.

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.

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

virtual CRef< CSeq_annot > ReadSeqAnnot(ILineReader &, ILineErrorListener *=0)

Read an object from a given line reader, render it as a single Seq-annot, if possible.

virtual void ReadSeqAnnots(vector< CRef< CSeq_annot > > &, CNcbiIstream &, ILineErrorListener *=0)

virtual CRef< CSerialObject > ReadObject(ILineReader &, ILineErrorListener *=0)

Read an object from a given line reader, render it as the most appropriate Genbank object.

CConstRef< CGC_Assembly > m_Assembly

CHgvsReader(const CGC_Assembly &assembly, int=0)

static CObjReaderLineException * Create(EDiagSev eSeverity, unsigned int uLine, const std::string &strMessage, EProblem eProblem=eProblem_GeneralParsingError, const std::string &strSeqId=string(""), const std::string &strFeatureName=string(""), const std::string &strQualifierName=string(""), const std::string &strQualifierValue=string(""), CObjReaderLineException::EErrCode eErrCode=eFormat, const TVecOfLines &vecOfOtherLines=TVecOfLines())

Please use this instead of the constructor because the ctor is protected.

Defines and provides stubs for a general interface to a variety of file readers.

unsigned int m_uLineNumber

void ProcessError(CObjReaderLineException &, ILineErrorListener *)

void ProcessWarning(CObjReaderLineException &, ILineErrorListener *)

Resolve chromosome names based on GC_Assembly.

Simple implementation of ILineReader for i(o)streams.

@ eProblem_GeneralParsingError

Abstract base class for lightweight line-by-line reading.

virtual const char * GetErrCodeString(void) const override

Get error code interpreted as text.

CSeq_id_Resolver::TResolvers & SetSeq_id_Resolvers()

In order of decreasing priority.

CRef< CVariation > AsVariation(const string &hgvs_expression, TOpFlags=fOpFlags_Default)

void AsVariation_feats(const CVariation &v, CSeq_annot::TData::TFtable &feats)

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

@ eDiag_Error

Error message.

@ eDiag_Warning

Warning message.

const string & GetMsg(void) const

Get message string.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Optimized implementation of CSerialObject::Assign, which is not so efficient.

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

@ eGetId_ForceGi

return only a gi-based seq-id

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

void Reset(void)

Reset reference object.

bool NotNull(void) const THROWS_NONE

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

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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

Truncate whitespace in a string (in-place)

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static string & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

void SetLocation(TLocation &value)

Assign a value to Location data member.

const TLocation & GetLocation(void) const

Get the Location member data.

TGi & SetGi(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

list< CRef< CSeq_feat > > TFtable

list< CRef< CVariantPlacement > > TPlacements

TCode GetCode(void) const

Get the Code member data.

const TMessage & GetMessage(void) const

Get the Message member data.

const TExceptions & GetExceptions(void) const

Get the Exceptions member data.

bool IsSetCode(void) const

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

bool IsSetMessage(void) const

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

list< CRef< CVariationException > > TExceptions

bool IsSetExceptions(void) const

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

Lightweight interface for getting lines of data with minimal memory copying.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

Defines NCBI C++ exception handling.

Multi-threading – classes, functions, and features.

Useful/utility classes and methods.

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4