NCBI C++ ToolKit
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Search Toolkit Book for CTSE_Chunk_Info
#include <objmgr/impl/tse_chunk_info.hpp>
Classes | |
struct | SFeatIds |
Protected Member Functions | |
void | x_SplitAttach (CTSE_Split_Info &split_info) |
void | x_TSEAttach (CTSE_Info &tse, ITSE_Assigner &tse_info) |
bool | x_Attached (void) const |
bool | x_GetRecords (const CSeq_id_Handle &id, bool bioseq) const |
void | GetBioseqsIds (TBioseqIds &ids) const |
bool | ContainsBioseq (const CSeq_id_Handle &id) const |
bool | x_AnnotIndexNeedsUpdate () const |
void | x_UpdateAnnotIndex (CTSE_Info &tse) |
void | x_UpdateAnnotIndexContents (CTSE_Info &tse) |
bool | x_ContainsFeatType (CSeqFeatData::E_Choice type) const |
bool | x_ContainsFeatType (CSeqFeatData::ESubtype subtype) const |
bool | x_ContainsFeatIds (CSeqFeatData::E_Choice type, EFeatIdType id_type) const |
bool | x_ContainsFeatIds (CSeqFeatData::ESubtype subtype, EFeatIdType id_type) const |
void | x_DropAnnotObjects (void) |
void | x_InitObjectIndexList (void) |
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virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
Private Member Functions | |
CTSE_Chunk_Info (const CTSE_Chunk_Info &) | |
CTSE_Chunk_Info & | operator= (const CTSE_Chunk_Info &) |
Friends | |
class | CTSE_Info |
class | CTSE_Split_Info |
class | CTSE_Default_Assigner |
Additional Inherited Members | |
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static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
Define method to throw null pointer exception. More... | |
static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
static EAllocFillMode | GetAllocFillMode (void) |
static void | SetAllocFillMode (EAllocFillMode mode) |
static void | SetAllocFillMode (const string &value) |
Set mode from configuration parameter value. More... | |
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static void | EnableDebugDump (bool on) |
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static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
Define possible object states. More... | |
static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
Heap signature was found. More... | |
static const TCount | eCounterBitsPlaceMask |
Mask for 'in heap' state flags. More... | |
static const int | eCounterStep = 1 << 2 |
Skip over the "in heap" bits. More... | |
static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
static const TCount | eCounterStateMask |
Valid object, and object in heap. More... | |
Definition at line 74 of file tse_chunk_info.hpp.
Definition at line 111 of file tse_chunk_info.hpp.
Definition at line 110 of file tse_chunk_info.hpp.
typedef list< CRef<CSeq_align> > CTSE_Chunk_Info::TAssembly |
Definition at line 119 of file tse_chunk_info.hpp.
Definition at line 102 of file tse_chunk_info.hpp.
typedef vector<TAssemblyInfo> CTSE_Chunk_Info::TAssemblyInfos |
Definition at line 103 of file tse_chunk_info.hpp.
typedef int CTSE_Chunk_Info::TBioseq_setId |
Definition at line 93 of file tse_chunk_info.hpp.
Definition at line 94 of file tse_chunk_info.hpp.
typedef vector<TBioseqId> CTSE_Chunk_Info::TBioseqIds |
Definition at line 101 of file tse_chunk_info.hpp.
typedef vector<TBioseq_setId> CTSE_Chunk_Info::TBioseqPlaces |
Definition at line 100 of file tse_chunk_info.hpp.
typedef CBlobIdKey CTSE_Chunk_Info::TBlobId |
Definition at line 82 of file tse_chunk_info.hpp.
typedef int CTSE_Chunk_Info::TBlobVersion |
Definition at line 83 of file tse_chunk_info.hpp.
typedef int CTSE_Chunk_Info::TChunkId |
Definition at line 84 of file tse_chunk_info.hpp.
typedef pair<TDescTypeMask, TPlace> CTSE_Chunk_Info::TDescInfo |
Definition at line 97 of file tse_chunk_info.hpp.
typedef vector<TDescInfo> CTSE_Chunk_Info::TDescInfos |
Definition at line 99 of file tse_chunk_info.hpp.
typedef unsigned CTSE_Chunk_Info::TDescTypeMask |
Definition at line 96 of file tse_chunk_info.hpp.
typedef int CTSE_Chunk_Info::TFeatIdInt |
Definition at line 176 of file tse_chunk_info.hpp.
typedef vector<TFeatIdInt> CTSE_Chunk_Info::TFeatIdIntList |
Definition at line 178 of file tse_chunk_info.hpp.
Definition at line 184 of file tse_chunk_info.hpp.
typedef string CTSE_Chunk_Info::TFeatIdStr |
Definition at line 177 of file tse_chunk_info.hpp.
typedef list<TFeatIdStr> CTSE_Chunk_Info::TFeatIdStrList |
Definition at line 179 of file tse_chunk_info.hpp.
typedef pair<TLocationId, TLocationRange> CTSE_Chunk_Info::TLocation |
Definition at line 108 of file tse_chunk_info.hpp.
Definition at line 106 of file tse_chunk_info.hpp.
typedef CRange<TSeqPos> CTSE_Chunk_Info::TLocationRange |
Definition at line 107 of file tse_chunk_info.hpp.
typedef vector<TLocation> CTSE_Chunk_Info::TLocationSet |
Definition at line 109 of file tse_chunk_info.hpp.
Definition at line 114 of file tse_chunk_info.hpp.
typedef list<TObjectIndex> CTSE_Chunk_Info::TObjectIndexList |
Definition at line 115 of file tse_chunk_info.hpp.
typedef pair<TBioseqId, TBioseq_setId> CTSE_Chunk_Info::TPlace |
Definition at line 95 of file tse_chunk_info.hpp.
typedef vector<TPlace> CTSE_Chunk_Info::TPlaces |
Definition at line 98 of file tse_chunk_info.hpp.
typedef list< CRef<CSeq_literal> > CTSE_Chunk_Info::TSequence |
Definition at line 118 of file tse_chunk_info.hpp.
anonymous enum |
Enumerator | |
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kMain_ChunkId | |
kMasterWGS_ChunkId | |
kDelayedMain_ChunkId |
Definition at line 86 of file tse_chunk_info.hpp.
CTSE_Chunk_Info::CTSE_Chunk_Info | ( | TChunkId | id | ) |
Definition at line 66 of file tse_chunk_info.cpp.
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Definition at line 76 of file tse_chunk_info.cpp.
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Definition at line 240 of file tse_chunk_info.cpp.
References m_BioseqIds.
Referenced by CTSE_Split_Info::ContainsBioseq(), CTSE_Split_Info::x_AddChunksForGetRecords(), x_GetRecords(), and x_SplitAttach().
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Definition at line 246 of file tse_chunk_info.hpp.
References m_AnnotContents.
Definition at line 234 of file tse_chunk_info.hpp.
References m_AnnotPlaces.
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Definition at line 254 of file tse_chunk_info.hpp.
References m_AssemblyInfos.
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Definition at line 242 of file tse_chunk_info.hpp.
References m_BioseqIds.
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Definition at line 238 of file tse_chunk_info.hpp.
References m_BioseqPlaces.
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Definition at line 234 of file tse_chunk_info.cpp.
References m_BioseqIds.
CTSE_Chunk_Info::TBlobId CTSE_Chunk_Info::GetBlobId | ( | void | ) | const |
Definition at line 89 of file tse_chunk_info.cpp.
References _ASSERT, CTSE_Split_Info::GetBlobId(), m_SplitInfo, and x_Attached().
Referenced by CBAMDataLoader::EstimateLoadSeconds(), CBlastDbDataLoader::GetChunk(), CBAMDataLoader::GetChunk(), CCSRADataLoader::GetChunk(), CWGSDataLoader::GetChunk(), CGBDataLoader_Native::GetChunk(), CSNPDataLoader::GetChunk(), CLDS2_DataLoader::GetChunk(), CVDBGraphDataLoader_Impl::GetChunkOnce(), CRemoteBlastDbDataLoader::GetChunks(), CCSRARefSeqInfo::LoadAnnotAlignChunk(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CPSGDataLoader_Impl::LoadChunksOnce(), CCSRARefSeqInfo::LoadRefSeqChunk(), CPSGL_GetChunk_Processor::PrintChunk(), CPSGL_LocalCDDBlob_Processor::ProcessItemFast(), CPSGL_Blob_Processor::SetLockedChunkInfo(), x_CreateEmptyLocalCDDEntry(), x_InitObjectIndexList(), and CPSGDataLoader_Impl::x_ReadCDDChunk().
CTSE_Chunk_Info::TBlobVersion CTSE_Chunk_Info::GetBlobVersion | ( | void | ) | const |
Definition at line 96 of file tse_chunk_info.cpp.
References _ASSERT, CTSE_Split_Info::GetBlobVersion(), m_SplitInfo, and x_Attached().
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Definition at line 339 of file tse_chunk_info.hpp.
References m_ChunkId.
Referenced by CTSE_Split_Info::AddChunk(), CTSE_Default_Assigner::AddSeq_data(), CPSGL_LocalCDDBlob_Processor::CPSGL_LocalCDDBlob_Processor(), CBamRefSeqInfo::CreateChunks(), CBamRefSeqInfo::EstimateLoadSeconds(), CSplitDataLoader::GetChunk(), CGBDataLoader_Native::GetChunk(), CCSRADataLoader_Impl::GetChunkOnce(), CSNPDataLoader_Impl::GetChunkOnce(), CVDBGraphDataLoader_Impl::GetChunkOnce(), CLoadLockBlob::GetSelectedChunkId(), CLoadLockBlob::IsLoadedChunk(), CBamRefSeqInfo::LoadAlignChunk(), CCSRARefSeqInfo::LoadAnnotAlignChunk(), CCSRARefSeqInfo::LoadAnnotChunk(), CSNPSeqInfo::LoadAnnotChunk(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CWGSFileInfo::LoadChunk(), CBamRefSeqInfo::LoadChunk(), CPSGDataLoader_Impl::LoadChunksOnce(), CWGSMasterDescrSetter::Loaded(), CBamRefSeqInfo::LoadPileupChunk(), CCSRARefSeqInfo::LoadRefSeqChunk(), CBamRefSeqInfo::LoadSeqChunk(), CPSGL_GetChunk_Processor::PrintChunk(), CLoadLockBlob::SelectChunk(), CLoadLockSetter::SetLoaded(), CPSGL_Blob_Processor::SetLockedChunkInfo(), CPSGL_Blob_Processor::SetLockedDelayedChunkInfo(), x_AddAnnotPlace(), x_AddAssemblyInfo(), x_AddBioseqPlace(), x_AddDescInfo(), CBamRefSeqInfo::x_AddSeqChunk(), CBamRefSeqInfo::x_InitAlignIterator(), x_LoadAnnot(), x_LoadBioseqs(), CPSGDataLoader_Impl::x_ReadCDDChunk(), CAnnot_Collector::x_SearchRange(), CLoadLockSetter::x_SelectChunk(), x_SplitAttach(), x_TSEAttach(), and x_UpdateAnnotIndexContents().
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Definition at line 230 of file tse_chunk_info.hpp.
References m_DescInfos.
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Definition at line 375 of file tse_chunk_info.hpp.
References m_LoadBytes.
Referenced by GetLoadCost().
pair< Uint4, double > CTSE_Chunk_Info::GetLoadCost | ( | ) | const |
Definition at line 807 of file tse_chunk_info.cpp.
References CDataLoader::EstimateLoadBytes(), CDataLoader::EstimateLoadSeconds(), CTSE_Split_Info::GetDataLoader(), GetLoadBytes(), GetLoadSeconds(), and m_SplitInfo.
Referenced by CAnnot_Collector::x_SearchRange().
CInitGuard * CTSE_Chunk_Info::GetLoadInitGuard | ( | void | ) |
Definition at line 260 of file tse_chunk_info.cpp.
References CTSE_Split_Info::GetMutexPool(), IsLoaded(), m_LoadLock, and m_SplitInfo.
Referenced by CPSGL_Blob_Processor::AssignChunks(), CPSGL_Blob_Processor::Chunk_ToOM(), CPSGL_CDDAnnot_Processor::ProcessReplySlow(), CPSGL_Blob_Processor::TSE_ToOM(), and CLoadLockSetter::x_Init().
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Definition at line 382 of file tse_chunk_info.hpp.
References m_LoadSeconds.
Referenced by GetLoadCost().
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Definition at line 250 of file tse_chunk_info.hpp.
References m_Seq_data.
Referenced by CBlastDbDataLoader::GetChunk(), and CRemoteBlastDbDataLoader::GetChunks().
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Definition at line 367 of file tse_chunk_info.hpp.
References _ASSERT, and m_SplitInfo.
Referenced by CSNPSeqInfo::LoadAnnotChunk(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CWGSFileInfo::LoadChunk(), CBamRefSeqInfo::LoadMainChunk(), CWGSMasterSupport::LoadWGSMaster(), CBamRefSeqInfo::x_AddSeqChunk(), x_InitObjectIndexList(), and CAnnot_Collector::x_SearchRange().
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Definition at line 353 of file tse_chunk_info.hpp.
References m_LoadLock.
Referenced by CTSE_Split_Info::AddChunk(), CPSGL_Blob_Processor::Chunk_ToOM(), CBlastDbDataLoader::GetChunk(), CSplitDataLoader::GetChunk(), CLDS2_DataLoader::GetChunk(), CRemoteBlastDbDataLoader::GetChunks(), GetLoadInitGuard(), CLoadLockSetter::IsLoaded(), CLoadLockBlob::IsLoadedChunk(), Load(), CPSGDataLoader_Impl::LoadChunksOnce(), SetLoadListener(), CPSGL_Blob_Processor::TSE_ToOM(), CTSE_Split_Info::x_AddChunksForGetRecords(), x_GetRecords(), CTSE_Split_Info::x_GetRecords(), x_LoadAnnot(), x_LoadAssembly(), x_LoadBioseq(), x_LoadBioseqs(), x_LoadDescr(), x_LoadSeq_entry(), x_LoadSequence(), CPSGDataLoader_Impl::x_ReadCDDChunk(), and x_SplitAttach().
void CTSE_Chunk_Info::Load | ( | void | ) | const |
Definition at line 269 of file tse_chunk_info.cpp.
References _ASSERT, CDataLoader::GetChunk(), CTSE_Split_Info::GetDataLoader(), CTSE_Split_Info::GetMutexPool(), init(), IsLoaded(), m_LoadLock, m_SplitInfo, Ref(), and x_Attached().
Referenced by CSeq_annot_Finder::x_Find(), x_GetRecords(), CTSE_Split_Info::x_LoadChunk(), CTSE_Split_Info::x_LoadDelayedMainChunk(), CSeqMap::x_LoadObject(), and CTSE_Split_Info::x_UpdateCore().
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Definition at line 346 of file tse_chunk_info.hpp.
References m_LoadLock.
Referenced by CSeq_annot_Finder::x_Find(), CSeqMap::x_GetChunkToLoad(), CTSE_Split_Info::x_NeedsDelayedMainChunk(), CAnnot_Collector::x_SearchRange(), and x_TSEAttach().
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Definition at line 205 of file tse_chunk_info.hpp.
References m_LoadLock.
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void CTSE_Chunk_Info::SetLoaded | ( | CObject * | obj = 0 | ) |
Definition at line 281 of file tse_chunk_info.cpp.
References CObject::CObject(), CTSEChunkLoadListener::Loaded(), m_ListenerMutex, m_LoadListener, m_LoadLock, and CInitMutex< C >::Reset().
Referenced by CPSGL_Blob_Processor::AssignChunks(), CPSGL_Blob_Processor::Chunk_ToOM(), CBlastDbDataLoader::GetChunk(), CSplitDataLoader::GetChunk(), CLDS2_DataLoader::GetChunk(), CVDBGraphDataLoader_Impl::GetChunkOnce(), CRemoteBlastDbDataLoader::GetChunks(), CBamRefSeqInfo::LoadAlignChunk(), CCSRARefSeqInfo::LoadAnnotAlignChunk(), CSNPSeqInfo::LoadAnnotChunk(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CWGSFileInfo::LoadChunk(), CBamRefSeqInfo::LoadMainChunk(), CBamRefSeqInfo::LoadPileupChunk(), CCSRARefSeqInfo::LoadRefSeqChunk(), CBamRefSeqInfo::LoadSeqChunk(), CWGSMasterSupport::LoadWGSMaster(), CPSGL_CDDAnnot_Processor::ProcessReplySlow(), CLoadLockSetter::SetLoaded(), CPSGL_Blob_Processor::TSE_ToOM(), x_CreateEmptyLocalCDDEntry(), and CPSGDataLoader_Impl::x_ReadCDDChunk().
void CTSE_Chunk_Info::SetLoadListener | ( | CRef< CTSEChunkLoadListener > | listener | ) |
Definition at line 297 of file tse_chunk_info.cpp.
References IsLoaded(), CTSEChunkLoadListener::Loaded(), m_ListenerMutex, and m_LoadListener.
Referenced by CWGSMasterDescrSetter::RegisterCallbacks().
Definition at line 348 of file tse_chunk_info.cpp.
Referenced by CCSRARefSeqInfo::LoadAnnotMainChunk(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), x_AddAnnotPlace(), CLDS2_DataLoader::x_LoadTSE(), and CSplitDataLoader::x_SplitAnnot().
Definition at line 360 of file tse_chunk_info.cpp.
References GetChunkId(), m_AnnotPlaces, m_SplitInfo, and CTSE_Split_Info::x_AddAnnotPlace().
void CTSE_Chunk_Info::x_AddAnnotPlace | ( | TBioseq_setId | id | ) |
Definition at line 354 of file tse_chunk_info.cpp.
References x_AddAnnotPlace().
void CTSE_Chunk_Info::x_AddAnnotType | ( | const CAnnotName & | annot_name, |
const SAnnotTypeSelector & | annot_type, | ||
const TLocationId & | location_id | ||
) |
Definition at line 405 of file tse_chunk_info.cpp.
References _ASSERT, COpenRange< TSeqPos >::GetWhole(), location, m_AnnotContents, and x_Attached().
Referenced by CBamRefSeqInfo::CreateChunks(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadAnnotMainSplit(), CProcessor_AnnotInfo::LoadBlob(), CBamRefSeqInfo::LoadMainSplit(), CVDBGraphDataLoader_Impl::LoadSplitEntry(), CProcessor_ExtAnnot::Process(), s_CreateNAChunk(), CSplitParser::x_Attach(), x_CreateLocalCDDEntryChunk(), CLDS2_DataLoader::x_LoadTSE(), CSplitDataLoader::x_SplitAligns(), CSplitDataLoader::x_SplitFeats(), and CSplitDataLoader::x_SplitGraphs().
void CTSE_Chunk_Info::x_AddAnnotType | ( | const CAnnotName & | annot_name, |
const SAnnotTypeSelector & | annot_type, | ||
const TLocationId & | location_id, | ||
const TLocationRange & | location_range | ||
) |
Definition at line 394 of file tse_chunk_info.cpp.
References _ASSERT, m_AnnotContents, and x_Attached().
void CTSE_Chunk_Info::x_AddAnnotType | ( | const CAnnotName & | annot_name, |
const SAnnotTypeSelector & | annot_type, | ||
const TLocationSet & | location | ||
) |
Definition at line 416 of file tse_chunk_info.cpp.
References _ASSERT, map_checker< Container >::insert(), location, m_AnnotContents, and x_Attached().
Definition at line 339 of file tse_chunk_info.cpp.
References GetChunkId(), m_AssemblyInfos, m_SplitInfo, and CTSE_Split_Info::x_AddAssemblyInfo().
Definition at line 378 of file tse_chunk_info.cpp.
References _ASSERT, m_BioseqIds, and x_Attached().
Referenced by CProcessor_ExtAnnot::Process(), and CBamRefSeqInfo::x_AddSeqChunk().
void CTSE_Chunk_Info::x_AddBioseqPlace | ( | TBioseq_setId | id | ) |
Definition at line 369 of file tse_chunk_info.cpp.
References GetChunkId(), m_BioseqPlaces, m_SplitInfo, and CTSE_Split_Info::x_AddBioseqPlace().
Referenced by CProcessor_ExtAnnot::Process(), CBamRefSeqInfo::x_AddSeqChunk(), and CSplitParser::x_Attach().
Definition at line 330 of file tse_chunk_info.cpp.
References GetChunkId(), info, m_DescInfos, m_SplitInfo, and CTSE_Split_Info::x_AddDescInfo().
void CTSE_Chunk_Info::x_AddDescInfo | ( | TDescTypeMask | type_mask, |
const TBioseqId & | id | ||
) |
Definition at line 316 of file tse_chunk_info.cpp.
Referenced by CWGSMasterDescrSetter::AddChunkToWait(), x_AddDescInfo(), and CSplitDataLoader::x_SplitDescr().
void CTSE_Chunk_Info::x_AddDescInfo | ( | TDescTypeMask | type_mask, |
TBioseq_setId | id | ||
) |
Definition at line 323 of file tse_chunk_info.cpp.
References x_AddDescInfo().
void CTSE_Chunk_Info::x_AddFeat_ids | ( | const SAnnotTypeSelector & | type, |
const TFeatIdIntList & | ids | ||
) |
Definition at line 432 of file tse_chunk_info.cpp.
References map_checker< Container >::insert(), m_ExplicitFeatIds, m_FeatIds, and type.
void CTSE_Chunk_Info::x_AddFeat_ids | ( | const SAnnotTypeSelector & | type, |
const TFeatIdStrList & | ids | ||
) |
Definition at line 450 of file tse_chunk_info.cpp.
References map_checker< Container >::insert(), m_ExplicitFeatIds, m_FeatIds, and type.
void CTSE_Chunk_Info::x_AddFeat_ids | ( | void | ) |
Definition at line 426 of file tse_chunk_info.cpp.
References m_ExplicitFeatIds.
Referenced by CSplitParser::x_Attach().
void CTSE_Chunk_Info::x_AddSeq_data | ( | const TLocationSet & | location | ) |
Definition at line 385 of file tse_chunk_info.cpp.
References location, m_Seq_data, m_SplitInfo, and CTSE_Split_Info::x_AddSeq_data().
Referenced by CCSRARefSeqInfo::LoadRefSeqMainEntry(), CCachedSequence::x_AddSplitSeqChunk(), CSplitParser::x_Attach(), and CSplitDataLoader::x_SplitSeqData().
void CTSE_Chunk_Info::x_AddUsedMemory | ( | size_t | size | ) |
Definition at line 788 of file tse_chunk_info.cpp.
References _ASSERT, m_SplitInfo, ncbi::grid::netcache::search::fields::size, CTSE_Split_Info::x_AddUsedMemory(), and x_Attached().
Referenced by CBamRefSeqInfo::LoadAlignChunk(), CCSRARefSeqInfo::LoadAnnotAlignChunk(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CBamRefSeqInfo::LoadPileupChunk(), and CCSRARefSeqInfo::LoadRefSeqChunk().
void CTSE_Chunk_Info::x_AddXref_ids | ( | const SAnnotTypeSelector & | type, |
const TFeatIdIntList & | ids | ||
) |
Definition at line 441 of file tse_chunk_info.cpp.
References map_checker< Container >::insert(), m_ExplicitFeatIds, m_XrefIds, and type.
Referenced by CSplitParser::x_Attach().
void CTSE_Chunk_Info::x_AddXref_ids | ( | const SAnnotTypeSelector & | type, |
const TFeatIdStrList & | ids | ||
) |
Definition at line 459 of file tse_chunk_info.cpp.
References map_checker< Container >::insert(), m_ExplicitFeatIds, m_XrefIds, and type.
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Definition at line 360 of file tse_chunk_info.hpp.
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Definition at line 81 of file tse_chunk_info.cpp.
References m_SplitInfo.
Referenced by GetBlobId(), GetBlobVersion(), Load(), x_AddAnnotType(), x_AddBioseqId(), x_AddUsedMemory(), x_LoadAnnot(), x_LoadAssembly(), x_LoadBioseq(), x_LoadBioseqs(), x_LoadDescr(), x_LoadSeq_entry(), x_LoadSequence(), x_SplitAttach(), and x_TSEAttach().
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Definition at line 637 of file tse_chunk_info.cpp.
References eFeatId_id, m_ExplicitFeatIds, m_FeatIds, m_XrefIds, x_ContainsFeatType(), and x_HasFeatIds().
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Definition at line 650 of file tse_chunk_info.cpp.
References eFeatId_id, m_ExplicitFeatIds, m_FeatIds, m_XrefIds, x_ContainsFeatType(), and x_HasFeatIds().
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Definition at line 615 of file tse_chunk_info.cpp.
References ITERATE, m_AnnotContents, and x_HasFeatType().
Referenced by x_ContainsFeatIds().
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Definition at line 626 of file tse_chunk_info.cpp.
References ITERATE, m_AnnotContents, and x_HasFeatType().
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Definition at line 715 of file tse_chunk_info.cpp.
References m_ObjectIndexList.
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Definition at line 246 of file tse_chunk_info.cpp.
References ContainsBioseq(), IsLoaded(), and Load().
Referenced by CTSE_Split_Info::x_GetRecords().
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Definition at line 482 of file tse_chunk_info.cpp.
References _ASSERT, SAnnotObjectsIndex::AddInfo(), SAnnotObjectsIndex::AddMap(), ERR_POST_X, GetBlobId(), SAnnotObjectsIndex::GetInfos(), SAnnotObjectsIndex::GetKey(), SAnnotObjectsIndex::GetKeys(), SAnnotObjectsIndex::GetName(), GetSplitInfo(), info, SAnnotObject_Key::IsSingle(), ITERATE, ncbi::grid::netcache::search::fields::key, m_AnnotContents, SAnnotObject_Index::m_AnnotObject_Info, m_ObjectIndexList, SAnnotObjectsIndex::PackKeys(), SAnnotObjectsIndex::RemoveLastMap(), and SAnnotObjectsIndex::SetIndexed().
Referenced by x_UpdateAnnotIndexContents().
void CTSE_Chunk_Info::x_LoadAnnot | ( | const TPlace & | place, |
const CSeq_annot & | annot | ||
) |
Definition at line 732 of file tse_chunk_info.cpp.
References _ASSERT, GetChunkId(), IsLoaded(), m_SplitInfo, x_Attached(), and CTSE_Split_Info::x_LoadAnnot().
Referenced by CSplitDataLoader::GetChunk(), CLDS2_DataLoader::GetChunk(), CVDBGraphDataLoader_Impl::GetChunkOnce(), CSplitParser::Load(), CBamRefSeqInfo::LoadAlignChunk(), CCSRARefSeqInfo::LoadAnnotAlignChunk(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CBamRefSeqInfo::LoadMainChunk(), and CBamRefSeqInfo::LoadPileupChunk().
Definition at line 770 of file tse_chunk_info.cpp.
References _ASSERT, IsLoaded(), m_SplitInfo, x_Attached(), and CTSE_Split_Info::x_LoadAssembly().
Referenced by CSplitParser::Load().
Definition at line 741 of file tse_chunk_info.cpp.
References _ASSERT, IsLoaded(), Ref(), x_Attached(), and x_LoadBioseqs().
void CTSE_Chunk_Info::x_LoadBioseqs | ( | const TPlace & | place, |
const list< CRef< CBioseq > > & | bioseqs | ||
) |
Definition at line 752 of file tse_chunk_info.cpp.
References _ASSERT, GetChunkId(), IsLoaded(), m_SplitInfo, x_Attached(), and CTSE_Split_Info::x_LoadBioseqs().
Referenced by CSplitParser::Load(), CBamRefSeqInfo::LoadSeqChunk(), and x_LoadBioseq().
void CTSE_Chunk_Info::x_LoadDescr | ( | const TPlace & | place, |
const CSeq_descr & | descr | ||
) |
Definition at line 723 of file tse_chunk_info.cpp.
References _ASSERT, IsLoaded(), m_SplitInfo, x_Attached(), and CTSE_Split_Info::x_LoadDescr().
Referenced by CSplitDataLoader::GetChunk(), CSplitParser::Load(), and CWGSMasterDescrSetter::Loaded().
void CTSE_Chunk_Info::x_LoadSeq_entry | ( | CSeq_entry & | entry, |
CTSE_SetObjectInfo * | set_info = 0 |
||
) |
Definition at line 779 of file tse_chunk_info.cpp.
References _ASSERT, IsLoaded(), m_SplitInfo, x_Attached(), and CTSE_Split_Info::x_LoadSeq_entry().
Referenced by CLoadLockSetter::SetSeq_entry().
Definition at line 761 of file tse_chunk_info.cpp.
References _ASSERT, IsLoaded(), m_SplitInfo, x_Attached(), and CTSE_Split_Info::x_LoadSequence().
Referenced by CBlastDbDataLoader::GetChunk(), CSplitDataLoader::GetChunk(), CRemoteBlastDbDataLoader::GetChunks(), CSplitParser::Load(), and CCSRARefSeqInfo::LoadRefSeqChunk().
void CTSE_Chunk_Info::x_SetLoadBytes | ( | Uint4 | bytes | ) |
Definition at line 795 of file tse_chunk_info.cpp.
References m_LoadBytes.
Referenced by CBamRefSeqInfo::CreateChunks(), CCSRARefSeqInfo::LoadAnnotMainChunk(), and CBamRefSeqInfo::x_AddSeqChunk().
void CTSE_Chunk_Info::x_SetLoadSeconds | ( | double | seconds | ) |
Definition at line 801 of file tse_chunk_info.cpp.
References m_LoadSeconds.
Referenced by CCSRARefSeqInfo::LoadAnnotMainChunk().
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Definition at line 105 of file tse_chunk_info.cpp.
References _ASSERT, ContainsBioseq(), GetChunkId(), set< Key, Compare >::insert(), IsLoaded(), ITERATE, m_AnnotContents, m_AnnotPlaces, m_AssemblyInfos, m_BioseqIds, m_BioseqPlaces, m_DescInfos, m_Seq_data, m_SplitInfo, ct::sort(), CTSE_Split_Info::x_AddAnnotPlace(), CTSE_Split_Info::x_AddAssemblyInfo(), CTSE_Split_Info::x_AddBioseqPlace(), CTSE_Split_Info::x_AddDescInfo(), CTSE_Split_Info::x_AddSeq_data(), x_Attached(), CTSE_Split_Info::x_SetContainedSeqIds(), and CTSE_Split_Info::x_UpdateAnnotIndex().
Referenced by CTSE_Split_Info::AddChunk().
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Definition at line 195 of file tse_chunk_info.cpp.
References _ASSERT, ITSE_Assigner::AddAnnotPlace(), ITSE_Assigner::AddAssemblyInfo(), ITSE_Assigner::AddBioseqPlace(), ITSE_Assigner::AddDescInfo(), ITSE_Assigner::AddSeq_data(), GetChunkId(), ITERATE, m_AnnotPlaces, m_AssemblyInfos, m_BioseqPlaces, m_DescInfos, m_Seq_data, NotLoaded(), x_Attached(), and x_UpdateAnnotIndex().
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Definition at line 471 of file tse_chunk_info.cpp.
References eEmptyGuard, CTSE_Info::GetAnnotLock(), CTSE_Info::GetDataSource(), CDSAnnotLockWriteGuard::Guard(), CTSE_Info::HasDataSource(), and x_UpdateAnnotIndexContents().
Referenced by CTSE_Default_Assigner::UpdateAnnotIndex(), x_TSEAttach(), and CTSE_Split_Info::x_UpdateAnnotIndex().
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Definition at line 663 of file tse_chunk_info.cpp.
References CSeq_annot_Base::C_Data::e_Ftable, eFeatId_id, eFeatId_xref, GetChunkId(), CTSE_Info::GetName(), i, info, ITERATE, m_AnnotContents, SAnnotObject_Index::m_AnnotObject_Info, m_ExplicitFeatIds, m_FeatIds, m_ObjectIndexList, m_XrefIds, CTSEAnnotObjectMapper::Map(), x_InitObjectIndexList(), CTSE_Info::x_MapChunkByFeatId(), and CTSE_Info::x_MapChunkByFeatType().
Referenced by x_UpdateAnnotIndex().
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Definition at line 306 of file tse_chunk_info.hpp.
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Definition at line 303 of file tse_chunk_info.hpp.
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Definition at line 304 of file tse_chunk_info.hpp.
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Definition at line 324 of file tse_chunk_info.hpp.
Referenced by GetAnnotContents(), x_AddAnnotType(), x_ContainsFeatType(), x_InitObjectIndexList(), x_SplitAttach(), and x_UpdateAnnotIndexContents().
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Definition at line 321 of file tse_chunk_info.hpp.
Referenced by GetAnnotPlaces(), x_AddAnnotPlace(), x_SplitAttach(), and x_TSEAttach().
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Definition at line 326 of file tse_chunk_info.hpp.
Referenced by GetAssemblyInfos(), x_AddAssemblyInfo(), x_SplitAttach(), and x_TSEAttach().
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Definition at line 323 of file tse_chunk_info.hpp.
Referenced by ContainsBioseq(), GetBioseqIds(), GetBioseqsIds(), x_AddBioseqId(), and x_SplitAttach().
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Definition at line 322 of file tse_chunk_info.hpp.
Referenced by GetBioseqPlaces(), x_AddBioseqPlace(), x_SplitAttach(), and x_TSEAttach().
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Definition at line 313 of file tse_chunk_info.hpp.
Referenced by GetChunkId().
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Definition at line 320 of file tse_chunk_info.hpp.
Referenced by GetDescInfos(), x_AddDescInfo(), x_SplitAttach(), and x_TSEAttach().
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Definition at line 318 of file tse_chunk_info.hpp.
Referenced by x_AddFeat_ids(), x_AddXref_ids(), x_ContainsFeatIds(), and x_UpdateAnnotIndexContents().
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Definition at line 328 of file tse_chunk_info.hpp.
Referenced by x_AddFeat_ids(), x_ContainsFeatIds(), and x_UpdateAnnotIndexContents().
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Definition at line 333 of file tse_chunk_info.hpp.
Referenced by SetLoaded(), and SetLoadListener().
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Definition at line 315 of file tse_chunk_info.hpp.
Referenced by GetLoadBytes(), and x_SetLoadBytes().
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Definition at line 334 of file tse_chunk_info.hpp.
Referenced by SetLoaded(), and SetLoadListener().
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Definition at line 331 of file tse_chunk_info.hpp.
Referenced by GetLoadInitGuard(), IsLoaded(), Load(), NotLoaded(), operator CInitMutex_Base &(), SetLoaded(), and CTSE_Split_Info::x_LoadChunks().
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Definition at line 316 of file tse_chunk_info.hpp.
Referenced by GetLoadSeconds(), and x_SetLoadSeconds().
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Definition at line 332 of file tse_chunk_info.hpp.
Referenced by x_DropAnnotObjects(), x_InitObjectIndexList(), and x_UpdateAnnotIndexContents().
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Definition at line 325 of file tse_chunk_info.hpp.
Referenced by GetSeq_dataInfos(), x_AddSeq_data(), x_SplitAttach(), and x_TSEAttach().
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Definition at line 312 of file tse_chunk_info.hpp.
Referenced by GetBlobId(), GetBlobVersion(), GetLoadCost(), GetLoadInitGuard(), GetSplitInfo(), Load(), x_AddAnnotPlace(), x_AddAssemblyInfo(), x_AddBioseqPlace(), x_AddDescInfo(), x_AddSeq_data(), x_AddUsedMemory(), x_Attached(), x_LoadAnnot(), x_LoadAssembly(), x_LoadBioseqs(), x_LoadDescr(), x_LoadSeq_entry(), x_LoadSequence(), and x_SplitAttach().
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Definition at line 329 of file tse_chunk_info.hpp.
Referenced by x_AddXref_ids(), x_ContainsFeatIds(), and x_UpdateAnnotIndexContents().