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

index_extn =

;

index_extn[1] = file_id;

data_extn = index_extn;

& index_extn,

& data_extn,

: m_AtlasHolder (lockedp,

),

m_Atlas (m_AtlasHolder.

()),

m_IndexFile (m_Atlas),

m_DataFile (m_Atlas),

m_IndexLease (m_Atlas),

m_DataLease (m_Atlas),

m_OffsetArrayStart (0)

(lockedp ==

) {

(! (found1 && found2)) {

);

index = (select_file ==

);

* ptr =

.GetFileDataPtr(lease, begin, end);

kFixedFieldBytes = 32;

fmt_version = header.

();

(fmt_version != 1) {

);

column_type = header.

();

(column_type != 1) {

);

);

);

(begin > 0 && end > begin);

);

(

j = 0; j <

; j++) {

);

);

(lockedp ==

) {

iend = istart + (2 * item_size);

dstart =

.ReadInt4();

dend =

.ReadInt4();

: m_VolIndices(indices), m_HaveMap(

)

`Blob' Class for SeqDB (and WriteDB).

void SkipPadBytes(int align, EPadding fmt)

Align the offset by skipping bytes.

int GetReadOffset() const

Get the current read pointer offset.

Int4 ReadInt4()

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

@ eString

Pad using NUL terminated string of '#' bytes.

int Size() const

Get size of blob contents.

void ReferTo(CTempString data)

Refer to an existing memory area.

CTempString ReadString(EStringFormat fmt)

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

void Clear()

Clear all owned data and reference an empty string.

Int8 ReadInt8()

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

Int8 ReadVarInt()

Read a variable length integer from the blob.

bool DoesFileExist(const string &fname)

Check if file exists.

void Lock(CSeqDBLockHold &locked)

Lock the atlas.

void Unlock(CSeqDBLockHold &locked)

Unlock the atlas.

string m_Title

The title identifies this column's purpose.

Int4 m_NumOIDs

Number of OIDs (Blobs) in this column.

CSeqDBColumn(const string &basename, const string &index_extn, const string &data_extn, CSeqDBLockHold *lockedp)

Constructor.

static bool ColumnExists(const string &basename, const string &extn, CSeqDBAtlas &atlas)

Determine if the column exists.

void x_ReadMetaData(CSeqDBLockHold &locked)

Open files and read field data from the atlas.

void Flush()

Flush any held memory.

ESelectFile

Which file to access.

@ e_Index

Use index file.

Int8 m_DataLength

Total length of data stored in the data file.

Int4 m_OffsetArrayStart

Start offset (in the index file) of the offset array.

int GetNumOIDs() const

Get the number of OIDs stored here.

CSeqDBRawFile m_DataFile

Data file.

map< string, string > m_MetaData

All key/value metadata for this column.

const map< string, string > & GetMetaData()

Get the column's Key/Value meta data.

CSeqDBFileMemMap m_DataLease

Data file lease.

void x_GetFileRange(TIndx begin, TIndx end, ESelectFile select_file, bool lifetime, CBlastDbBlob &blob, CSeqDBLockHold &locked)

Get a range of the index or data file.

static const CBlastDbBlob::EStringFormat kStringFmt

String format used by column files.

void GetBlob(int oid, CBlastDbBlob &blob, bool keep, CSeqDBLockHold *lockedp)

Fetch the data blob for the given oid.

string m_Date

The create date of the column files.

CSeqDBAtlas & m_Atlas

Reference to the atlas.

const string & GetTitle() const

Get the column title.

CSeqDBRawFile m_IndexFile

Index file.

Int4 m_MetaDataStart

Start offset (in the index file) of the metadata section.

CSeqDBFileMemMap m_IndexLease

Index file lease.

~CSeqDBColumn()

Destructor.

void x_ReadFields(CSeqDBLockHold &locked)

Open files and read field data from the atlas.

CSeqDBAtlas::TIndx TIndx

File offset type.

void Clear()

Clears the memory mapobject.

TIndx GetFileLength() const

Get the length of the file.

bool Open(const CSeqDB_Path &name)

MMap or Open a file.

Hold a memory region refcount, return to atlas when destroyed.

CSeqDB_ColumnEntry(const vector< int > &indices)

Constructor.

map< string, string > m_Map

The combined metadata map for this column.

void SetMapValue(const string &k, const string &v)

Add a meta-data key/value association.

void GetBlob(int oid, CBlastDbBlob &blob)

Fetch the data blob for the given oid.

const map< string, string > & GetMetaData()

Get the column's key/value meta data.

CSeqDB_ColumnReader(const string &basename, char file_id='a')

Read a BlastDb format column.

const string & GetTitle() const

Get the column title.

int GetNumOIDs() const

Get the number of rows stored in this column.

class CSeqDBColumn * m_Impl

Implementation object.

~CSeqDB_ColumnReader()

Destructor.

const string & GetValue(const string &key)

Look up one metadata value.

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

const_iterator end() const

const_iterator find(const key_type &key) const

Defines column reader class for SeqDB.

#define NCBI_THROW(exception_class, err_code, message)

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

int64_t Int8

8-byte (64-bit) signed integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

unsigned int

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

const TYPE & Get(const CNamedParameterList *param)

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

static uint32_t offset_size

static PCRE2_SIZE * offsets

Defines database column access classes.

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

const U & SeqDB_MapFind(const std::map< T, U > &m, const T &k, const U &dflt)

Find a map value or return a default.

#define SEQDB_FILE_ASSERT(YESNO)

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