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NCBI C++ ToolKit: src/algo/blast/dbindex/dbindex.cpp Source File

<

t_

>

[

( t_int )];

<

t_

>

ReadInt( std::istream & is, t_int & v )

UIntHolder< t_int > h;

is.read( h.buf,

( t_int ) );

<

t_

>

WriteInt( std::ostream & os,

t_int & v )

UIntHolder< t_int > h;

os.write( h.buf,

( t_int ) );

( is.eof() || is.bad() ) {

std::ostringstream os;

os << idxname <<

<< setw(2) << setfill(

)

<< volume <<

;

{

;

[4]; } x;

x.a = (

)0x01020304ULL;

<< _m; \

CheckStream( _s, _os.str() ); \

std::ostringstream os;

os <<

<< fname <<

;

std::ostringstream os;

os <<

<< fname;

file_size( (

)fl.

() );

std::ifstream is( fname.c_str() );

ReadInt( is, endianness );

endianness = (endianness == 0) ?

file_size, endianness,

, fname, is ) );

std::ostringstream os;

: actual_size_(

), endianness_( endianness ), version_(

)

: endianness_( GetSystemEndianness() ), version_(

)

(

!= EXPECTED_SIZE ) {

std::ostringstream os;

os <<

<< EXPECTED_SIZE <<

<<

;

ReadInt( is, num_seq_ );

ReadInt( is, num_vol_ );

num_seq_( n_seq ), num_vol_( n_vol )

std::ofstream os( fname.c_str() );

WriteInt( os, num_seq_ );

WriteInt( os, num_vol_ );

std::ifstream is( fname.c_str() );

(

( 0 );

< 7; ++

) { ReadInt( is,

); }

ReadInt( is, start );

( is.bad() ) start = end = 0;

CheckIndexEndianness(

*

)

MAX_KEY_SIZE = 15;

( key_size <= MAX_KEY_SIZE )

;

rev_key_size( 0 );

rev_key_size += ((key_size&0xFF)<<24);

rev_key_size += (((key_size>>8)&0xFF)<<16);

rev_key_size += (((key_size>>16)&0xFF)<<8);

rev_key_size += (key_size>>24);

( rev_key_size <= MAX_KEY_SIZE ) {

);

);

CheckIndexEndianness(

);

.hkey_width_ = (

long)(*ptr++);

= (

long)(*ptr++);

= (

long)(*ptr++);

CheckIndexEndianness(

);

.hkey_width_ = (

long)(*ptr++);

.stride_ = (

long)(*ptr++);

.ws_hint_ = (

long)(*ptr++);

:

;

:

;

:

;

(

)

;

( !index_stream ) {

index_stream.close();

:

LoadIndex< true >( fname, nomap );

+ 1:

LoadIndex< false >( fname, nomap );

);

{ stride >>= 1; ++

; }

( stride != 0 );

(

= 0;

< n_subjects; ++

) {

cerr <<

<<

<<

[

] - 1 << endl;

.push_back( make_pair(

- 1, chunk ) );

nlengths = *(*map)++;

nlengths /=

(

);

(

= 0;

< nlengths; ++

) {

cerr <<

<<

<<

<<

[

] << endl;

nlidmap = *(*map)++;

nlidmap /=

(

);

nlengths = *(*map)++;

nlengths /=

(

);

(

= 0;

< nlengths; ++

) {

cerr <<

<<

<<

<<

[

] << endl;

nlidmap = *(*map)++;

nlidmap /=

(

);

(

, start, stop, stride );

**

,

hkey_width,

stride,

ws_hint )

: total_( 0 ), hkey_width_( hkey_width ), stride_( stride ),

ws_hint_( ws_hint ), min_offset_(

( stride ) )

*

+= hash_table_size + 1;

Structures and functions prototypes used for BLAST gapped extension.

#define MAX_DBSEQ_LEN

Split subject sequences if longer than this.

Structures and API used for saving BLAST hits.

#define DBSEQ_CHUNK_OVERLAP

By how much should the chunks of a subject sequence overlap if it is too long and has to be split.

Types of exception the indexing library can throw.

@ eBadOption

Bad index creation/search option.

@ eBadVersion

Wrong index version.

@ eBadData

Bad index data.

@ eBadSequence

Bad input sequence data.

virtual const char * GetErrCodeString() const override

Get a human readable description of the exception type.

static SOptions DefaultSOptions()

Creates an SOptions instance initialized with default values.

static const unsigned long STRIDE

Only process every STRIDEth nmer.

static const unsigned char VERSION

Index version that this library handles.

static CRef< CDbIndex > Load(const std::string &fname, bool nomap=false)

Load index.

THashTable hash_table_

The hash table (mapping from Nmer values to the lists of offsets.

COffsetData_Base(TWord **map, unsigned long hkey_width, unsigned long stride, unsigned long ws_hint)

Object constructor.

TWord total_

Auxiliary data member used for importing the offset list data.

CDbIndex::TWord TWord

Index word type (public to support Solaris).

unsigned long hkey_width_

Hash key width in bp.

TLengths lengths_

Subject lengths storage.

TWord offset_mask_

Mask to extract offsets.

unsigned long stride_

Index stride value.

unsigned long max_chunk_size_

void Load(TWord **map, TSeqNum start, TSeqNum stop, unsigned long stride)

Loads index by mapping to the memory segment.

unsigned long min_offset_

Minimum offset used by the index.

Uint1 offset_bits_

Number of bits used to encode offset.

TWord total_

Size in bytes of the raw sequence storage.

TLIdMap lid_map_

Local id -> chunk map storage.

TSubjects subjects_

Mapping from database oids to the chunk info.

TChunks chunks_

Collection of individual chunk descriptors.

TSeqStore seq_store_

Storage for the raw subject sequence data.

unsigned long chunk_overlap_

void SetSeqDataFromMap(TWord **map)

Set up the sequence store from the memory segment.

CSubjectMap()

Trivial constructor.

TSCPairMap c2s_map_

CId -> (SId, RCId) map.

CDbIndex::TSeqNum TSeqNum

TVector::size_type size_type

void SetPtr(T *base, size_type sz)

Make the object hold an external sequence.

size_type size() const

Get the sequence size.

unsigned long GetIndexStride< true >(const SIndexHeader &header)

CRef< CIndexSuperHeader_Base > GetIndexSuperHeader(const std::string &fname)

Read superheader structure from the file.

#define M_CHECK_STREAM(_s, _f, _m)

unsigned long GetIndexStride< false >(const SIndexHeader &header)

const SIndexHeader ReadIndexHeader< false >(void *map)

unsigned long GetMinOffset(unsigned long stride)

Compute the minimum offset value needed encode offsets based on stride.

const SIndexHeader ReadIndexHeader< true >(void *map)

unsigned long GetIndexWSHint< false >(const SIndexHeader &header)

unsigned long GetCodeBits(unsigned long stride)

Compute the number of bits to encode special offsets based on stride.

unsigned long GetIndexWSHint< true >(const SIndexHeader &header)

unsigned long GetIndexVersion(CNcbiIstream &is)

Get the index format version for the index data represented by the input stream.

size_t GetIdxVolNumOIDs(const std::string &fname)

Read the index header information from the given file.

const unsigned long REPORT_NORMAL

Normal reporting.

void ReadWord(CNcbiIstream &is, word_t &data)

Read a word from the input stream.

CDbIndex::TSeqNum TSeqNum

Forwarding declarations for convenience.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

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

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

Int8 GetLength(void) const

Get size of file.

bool CheckAccess(TMode access_mode) const

Check access rights.

virtual bool Exists(void) const

Check existence of file.

uint8_t Uint1

1-byte (8-bit) unsigned integer

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 END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

const string version

version string

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

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

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

Simple record type used to specify index creation parameters.

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