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NCBI C++ ToolKit: include/algo/blast/dbindex/dbindex_sp.hpp Source File

<

word_t >

<

LEGACY >

<

LEGACY >

<

LEGACY >

<

iterator_t >

{

( offset_data,

, ws ); }

<

iterator_t >

stride,

ws_hint );

stride,

ws_hint );

h = offset_data.

() - 1;

s = offset_data.

();

w = offset_data.

();

(

== 0 )

;

{

!= 0; }

<

iterator_t >

**

,

hkey_width,

stride,

ws_hint )

:

(

, hkey_width, stride, ws_hint )

<

LEGACY >

<

LEGACY >

vector< string > & idmap,

();

SSearchOptions & search_options );

<

LEGACY >

vector< string > & idmap,

*

)

: mapfile_(

), map_start_( 0 ), version_(

),

, GetIndexWSHint< LEGACY >( header ) );

(

!= 0 ) {

, GetIndexWSHint< LEGACY >( header ) );

<

LEGACY >

( mapfile_ != 0 ) {

subject_map_; subject_map_ = 0;

offset_data_; offset_data_ = 0;

map_ = (

*)(mapfile_->Map( subject_map_offset_ ));

subject_map_ =

( &map_, start_, stop_, stride_ );

<

LEGACY >

<

LEGACY >

vector< string > idmap;

idmap_fname = fname +

;

( idmap_stream ) {

idmap_stream >> line;

idmap.push_back( line );

(

);

);

s.read( (

*)

,

);

header = ReadIndexHeader< LEGACY >(

);

header = ReadIndexHeader< LEGACY >(

->GetPtr() );

Types of exception the indexing library can throw.

Implementation of the BLAST database index.

const Uint1 * GetSeqStoreBase() const

Get the start of compressed raw sequence data.

size_t subject_map_offset_

Offset of the subject map in the index file.

unsigned long version_

Index format version.

virtual CConstRef< CSearchResults > DoSearch(const BLAST_SequenceBlk *query, const BlastSeqLoc *locs, const SSearchOptions &search_options)

The search procedure for this specialized index implementation.

TOffsetData * offset_data_

Offset lists.

static const unsigned long HEADER_SIZE

Size of the index file header for index format version >= 2.

TTraits::TOffsetData TOffsetData

CMemoryFile * mapfile_

Memory mapped file.

TWord * map_

Start of memory mapped file data.

TOffsetData::TIterator TOffsetIterator

TWord * map_start_

Start of the index data, when not mapped.

const TOffsetIterator OffsetIterator(TWord nmer, unsigned long mod) const

Create an offset list iterator corresponding to the given Nmer value.

TTraits::TSubjectMap TSubjectMap

virtual TSeqPos GetSeqLen(TSeqNum oid) const

Get the length of the subject sequence.

TSeqNum NumChunks() const

Get the total number of sequence chunks in the index.

const TSubjectMap & GetSubjectMap() const

Get the subject map instance from the index object.

CDbIndex_Traits< LEGACY > TTraits

Offset data and subject map types computer.

virtual void Remap()

If possible reduce the index footpring by unmapping the portion that does not contain sequence data.

~CDbIndex_Impl()

Object destructor.

CDbIndex_Impl(CMemoryFile *map, const SIndexHeader &header, const vector< string > &idmap, TWord *data=0)

Create an index object from mapped memory segment.

TSeqNum NumSubjects() const

Get the total number of logical sequences in the index.

unsigned long stride_

Stride value used during index creation.

virtual unsigned long Version() const

Get the index format version.

virtual const Uint1 * GetSeqData(TSeqNum oid) const

Get the sequence data of the subject sequence.

unsigned long hkey_width() const

Get the hash key width of the index.

Base class providing high level interface to index objects.

static CRef< CDbIndex > LoadIndex(CNcbiIstream &is)

Load index from an open stream.

TSeqNum start_

OID of the first sequence in the index.

TSeqNum stop_chunk_

Number of the last chunk of the last sequence.

Uint4 TWord

Type representing main memory unit of the index structure.

SIndexHeader header_

The index header structure.

TSeqNum start_chunk_

Number of the first chunk of the first sequence.

TSubjectMap * subject_map_

The subject map object.

vector< string > idmap_

Mapping from source ids to bioseq ids.

TSeqNum stop_

OID of the last sequence in the inex.

CSequenceIStream::TStreamPos TSeqNum

Type used to enumerate sequences in the index.

Class representing index hash table and offset list database.

THashTable hash_table_

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

TWord total_

Auxiliary data member used for importing the offset list data.

unsigned long getMinOffset() const

Accessor for minimum offset value.

unsigned long hkey_width() const

Get the width of the hash key in base pairs.

unsigned long getWSHint() const

Accessor for ws_hint value.

unsigned long getStride() const

Accessor for stride value.

Iterator specific functionality of offset list manager class.

TWord * data_start_

Start of the offset data.

TOffsets offsets_

Concatenated offset list data.

COffsetData_Base TBase

Base class alias.

CVectorWrap< TWord > TOffsets

Type used to store offset lists.

iterator_t TIterator

Type used to iterate over an offset list.

COffsetData(CNcbiIstream &is, unsigned long hkey_width, unsigned long stride, unsigned long ws_hint)

Construct the object from the data in the given input stream.

Iterator for 0-terminated pre-ordered offset lists.

const TWord * curr_

Current position in the offset list.

TOffsetValue getOffsetValue() const

bool More()

Check if more data is available in the iterator.

bool boundary_

Flag indicating the current offset is actually a extra information for boundary cases.

COffsetData_Base::TOffsetValue TOffsetValue

CPreOrderedOffsetIterator()

unsigned long more_

Flag indicating that more values are available.

bool Next()

Advance the iterator.

unsigned long mod_

Determines which offsets to skip.

COffsetData< CPreOrderedOffsetIterator > TOffsetData

Type of offset data class supported by this iterator.

TWord offset_

Current cached offset value.

unsigned long min_offset_

Minimum offset used by the index.

CPreOrderedOffsetIterator(const TOffsetData &offset_data, TWord key, unsigned long ws)

Object constructor.

TWord Offset() const

Iterator dereference.

Type representing subject map data.

const Uint1 * GetSeqStoreBase() const

Return the start of the raw storage for compressed subject sequence data.

TSeqNum NumSubjects() const

Get the total number of logical sequences in the map.

TSeqNum NumChunks() const

Get the total number of sequence chunks in the map.

TSeqPos GetSeqLen(TSeqNum oid) const

Get the length of the subject sequence.

const Uint1 * GetSeqData(TSeqNum oid) const

Get the sequence data of the subject sequence.

TVector::size_type size_type

void SetPtr(T *base, size_type sz)

Make the object hold an external sequence.

void ReadWord(CNcbiIstream &is, word_t &data)

Read a word from the input stream.

unsigned long GetIndexStride(const SIndexHeader &header)

Get the stride value associated with the index.

const SIndexHeader ReadIndexHeader(void *map)

Read the index header information from the given input stream.

CDbIndex::TSeqNum TSeqNum

Forwarding declarations for convenience.

CMemoryFile * MapFile(const std::string &fname)

Memory map a file and return a pointer to the mapped area.

unsigned long GetIndexWSHint(const SIndexHeader &header)

Get the ws_hint value associated with the index.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define NCBI_THROW(exception_class, err_code, message)

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

Int8 GetLength(void) const

Get size of file.

bool Unmap(void)

Unmap file if mapped.

void * GetPtr(void) const

Get pointer to beginning of data.

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed 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 struct ncbi::grid::netcache::search::fields::KEY key

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

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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

Structure to hold a sequence.

Used to hold a set of positions, mostly used for filtering.

Simple record type used to specify index search parameters.

Some computed type definitions.

COffsetData< CPreOrderedOffsetIterator > TOffsetData

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