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NCBI C++ ToolKit: src/objtools/data_loaders/genbank/psg_processors.cpp Source File

<

Class>

(ptr?

:

);

;

shared_ptr<CPSG_ReplyItem>& item)

(

()<<

<<

(status)<<

<<item.get()<<

);

bioseq_info = dynamic_pointer_cast<CPSG_BioseqInfo>(item);

shared_ptr<SPsgBioseqInfo>

;

(

()<<

<<

(status)<<

<<item.get()<<

<<

.get());

shared_ptr<CPSG_Reply>& reply)

(

()<<

<<

(status)<<

);

(

+

: m_Blob_id(blob_id),

& blob_id,

;

shared_ptr<CPSG_ReplyItem>& item)

(

blob_info = dynamic_pointer_cast<CPSG_BlobInfo>(item) ) {

shared_ptr<SPsgBlobInfo>

= make_shared<SPsgBlobInfo>(*blob_info);

shared_ptr<CPSG_Reply>& reply)

(

+

& blob_id,

;

shared_ptr<CPSG_ReplyItem>& item)

(

()<<

<<

(status)<<

<<item.get()<<

);

bioseq_info = dynamic_pointer_cast<CPSG_BioseqInfo>(item);

shared_ptr<SPsgBioseqInfo>

;

(

()<<

<<

(status)<<

<<item.get()<<

<<

.get());

(

blob_info = dynamic_pointer_cast<CPSG_BlobInfo>(item) ) {

shared_ptr<SPsgBlobInfo>

= make_shared<SPsgBlobInfo>(*blob_info);

shared_ptr<CPSG_Reply>& reply)

(

()<<

<<

(status)<<

);

(

+

(

+

m_IsWPAcc(is_WP_acc),

;

shared_ptr<CPSG_ReplyItem>& item)

(

()<<

<<

(status)<<

<<item.get()<<

);

(

ipg_info = dynamic_pointer_cast<CPSG_IpgInfo>(item) ) {

= tax_id = ipg_info->GetTaxId();

(ipg_info->GetNucleotide().empty()) {

= tax_id = ipg_info->GetTaxId();

(

()<<

<<

(status)<<

<<item.get()<<

<<

);

(

()<<

<<

(status)<<

<<item.get()<<

);

(

);

shared_ptr<CPSG_Reply>& reply)

(

()<<

<<

(status)<<

);

m_SeqIdSet(seq_id_set),

m_DataSource(data_source),

;

shared_ptr<CPSG_ReplyItem>& item)

( item->GetType() ) {

= dynamic_pointer_cast<CPSG_NamedAnnotInfo>(item);

= dynamic_pointer_cast<CPSG_NamedAnnotStatus>(item);

(

);

= dynamic_pointer_cast<CPSG_BlobInfo>(item);

= dynamic_pointer_cast<CPSG_BlobData>(item);

shared_ptr<CPSG_Reply>& reply)

shared_ptr<CPSG_Reply>& reply)

(

+

.front().AsString());

( chunk_load_lock.

() && *chunk_load_lock.

() ) {

;

shared_ptr<CPSG_ReplyItem>& item)

bioseq_info = dynamic_pointer_cast<CPSG_BioseqInfo>(item);

shared_ptr<SPsgBioseqInfo>

;

dl_blob_id =

->GetDLBlobId();

(

()<<

<<

(status)<<

<<item.get()<<

<<

.get());

shared_ptr<CPSG_Reply>& reply)

(

()<<

);

( !psg_blob_id.empty() ) {

( psg_blob_id.empty() ) {

shared_ptr<CPSG_Reply>& reply)

(

()<<

<<(

)status<<

);

shared_ptr<CPSG_Reply>& reply)

(

()<<

<<(

)status<<

);

m_Blob_id(dl_blob_id.ToPsgId())

;

shared_ptr<CPSG_Reply>& reply)

shared_ptr<CPSG_Reply>& reply)

;

shared_ptr<CPSG_Reply>& reply)

add_wgs_master)

;

pair<CRef<CTSE_Chunk_Info>,

>

main_count = 0;

zoom_count = 0;

vector<SAnnotTypeSelector>

;

(

feat_type_info_iter : annot_info.

() ) {

feat_type = finfo.

();

( feat_type == 0 ) {

(

feat_subtype : finfo.

() ) {

(

.size() == 1 ) {

name = *

.begin();

<<name<<

<<main_count<<

<<zoom_count);

make_pair(chunk, name);

shared_ptr<CPSG_ReplyItem>& item)

(item->GetType()) {

(

annot_status = dynamic_pointer_cast<CPSG_NamedAnnotStatus>(item) ) {

(

);

(

& s : annot_status->GetId2AnnotStatusList() ) {

(

);

shared_ptr<CPSG_ReplyItem>& item)

(item->GetType()) {

(

annot_info = dynamic_pointer_cast<CPSG_NamedAnnotInfo>(item) ) {

.m_NA = annot_info->GetName();

.m_Blob_id = annot_info->GetBlobId().GetId();

( !name.empty() ) {

dl_blob_id->SetTSEName(name);

.m_TSE_Lock = load_lock;

.push_back(make_pair(status, annot_info));

shared_ptr<CPSG_Reply>& reply)

add_wgs_master)

m_CDDChunkInfo(cdd_chunk_info),

;

shared_ptr<CPSG_ReplyItem>& item)

(item->GetType()) {

(

annot_status = dynamic_pointer_cast<CPSG_NamedAnnotStatus>(item) ) {

(

);

(

);

(

annot_info = dynamic_pointer_cast<CPSG_NamedAnnotInfo>(item) ) {

na = annot_info->GetName();

shared_ptr<CPSG_Reply>& reply)

(

()<<

<<

(status)<<

);

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

const string & GetName(void) const

CTSE_LoadLock GetTSE_LoadLock(const TBlobId &blob_id)

CID2S_Feat_type_Info –.

CID2S_Seq_annot_Info –.

mapped_type Add(const key_type &key, const SPsgAnnotInfo::TInfos &infos)

mapped_type Add(const key_type &key, const CPSG_BioseqInfo &info)

void Add(const TKey &key, const TValue &value)

CPSGCache_Base< CPSGBlobInfoCache::key_type, EPSG_Status > m_NoBlobInfoCache

CPSGCache_Base< CPSGBioseqInfoCache::key_type, bool > m_NoBioseqInfoCache

CPSGBlobInfoCache m_BlobInfoCache

CPSGIpgTaxIdCache m_IpgTaxIdCache

CPSGBioseqInfoCache m_BioseqInfoCache

CPSGCache_Base< CPSGAnnotInfoCache::key_type, bool > m_NoAnnotInfoCache

CPSGCache_Base< string, bool > m_NoCDDCache

CPSGAnnotInfoCache m_AnnotInfoCache

shared_ptr< CPSG_BioseqInfo > m_BioseqInfo

const CSeq_id_Handle & GetSeq_id() const

ostream & PrintProcessorArgs(ostream &out) const override

EPSG_Status m_BioseqInfoStatus

EProcessResult ProcessReplyFast(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

const char * GetProcessorName() const override

~CPSGL_BioseqInfo_Processor() override

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

CFastMutex m_BioseqInfoMutex

CPSGL_BioseqInfo_Processor(const CSeq_id_Handle &seq_id, CPSGCaches *caches=nullptr)

shared_ptr< SPsgBioseqInfo > m_BioseqInfoResult

EProcessResult ProcessReplyFast(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

EPSG_Status m_BlobInfoStatus

shared_ptr< CPSG_BlobInfo > m_BlobInfo

ostream & PrintProcessorArgs(ostream &out) const override

CFastMutex m_BlobInfoMutex

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

~CPSGL_BlobInfo_Processor() override

const char * GetProcessorName() const override

CPSGL_BlobInfo_Processor(const CSeq_id_Handle &seq_id, CPSGCaches *caches=nullptr)

shared_ptr< SPsgBlobInfo > m_BlobInfoResult

void SetDLBlobId(const string &psg_blob_id, const CConstRef< CPsgBlobId > &dl_blob_id)

bool GotUnauthorized() const

void SetLockedDelayedChunkInfo(const string &psg_blob_id, CTSE_Chunk_Info &locked_chunk_info)

EProcessResult ProcessItemSlow(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

EProcessResult ProcessTSE_Lock(const string &blob_id, CTSE_Lock &tse_lock, EWaitForLock wait_for_lock=eNoWaitForLock)

void SetLockedChunkInfo(CTSE_Chunk_Info &locked_chunk_info)

int GetBlobInfoState(const string &psg_blob_id)

CDataSource * m_DataSource

bool GotForbidden() const

CDataSource * m_DataSource

shared_ptr< CPSG_NamedAnnotStatus > m_AnnotStatus

EProcessResult ProcessReplySlow(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

shared_ptr< CPSG_NamedAnnotInfo > m_AnnotInfo

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

CPSGL_CDDAnnot_Processor(const SCDDIds &cdd_ids, const TSeqIdSet &id_set, CDataSource *data_source, CPSGCaches *caches=nullptr)

ostream & PrintProcessorArgs(ostream &out) const override

const char * GetProcessorName() const override

shared_ptr< CPSG_BlobInfo > m_BlobInfo

EProcessResult ProcessReplyFast(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

shared_ptr< CPSG_BlobData > m_BlobData

vector< CSeq_id_Handle > TSeqIdSet

~CPSGL_CDDAnnot_Processor() override

EProcessResult ProcessReplyFinal() override

CPSGL_GetBlob_Processor(const CPsgBlobId &dl_blob_id, CDataSource *data_source, CPSGCaches *caches=nullptr, bool add_wgs_master=false)

~CPSGL_GetBlob_Processor() override

ostream & PrintProcessorArgs(ostream &out) const override

EProcessResult ProcessReplyFast(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

EProcessResult ProcessReplySlow(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

const char * GetProcessorName() const override

CPSGL_GetChunk_Processor(CTSE_Chunk_Info &chunk, CDataSource *data_source, CPSGCaches *caches=nullptr, bool add_wgs_master=false)

void AddChunk(CTSE_Chunk_Info &chunk)

EProcessResult ProcessReplySlow(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

ostream & PrintProcessorArgs(ostream &out) const override

~CPSGL_GetChunk_Processor() override

const char * GetProcessorName() const override

vector< CTSE_Chunk_Info * > m_Chunks

ostream & PrintChunk(ostream &out, CTSE_Chunk_Info &chunk) const

CPSGL_Get_Processor(const CSeq_id_Handle &seq_id, CDataSource *data_source, CPSGCaches *caches=nullptr, bool add_wgs_master=false)

EProcessResult ProcessReplySlow(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

const string & GetPSGBlobId() const

CConstRef< CPsgBlobId > CreateDLBlobId(STSESlot *tse_slot) override

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

EPSG_Status m_BioseqInfoStatus

EProcessResult x_PreProcessReply(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply)

~CPSGL_Get_Processor() override

shared_ptr< SPsgBioseqInfo > m_BioseqInfoResult

ostream & PrintProcessorArgs(ostream &out) const override

EProcessResult ProcessReplyFinal() override

const char * GetProcessorName() const override

CConstRef< CPsgBlobId > GetDLBlobId() const

EProcessResult ProcessReplyFast(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

~CPSGL_Info_Processor() override

ostream & PrintProcessorArgs(ostream &out) const override

const CSeq_id_Handle & GetSeq_id() const

shared_ptr< SPsgBioseqInfo > m_BioseqInfoResult

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

EPSG_Status m_BioseqInfoStatus

EPSG_Status m_BlobInfoStatus

shared_ptr< CPSG_BioseqInfo > m_BioseqInfo

shared_ptr< SPsgBlobInfo > m_BlobInfoResult

EProcessResult ProcessReplyFast(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

CPSGL_Info_Processor(const CSeq_id_Handle &seq_id, CPSGCaches *caches=nullptr)

shared_ptr< CPSG_BlobInfo > m_BlobInfo

const char * GetProcessorName() const override

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

CFastMutex m_IpgTaxIdMutex

CPSGL_IpgTaxId_Processor(const CSeq_id_Handle &seq_id, bool is_WP_acc, CPSGCaches *caches=nullptr)

const char * GetProcessorName() const override

EProcessResult ProcessReplyFast(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

~CPSGL_IpgTaxId_Processor() override

ostream & PrintProcessorArgs(ostream &out) const override

EProcessResult ProcessReplySlow(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

CPSGL_LocalCDDBlob_Processor(CTSE_Chunk_Info &cdd_chunk_info, const SCDDIds &cdd_ids, CDataSource *data_source, CPSGCaches *caches=nullptr, bool add_wgs_master=false)

~CPSGL_LocalCDDBlob_Processor() override

CConstRef< CPsgBlobId > CreateDLBlobId(STSESlot *tse_slot) override

ostream & PrintProcessorArgs(ostream &out) const override

CFastMutex m_CDDProcessorMutex

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

CTSE_Chunk_Info & m_CDDChunkInfo

const char * GetProcessorName() const override

EProcessResult ProcessItemSlow(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

const char * GetProcessorName() const override

vector< CSeq_id_Handle > TSeq_ids

CFastMutex m_NAProcessorMutex

ostream & PrintProcessorArgs(ostream &out) const override

~CPSGL_NA_Processor() override

CPSGL_NA_Processor(const TSeq_ids &ids, CDataSource *data_source, CPSGCaches *caches=nullptr, bool add_wgs_master=false)

EProcessResult ProcessReplyFinal() override

EProcessResult ProcessItemFast(EPSG_Status status, const shared_ptr< CPSG_ReplyItem > &item) override

EProcessResult ProcessReplySlow(EPSG_Status status, const shared_ptr< CPSG_Reply > &reply) override

EProcessResult x_Failed(const string &message)

SProcessorDescrPrinter Descr() const

static string x_FormatAndSetError(EPSG_Status &status)

static string x_Format(EPSG_Status status)

const string & GetId() const

Get ID.

Named Annotations (NAs) metainfo – reply to CPSG_Request_NamedAnnotInfo.

CPSG_BlobId GetBlobId() const

Coordinates of the blob that contains the NA data.

TId2AnnotInfoList GetId2AnnotInfoList() const

Named Annotations (NAs) status – reply to CPSG_Request_NamedAnnotInfo.

TId2AnnotStatusList GetId2AnnotStatusList() const

const string & ToPsgId() const

static void x_ParseLocation(TLocationSet &vec, const CID2S_Seq_loc &loc)

TBlobId GetBlobId(void) const

void SetLoaded(CObject *obj=0)

vector< TLocation > TLocationSet

TChunkId GetChunkId(void) const

void x_AddAnnotType(const CAnnotName &annot_name, const SAnnotTypeSelector &annot_type, const TLocationId &location_id)

CInitGuard * GetLoadInitGuard(void)

CTSE_Split_Info & GetSplitInfo(void)

bool x_NeedsDelayedMainChunk(void) const

void SetSeq_entry(CSeq_entry &entry, CTSE_SetObjectInfo *set_info=0)

bool IsLoaded(void) const

CTSE_Chunk_Info & GetChunk(TChunkId chunk_id)

void AddChunk(CTSE_Chunk_Info &chunk_info)

std::ofstream out("events_result.xml")

main entry point for tests

static const struct name_t names[]

static const struct type types[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

element_type * get(void) const

Get pointer.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Info(CExceptionArgs_Base &args)

#define MSerial_AsnText

I/O stream manipulators –.

string ToString(void) const

bool ExtractZoomLevel(const string &full_name, string *acc_ptr, int *zoom_level_ptr)

Extract optional zoom level suffix from named annotation string.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

const TSubtypes & GetSubtypes(void) const

Get the Subtypes member data.

const TSeq_loc & GetSeq_loc(void) const

Get the Seq_loc member data.

bool IsSetGraph(void) const

Check if a value has been assigned to Graph data member.

bool IsSetAlign(void) const

Check if a value has been assigned to Align data member.

bool IsSetSubtypes(void) const

Check if a value has been assigned to Subtypes data member.

const TName & GetName(void) const

Get the Name member data.

const TFeat & GetFeat(void) const

Get the Feat member data.

bool IsSetFeat(void) const

Check if a value has been assigned to Feat data member.

TType GetType(void) const

Get the Type member data.

E_Choice

Choice variants.

std::istream & in(std::istream &in_, double &x_)

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

CTSE_Lock x_CreateLocalCDDEntry(CDataSource *data_source, const SCDDIds &ids)

const char kCDDAnnotName[]

unsigned s_GetDebugLevel()

CObjectIStream * GetBlobDataStream(const CPSG_BlobInfo &blob_info, const CPSG_BlobData &blob_data)

const bool kCreateLocalCDDEntries

void UpdateOMBlobId(CTSE_LoadLock &load_lock, const CConstRef< CPsgBlobId > &dl_blob_id)

string x_MakeLocalCDDEntryId(const SCDDIds &cdd_ids)

void x_CreateEmptyLocalCDDEntry(CDataSource *data_source, CTSE_Chunk_Info *chunk)

bool x_IsEmptyCDD(const CTSE_Info &tse)

EPSG_Status

Retrieval result.

@ eSuccess

Successfully retrieved.

@ eForbidden

User is not authorized for the retrieval.

@ eError

An error was encountered while trying to send request or to read and to process the reply.

static pair< CRef< CTSE_Chunk_Info >, string > s_CreateNAChunk(const CPSG_NamedAnnotInfo &psg_annot_info)

static string x_FormatPtr(const shared_ptr< Class > &ptr)

static bool s_SameId(const CPSG_BlobId *id1, const CPSG_BlobId &id2)

static bool s_HasFailedStatus(const CPSG_NamedAnnotStatus &na_status)

list< shared_ptr< CPSG_NamedAnnotInfo > > TInfos

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