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NCBI C++ ToolKit: src/objtools/blast/seqdb_reader/seqdbfile.cpp Source File

+

(*value);

+

(*value);

*

)

& dbfilename,

m_FileName(dbfilename),

((prot_nucl !=

) && (prot_nucl !=

)) {

);

);

((prot_nucl !=

) && (prot_nucl !=

)) {

);

f_format_version = 0;

f_db_seqtype = 0;

off1(0), off2(0), off3(0), offend(0);

dbv5 = ( 5 == f_format_version );

(!dbv5 && (f_format_version != 4)) {

);

off2 = off1 + region_bytes;

off3 = off2 + region_bytes;

offend = off3 + region_bytes;

db_seqtype = ((f_db_seqtype == 1) ?

:

);

);

(db_seqtype ==

) {

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.

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.

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 Init(const string &filename)

Initializes a memory map object.

string m_LMDBFile

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

TIndx m_EndSeq

Offset of the end of the sequence section.

Uint4 m_NumOIDs

The number of oids in this volume.

TIndx m_OffHdr

offset of the start of the header section.

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.

Uint4 m_Volume

Volume number (only set in version 5 DBs)

Uint8 m_VolLen

The length of the volume (in bases).

TIndx m_OffSeq

Offset of the start of the sequence section.

TIndx m_OffAmb

Offset of the start of the ambiguity section.

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

Constructor.

string m_Date

The construction date of the volume.

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

Read a four byte numerical object from the file.

string m_FileName

The name of this file.

CSeqDBAtlas::TIndx TIndx

Type which spans possible file offsets.

bool Open(const CSeqDB_Path &name)

MMap or Open a file.

#define NCBI_THROW(exception_class, err_code, message)

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

int32_t Int4

4-byte (32-bit) signed integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed 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.

unsigned int

A callback function used to compare two keys in a database.

const GenericPointer< typename T::ValueType > T2 value

CSeqDBAtlas::TIndx TIndx

Index file.

File access objects for CSeqDB.

T SeqDB_GetStdOrd(const T *stdord_obj)

Read a network order integer value.

T SeqDB_GetBroken(const T *stdord_obj)

Read a non-network-order integer value.

static SLJIT_INLINE sljit_ins msg(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

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