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NCBI C++ ToolKit: src/objtools/huge_asn/huge_file.cpp Source File

memfile = std::make_unique<CMemoryFile>(filename,

= (

*)memfile->GetPtr();

std::unique_ptr<std::ifstream> stream{

std::ifstream(filename, ios::binary)};

(!stream->is_open())

std::istream istr(&strbuf);

(object_type ==

)

unique_ptr<CObjectIStream>

;

std::unique_ptr<std::ifstream> stream{

std::ifstream(

, ios::binary)};

->UseMemoryPool();

Wraps CFormatGuess, and if CFormatGuess's result is Unknown, it tries every file reader until one wor...

CFormatGuess::EFormat GuessFormatAndContent(CFileContentInfo &contentInfo)

CFormatGuess::CFormatHints & GetFormatHints(void)

Get format hints.

void SetRecognizedGenbankTypes(const set< TTypeInfo > &recognizedGenbankTypes)

CFormatHints & AddPreferredFormat(TFormat fmt)

Mark the format as preferred.

CFormatHints & DisableAllNonpreferred(void)

Disable all formats not marked as preferred.

@ eBZip2

bzip2 compressed file

@ eBinaryASN

Binary ASN.1.

@ eLzo

lzo compressed file

@ eGtf

New GTF, CGtfReader.

@ eGZip

GNU zip compressed file.

@ eZip

zip compressed file

@ eGff3

GFF3, CGff3Reader.

@ eFasta

FASTA format sequence record, CFastaReader.

@ eZstd

Zstandard (zstd) compressed data.

unique_ptr< CObjectIStream > MakeObjStream(std::streampos pos=0) const

std::unique_ptr< CMemoryFile > m_memfile

std::unique_ptr< std::istream > m_stream

const set< TTypeInfo > * m_supported_types

std::unique_ptr< std::streambuf > m_streambuf

CFormatGuess::EFormat m_format

TTypeInfo RecognizeContent(std::streampos pos)

void Open(const std::string &filename, const set< TTypeInfo > *supported_types)

void OpenPlain(const std::string &filename)

std::streampos m_filesize

bool x_TryOpenStreamFile(const string &filename, std::streampos filesize)

bool x_TryOpenMemoryFile(const string &filename)

ESerialDataFormat m_serial_format

CTypeInfo class contains all information about C++ types (both basic and classes): members and layout...

static const char * str(char *buf, int n)

@ eTakeOwnership

An object can take ownership of another.

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

#define NCBI_THROW2(exception_class, err_code, message, extra)

Throw exception with extra parameter.

TErrCode GetErrCode(void) const

Int8 GetLength(void) const

Get size of file.

@ eMMS_Private

Changes are private (write do not change file)

@ eMMP_Read

Data can be read.

@ eSerial_AsnText

ASN.1 text.

@ eSerial_AsnBinary

ASN.1 binary.

static CObjectIStream * Create(ESerialDataFormat format)

Create serial object reader.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

@ eDelayBufferPolicyAlwaysParse

Parse always.

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.

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

Check if a string starts with a specified prefix value.

const CharType(& source)[N]

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

CFileContentInfoGenbank mInfoGenbank

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