Type representing subject map data. More...

#include <algo/blast/dbindex/dbindex.hpp>

Collaboration diagram for CSubjectMap:

Public Types
typedef pair< TSeqNum, TSeqPos >	TSOPair

typedef pair< TSeqNum, TSeqNum >	TSCPair

typedef vector< TSCPair >	TSCPairMap

Public Member Functions
	CSubjectMap ()
	Trivial constructor. More...

	CSubjectMap (TWord **map, TSeqNum start, TSeqNum stop, unsigned long stride)
	Constructs object by mapping to the memory segment. More...

	CSubjectMap (TWord **map, const SIndexHeader &header)

void	Load (TWord **map, TSeqNum start, TSeqNum stop, unsigned long stride)
	Loads index by mapping to the memory segment. More...

const TWord *	GetSubjectMap () const
	Provides a mapping from real subject ids and chunk numbers to internal logical subject ids. More...

const Uint1 *	GetSeqStoreBase () const
	Return the start of the raw storage for compressed subject sequence data. More...

TWord	GetSeqStoreSize () const
	Return the size in bytes of the eaw sequence storage. More...

TSeqNum	NumChunks () const
	Get the total number of sequence chunks in the map. More...

TSeqNum	GetNumChunks (TSeqNum lid) const
	Get number of chunks combined into a given logical sequence. More...

TSeqNum	MapSubject (TSeqNum subject, TSeqNum chunk) const
	Get the logical sequence id from the database oid and the chunk number. More...

unsigned long	GetStride () const
	Accessor for stride value. More...

std::pair< TSeqNum, TSeqPos >	DecodeOffset (TWord offset) const
	Decode offset. More...

void	SetSubjInfo (TSeqNum subj, TWord &start, TWord &end) const
	Return the subject information based on the given logical subject id. More...

std::pair< TSeqNum, TSeqPos >	MapSubjOff (TSeqNum lid, TSeqPos soff) const
	Map logical sequence id and logical sequence offset to relative chunk number and chunk offset. More...

TSeqNum	MapLId2Chunk (TSeqNum lid, TSeqNum lchunk) const
	Map logical id and relative chunk to absolute chunk id. More...

TSeqNum	NumSubjects () const
	Get the total number of logical sequences in the map. More...

TSeqPos	GetSeqLen (TSeqNum oid) const
	Get the length of the subject sequence. More...

const Uint1 *	GetSeqData (TSeqNum oid) const
	Get the sequence data of the subject sequence. More...

TWord	getSubjectLength (TSeqNum sid) const

TSeqNum	getCId (TSeqNum sid, TSeqNum rcid) const

TSCPair	getSRCId (TSeqNum cid) const

TWord	getChunkLength (TSeqNum cid) const

TSeqNum	getCIdByLRCId (TSeqNum lid, TSeqNum rcid) const

TSOPair	getRCIdOffByLIdOff (TSeqNum lid, TSeqPos loff) const

TSeqPos	getSOff (TSeqNum sid, TSeqNum rcid, TSeqPos coff) const

TSeqNum	getNumSubjects () const

TSeqNum	getNumChunks () const

TSeqNum	getNumChunks (TSeqNum sid) const

const Uint1 *	getSeqData (TSeqNum sid) const

TSeqNum	getLId (const TOffsetValue &v) const

TSeqPos	getLOff (const TOffsetValue &v) const

Private Types
typedef CDbIndex::TSeqNum	TSeqNum

typedef CDbIndex::TWord	TWord

typedef CDbIndex::TOffsetValue	TOffsetValue

typedef CVectorWrap< TWord >	TSubjects
	Type used to map database oids to the chunk info. More...

typedef CVectorWrap< Uint1 >	TSeqStore
	Type used for compressed subject sequence data storage. More...

typedef CVectorWrap< TWord >	TChunks
	Type for storing the chunk data. More...

typedef CVectorWrap< TWord >	TLengths
	Subject lengths storage type. More...

typedef CVectorWrap< TWord >	TLIdMap
	Local id -> chunks map storage type. More...

Private Member Functions
void	SetSeqDataFromMap (TWord **map)
	Set up the sequence store from the memory segment. More...

Private Attributes
TSubjects	subjects_
	Mapping from database oids to the chunk info. More...

TSeqStore	seq_store_
	Storage for the raw subject sequence data. More...

TWord	total_
	Size in bytes of the raw sequence storage. More...

TChunks	chunks_
	Collection of individual chunk descriptors. More...

unsigned long	stride_
	Index stride value. More...

unsigned long	min_offset_
	Minimum offset used by the index. More...

TLengths	lengths_
	Subject lengths storage. More...

TLIdMap	lid_map_
	Local id -> chunk map storage. More...

Uint1	offset_bits_
	Number of bits used to encode offset. More...

TWord	offset_mask_
	Mask to extract offsets. More...

TSCPairMap	c2s_map_
	CId -> (SId, RCId) map. More...

unsigned long	max_chunk_size_

unsigned long	chunk_overlap_

Detailed Description

Type representing subject map data.

Definition at line 1027 of file dbindex.hpp.

Member Typedef Documentation

◆ TChunks

typedef CVectorWrap< TWord > CSubjectMap::TChunks

private

Type for storing the chunk data.

For raw offset encoding the offset into the vector serves also as the internal logical sequence id.

Definition at line 1045 of file dbindex.hpp.

◆ TLengths

typedef CVectorWrap< TWord > CSubjectMap::TLengths

private

Subject lengths storage type.

Definition at line 1047 of file dbindex.hpp.

◆ TLIdMap

typedef CVectorWrap< TWord > CSubjectMap::TLIdMap

private

Local id -> chunks map storage type.

Definition at line 1048 of file dbindex.hpp.

◆ TOffsetValue

typedef CDbIndex::TOffsetValue CSubjectMap::TOffsetValue

private

Definition at line 1033 of file dbindex.hpp.

◆ TSCPair

typedef pair< TSeqNum, TSeqNum > CSubjectMap::TSCPair

Definition at line 1261 of file dbindex.hpp.

◆ TSCPairMap

typedef vector< TSCPair > CSubjectMap::TSCPairMap

Definition at line 1262 of file dbindex.hpp.

◆ TSeqNum

typedef CDbIndex::TSeqNum CSubjectMap::TSeqNum

private

Definition at line 1031 of file dbindex.hpp.

◆ TSeqStore

typedef CVectorWrap< Uint1 > CSubjectMap::TSeqStore

private

Type used for compressed subject sequence data storage.

Definition at line 1039 of file dbindex.hpp.

◆ TSOPair

typedef pair< TSeqNum, TSeqPos > CSubjectMap::TSOPair

Definition at line 1260 of file dbindex.hpp.

◆ TSubjects

typedef CVectorWrap< TWord > CSubjectMap::TSubjects

private

Type used to map database oids to the chunk info.

Definition at line 1036 of file dbindex.hpp.

◆ TWord

typedef CDbIndex::TWord CSubjectMap::TWord

private

Definition at line 1032 of file dbindex.hpp.

Constructor & Destructor Documentation

◆ CSubjectMap() [1/3]

CSubjectMap::CSubjectMap ( )

inline

Trivial constructor.

Definition at line 1053 of file dbindex.hpp.

◆ CSubjectMap() [2/3]

CSubjectMap::CSubjectMap	(	TWord **	map,
		TSeqNum	start,
		TSeqNum	stop,
		unsigned long	stride
	)

Constructs object by mapping to the memory segment.

Parameters

map	[I/O] pointer to the memory segment
start	[I] database oid of the first sequence in the map
stop	[I] database oid of the last sequence in the map
stride	[I] index stride value

Definition at line 525 of file dbindex.cpp.

References i, lengths_, lid_map_, Load(), offset_bits_, offset_mask_, and CVectorWrap< T >::SetPtr().

◆ CSubjectMap() [3/3]

CSubjectMap::CSubjectMap	(	TWord **	map,
		const SIndexHeader &	header
	)

Definition at line 499 of file dbindex.cpp.

References SIndexHeader::chunk_overlap_, chunk_overlap_, i, lengths_, lid_map_, Load(), SIndexHeader::max_chunk_size_, max_chunk_size_, offset_bits_, offset_mask_, CVectorWrap< T >::SetPtr(), SIndexHeader::start_, SIndexHeader::stop_, and SIndexHeader::stride_.

Member Function Documentation

◆ DecodeOffset()

std::pair< TSeqNum, TSeqPos > CSubjectMap::DecodeOffset ( TWord offset ) const

inline

Decode offset.

Parameters

offset The encoded offset value.

Returns: A pair with first element being the local subject sequence id and the second element being the subject offset.

Definition at line 1149 of file dbindex.hpp.

References min_offset_, offset, offset_bits_, offset_mask_, and stride_.

Referenced by CSearch< LEGACY, NHITS >::DecodeOffset().

◆ getChunkLength()

TWord CSubjectMap::getChunkLength ( TSeqNum cid ) const

inline

Definition at line 1270 of file dbindex.hpp.

References ASSERT, chunk_overlap_, chunks_, getSRCId(), getSubjectLength(), max_chunk_size_, CVectorWrap< T >::size(), subjects_, and t.

Referenced by CDbIndex::getChunkLength().

◆ getCId()

TSeqNum CSubjectMap::getCId	(	TSeqNum	sid,
		TSeqNum	rcid
	)		const

inline

Definition at line 1252 of file dbindex.hpp.

References ASSERT, chunks_, result, CVectorWrap< T >::size(), and subjects_.

Referenced by CDbIndex::getCId().

◆ getCIdByLRCId()

TSeqNum CSubjectMap::getCIdByLRCId	(	TSeqNum	lid,
		TSeqNum	rcid
	)		const

inline

Definition at line 1290 of file dbindex.hpp.

References ASSERT, lid_map_, and CVectorWrap< T >::size().

Referenced by CDbIndex::getCIdByLRCId().

◆ getLId()

TSeqNum CSubjectMap::getLId ( const TOffsetValue & v ) const

inline

Definition at line 1356 of file dbindex.hpp.

References CDbIndex::SOffsetValue::offset, and offset_bits_.

Referenced by CDbIndex::getLId().

◆ getLOff()

TSeqPos CSubjectMap::getLOff ( const TOffsetValue & v ) const

inline

Definition at line 1359 of file dbindex.hpp.

References CDbIndex::SOffsetValue::offset, offset_mask_, and stride_.

Referenced by CDbIndex::getLOff().

◆ getNumChunks() [1/2]

TSeqNum CSubjectMap::getNumChunks ( ) const

inline

Definition at line 1337 of file dbindex.hpp.

References chunks_, and CVectorWrap< T >::size().

Referenced by CDbIndex::getNumChunks().

◆ GetNumChunks()

TSeqNum CSubjectMap::GetNumChunks ( TSeqNum lid ) const

inline

Get number of chunks combined into a given logical sequence.

Parameters

lid	The logical sequence id.

Returns: Corresponding number of chunks.

Definition at line 1110 of file dbindex.hpp.

References lid_map_.

Referenced by CSearch_Base< LEGACY, NHITS, derived_t >::operator()(), and CTrackedSeeds_Base< TWO_HIT >::SetLId().

◆ getNumChunks() [2/2]

TSeqNum CSubjectMap::getNumChunks ( TSeqNum sid ) const

inline

Definition at line 1339 of file dbindex.hpp.

References ASSERT, chunks_, CVectorWrap< T >::size(), and subjects_.

◆ getNumSubjects()

TSeqNum CSubjectMap::getNumSubjects ( ) const

inline

Definition at line 1336 of file dbindex.hpp.

References CVectorWrap< T >::size(), and subjects_.

Referenced by CDbIndex::getNumSubjects().

◆ getRCIdOffByLIdOff()

TSOPair CSubjectMap::getRCIdOffByLIdOff	(	TSeqNum	lid,
		TSeqPos	loff
	)		const

inline

Definition at line 1299 of file dbindex.hpp.

References ASSERT, CVectorWrap< T >::begin(), chunks_, CDbIndex::CR, CR, lid_map_, seq_store_, and CVectorWrap< T >::size().

Referenced by CDbIndex::getRCIdOffByLIdOff().

◆ GetSeqData()

const Uint1* CSubjectMap::GetSeqData ( TSeqNum oid ) const

inline

Get the sequence data of the subject sequence.

Parameters

oid	Ordinal id of the subject sequence.

Returns: Pointer to the sequence data.

Definition at line 1239 of file dbindex.hpp.

References chunks_, seq_store_, and subjects_.

Referenced by CDbIndex_Impl< LEGACY >::GetSeqData().

◆ getSeqData()

const Uint1* CSubjectMap::getSeqData ( TSeqNum sid ) const

inline

Definition at line 1348 of file dbindex.hpp.

References ASSERT, chunks_, seq_store_, CVectorWrap< T >::size(), and subjects_.

Referenced by CDbIndex::getSeqData().

◆ GetSeqLen()

TSeqPos CSubjectMap::GetSeqLen ( TSeqNum oid ) const

inline

Get the length of the subject sequence.

Parameters

oid	Ordinal id of the subject sequence.

Returns: Length of the sequence in bases.

Definition at line 1230 of file dbindex.hpp.

References lengths_.

Referenced by CDbIndex_Impl< LEGACY >::GetSeqLen().

◆ GetSeqStoreBase()

const Uint1* CSubjectMap::GetSeqStoreBase ( ) const

inline

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

Returns: start of the sequence data storage

Definition at line 1091 of file dbindex.hpp.

References seq_store_.

Referenced by CDbIndex_Impl< LEGACY >::GetSeqStoreBase().

◆ GetSeqStoreSize()

TWord CSubjectMap::GetSeqStoreSize ( ) const

inline

Return the size in bytes of the eaw sequence storage.

Returns: Size of the sequence data storage.

Definition at line 1097 of file dbindex.hpp.

References total_.

◆ getSOff()

TSeqPos CSubjectMap::getSOff	(	TSeqNum	sid,
		TSeqNum	rcid,
		TSeqPos	coff
	)		const

inline

Definition at line 1326 of file dbindex.hpp.

References ASSERT, chunk_overlap_, chunks_, lengths_, max_chunk_size_, CVectorWrap< T >::size(), and subjects_.

Referenced by CDbIndex::getSOff().

◆ getSRCId()

TSCPair CSubjectMap::getSRCId ( TSeqNum cid ) const

inline

Definition at line 1264 of file dbindex.hpp.

References ASSERT, c2s_map_, chunks_, and CVectorWrap< T >::size().

Referenced by getChunkLength(), and CDbIndex::getSRCId().

◆ GetStride()

unsigned long CSubjectMap::GetStride ( ) const

inline

Accessor for stride value.

Returns: the stride value used by the index

Definition at line 1140 of file dbindex.hpp.

References stride_.

◆ getSubjectLength()

TWord CSubjectMap::getSubjectLength ( TSeqNum sid ) const

inline

Definition at line 1246 of file dbindex.hpp.

References ASSERT, lengths_, CVectorWrap< T >::size(), and subjects_.

Referenced by getChunkLength(), and CDbIndex::getSubjectLength().

◆ GetSubjectMap()

const TWord* CSubjectMap::GetSubjectMap ( ) const

inline

Provides a mapping from real subject ids and chunk numbers to internal logical subject ids.

Returns: start of the (subject,chunk)->id mapping

Definition at line 1085 of file dbindex.hpp.

References subjects_.

Referenced by CSearch_Base< LEGACY, NHITS, derived_t >::operator()().

◆ Load()

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

Loads index by mapping to the memory segment.

Parameters

map	[I/O] pointer to the memory segment
start	[I] database oid of the first sequence in the map
stop	[I] database oid of the last sequence in the map
stride	[I] index stride value

Definition at line 450 of file dbindex.cpp.

References c2s_map_, chunks_, GetMinOffset(), i, min_offset_, CVectorWrap< T >::SetPtr(), SetSeqDataFromMap(), CVectorWrap< T >::size(), stride_, subjects_, and total_.

Referenced by CSubjectMap().

◆ MapLId2Chunk()

TSeqNum CSubjectMap::MapLId2Chunk	(	TSeqNum	lid,
		TSeqNum	lchunk
	)		const

inline

Map logical id and relative chunk to absolute chunk id.

Parameters

lid	logical sequence id
lchunk	chunk number within the logical sequence

Returns: chunk id of the corresponding chunk

Definition at line 1211 of file dbindex.hpp.

References lid_map_.

◆ MapSubject()

TSeqNum CSubjectMap::MapSubject	(	TSeqNum	subject,
		TSeqNum	chunk
	)		const

inline

Get the logical sequence id from the database oid and the chunk number.

Parameters

subject	[I] database oid
chunk	[I] the chunk number

Returns: logical sequence id corresponding to subject and chunk

Definition at line 1122 of file dbindex.hpp.

References chunks_, result, CVectorWrap< T >::size(), subject, and subjects_.

◆ MapSubjOff()

std::pair< TSeqNum, TSeqPos > CSubjectMap::MapSubjOff	(	TSeqNum	lid,
		TSeqPos	soff
	)		const

inline

Map logical sequence id and logical sequence offset to relative chunk number and chunk offset.

Parameters

lid	The logical sequence id.
soff	The logical sequence offset.

Returns: Pair of relative chunk number and chunk offset.

Definition at line 1180 of file dbindex.hpp.

References ASSERT, CVectorWrap< T >::begin(), chunks_, CDbIndex::CR, CR, and lid_map_.

◆ NumChunks()

TSeqNum CSubjectMap::NumChunks ( ) const

inline

Get the total number of sequence chunks in the map.

Returns: number of chunks in the map

Definition at line 1102 of file dbindex.hpp.

References chunks_, and CVectorWrap< T >::size().

Referenced by CDbIndex_Impl< LEGACY >::NumChunks().

◆ NumSubjects()

TSeqNum CSubjectMap::NumSubjects ( ) const

inline

Get the total number of logical sequences in the map.

Returns: number of chunks in the map

Definition at line 1221 of file dbindex.hpp.

References lid_map_, and CVectorWrap< T >::size().

Referenced by CDbIndex_Impl< LEGACY >::NumSubjects().

◆ SetSeqDataFromMap()

void CSubjectMap::SetSeqDataFromMap ( TWord ** map )

private

Set up the sequence store from the memory segment.

Parameters

map	[I/O] points to the memory segment

Definition at line 489 of file dbindex.cpp.

References seq_store_, CVectorWrap< T >::SetPtr(), and total_.

Referenced by Load().

◆ SetSubjInfo()

void CSubjectMap::SetSubjInfo	(	TSeqNum	subj,
		TWord &	start,
		TWord &	end
	)		const

inline

Return the subject information based on the given logical subject id.

Parameters

subj	[I] logical subject id
start	[0] starting offset of subj in the sequence store
end	[0] 1 + ending offset of subj in the sequence store

Definition at line 1164 of file dbindex.hpp.

References lid_map_.

Referenced by CSearch< LEGACY, NHITS >::SetSubjInfo().

Member Data Documentation

◆ c2s_map_

TSCPairMap CSubjectMap::c2s_map_

private

CId -> (SId, RCId) map.

Definition at line 1383 of file dbindex.hpp.

Referenced by getSRCId(), and Load().

◆ chunk_overlap_

unsigned long CSubjectMap::chunk_overlap_

private

Definition at line 1386 of file dbindex.hpp.

Referenced by CSubjectMap(), getChunkLength(), and getSOff().

◆ chunks_

TChunks CSubjectMap::chunks_

private

Collection of individual chunk descriptors.

Definition at line 1374 of file dbindex.hpp.

Referenced by getChunkLength(), getCId(), getNumChunks(), getRCIdOffByLIdOff(), GetSeqData(), getSeqData(), getSOff(), getSRCId(), Load(), MapSubject(), MapSubjOff(), and NumChunks().

◆ lengths_

TLengths CSubjectMap::lengths_

private

Subject lengths storage.

Definition at line 1379 of file dbindex.hpp.

Referenced by CSubjectMap(), GetSeqLen(), getSOff(), and getSubjectLength().

◆ lid_map_

TLIdMap CSubjectMap::lid_map_

private

Local id -> chunk map storage.

Definition at line 1380 of file dbindex.hpp.

Referenced by CSubjectMap(), getCIdByLRCId(), GetNumChunks(), getRCIdOffByLIdOff(), MapLId2Chunk(), MapSubjOff(), NumSubjects(), and SetSubjInfo().

◆ max_chunk_size_

unsigned long CSubjectMap::max_chunk_size_

private

Definition at line 1385 of file dbindex.hpp.

Referenced by CSubjectMap(), getChunkLength(), and getSOff().

◆ min_offset_

unsigned long CSubjectMap::min_offset_

private

Minimum offset used by the index.

Definition at line 1377 of file dbindex.hpp.

Referenced by DecodeOffset(), and Load().

◆ offset_bits_

Uint1 CSubjectMap::offset_bits_

private

Number of bits used to encode offset.

Definition at line 1381 of file dbindex.hpp.

Referenced by CSubjectMap(), DecodeOffset(), and getLId().

◆ offset_mask_

TWord CSubjectMap::offset_mask_

private

Mask to extract offsets.

Definition at line 1382 of file dbindex.hpp.

Referenced by CSubjectMap(), DecodeOffset(), and getLOff().

◆ seq_store_

TSeqStore CSubjectMap::seq_store_

private

Storage for the raw subject sequence data.

Definition at line 1370 of file dbindex.hpp.

Referenced by getRCIdOffByLIdOff(), GetSeqData(), getSeqData(), GetSeqStoreBase(), and SetSeqDataFromMap().

◆ stride_

unsigned long CSubjectMap::stride_

private

Index stride value.

Definition at line 1376 of file dbindex.hpp.

Referenced by DecodeOffset(), getLOff(), GetStride(), and Load().

◆ subjects_

TSubjects CSubjectMap::subjects_

private

Mapping from database oids to the chunk info.

Definition at line 1369 of file dbindex.hpp.

Referenced by getChunkLength(), getCId(), getNumChunks(), getNumSubjects(), GetSeqData(), getSeqData(), getSOff(), getSubjectLength(), GetSubjectMap(), Load(), and MapSubject().

◆ total_

TWord CSubjectMap::total_

private

Size in bytes of the raw sequence storage.

(only valid after the complete object has been constructed)

Definition at line 1371 of file dbindex.hpp.

Referenced by GetSeqStoreSize(), Load(), and SetSeqDataFromMap().

The documentation for this class was generated from the following files:

include/algo/blast/dbindex/dbindex.hpp
src/algo/blast/dbindex/dbindex.cpp

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ TChunks

◆ TLengths

◆ TLIdMap

◆ TOffsetValue

◆ TSCPair

◆ TSCPairMap

◆ TSeqNum

◆ TSeqStore

◆ TSOPair

◆ TSubjects

◆ TWord

Constructor & Destructor Documentation

◆ CSubjectMap() [1/3]

◆ CSubjectMap() [2/3]

◆ CSubjectMap() [3/3]

Member Function Documentation

◆ DecodeOffset()

◆ getChunkLength()

◆ getCId()

◆ getCIdByLRCId()

◆ getLId()

◆ getLOff()

◆ getNumChunks() [1/2]

◆ GetNumChunks()

◆ getNumChunks() [2/2]

◆ getNumSubjects()

◆ getRCIdOffByLIdOff()

◆ GetSeqData()

◆ getSeqData()

◆ GetSeqLen()

◆ GetSeqStoreBase()

◆ GetSeqStoreSize()

◆ getSOff()

◆ getSRCId()

◆ GetStride()

◆ getSubjectLength()

◆ GetSubjectMap()

◆ Load()

◆ MapLId2Chunk()

◆ MapSubject()

◆ MapSubjOff()

◆ NumChunks()

◆ NumSubjects()

◆ SetSeqDataFromMap()

◆ SetSubjInfo()

Member Data Documentation

◆ c2s_map_

◆ chunk_overlap_

◆ chunks_

◆ lengths_

◆ lid_map_

◆ max_chunk_size_

◆ min_offset_

◆ offset_bits_

◆ offset_mask_

◆ seq_store_

◆ stride_

◆ subjects_

◆ total_