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

: m_Owner(

), m_ReadOffset(0), m_WriteOffset(0)

: m_Owner(

), m_ReadOffset(0), m_WriteOffset(0)

(

= *offsetp;

<

.size();

++) {

rv = (rv << 7) | (ch & 0x7F);

rv = (rv << 6) | (ch & 0x3F);

*offsetp =

(

+1);

(ch & 0x40) ? -rv : rv;

);

x_ReadIntFixed<int, 1>(&

);

x_ReadIntFixed<int, 2>(&

);

x_ReadIntFixed<Int4, 4>(&

);

x_ReadIntFixed<Int8, 8>(&

);

sz = x_ReadIntFixed<int,4>(offsetp);

* datap =

;

(

= *offsetp;

< ts.

();

++) {

(ts[

] == (

)0) {

zoffset =

(

);

);

datap = ts.

() + *offsetp;

sz = zoffset - *offsetp;

*offsetp = zoffset+1;

begin = *offsetp;

end = begin +

;

(begin > end || end > (

)s.

()) {

);

s.

() + begin;

(((x >> 62) == -1) || ((x >> 62) == 0));

end_ptr =

(

);

[--ptr] = (ux & 0x3F);

[--ptr] = (ux & 0x7F) | 0x80;

bytes = end_ptr - ptr;

ux = ((

)((x >= 0) ? x : -x)) >> 6;

x_WriteIntFixed<int,1>(x,

);

x_WriteIntFixed<int,1>(x, &

);

x_WriteIntFixed<int,2>(x,

);

x_WriteIntFixed<int,2>(x, &

);

x_WriteIntFixed<int,4>(x,

);

x_WriteIntFixed<int,4>(x, &

);

x_WriteIntFixed<Int8, 8>(x,

);

x_WriteIntFixed<Int8, 8>(x, &

);

x_WriteIntFixed_LE<int,1>(x,

);

x_WriteIntFixed_LE<int,1>(x, &

);

x_WriteIntFixed_LE<int,2>(x,

);

x_WriteIntFixed_LE<int,2>(x, &

);

x_WriteIntFixed_LE<int,4>(x,

);

x_WriteIntFixed_LE<int,4>(x, &

);

x_WriteIntFixed_LE<Int8, 8>(x,

);

x_WriteIntFixed_LE<Int8, 8>(x, &

);

x_WriteIntFixed<int,4>(

(

.size()), offsetp);

end_off - start_off;

orig_size =

;

(offsetp ==

) {

*offsetp += orig_size;

cur_cap =

(

.capacity());

(cur_cap < need) {

(new_cap < need) {

(

.size());

pads = pads ? (align - pads) : 0;

(

= 0;

< pads;

++) {

(

= 1;

< pads;

++) {

pads = pads ? (align-pads) : 0;

(

= 0;

< (

)

.size();

++) {

void SkipPadBytes(int align, EPadding fmt)

Align the offset by skipping bytes.

int GetReadOffset() const

Get the current read pointer offset.

CTempString m_DataRef

Non-owned data (only used for `read' streams).

Int4 ReadInt4()

Read a 4 byte integer at the pointer (and move the pointer).

int ReadInt2()

Read a 2 byte integer at the pointer (and move the pointer).

int ReadInt1()

Read a 1 byte integer at the pointer (and move the pointer).

CBlastDbBlob(int size=0)

Create a new object, reserving 'size' bytes for writing.

void x_WriteRaw(const char *ptr, int size, int *offsetp)

Write raw bytes as ptr + size at a given offset.

@ eString

Pad using NUL terminated string of '#' bytes.

@ eSimple

Just write NUL bytes until aligned.

static int VarIntSize(Int8 x)

Compute bytes used for a variable length integer.

int Size() const

Get size of blob contents.

void ReferTo(CTempString data)

Refer to an existing memory area.

int GetWriteOffset() const

Get the current write pointer offset.

void WriteRaw(const char *begin, int size)

Write raw data to the blob (moving the write pointer).

void WritePadBytes(int align, EPadding fmt)

Align the offset by writing pad bytes.

EStringFormat

String termination style.

@ eSizeVar

Write string length as VarInt, then string data.

@ eNUL

Write a NUL terminated string.

@ eSize4

Write string length as Int4, then string data.

void WriteInt2(int x)

Write a 1 byte integer to the blob.

CTempString ReadString(EStringFormat fmt)

Read string data from the blob (moving the read pointer).

void x_Copy(int total)

Copy referenced data to owned data.

void Clear()

Clear all owned data and reference an empty string.

void WriteInt4(Int4 x)

Write a 4 byte integer to the blob.

int x_WriteVarInt(Int8 x, int *offsetp)

Write a variable length integer into the buffer.

void WriteInt8(Int8 x)

Write an 8 byte integer to the blob.

int m_WriteOffset

The `write pointer' for stream-like access.

Int8 x_ReadVarInt(int *offsetp) const

Read a variable length integer from the buffer.

void WriteInt8_LE(Int8 x)

vector< char > m_DataHere

Data owned by this object.

Int8 ReadInt8()

Read an 8 byte integer at the pointer (and move the pointer).

void SeekRead(int offset)

Move the read pointer to a specific location.

CRef< CObject > m_Lifetime

Lifetime maintenance object for referenced data.

int x_WriteString(CTempString str, EStringFormat fmt, int *offsetp)

Write string data to the blob.

void WriteInt1(int x)

Write a 1 byte integer to the blob.

void x_Reserve(int size)

Write raw bytes as a CTempString.

CTempString Str() const

Get blob contents as a CTempString.

void WriteInt4_LE(Int4 x)

int WriteString(CTempString str, EStringFormat fmt)

Write string data to the blob.

void SeekWrite(int offset)

Seek write pointer to a specific location.

const char * x_ReadRaw(int size, int *offsetp) const

Read raw bytes from a given offset.

const char * ReadRaw(int size)

Read raw data (moving the read pointer).

CTempString x_ReadString(EStringFormat fmt, int *offsetp) const

Read string data from the blob.

bool m_Owner

True if this object owns the target data.

int m_ReadOffset

The `read pointer' for stream-like access.

Int8 ReadVarInt()

Read a variable length integer from the blob.

int WriteVarInt(Int8 x)

Write a variable length integer to the blob.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

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

#define NCBI_THROW(exception_class, err_code, message)

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

void Reset(void)

Reset reference object.

int32_t Int4

4-byte (32-bit) signed 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.

const char * data(void) const

Return a pointer to the array represented.

size_type size(void) const

Return the length of the represented array.

unsigned int

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

const struct ncbi::grid::netcache::search::fields::SIZE size

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

Defines BlastDb `Blob' class for SeqDB and WriteDB.

Defines exception class and several constants for SeqDB.

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

#define SEQDB_FILE_ASSERT(YESNO)

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