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NCBI C++ ToolKit: CId2ReaderBase Class Reference

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#include <objtools/data_loaders/genbank/impl/reader_id2_base.hpp>

Definition at line 76 of file reader_id2_base.hpp.

◆ TAvoidRequests ◆ TErrorFlags ◆ TProcessors ◆ anonymous enum Enumerator fAvoidRequest_nested_get_blob_info fAvoidRequest_for_Seq_id_label fAvoidRequest_for_Seq_id_taxid fAvoidRequest_for_Seq_id_hash fAvoidRequest_for_Seq_id_length fAvoidRequest_for_Seq_id_type

Definition at line 309 of file reader_id2_base.hpp.

◆ EDebugLevel Enumerator eTraceError eTraceOpen eTraceConn eTraceASN eTraceBlob eTraceBlobData

Definition at line 152 of file reader_id2_base.hpp.

◆ EErrorFlags Enumerator fError_warning fError_no_data fError_bad_command fError_bad_connection fError_warning_dead fError_restricted fError_withdrawn fError_suppressed_perm fError_suppressed_temp fError_inactivity_timeout fError_failed_command

Definition at line 202 of file reader_id2_base.hpp.

◆ CId2ReaderBase() CId2ReaderBase::CId2ReaderBase ( void )

Definition at line 248 of file reader_id2_base.cpp.

References ERR_POST_X, CPluginManagerGetter< Interface >::Get(), info, ITERATE, m_Processors, NCBI_PARAM_TYPE(), Ref(), CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), NStr::Split(), and x_SetContextData().

◆ ~CId2ReaderBase() ◆ GetBlobId() ◆ GetDebugLevel() int CId2ReaderBase::GetDebugLevel ( void ) static

Definition at line 127 of file reader_id2_base.cpp.

References NCBI_PARAM_TYPE(), and ncbi::grid::netcache::search::s_Value().

Referenced by CId2Reader::x_ConnectAtSlot(), CPubseq2Reader::x_ConnectAtSlot(), CId2Reader::x_DisconnectAtSlot(), x_DumpPacket(), x_DumpReply(), CId2Reader::x_InitConnection(), CPubseq2Reader::x_InitConnection(), x_ProcessPacket(), x_ReceiveFromConnection(), x_ReceiveID2ReplyStage(), x_SendID2Packet(), x_SendToConnection(), and x_UpdateLoadedSet().

◆ GetSNP_Scale_Limit() ◆ GetVDB_CDD_Enabled() bool CId2ReaderBase::GetVDB_CDD_Enabled ( ) static ◆ GetVDB_SNP_Enabled() bool CId2ReaderBase::GetVDB_SNP_Enabled ( ) static ◆ GetVDB_WGS_Enabled() bool CId2ReaderBase::GetVDB_WGS_Enabled ( ) static ◆ LoadAccVers()

Reimplemented from CReader.

Definition at line 634 of file reader_id2_base.cpp.

References CReadDispatcher::CannotProcess(), count, data, CID2_Request_Get_Seq_id_Base::eSeq_id_type_all, CLoadLockAcc::GetAcc(), CLoadLockAcc::GetAccVer(), GetMaxIdsRequestSize(), GetSeqId(), i, CLoadLockAcc::IsFound(), CLoadLockAcc::IsLoadedAccVer(), CReader::LoadAccVers(), result, CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), and x_ProcessPacket().

◆ LoadBlob()

Implements CReader.

Definition at line 1455 of file reader_id2_base.cpp.

References _ASSERT, CProcessor::eType_ExtAnnot, CReadDispatcher::GetProcessor(), CProcessor_ExtAnnot::IsExtAnnot(), CLoadLockBlob::IsLoadedBlob(), kMain_ChunkId, CReader::m_Dispatcher, Process(), result, CID2_Request_Get_Blob_Info_Base::SetBlob_id(), CID2_Request_Get_Blob_Info_Base::SetGet_data(), CID2_Request_Base::SetRequest(), x_ProcessRequest(), and x_SetResolve().

◆ LoadBlobs() [1/3]

Reimplemented from CReader.

Definition at line 1403 of file reader_id2_base.cpp.

References _ASSERT, CProcessor::eType_ExtAnnot, CID2_Request_Packet_Base::Get(), CLoadLockBlobIds::GetBlob_ids(), GetMaxChunksRequestSize(), CReadDispatcher::GetProcessor(), info, CProcessor_ExtAnnot::IsExtAnnot(), CLoadLockBlob::IsLoadedBlob(), ITERATE, kMain_ChunkId, LimitChunksRequests(), CProcessor_AnnotInfo::LoadBlob(), CReader::m_Dispatcher, mask, Process(), result, CID2_Request_Packet_Base::Set(), CID2_Request_Get_Blob_Info_Base::SetBlob_id(), CID2_Request_Get_Blob_Info_Base::SetGet_data(), CID2_Request_Base::SetRequest(), x_ProcessPacket(), x_SetDetails(), and x_SetResolve().

◆ LoadBlobs() [2/3]

Reimplemented from CReader.

Definition at line 1369 of file reader_id2_base.cpp.

References CWriter::eBlobWriter, fAvoidRequest_nested_get_blob_info, fBlobHasAllLocal, CSeq_id_Handle::GetSeqId(), CReadDispatcher::GetWriter(), CReader::LoadBlobs(), LoadSeq_idBlob_ids(), m_AvoidRequest, CReader::m_Dispatcher, mask, result, CID2_Request_Get_Blob_Info_Base::SetBlob_id(), CID2_Request_Get_Blob_Info_Base::SetGet_data(), CID2_Request_Base::SetRequest(), x_ProcessRequest(), x_SetDetails(), x_SetExclude_blobs(), and x_SetResolve().

◆ LoadBlobs() [3/3]

Reimplemented from CReader.

Definition at line 1699 of file reader_id2_base.cpp.

References _ASSERT, CProcessor::eType_ExtAnnot, fBlobHasCore, CID2_Request_Packet_Base::Get(), GetMaxChunksRequestSize(), CReadDispatcher::GetProcessor(), info, CProcessor_ExtAnnot::IsExtAnnot(), CLoadLockBlob::IsLoadedBlob(), kMain_ChunkId, LimitChunksRequests(), CProcessor_AnnotInfo::LoadBlob(), CReader::m_Dispatcher, Process(), result, CID2_Request_Packet_Base::Set(), CID2_Request_Get_Blob_Info_Base::SetBlob_id(), CID2_Request_Get_Blob_Info_Base::SetGet_data(), CID2_Request_Base::SetRequest(), x_ProcessPacket(), x_SetDetails(), and x_SetResolve().

◆ LoadBlobSet()

Reimplemented from CReader.

Definition at line 1778 of file reader_id2_base.cpp.

References fAvoidRequest_nested_get_blob_info, fBlobHasCore, CID2_Request_Packet_Base::Get(), CLoadLockBlobIds::GetBlob_ids(), GetMaxChunksRequestSize(), info, set< Key, Compare >::insert(), CLoadLockBlob::IsLoadedBlob(), ITERATE, LimitChunksRequests(), CReader::LoadBlobSet(), m_AvoidRequest, result, SeparateChunksRequests(), CID2_Request_Packet_Base::Set(), CID2_Request_Get_Blob_Info_Base::SetBlob_id(), CID2_Request_Get_Blob_Info_Base::SetGet_data(), CID2_Request_Base::SetRequest(), x_LoadSeq_idBlob_idsSet(), x_ProcessPacket(), x_SetDetails(), x_SetExclude_blobs(), and x_SetResolve().

◆ LoadBlobState() ◆ LoadBlobVersion() ◆ LoadBulkIds()

Reimplemented from CReader.

Definition at line 555 of file reader_id2_base.cpp.

References CReadDispatcher::CannotProcess(), count, data, CID2_Request_Get_Seq_id_Base::eSeq_id_type_all, GetMaxIdsRequestSize(), CLoadLockSeqIds::GetSeq_ids(), GetSeqId(), i, CReader::LoadBulkIds(), result, CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), and x_ProcessPacket().

◆ LoadChunk()

Reimplemented from CReader.

Definition at line 1480 of file reader_id2_base.cpp.

References ERR_POST_X, CLoadLockBlob::GetKnownBlobVersion(), CLoadLockBlob::GetSplitInfo(), CTSE_Split_Info::GetSplitVersion(), CLoadLockSetter::IsLoaded(), CLoadLockBlob::IsLoadedChunk(), kDelayedMain_ChunkId, result, CID2_Request_Get_Blob_Info_Base::SetBlob_id(), CID2S_Request_Get_Chunks_Base::SetBlob_id(), CID2S_Request_Get_Chunks_Base::SetChunks(), CID2_Request_Get_Blob_Info_Base::SetGet_data(), CLoadLockSetter::SetLoaded(), CID2_Request_Base::SetRequest(), CID2S_Request_Get_Chunks_Base::SetSplit_version(), x_ProcessRequest(), and x_SetResolve().

Referenced by LoadChunks().

◆ LoadChunks() [1/2]

Reimplemented from CReader.

Definition at line 1628 of file reader_id2_base.cpp.

References _ASSERT, CLoadLockBlob::GetKnownBlobVersion(), GetMaxChunksRequestSize(), CLoadLockBlob::GetSplitInfo(), CTSE_Split_Info::GetSplitVersion(), CLoadLockBlob::IsLoadedBlob(), CLoadLockBlob::IsLoadedChunk(), kDelayedMain_ChunkId, LimitChunksRequests(), CReader::LoadChunks(), LoadedChunksPacket(), result, CLoadLockBlob::SelectChunk(), SeparateChunksRequests(), CID2_Request_Packet_Base::Set(), CID2_Request_Get_Blob_Info_Base::SetBlob_id(), CID2S_Request_Get_Chunks_Base::SetBlob_id(), CID2S_Request_Get_Chunks_Base::SetChunks(), CID2_Request_Get_Blob_Info_Base::SetGet_data(), CID2_Request_Base::SetRequest(), CID2S_Request_Get_Chunks_Base::SetSplit_version(), x_ProcessPacket(), and x_SetResolve().

◆ LoadChunks() [2/2]

Reimplemented from CReader.

Definition at line 1551 of file reader_id2_base.cpp.

References _ASSERT, CID2_Request_Packet_Base::Get(), CLoadLockBlob::GetKnownBlobVersion(), GetMaxChunksRequestSize(), CLoadLockBlob::GetSplitInfo(), CTSE_Split_Info::GetSplitVersion(), CLoadLockBlob::IsLoadedBlob(), CLoadLockBlob::IsLoadedChunk(), ITERATE, kDelayedMain_ChunkId, LimitChunksRequests(), LoadChunk(), CReader::LoadChunks(), LoadedChunksPacket(), result, CLoadLockBlob::SelectChunk(), SeparateChunksRequests(), CID2_Request_Packet_Base::Set(), CID2_Request_Get_Blob_Info_Base::SetBlob_id(), CID2S_Request_Get_Chunks_Base::SetBlob_id(), CID2S_Request_Get_Chunks_Base::SetChunks(), CID2_Request_Get_Blob_Info_Base::SetGet_data(), CID2_Request_Base::SetRequest(), CID2S_Request_Get_Chunks_Base::SetSplit_version(), x_ProcessPacket(), x_ProcessRequest(), and x_SetResolve().

◆ LoadGis()

Reimplemented from CReader.

Definition at line 713 of file reader_id2_base.cpp.

References CReadDispatcher::CannotProcess(), count, data, CID2_Request_Get_Seq_id_Base::eSeq_id_type_all, CLoadLockGi::GetGi(), GetMaxIdsRequestSize(), GetSeqId(), i, CLoadLockGi::IsFound(), CLoadLockGi::IsLoadedGi(), CReader::LoadGis(), result, CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), and x_ProcessPacket().

◆ LoadHashes()

Reimplemented from CReader.

Definition at line 969 of file reader_id2_base.cpp.

References CReadDispatcher::CannotProcess(), count, CID2_Request_Get_Seq_id_Base::eSeq_id_type_hash, fAvoidRequest_for_Seq_id_hash, CLoadLockHash::GetHash(), GetMaxIdsRequestSize(), GetSeqId(), i, CLoadLockHash::IsLoadedHash(), CReader::LoadHashes(), m_AvoidRequest, result, CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), and x_ProcessPacket().

◆ LoadLabels()

Reimplemented from CReader.

Definition at line 792 of file reader_id2_base.cpp.

References CReadDispatcher::CannotProcess(), count, CID2_Request_Get_Seq_id_Base::eSeq_id_type_all, CID2_Request_Get_Seq_id_Base::eSeq_id_type_label, fAvoidRequest_for_Seq_id_label, CLoadLockLabel::GetLabel(), GetMaxIdsRequestSize(), CLoadLockSeqIds::GetSeq_ids(), GetSeqId(), i, CLoadLockLabel::IsLoadedLabel(), label, CReader::LoadLabels(), m_AvoidRequest, result, CID2_Request_Packet_Base::Set(), CLoadLockLabel::SetLoadedLabel(), CID2_Request_Base::SetRequest(), and x_ProcessPacket().

◆ LoadLengths()

Reimplemented from CReader.

Definition at line 1072 of file reader_id2_base.cpp.

References CReadDispatcher::CannotProcess(), count, CID2_Request_Get_Seq_id_Base::eSeq_id_type_all, CID2_Request_Get_Seq_id_Base::eSeq_id_type_seq_length, fAvoidRequest_for_Seq_id_length, CLoadLockLength::GetLength(), GetMaxIdsRequestSize(), GetSeqId(), i, CLoadLockLength::IsLoadedLength(), CReader::LoadLengths(), m_AvoidRequest, result, CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), and x_ProcessPacket().

◆ LoadSeq_idAccVer() ◆ LoadSeq_idBlob_ids()

All LoadXxx() methods should return false if there is no requested data in the reader.

This will notify dispatcher that there is no sense to retry.

Reimplemented from CReader.

Definition at line 1288 of file reader_id2_base.cpp.

References CSeq_id::eSNPScaleLimit_Default, SAnnotSelector::GetNamedAnnotAccessions(), CSeq_id_Handle::GetSeqId(), GetSNP_Scale_Limit(), SAnnotSelector::GetSNPScaleLimit(), CSeq_id::GetSNPScaleLimit_Name(), SAnnotSelector::IsIncludedAnyNamedAnnotAccession(), ITERATE, result, CID2_Request_Base::SetParams(), CID2_Request_Base::SetRequest(), CID2_Request_Get_Blob_Id_Base::SetSources(), x_ProcessRequest(), and x_SetResolve().

Referenced by LoadBlobs(), and x_LoadSeq_idBlob_idsSet().

◆ LoadSeq_idGi() ◆ LoadSeq_idLabel() ◆ LoadSeq_idSeq_ids() ◆ LoadSeq_idTaxId() ◆ LoadSequenceHash() ◆ LoadSequenceLength() ◆ LoadSequenceType() ◆ LoadStates() ◆ LoadTaxIds()

Reimplemented from CReader.

Definition at line 889 of file reader_id2_base.cpp.

References CReadDispatcher::CannotProcess(), count, CID2_Request_Get_Seq_id_Base::eSeq_id_type_taxid, fAvoidRequest_for_Seq_id_taxid, GetMaxIdsRequestSize(), GetSeqId(), CLoadLockTaxId::GetTaxId(), i, CLoadLockTaxId::IsLoadedTaxId(), CReader::LoadTaxIds(), m_AvoidRequest, result, CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), and x_ProcessPacket().

◆ LoadTypes()

Reimplemented from CReader.

Definition at line 1153 of file reader_id2_base.cpp.

References CReadDispatcher::CannotProcess(), count, data, CID2_Request_Get_Seq_id_Base::eSeq_id_type_all, CID2_Request_Get_Seq_id_Base::eSeq_id_type_seq_mol, fAvoidRequest_for_Seq_id_type, GetMaxIdsRequestSize(), GetSeqId(), CLoadLockType::GetType(), i, CLoadLockType::IsFound(), CLoadLockType::IsLoadedType(), CReader::LoadTypes(), m_AvoidRequest, result, CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), and x_ProcessPacket().

◆ SetParams() ◆ SetSNP_Scale_Limit() ◆ SetVDB_CDD_Enabled() void CId2ReaderBase::SetVDB_CDD_Enabled ( bool enabled = true ) static ◆ SetVDB_SNP_Enabled() void CId2ReaderBase::SetVDB_SNP_Enabled ( bool enabled = true ) static ◆ SetVDB_WGS_Enabled() void CId2ReaderBase::SetVDB_WGS_Enabled ( bool enabled = true ) static ◆ sx_CheckErrorFlag() ◆ x_AssignSerialNumbers()

Definition at line 2200 of file reader_id2_base.cpp.

References CAtomicCounter::Add(), DEFINE_STATIC_FAST_MUTEX, CID2_Request_Packet_Base::Get(), CAtomicCounter::Get(), i, info, m_RequestSerialNumber, NON_CONST_ITERATE, CAtomicCounter::Set(), CID2_Request_Packet_Base::Set(), and x_SetContextData().

Referenced by x_ProcessPacket().

◆ x_ConnDescription() virtual string CId2ReaderBase::x_ConnDescription ( TConn conn ) const protectedpure virtual ◆ x_DisableProcessors() void CId2ReaderBase::x_DisableProcessors ( ) protected ◆ x_DoneReply() ◆ x_DumpPacket() ◆ x_DumpReply()

Definition at line 1999 of file reader_id2_base.cpp.

References Begin(), conn, count, CProcessor_ID2::DumpDataAsText(), ERR_POST_X, eTraceASN, eTraceBlob, eTraceBlobData, eTraceConn, GetDebugLevel(), i, ITERATE, max(), MSerial_AsnText, msg(), NcbiCout, ncbi::grid::netcache::search::fields::size, and x_GetReaderName.

Referenced by x_ReceiveFromConnection(), x_ReceiveID2ReplyStage(), and x_SendID2Packet().

◆ x_EndOfPacket() void CId2ReaderBase::x_EndOfPacket ( TConn conn ) protectedvirtual ◆ x_GetBlobState()

Definition at line 2660 of file reader_id2_base.cpp.

References map_checker< Container >::end(), fError_no_data, fError_restricted, fError_suppressed_perm, fError_suppressed_temp, fError_warning_dead, fError_withdrawn, map_checker< Container >::find(), CBioseq_Handle::fState_confidential, CBioseq_Handle::fState_dead, CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_suppress_perm, CBioseq_Handle::fState_suppress_temp, CBioseq_Handle::fState_withdrawn, SId2LoadedSet::m_BlobStates, and x_GetMessageError().

Referenced by x_ProcessGetBlob(), x_ProcessGetBlobId(), and x_ProcessGetSplitInfo().

◆ x_GetBlobStateFromID2()

Definition at line 2629 of file reader_id2_base.cpp.

References eID2_Blob_State_dead, eID2_Blob_State_protected, eID2_Blob_State_suppressed, eID2_Blob_State_suppressed_temp, eID2_Blob_State_withdrawn, CBioseq_Handle::fState_confidential, CBioseq_Handle::fState_dead, CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_suppress_perm, CBioseq_Handle::fState_suppress_temp, CBioseq_Handle::fState_withdrawn, and SId2LoadedSet::m_BlobStates.

Referenced by x_ProcessGetBlob(), x_ProcessGetBlobId(), and x_ProcessGetSplitInfo().

◆ x_GetError() [1/2]

Definition at line 2485 of file reader_id2_base.cpp.

Referenced by x_GetError(), x_GetReplyIndex(), and x_ProcessReply().

◆ x_GetError() [2/2] ◆ x_GetMessageError() [1/2]

Definition at line 2540 of file reader_id2_base.cpp.

Referenced by x_GetBlobState(), x_GetMessageError(), x_ProcessEmptyReply(), and x_ProcessGetSeqIdSeqId().

◆ x_GetMessageError() [2/2] ◆ x_GetReplyIndex()

Definition at line 2239 of file reader_id2_base.cpp.

References conn, ERR_POST_X, fError_bad_connection, fError_failed_command, fError_inactivity_timeout, CID2_Reply_Base::GetReply(), CID2_Reply_Base::GetSerial_number(), CID2_Reply_Base::C_Reply::IsEmpty(), CID2_Reply_Base::IsSetDiscard(), CID2_Reply_Base::IsSetSerial_number(), NCBI_THROW_FMT, SId2PacketInfo::request_count, SId2PacketInfo::requests, result, SId2PacketInfo::start_serial_num, x_ConnDescription(), and x_GetError().

Referenced by x_ProcessPacket().

◆ x_LoadSeq_idBlob_idsSet()

Definition at line 1744 of file reader_id2_base.cpp.

References CID2_Request_Packet_Base::Get(), GetMaxChunksRequestSize(), ITERATE, LimitChunksRequests(), LoadSeq_idBlob_ids(), result, SeparateChunksRequests(), CID2_Request_Packet_Base::Set(), CID2_Request_Base::SetRequest(), x_ProcessPacket(), and x_SetResolve().

Referenced by LoadBlobSet().

◆ x_ProcessEmptyReply()

Definition at line 2752 of file reader_id2_base.cpp.

References CID2_Request_Base::C_Request::e_Get_blob_id, CID2_Request_Base::C_Request::e_Get_blob_info, CID2_Request_Base::C_Request::e_Get_seq_id, fError_no_data, CBioseq_Handle::fState_no_data, CSeq_id_Handle::GetHandle(), CID2_Request_Base::GetRequest(), result, CReader::SetAndSaveNoSeq_idBlob_ids(), x_GetMessageError(), and x_ProcessGetSeqId().

Referenced by x_ProcessReply().

◆ x_ProcessGetBlob()

Definition at line 3097 of file reader_id2_base.cpp.

References _ASSERT, data, ERR_POST_X, CID2_Blob_Id_Base::eSub_sat_snp, CProcessor::eType_ID2, CProcessor::eType_Seq_entry_SNP, fAvoidRequest_nested_get_blob_info, CBioseq_Handle::fState_no_data, CID2_Reply_Get_Blob_Base::GetBlob_id(), CID2_Reply_Get_Blob_Base::GetBlob_state(), GetBlobId(), CID2_Reply_Get_Blob_Base::GetData(), CReadDispatcher::GetProcessor(), CID2_Reply_Get_Blob_Base::GetSplit_version(), CID2_Blob_Id_Base::GetSub_sat(), CID2_Blob_Id_Base::GetVersion(), Info(), CLoadLockBlob::IsLoadedBlob(), CLoadLockBlobVersion::IsLoadedBlobVersion(), CLoadLockBlob::IsLoadedChunk(), CID2_Reply_Get_Blob_Base::IsSetBlob_state(), CID2_Reply_Get_Blob_Base::IsSetData(), CID2_Blob_Id_Base::IsSetVersion(), kDelayedMain_ChunkId, kMain_ChunkId, m_AvoidRequest, SId2LoadedSet::m_BlobStates, CReader::m_Dispatcher, SId2LoadedSet::m_Skeletons, CLoadLockBlob::NeedsDelayedMainChunk(), CProcessor::ProcessBlobFromID2Data(), result, CLoadLockBlob::SelectChunk(), CReader::SetAndSaveBlobVersion(), CReader::SetAndSaveNoBlob(), Warning(), x_GetBlobState(), and x_GetBlobStateFromID2().

Referenced by x_ProcessReply().

◆ x_ProcessGetBlobId()

Definition at line 2995 of file reader_id2_base.cpp.

References CProcessor_ExtAnnot::eSat_VDB_WGS_MAX, CProcessor_ExtAnnot::eSat_VDB_WGS_MIN, CID2_Blob_Id_Base::eSub_sat_main, fBlobHasAllLocal, fBlobHasExtAnnot, fBlobHasNamedAlign, fBlobHasNamedAnnot, fBlobHasNamedFeat, fBlobHasNamedGraph, fError_warning, CBioseq_Handle::fState_no_data, CBioseq_Handle::fState_other_error, CID2_Reply_Get_Blob_Id_Base::GetAnnot_info(), CID2_Reply_Get_Blob_Id_Base::GetBlob_id(), CID2_Reply_Get_Blob_Id_Base::GetBlob_state(), GetBlobId(), CSeq_id_Base::GetGeneral(), CSeq_id_Handle::GetHandle(), CObject_id::GetId8(), CBlob_id::GetSat(), CBlob_id::GetSatKey(), CID2_Reply_Get_Blob_Id_Base::GetSeq_id(), CBlob_id::GetSubSat(), CDbtag_Base::GetTag(), CID2_Blob_Id_Base::GetVersion(), info, CSeq_id_Base::IsGeneral(), CObject_id_Base::IsId(), CID2_Reply_Get_Blob_Id_Base::IsSetAnnot_info(), CID2_Reply_Get_Blob_Id_Base::IsSetBlob_state(), CID2_Blob_Id_Base::IsSetVersion(), ITERATE, SId2BlobInfo::m_AnnotInfo, SId2LoadedSet::m_Blob_ids, SId2LoadedSet::m_BlobStates, SId2BlobInfo::m_ContentMask, mask, result, CReader::SetAndSaveBlobVersion(), CReader::SetAndSaveNoSeq_idBlob_ids(), NStr::StartsWith(), x_GetBlobState(), and x_GetBlobStateFromID2().

Referenced by x_ProcessReply().

◆ x_ProcessGetBlobSeqIds() ◆ x_ProcessGetChunk() ◆ x_ProcessGetSeqId() ◆ x_ProcessGetSeqIdSeqId()

Definition at line 2820 of file reader_id2_base.cpp.

Referenced by x_ProcessGetSeqId().

◆ x_ProcessGetSplitInfo()

Definition at line 3197 of file reader_id2_base.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::erase(), ERR_POST_X, CProcessor::eType_ID2, fAvoidRequest_nested_get_blob_info, map_checker< Container >::find(), CBioseq_Handle::fState_no_data, CID2S_Reply_Get_Split_Info_Base::GetBlob_id(), CID2S_Reply_Get_Split_Info_Base::GetBlob_state(), GetBlobId(), CID2S_Reply_Get_Split_Info_Base::GetData(), CReadDispatcher::GetProcessor(), CID2S_Reply_Get_Split_Info_Base::GetSplit_version(), CID2_Blob_Id_Base::GetVersion(), Info(), CLoadLockBlob::IsLoadedBlob(), CLoadLockBlobVersion::IsLoadedBlobVersion(), CLoadLockBlob::IsLoadedChunk(), CID2S_Reply_Get_Split_Info_Base::IsSetBlob_state(), CID2S_Reply_Get_Split_Info_Base::IsSetData(), CID2_Blob_Id_Base::IsSetVersion(), kDelayedMain_ChunkId, kMain_ChunkId, m_AvoidRequest, CReader::m_Dispatcher, SId2LoadedSet::m_Skeletons, CLoadLockBlob::NeedsDelayedMainChunk(), result, CLoadLockBlob::SelectChunk(), CReader::SetAndSaveBlobVersion(), CReader::SetAndSaveNoBlob(), x_GetBlobState(), and x_GetBlobStateFromID2().

Referenced by x_ProcessReply().

◆ x_ProcessPacket()

Definition at line 2299 of file reader_id2_base.cpp.

References eTraceError, GetDebugLevel(), MSerial_AsnText, NCBI_RETHROW, SId2PacketInfo::remaining_count, SId2PacketInfo::request_count, SId2PacketInfo::requests, CRef< C, Locker >::Reset(), result, x_AssignSerialNumbers(), x_ConnDescription(), x_DoneReply(), x_EndOfPacket(), x_GetReaderName, x_GetReplyIndex(), x_ProcessReply(), x_ReceiveID2Reply(), x_SendID2Packet(), and x_UpdateLoadedSet().

Referenced by LoadAccVers(), LoadBlobs(), LoadBlobSet(), LoadBulkIds(), LoadChunks(), LoadGis(), LoadHashes(), LoadLabels(), LoadLengths(), LoadStates(), LoadTaxIds(), LoadTypes(), x_LoadSeq_idBlob_idsSet(), and x_ProcessRequest().

◆ x_ProcessReply()

Definition at line 2698 of file reader_id2_base.cpp.

References CID2_Reply_Base::C_Reply::e_Empty, CID2_Reply_Base::C_Reply::e_Get_blob, CID2_Reply_Base::C_Reply::e_Get_blob_id, CID2_Reply_Base::C_Reply::e_Get_blob_seq_ids, CID2_Reply_Base::C_Reply::e_Get_chunk, CID2_Reply_Base::C_Reply::e_Get_seq_id, CID2_Reply_Base::C_Reply::e_Get_split_info, ERR_POST_X, fError_bad_connection, fError_failed_command, CID2_Reply_Base::GetReply(), MSerial_AsnText, NCBI_THROW, result, x_GetError(), x_ProcessEmptyReply(), x_ProcessGetBlob(), x_ProcessGetBlobId(), x_ProcessGetBlobSeqIds(), x_ProcessGetChunk(), x_ProcessGetSeqId(), and x_ProcessGetSplitInfo().

Referenced by x_ProcessPacket().

◆ x_ProcessRequest()

Definition at line 1864 of file reader_id2_base.cpp.

References Ref(), result, CID2_Request_Packet_Base::Set(), and x_ProcessPacket().

Referenced by LoadBlob(), LoadBlobs(), LoadBlobState(), LoadBlobVersion(), LoadChunk(), LoadChunks(), LoadSeq_idAccVer(), LoadSeq_idBlob_ids(), LoadSeq_idGi(), LoadSeq_idLabel(), LoadSeq_idSeq_ids(), LoadSeq_idTaxId(), LoadSequenceHash(), LoadSequenceLength(), and LoadSequenceType().

◆ x_ReceiveFromConnection() ◆ x_ReceiveID2Reply() ◆ x_ReceiveID2ReplyStage()

Definition at line 2144 of file reader_id2_base.cpp.

References _ASSERT, conn, eTraceConn, GetDebugLevel(), info, m_Processors, NCBI_RETHROW, SId2ProcessorStage::packet_context, SId2ProcessorStage::replies, x_ConnDescription(), x_DumpReply(), x_GetReaderName, and x_ReceiveReply().

Referenced by x_ReceiveID2Reply().

◆ x_ReceiveReply() [1/2] ◆ x_ReceiveReply() [2/2] virtual void CId2ReaderBase::x_ReceiveReply ( TConn conn, CID2_Reply & reply ) protectedpure virtual ◆ x_SendID2Packet()

Definition at line 2095 of file reader_id2_base.cpp.

References conn, eTraceConn, CID2_Request_Packet_Base::Get(), GetDebugLevel(), i, info, m_Processors, NCBI_RETHROW, CProcessor::OffsetAllGisFromOM(), SId2ProcessorStage::packet_context, SId2ProcessorStage::replies, result, x_ConnDescription(), x_DumpPacket(), x_DumpReply(), x_GetReaderName, and x_SendPacket().

Referenced by x_ProcessPacket().

◆ x_SendPacket() ◆ x_SendToConnection() ◆ x_SetContextData() void CId2ReaderBase::x_SetContextData ( CID2_Request & request ) protected

Definition at line 1921 of file reader_id2_base.cpp.

References CSeq_id::eSNPScaleLimit_Default, CRequestContext::GetClientIP(), GetDiagContext(), CRequestContext::GetNextSubHitID(), CID2_Request_Base::GetRequest(), CDiagContext::GetRequestContext(), CRequestContext::GetSessionID(), GetSNP_Scale_Limit(), CSeq_id::GetSNPScaleLimit_Name(), GetVDB_CDD_Enabled(), GetVDB_SNP_Enabled(), GetVDB_WGS_Enabled(), CID2_Request_Base::C_Request::IsInit(), CRequestContext::IsSetClientIP(), CRequestContext::IsSetHitID(), CRequestContext::IsSetSessionID(), and CID2_Request_Base::SetParams().

Referenced by CId2ReaderBase(), x_AssignSerialNumbers(), CId2Reader::x_InitConnection(), and CPubseq2Reader::x_InitConnection().

◆ x_SetDetails() ◆ x_SetExclude_blobs() ◆ x_SetResolve() [1/2] ◆ x_SetResolve() [2/2]

Definition at line 296 of file reader_id2_base.cpp.

References _ASSERT, CSeq_id_Base::e_not_set, CID2_Request_Get_Blob_Id_Base::GetSeq_id(), CID2_Request_Get_Seq_id_Base::GetSeq_id(), CID2_Seq_id_Base::GetSeq_id(), CID2_Request_Get_Blob_Id_Base::SetExternal(), CID2_Request_Get_Blob_Id_Base::SetSeq_id(), and CSeq_id_Base::Which().

Referenced by LoadBlob(), LoadBlobs(), LoadBlobSet(), LoadBlobState(), LoadBlobVersion(), LoadChunk(), LoadChunks(), LoadSeq_idBlob_ids(), LoadStates(), x_LoadSeq_idBlob_idsSet(), and x_SetExclude_blobs().

◆ x_UpdateLoadedSet()

Definition at line 2379 of file reader_id2_base.cpp.

References CombineWithZoomLevel(), data, eTakeOwnership, eTraceASN, ExtractZoomLevel(), fBlobHasNamedAnnot, GetDebugLevel(), CID2S_Seq_annot_Info_Base::GetName(), CID2S_Seq_annot_Info_Base::IsSetAlign(), CID2S_Seq_annot_Info_Base::IsSetFeat(), CID2S_Seq_annot_Info_Base::IsSetGraph(), CID2S_Seq_annot_Info_Base::IsSetName(), CID2S_Seq_annot_Info_Base::IsSetSeq_loc(), ITERATE, MSerial_AsnText, NON_CONST_ITERATE, CID2S_Seq_annot_Info_Base::ResetGraph(), result, SerialClone(), CReader::SetAndSaveSeq_idBlob_ids(), CReader::SetAndSaveSeq_idSeq_ids(), CBlob_Info::SetAnnotInfo(), and x_GetReaderName.

Referenced by x_ProcessPacket().

◆ CId2ReaderProcessorResolver ◆ m_AvoidRequest

Definition at line 318 of file reader_id2_base.hpp.

Referenced by LoadBlobs(), LoadBlobSet(), LoadHashes(), LoadLabels(), LoadLengths(), LoadSeq_idLabel(), LoadSeq_idTaxId(), LoadSequenceHash(), LoadSequenceLength(), LoadSequenceType(), LoadTaxIds(), LoadTypes(), x_GetError(), x_GetMessageError(), x_ProcessGetBlob(), and x_ProcessGetSplitInfo().

◆ m_Processors ◆ m_RequestSerialNumber

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

include/objtools/data_loaders/genbank/impl/reader_id2_base.hpp
src/objtools/data_loaders/genbank/reader_id2_base.cpp

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