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NCBI C++ ToolKit: src/objtools/data_loaders/blastdb/cached_sequence.cpp Source File

use_fixed_size_slices,

: m_SIH(idh), m_BlastDb(db), m_OID(oid),

m_UseFixedSizeSlices(use_fixed_size_slices),

m_SliceSize(slice_size)

m_Length = m_BlastDb.GetSeqLength(m_OID);

bioseq->

().SetLength(m_Length);

m_TSE->SetSeq(*bioseq);

( blast_deflines.

() ) {

blast_deflines->

()) {

(! (*one_defline)->CanGetSeqid()) {

(*one_defline)->SetSeqid()) {

retval.push_back(*seqid);

((end - pos) > slice_size) {

end = pos + slice_size;

dseq->SetLiteral().SetLength(end - pos);

.push_back(dseq);

loc_set.push_back(loc);

chunks.push_back(chunk);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

#define kSliceGrowthFactor

When fixed size slices are not used, each subsequent slice grows its size by this factor.

@ kRmtSequenceSliceSize

Same as above, but used for fetching sequences from remote BLAST databases.

@ kFastSequenceLoadSize

If sequence is shorter than this size, it will not be split and it will be loaded full as soon as its...

CRef< CSeq_literal > CreateSeqDataChunk(IBlastDbAdapter &blastdb, int oid, TSeqPos begin, TSeqPos end)

Creates a chunk that corresponds to a given OID and its beginning and ending offsets.

static CBioseq::TId s_ExtractSeqIds(const CBioseq &bioseq)

Defines the CCachedSequence class.

const CSeq_id * GetFirstId() const

Manages a TSE and its subordinate chunks for all implementations of the IBlastDbAdapter interface.

void RegisterIds(CBlastDbDataLoader::TIdMap &idmap)

Add this sequence's identifiers to a lookup table held by the data loader.

TSeqPos m_SliceSize

Specifies the slice size for splitting the sequence data.

vector< CRef< CTSE_Chunk_Info > > TCTSE_Chunk_InfoVector

A list of 'chunk' objects, generic sequence related data elements.

bool m_UseFixedSizeSlices

Determines whether sequences should be fetched in fixed size slices or in incrementally larger sizes.

CSeq_id_Handle m_SIH

SeqID handle.

CRef< CSeq_entry > m_TSE

The Seq entry we handle.

void SplitSeqData(TCTSE_Chunk_InfoVector &chunks)

Load or split the sequence data chunks.

void x_AddSplitSeqChunk(TCTSE_Chunk_InfoVector &chunks, const CSeq_id_Handle &id, TSeqPos begin, TSeqPos end)

Add a chunk of sequence data.

int m_OID

Locates this sequence within m_BlastDb.

TSeqPos m_Length

Sequence length in bases.

IBlastDbAdapter & m_BlastDb

Database reference.

void x_AddFullSeq_data(void)

Add an the entire sequence data to this object's TSE as raw data in its Seq-data field.

static CRef< CBlast_def_line_set > ExtractBlastDefline(const CBioseq &bioseq)

Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB.

vector< TLocation > TLocationSet

CRange< TSeqPos > TLocationRange

void x_AddSeq_data(const TLocationSet &location)

pair< TLocationId, TLocationRange > TLocation

Interface that provides a common interface to retrieve sequence data from local vs.

virtual CRef< CSeq_data > GetSequence(int oid, int begin=0, int end=0)=0

Get all or part of the sequence data as a Seq-data object.

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#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.

list< CRef< CSeq_id > > TSeqid

Tdata & Set(void)

Assign a value to data member.

list< CRef< CBlast_def_line > > Tdata

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

void SetLength(TLength value)

Assign a value to Length data member.

TId & SetId(void)

Assign a value to Id data member.

void SetSeq_data(TSeq_data &value)

Assign a value to Seq_data data member.

void SetExt(TExt &value)

Assign a value to Ext data member.

list< CRef< CSeq_id > > TId

void SetInst(TInst &value)

Assign a value to Inst data member.

void SetRepr(TRepr value)

Assign a value to Repr data member.

list< CRef< CDelta_seq > > Tdata

@ eRepr_delta

sequence made by changes (delta) to others

@ eRepr_raw

continuous sequence

@ eMol_na

just a nucleic acid

Int4 delta(size_t dimension_, const Int4 *score_)

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