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NCBI C++ ToolKit: include/objtools/blast/seqdb_reader/impl/seqdbfile.hpp Source File

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bool GetFileSizeL(const string &fname, TIndx &length)

Get size of a file.

CNcbiStreamoff TIndx

The type used for file offsets.

CSeqDBRawFile m_File

The raw file object.

char x_GetSeqType() const

Get the volume's sequence data type.

void x_SetFileType(char prot_nucl)

Sets the sequence data type.

CSeqDBAtlas::TIndx TIndx

Type which spans possible file offsets.

void x_ReadBytes(char *buf, TIndx start, TIndx end) const

Read part of the file into a buffer.

CSeqDBAtlas & m_Atlas

The memory layer management object.

char m_ProtNucl

Either 'p' for protein or 'n' for nucleotide.

CSeqDBFileMemMap m_Lease

A memory lease used by this file.

TIndx x_ReadSwapped(CSeqDBFileMemMap &lease, TIndx offset, T *value)

Read a numerical object from the file.

virtual ~CSeqDBExtFile()

Destructor.

void UnLease()

Release memory held in the atlas layer by this object.

string m_FileName

The name of this file.

CSeqDBExtFile(CSeqDBAtlas &atlas, const string &dbfilename, char prot_nucl)

Constructor.

const char * GetFileDataPtr(const string &fname, TIndx offset)

Get a pointer to the specified offset.

void Clear()

Clears the memory mapobject.

const char * GetFileDataPtr(TIndx start) const

Read part of the file into a buffer.

CSeqDBHdrFile(CSeqDBAtlas &atlas, const string &dbname, char prot_nucl)

Constructor.

void ReadBytes(char *buf, TIndx start, TIndx end) const

Read part of the file into a buffer.

CSeqDBAtlas::TIndx TIndx

Type which spans possible file offsets.

virtual ~CSeqDBHdrFile()

Destructor.

Uint4 * x_GetAmb() const

Get ambiguity data (assumes locked).

string m_LMDBFile

Name of matching SQLite file (empty if version 4 DB)

TIndx m_EndSeq

Offset of the end of the sequence section.

string GetDate() const

Get the construction date of the volume.

Uint4 m_NumOIDs

The number of oids in this volume.

TIndx m_OffHdr

offset of the start of the header section.

void GetHdrStartEnd(int oid, TIndx &start, TIndx &end) const

Get the location of a sequence's header data.

void UnLease()

Release any memory leases temporarily held here.

string GetTitle() const

Get the volume title.

int GetNumOIDs() const

Get the number of oids in this volume.

string GetLMDBFileName() const

bool GetAmbStartEnd(int oid, TIndx &start, TIndx &end) const

Get the location of a sequence's ambiguity data.

Uint4 m_MaxLen

The length of the longest sequence in this volume.

TIndx m_EndAmb

Offset of the end of the ambiguity section.

string m_Title

The volume title.

TIndx m_EndHdr

Offset of the end of the header section.

Uint8 GetVolumeLength() const

Get the length of the volume (in bases).

Uint4 * x_GetHdr() const

Get header data (assumes locked).

Uint4 m_Volume

Volume number (only set in version 5 DBs)

int GetMinLength() const

Get the length of the shortest sequence in this volume.

Uint8 m_VolLen

The length of the volume (in bases).

TIndx m_OffSeq

Offset of the start of the sequence section.

virtual ~CSeqDBIdxFile()

Destructor.

void GetSeqStart(int oid, TIndx &start) const

Get the location of a sequence's packed sequence data.

char GetSeqType() const

Get the sequence data type.

TIndx m_OffAmb

Offset of the start of the ambiguity section.

CSeqDBIdxFile(CSeqDBAtlas &atlas, const string &dbname, char prot_nucl)

Constructor.

int GetMaxLength() const

Get the length of the longest sequence in this volume.

string m_Date

The construction date of the volume.

Uint4 m_MinLen

The length of the shortest sequence in this volume.

void GetSeqStartEnd(int oid, TIndx &start, TIndx &end) const

Get the location of a sequence's packed sequence data.

Uint4 * x_GetSeq() const

Get sequence data (assumes locked).

TIndx GetFileLength() const

Get the length of the file.

TIndx ReadSwapped(CSeqDBFileMemMap &lease, TIndx offset, Uint4 *value) const

Read a four byte numerical object from the file.

void ReadBytes(CSeqDBFileMemMap &lease, char *buf, TIndx start, TIndx end) const

Read part of the file into a buffer.

TIndx m_Length

The length of this file.

string m_FileName

The name of this file.

CSeqDBRawFile(CSeqDBAtlas &atlas)

Constructor.

CSeqDBAtlas::TIndx TIndx

Type which spans possible file offsets.

bool Open(const CSeqDB_Path &name)

MMap or Open a file.

const char * GetFileDataPtr(CSeqDBFileMemMap &lease, TIndx start, TIndx end) const

Get a pointer to a section of the file.

CSeqDBAtlas & m_Atlas

The memory management layer object.

CSeqDBSeqFile(CSeqDBAtlas &atlas, const string &dbname, char prot_nucl)

Constructor.

CSeqDBAtlas::TIndx TIndx

Type which spans possible file offsets.

void ReadBytes(char *buf, TIndx start, TIndx end) const

Read part of the file into a buffer.

virtual ~CSeqDBSeqFile()

Destructor.

const char * GetFileDataPtr(TIndx start) const

Get a pointer into the file contents.

const string & GetPathS() const

Get the path as a string.

bool Valid() const

Returns true if this object has a value.

The NCBI C++ standard methods for dealing with std::string.

#define NCBI_THROW(exception_class, err_code, message)

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

const GenericPointer< typename T::ValueType > T2 value

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

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

The SeqDB memory management layer.

Defines exception class and several constants for SeqDB.

CSeqDBAtlas::TIndx TIndx

Index file.

This file defines several SeqDB utility functions related to byte order and file system portability.

#define SEQDB_FILE_ASSERT(YESNO)

T SeqDB_GetStdOrd(const T *stdord_obj)

Read a network order integer value.

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