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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/asn__cache__store_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/data_loaders/asn_cache/asn_cache_store.cpp Source File

TBuffer = std::vector<unsigned char>;

->SetCacheSize(128 * 1024 * 1024);

( !

(main_fname).Exists() ) {

+ main_fname);

(

(fname).Exists()) {

(

<<

<< e);

vector<CAsnIndex::SIndexInfo>&

,

was_id_found =

;

cursor.From << seq_id <<

;

(cursor.Fetch() ==

) {

(current_info.seq_id != seq_id) {

should_report = (!

||

== current_info.version) &&

(

[0].version < current_info.version ||

(

[0].version == current_info.version &&

[0].timestamp < current_info.timestamp))) ||

(

&&

[0].timestamp < current_info.timestamp))

was_id_found =

;

.push_back(current_info);

vector<CAsnIndex::SIndexInfo> info_vector;

= info_vector[0];

time_t& this_timestamp)

this_timestamp =

.timestamp;

& sequence_length,

timestamp =

.timestamp;

sequence_length =

.sequence_length;

tax_id =

.taxonomy_id;

vector<CSeq_id_Handle>& all_ids,

was_seqid_blob_found =

;

<<

<<

.gi

<<

<<

.timestamp

<<

<<

.offs

<<

<<

.size);

( was_seqid_blob_found ){

(

<<

<<

.offs <<

<<

.size );

(

<<

.AsString() <<

<<

.gi

<<

<<

.timestamp );

was_seqid_blob_found =

;

(!cheap_only) {

was_seqid_blob_found =

;

was_seqid_blob_found;

was_blob_found =

;

(! was_blob_found ) {

<<

<<

.gi

<<

<<

.timestamp

<<

<<

.chunk

<<

<<

.offs

<<

<<

.size);

(

<<

.chunk

<<

<<

.offs <<

<<

.size );

<<

<<

.timestamp );

vector<CAsnIndex::SIndexInfo>

;

(! was_blob_found ) {

(vector<CAsnIndex::SIndexInfo>, blob_it,

) {

blobs.push_back(blob);

!blobs.empty();

vector< CRef<CCache_blob> > blobs;

.resize(blobs.size());

(*blob_it)->UnPack(

[blob_it - blobs.begin()]);

CAsnCacheStore::EfficientlyGetSeqIds()

vector< CRef<CSeq_entry> >

;

vector< CRef<CCache_blob> > blobs;

(*blob_it)->UnPack(*entry);

vector<CAsnIndex::SIndexInfo> &

)

std::set<CAsnIndex::TGi> gi_set;

gi = index_ref.GetGi();

gi_set.size();

cb(index_ref.GetSeqId(),

index_ref.GetVersion(),

index_ref.GetTimestamp());

cb(index_ref.GetSeqId(),

index_ref.GetVersion(),

index_ref.GetTimestamp(),

index_ref.GetChunkId(),

index_ref.GetOffset(),

index_ref.GetSeqLength(),

index_ref.GetTaxId());

: m_Index(db_paths.

())

(

& db_path: db_paths ) {

std::unique_ptr<IAsnCacheStore> store(

(db_path) );

.push_back(std::move(store));

std::shuffle(

.begin(),

.end(), default_random_engine());

std::shuffle(

.begin(),

.end(), default_random_engine());

std::shuffle(

.begin(),

.end(), default_random_engine());

std::shuffle(

.begin(),

.end(), default_random_engine());

vector<objects::CSeq_id_Handle>& all_ids,

std::shuffle(

.begin(),

.end(), default_random_engine());

CAsnCacheStoreMany::EfficientlyGetSeqIds()

std::shuffle(

.begin(),

.end(), default_random_engine());

entry =

[

]->GetEntry(

);

std::shuffle(

.begin(),

.end(), default_random_engine());

vector<CRef<CSeq_entry> >();

std::shuffle(

.begin(),

.end(), default_random_engine());

objects::CSeq_id_Handle& accession,

& sequence_length,

std::shuffle(

.begin(),

.end(), default_random_engine());

(

[

]->

(

, accession, gi, timestamp, sequence_length, tax_id) ) {

std::shuffle(

.begin(),

.end(), default_random_engine());

vector<CAsnIndex::SIndexInfo> &

)

std::shuffle(

.begin(),

.end(), default_random_engine());

(

& store:

) {

+= store->GetGiCount();

(

& store:

) {

store->EnumSeqIds(cb);

(

& store:

) {

store->EnumIndex(cb);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Contains the class definiton for CAsnCache, the main client class for accessing the ASN cache data.

CConstRef< objects::CBioseq > ExtractBioseq(CConstRef< objects::CSeq_entry > entry, const objects::CSeq_id_Handle &id)

void GetNormalizedSeqId(const objects::CSeq_id_Handle &id, string &id_str, Uint4 &version)

Berkeley BDB file cursor.

bool GetMultipleIndexEntries(const objects::CSeq_id_Handle &id, vector< CAsnIndex::SIndexInfo > &info)

void EnumSeqIds(IAsnCacheStore::TEnumSeqidCallback cb) const

CRef< objects::CSeq_entry > GetEntry(const objects::CSeq_id_Handle &id)

Check if the SeqId cache, for efficient retrieval of SeqIds, is available.

size_t GetGiCount() const

bool GetBlob(const objects::CSeq_id_Handle &id, objects::CCache_blob &blob)

Return the cache blob, packed and uninterpreted.

bool GetSeqIds(const objects::CSeq_id_Handle &id, vector< objects::CSeq_id_Handle > &all_ids, bool cheap_only)

Return the set of seq-ids associated with a given ID.

CAsnCacheStoreMany()=delete

std::vector< std::unique_ptr< IAsnCacheStore > > m_Stores

bool GetMultipleRaw(const objects::CSeq_id_Handle &id, vector< vector< unsigned char >> &buffer)

bool GetRaw(const objects::CSeq_id_Handle &id, vector< unsigned char > &buffer)

Return the raw blob in an unformatted buffer.

bool GetMultipleBlobs(const objects::CSeq_id_Handle &id, vector< CRef< objects::CCache_blob > > &blob)

bool GetIdInfo(const objects::CSeq_id_Handle &id, CAsnIndex::TGi &gi, time_t &timestamp)

Return the GI and timestamp for a given seq_id.

bool GetIndexEntry(const objects::CSeq_id_Handle &id, CAsnIndex::SIndexInfo &info)

Get the full ASN cache index entry.

std::vector< int > m_Index

void EnumIndex(IAsnCacheStore::TEnumIndexCallback cb) const

vector< CRef< objects::CSeq_entry > > GetMultipleEntries(const objects::CSeq_id_Handle &id)

std::unique_ptr< CAsnIndex > m_Index

static bool s_GetChunkAndOffset(const objects::CSeq_id_Handle &idh, CAsnIndex &index, vector< CAsnIndex::SIndexInfo > &info, bool multiple)

bool GetSeqIds(const objects::CSeq_id_Handle &id, vector< objects::CSeq_id_Handle > &all_ids, bool cheap_only)

Return the set of seq-ids associated with a given ID.

bool GetBlob(const objects::CSeq_id_Handle &id, objects::CCache_blob &blob)

Return the cache blob, packed and uninterpreted.

bool GetMultipleIndexEntries(const objects::CSeq_id_Handle &id, vector< CAsnIndex::SIndexInfo > &info)

std::unique_ptr< CChunkFile > m_CurrChunk

vector< CRef< objects::CSeq_entry > > GetMultipleEntries(const objects::CSeq_id_Handle &id)

CRef< objects::CSeq_entry > GetEntry(const objects::CSeq_id_Handle &id)

Check if the SeqId cache, for efficient retrieval of SeqIds, is available.

bool GetMultipleBlobs(const objects::CSeq_id_Handle &id, vector< CRef< objects::CCache_blob > > &blob)

size_t GetGiCount() const

std::unique_ptr< CSeqIdChunkFile > m_SeqIdChunk

CAsnIndex & x_GetIndexRef() const

bool GetMultipleRaw(const objects::CSeq_id_Handle &id, vector< vector< unsigned char >> &buffer)

bool GetIndexEntry(const objects::CSeq_id_Handle &id, CAsnIndex::SIndexInfo &info)

Get the full ASN cache index entry.

bool x_GetBlob(const CAsnIndex::SIndexInfo &info, objects::CCache_blob &blob)

std::unique_ptr< CAsnIndex > m_SeqIdIndex

void EnumIndex(IAsnCacheStore::TEnumIndexCallback cb) const

bool GetRaw(const objects::CSeq_id_Handle &id, vector< unsigned char > &buffer)

Return the raw blob in an unformatted buffer.

bool GetIdInfo(const objects::CSeq_id_Handle &id, CAsnIndex::TGi &gi, time_t &timestamp)

Return the GI and timestamp for a given seq_id.

CAsnIndex::TChunkId m_CurrChunkId

void EnumSeqIds(IAsnCacheStore::TEnumSeqidCallback cb) const

This is a simple BDB structure holding information about a given accession and its indexed location.

Berkeley DB file cursor class.

void UnPack(CSeq_entry &entry) const

std::function< void(string, uint32_t, uint64_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t, uint32_t)> TEnumIndexCallback

std::function< void(string, uint32_t, uint64_t, uint32_t)> TEnumSeqidCallback

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

@ eFollowLinks

Follow symbolic links.

void SetCondition(ECondition cond_from, ECondition cond_to=eNotSet)

Set search condition(type of interval)

EBDB_ErrCode Fetch(EFetchDirection fdir=eDefault)

Fetch record.

#define ERR_POST(message)

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

void Error(CExceptionArgs_Base &args)

#define NCBI_THROW(exception_class, err_code, message)

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

static string NormalizePath(const string &path, EFollowLinks follow_links=eIgnoreLinks)

Normalize a path.

static string CreateAbsolutePath(const string &path, ERelativeToWhat rtw=eRelativeToCwd)

Get an absolute path from some, possibly relative, path.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

bool NotNull(void) const THROWS_NONE

Check if pointer is not null – same effect as NotEmpty().

uint32_t Uint4

4-byte (32-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

const string version

version string

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

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

static bool GetSeqId(const T &d, set< string > &labels, const string name="", bool detect=false, bool found=false)

static wxAcceleratorEntry entries[3]

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