NCBI C++ ToolKit
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Object Manager Core Classes
+ Collaboration diagram for Object Manager Core Classes:

Classes

class  CAnnotMapperException
 Seq-loc and seq-align mapper exceptions. More...
 
class  CMappingRange
 CMappingRange - describes a single interval to interval mapping. More...
 
class  CMappingRanges
 Storage for multiple mapping ranges. More...
 
class  CGraphRanges
 Helper class for mapping graphs. More...
 
class  CSeq_loc_Mapper_Options
 CSeq_loc_Mapper_Options –. More...
 
class  CSeq_loc_Mapper_Base
 CSeq_loc_Mapper_Base –. More...
 
struct  CSeq_loc_Mapper_Base::SMappedRange
 
class  IMapper_Sequence_Info
 IMapper_Sequence_Info. More...
 
class  CSeq_loc_Mapper_Message
 CSeq_loc_Mapper_Message. More...
 
struct  CMappingRangeRef_Less
 
struct  CMappingRangeRef_LessRev
 
class  CSeqTableException
 Seq-loc and seq-align mapper exceptions. More...
 
struct  PConvertToString< Value >
 
struct  PConvertToString< int >
 
struct  PConvertToString< const void * >
 
struct  PConvertToString< string >
 
struct  PConvertToString< CSeq_id_Handle >
 
class  CBlobId
 
class  CBlobIdFor< Value, Converter >
 
class  CBlobIdKey
 
struct  SRequestDetails
 
class  CLoaderMaker_Base
 
class  CSimpleLoaderMaker< TDataLoader >
 
class  CParamLoaderMaker< TDataLoader, TParam >
 
class  CDataLoader
 
struct  CDataLoader::SAccVerFound
 Better replacement of GetAccVer(), this method should be defined in data loaders, GetAccVer() is left for compatibility. More...
 
struct  CDataLoader::SGiFound
 Better replacement of GetGi(), this method should be defined in data loaders, GetGi() is left for compatibility. More...
 
struct  CDataLoader::STypeFound
 Better replacement of GetSequenceType(), this method should be defined in data loaders, GetSequenceType() is left for compatibility. More...
 
struct  CDataLoader::SHashFound
 Better replacement of GetSequenceHash(), this method should be defined in data loaders, GetSequenceHash() is left for compatibility. More...
 
class  CDllResolver_Getter< objects::CDataLoader >
 
class  CGC_Assembly_Parser
 CGC_Assembly_Parser –. More...
 
class  CAssemblyParserException
 Seq-loc and seq-align mapper exceptions. More...
 
class  CPrefetchManager_Impl
 
struct  SRegisterLoaderInfo< TLoader >
 SRegisterLoaderInfo –. More...
 
class  CObjectManager
 CObjectManager –. More...
 
class  CObjectManager::IDataLoaderFilter
 
class  CObjMgrException
 Base class for all object manager exceptions. More...
 
class  CSeqMapException
 SeqMap related exceptions. More...
 
class  CSeqVectorException
 SeqVector related exceptions. More...
 
class  CAnnotException
 Annotation iterators exceptions. More...
 
class  CLoaderException
 Data loader exceptions, used by GenBank loader. More...
 
class  CBlobStateException
 Blob state exceptions, used by GenBank loader. More...
 
class  CObjmgrUtilException
 Exceptions for objmgr/util library. More...
 
class  CAnnotSearchLimitException
 
class  CPrefetchTokenOld
 CPrefetchToken –. More...
 
class  CScopeSource
 
class  CPrefetchBioseq
 
class  CPrefetchFeat_CI
 
class  CPrefetchComplete< Handle >
 
class  CPrefetchComplete< CBioseq_Handle >
 
class  ISeq_idSource
 
class  CStdSeq_idSource< Container >
 
class  CPrefetchBioseqActionSource
 
class  CPrefetchFeat_CIActionSource
 
class  CStdPrefetch
 
struct  SPrefetchTypes
 
class  IPrefetchAction
 
class  IPrefetchActionSource
 
class  IPrefetchListener
 
class  CPrefetchManager
 
class  CPrefetchFailed
 This exception is used to report failed actions. More...
 
class  CPrefetchCanceled
 This exception is used to interrupt actions canceled by user. More...
 
class  CPrefetchSequence
 
class  CPrefetchRequest
 
class  CScope
 CScope –. More...
 
class  CSeq_loc_Mapper
 CSeq_loc_Mapper –. More...
 

Typedefs

typedef CRange< TSeqPosCMappingRange::TRange
 
typedef CRef< CInt_fuzzCMappingRange::TFuzz
 
typedef pair< TFuzz, TFuzzCMappingRange::TRangeFuzz
 
typedef CMappingRange::TRange CMappingRanges::TRange
 
typedef CRangeMultimap< CRef< CMappingRange >, TSeqPosCMappingRanges::TRangeMap
 
typedef TRangeMap::const_iterator CMappingRanges::TRangeIterator
 
typedef map< CSeq_id_Handle, TRangeMapCMappingRanges::TIdMap
 
typedef TIdMap::const_iterator CMappingRanges::TIdIterator
 
typedef vector< CRef< CMappingRange > > CMappingRanges::TSortedMappings
 
typedef CRange< TSeqPosCGraphRanges::TRange
 
typedef vector< TRangeCGraphRanges::TGraphRanges
 
typedef int CSeq_loc_Mapper_Options::TMapOptions
 
typedef int CSeq_loc_Mapper_Base::TMapOptions
 
typedef int CSeq_loc_Mapper_Base::TFuzzOption
 
typedef int CSeq_loc_Mapper_Base::TAnnotMapFlags
 
typedef set< CSeq_id_HandleCSeq_loc_Mapper_Base::TSynonyms
 
typedef CMappingRange::TRange CSeq_loc_Mapper_Base::TRange
 
typedef CMappingRanges::TRangeMap CSeq_loc_Mapper_Base::TRangeMap
 
typedef CMappingRanges::TRangeIterator CSeq_loc_Mapper_Base::TRangeIterator
 
typedef CMappingRanges::TSortedMappings CSeq_loc_Mapper_Base::TSortedMappings
 
typedef list< TRangeCSeq_loc_Mapper_Base::TDstRanges
 
typedef map< CSeq_id_Handle, TDstRangesCSeq_loc_Mapper_Base::TDstIdMap
 
typedef vector< TDstIdMapCSeq_loc_Mapper_Base::TDstStrandMap
 
typedef CRef< CInt_fuzzCSeq_loc_Mapper_Base::TFuzz
 
typedef pair< TFuzz, TFuzzCSeq_loc_Mapper_Base::TRangeFuzz
 
typedef list< SMappedRangeCSeq_loc_Mapper_Base::TMappedRanges
 
typedef vector< TMappedRangesCSeq_loc_Mapper_Base::TRangesByStrand
 
typedef map< CSeq_id_Handle, TRangesByStrandCSeq_loc_Mapper_Base::TRangesById
 
typedef map< CSeq_id_Handle, ESeqTypeCSeq_loc_Mapper_Base::TSeqTypeById
 
typedef CSeq_align::C_Segs::TDendiag CSeq_loc_Mapper_Base::TDendiag
 
typedef CSeq_align::C_Segs::TStd CSeq_loc_Mapper_Base::TStd
 
typedef map< CSeq_id_Handle, CSeq_id_HandleCSeq_loc_Mapper_Base::TSynonymMap
 
typedef map< CSeq_id_Handle, TSeqPosCSeq_loc_Mapper_Base::TLengthMap
 
typedef int CSeq_loc_Mapper_Base::TMiscFlags
 
typedef CSeq_loc_Mapper_Base::ESeqType IMapper_Sequence_Info::TSeqType
 
typedef CSeq_loc_Mapper_Base::TSynonyms IMapper_Sequence_Info::TSynonyms
 
typedef Value CBlobIdFor< Value, Converter >::value_type
 
typedef Converter CBlobIdFor< Value, Converter >::convert_to_string_type
 
typedef CBlobIdFor< Value, Converter > CBlobIdFor< Value, Converter >::TThisType
 
typedef CBlobIdFor< intCBlobIdInt
 
typedef CBlobIdFor< const void * > CBlobIdPtr
 
typedef CBlobIdFor< stringCBlobIdString
 
typedef CBlobIdFor< CSeq_id_HandleCBlobIdSeq_id
 
typedef CRange< TSeqPosSRequestDetails::TRange
 
typedef set< SAnnotTypeSelectorSRequestDetails::TAnnotTypesSet
 
typedef map< CAnnotName, TAnnotTypesSetSRequestDetails::TAnnotSet
 
typedef int SRequestDetails::TAnnotBlobType
 
typedef SRegisterLoaderInfo< CDataLoaderCLoaderMaker_Base::TRegisterInfo_Base
 
typedef SRegisterLoaderInfo< TDataLoader > CSimpleLoaderMaker< TDataLoader >::TRegisterInfo
 
typedef TParam CParamLoaderMaker< TDataLoader, TParam >::TParamType
 
typedef SRegisterLoaderInfo< TDataLoader > CParamLoaderMaker< TDataLoader, TParam >::TRegisterInfo
 
typedef CTSE_Lock CDataLoader::TTSE_Lock
 
typedef set< TTSE_LockCDataLoader::TTSE_LockSet
 
typedef CRef< CTSE_Chunk_InfoCDataLoader::TChunk
 
typedef vector< TChunkCDataLoader::TChunkSet
 
typedef set< stringCDataLoader::TProcessedNAs
 
typedef set< CSeq_id_HandleCDataLoader::TSeq_idSet
 
typedef vector< CSeq_id_HandleCDataLoader::TIds
 
typedef vector< boolCDataLoader::TLoaded
 Bulk loading interface for a small pieces of information per id. More...
 
typedef vector< TIdsCDataLoader::TBulkIds
 
typedef vector< TGiCDataLoader::TGis
 
typedef vector< stringCDataLoader::TLabels
 
typedef vector< TTaxIdCDataLoader::TTaxIds
 
typedef vector< TSeqPosCDataLoader::TSequenceLengths
 
typedef vector< CSeq_inst::TMolCDataLoader::TSequenceTypes
 
typedef vector< intCDataLoader::TSequenceStates
 
typedef vector< intCDataLoader::TSequenceHashes
 
typedef vector< boolCDataLoader::THashKnown
 
typedef map< CSeq_id_Handle, TTSE_LockSetCDataLoader::TTSE_LockSets
 
typedef vector< vector< CSeq_id_Handle > > CDataLoader::TSeqIdSets
 
typedef vector< CTSE_LockCDataLoader::TCDD_Locks
 
typedef CBlobIdKey CDataLoader::TBlobId
 
typedef int CDataLoader::TBlobVersion
 
typedef CRef< IEditSaverCDataLoader::TEditSaver
 
typedef int CGC_Assembly_Parser::TParserFlags
 
typedef set< CSeq_id_HandleCGC_Assembly_Parser::TSeqIds
 
typedef unsigned int CPrefetchManager_Impl::TPriority
 
typedef CRef< CDataSourceCObjectManager::TDataSourceLock
 
typedef int CObjectManager::TPriority
 
typedef vector< stringCObjectManager::TRegisteredNames
 
typedef SRegisterLoaderInfo< CDataLoaderCObjectManager::TRegisterLoaderInfo
 
typedef set< TDataSourceLockCObjectManager::TDataSourcesLock
 
typedef CPluginManager< CDataLoaderCObjectManager::TPluginManager
 
typedef set< TDataSourceLockCObjectManager::TSetDefaultSource
 
typedef map< string, CDataLoader * > CObjectManager::TMapNameToLoader
 
typedef map< const CObject *, TDataSourceLockCObjectManager::TMapToSource
 
typedef set< CScope_Impl * > CObjectManager::TSetScope
 
typedef CMutex CObjectManager::TRWLock
 
typedef CMutexGuard CObjectManager::TReadLockGuard
 
typedef CMutexGuard CObjectManager::TWriteLockGuard
 
typedef int CBlobStateException::TBlobState
 
typedef int CBlobStateException::TErrCode
 
typedef CPrefetchTokenOld_Impl::TIds CPrefetchTokenOld::TIds
 
typedef CBioseq_Handle CPrefetchBioseq::TResult
 
typedef CFeat_CI CPrefetchFeat_CI::TResult
 
typedef Handle CPrefetchComplete< Handle >::THandle
 
typedef THandle::TObject CPrefetchComplete< Handle >::TObject
 
typedef CConstRef< TObjectCPrefetchComplete< Handle >::TResult
 
typedef CBioseq_Handle CPrefetchComplete< CBioseq_Handle >::THandle
 
typedef THandle::TObject CPrefetchComplete< CBioseq_Handle >::TObject
 
typedef CConstRef< TObjectCPrefetchComplete< CBioseq_Handle >::TResult
 
typedef Container CStdSeq_idSource< Container >::TContainer
 
typedef TContainer::const_iterator CStdSeq_idSource< Container >::TIterator
 
typedef vector< CSeq_id_HandleCPrefetchBioseqActionSource::TIds
 
typedef vector< CSeq_id_HandleCPrefetchFeat_CIActionSource::TIds
 
typedef EState SPrefetchTypes::EEvent
 
typedef int SPrefetchTypes::TPriority
 
typedef int SPrefetchTypes::TProgress
 
typedef int CScope::TPriority
 priority type and special value for added objects More...
 
typedef vector< CSeq_id_HandleCScope::TIds
 
typedef vector< CBioseq_HandleCScope::TBioseqHandles
 
typedef vector< CTSE_HandleCScope::TCDD_Entries
 Get CDD annotations for all ids. More...
 
typedef CBlobIdKey CScope::TBlobId
 
typedef int CScope::TGetFlags
 
typedef int CScope::TSequenceHash
 Get sequence data hash value Return 0 if sequence is not found or if its hash is not known Note: 0 can be a real hash value, use flags to distinguish these cases. More...
 
typedef vector< CSeq_id_HandleCScope::TSeq_id_Handles
 Bulk retrieval methods Common argument typedef - vector of requested ids. More...
 
typedef vector< TIdsCScope::TBulkIds
 Get all ids of sequences Returns empty ids if the sequence is not found. More...
 
typedef vector< TGiCScope::TGIs
 Get GI of a sequence Returns ZERO_GI for sequence that aren't found or don't have GI. More...
 
typedef vector< stringCScope::TLabels
 Get short descriptions of sequences, usually "accession.version" Returns empty strings for sequences that aren't found. More...
 
typedef vector< TTaxIdCScope::TTaxIds
 Get taxonomy ids of sequences Return -1 for sequences that aren't found Return 0 for sequences that don't have taxonomy id. More...
 
typedef vector< TSeqPosCScope::TSequenceLengths
 Get lengths of sequences Return kInvalidSeqPos for sequences that aren't found. More...
 
typedef vector< CSeq_inst::TMolCScope::TSequenceTypes
 Get molecular types of sequences (protein/dna/rna) Return CSeq_inst::eMol_not_set for sequences that aren't found. More...
 
typedef vector< CBioseq_Handle::TBioseqStateFlagsCScope::TSequenceStates
 Get GenBank states of sequences Return (fState_not_found|fState_no_data) for sequences that aren't found. More...
 
typedef vector< TSequenceHashCScope::TSequenceHashes
 Get data hashes of sequences Return 0 for sequences that aren't found or they don't have hash Note: 0 can be a real hash value, use flags to distinguish these cases. More...
 
typedef vector< CSeq_entry_HandleCScope::TTSE_Handles
 

Enumerations

enum  CAnnotMapperException::EErrCode {
  CAnnotMapperException::eBadLocation , CAnnotMapperException::eUnknownLength , CAnnotMapperException::eBadAlignment , CAnnotMapperException::eBadFeature ,
  CAnnotMapperException::eCanNotMap , CAnnotMapperException::eOtherError
}
 
enum  CSeq_loc_Mapper_Base::EFeatMapDirection { CSeq_loc_Mapper_Base::eLocationToProduct , CSeq_loc_Mapper_Base::eProductToLocation }
 Mapping direction used when initializing the mapper with a feature. More...
 
enum  CSeq_loc_Mapper_Base::EMapOptions {
  CSeq_loc_Mapper_Base::fAlign_Dense_seg_TotalRange = 1 << 0 , CSeq_loc_Mapper_Base::fAlign_Sparse_ToFirst = 0 , CSeq_loc_Mapper_Base::fAlign_Sparse_ToSecond = 1 << 1 , CSeq_loc_Mapper_Base::fMapSingleLevel = 1 << 2 ,
  CSeq_loc_Mapper_Base::fTrimMappedLocation = 1 << 3
}
 Options for interpretations of locations. More...
 
enum  CSeq_loc_Mapper_Base::ESplicedRow { CSeq_loc_Mapper_Base::eSplicedRow_Prod = 0 , CSeq_loc_Mapper_Base::eSplicedRow_Gen = 1 }
 Spliced-seg row indexing constants. More...
 
enum  CSeq_loc_Mapper_Base::FFuzzOption { CSeq_loc_Mapper_Base::fFuzzOption_CStyle = 1 << 0 , CSeq_loc_Mapper_Base::fFuzzOption_RemoveLimTlOrTr = 1 << 1 }
 
enum  CSeq_loc_Mapper_Base::FAnnotMapFlag {
  CSeq_loc_Mapper_Base::fAnnotMap_Location = 1 << 0 , CSeq_loc_Mapper_Base::fAnnotMap_Product = 1 << 1 , CSeq_loc_Mapper_Base::fAnnotMap_Both = fAnnotMap_Location | fAnnotMap_Product , CSeq_loc_Mapper_Base::fAnnotMap_RemoveNonMapping = 1 << 2 ,
  CSeq_loc_Mapper_Base::fAnnotMap_ThrowOnFailure = 1 << 3 , CSeq_loc_Mapper_Base::fAnnotMap_Default = fAnnotMap_Both
}
 Flags defining seq-annot mapping options. More...
 
enum  CSeq_loc_Mapper_Base::EMapResult { CSeq_loc_Mapper_Base::eMapped_None = 0 , CSeq_loc_Mapper_Base::eMapped_Some , CSeq_loc_Mapper_Base::eMapped_All }
 Result of seq-annot mapping. More...
 
enum  CSeq_loc_Mapper_Base::ESeqType { CSeq_loc_Mapper_Base::eSeq_unknown = 0 , CSeq_loc_Mapper_Base::eSeq_nuc = 1 , CSeq_loc_Mapper_Base::eSeq_prot = 3 }
 
enum  CSeq_loc_Mapper_Base::EMergeFlags {
  CSeq_loc_Mapper_Base::eMergeNone , CSeq_loc_Mapper_Base::eMergeAbutting , CSeq_loc_Mapper_Base::eMergeContained , CSeq_loc_Mapper_Base::eMergeBySeg ,
  CSeq_loc_Mapper_Base::eMergeAll
}
 
enum  CSeq_loc_Mapper_Base::EGapFlags { CSeq_loc_Mapper_Base::eGapPreserve , CSeq_loc_Mapper_Base::eGapRemove }
 
enum  CSeq_loc_Mapper_Base::EMiscFlags {
  CSeq_loc_Mapper_Base::fTrimSplicedSegs = 1 << 0 , CSeq_loc_Mapper_Base::fKeepNonmapping = 1 << 1 , CSeq_loc_Mapper_Base::fCheckStrand = 1 << 2 , CSeq_loc_Mapper_Base::fIncludeSrcLocs = 1 << 3 ,
  CSeq_loc_Mapper_Base::fMixedAlignsAsSpliced = 1 << 4 , CSeq_loc_Mapper_Base::fErrorOnPartial = 1 << 5
}
 
enum  CSeq_loc_Mapper_Message::EObjectType {
  CSeq_loc_Mapper_Message::eNot_set , CSeq_loc_Mapper_Message::eSeq_loc , CSeq_loc_Mapper_Message::eSeq_feat , CSeq_loc_Mapper_Message::eSeq_align ,
  CSeq_loc_Mapper_Message::eSeq_graph
}
 
enum  CSeqTableException::EErrCode { CSeqTableException::eColumnNotFound , CSeqTableException::eRowNotFound , CSeqTableException::eIncompatibleValueType , CSeqTableException::eOtherError }
 
enum  SRequestDetails::FAnnotBlobType {
  SRequestDetails::fAnnotBlobNone = 0 , SRequestDetails::fAnnotBlobInternal = 1<<0 , SRequestDetails::fAnnotBlobExternal = 1<<1 , SRequestDetails::fAnnotBlobOrphan = 1<<2 ,
  SRequestDetails::fAnnotBlobAll
}
 
enum  CDataLoader::EChoice {
  CDataLoader::eBlob , CDataLoader::eBioseq , CDataLoader::eCore , CDataLoader::eBioseqCore ,
  CDataLoader::eSequence , CDataLoader::eFeatures , CDataLoader::eGraph , CDataLoader::eAlign ,
  CDataLoader::eAnnot , CDataLoader::eExtFeatures , CDataLoader::eExtGraph , CDataLoader::eExtAlign ,
  CDataLoader::eExtAnnot , CDataLoader::eOrphanAnnot , CDataLoader::eAll
}
 main blob is blob with sequence all other blobs are external and contain external annotations More...
 
enum  CGC_Assembly_Parser::FParserFlags {
  CGC_Assembly_Parser::fIgnoreLocalIds = 1 << 0 , CGC_Assembly_Parser::fIgnoreExternalIds = 1 << 1 , CGC_Assembly_Parser::fIgnoreAnnots = 1 << 2 , CGC_Assembly_Parser::fIgnoreDescr = 1 << 3 ,
  CGC_Assembly_Parser::fSkipDuplicates = 1 << 4 , CGC_Assembly_Parser::fDefault = fIgnoreLocalIds | fIgnoreAnnots | fIgnoreDescr | fSkipDuplicates
}
 Parser options. More...
 
enum  CAssemblyParserException::EErrCode { CAssemblyParserException::eUnsupported , CAssemblyParserException::eOtherError }
 
enum  CObjectManager::EIsDefault { CObjectManager::eDefault , CObjectManager::eNonDefault }
 Flag defining if the data loader is included in the "default" group. More...
 
enum  CObjectManager::EPriority {
  CObjectManager::kPriority_Entry = 9 , CObjectManager::kPriority_Local = 44 , CObjectManager::kPriority_Replace = 88 , CObjectManager::kPriority_Loader = 99 ,
  CObjectManager::kPriority_Extra = 111 , CObjectManager::kPriority_Default = -1 , CObjectManager::kPriority_NotSet = -1
}
 Default data source priority. More...
 
enum  CObjMgrException::EErrCode {
  CObjMgrException::eNotImplemented , CObjMgrException::eRegisterError , CObjMgrException::eFindConflict , CObjMgrException::eFindFailed ,
  CObjMgrException::eAddDataError , CObjMgrException::eModifyDataError , CObjMgrException::eInvalidHandle , CObjMgrException::eLockedData ,
  CObjMgrException::eTransaction , CObjMgrException::eMissingData , CObjMgrException::eOtherError
}
 
enum  CSeqMapException::EErrCode {
  CSeqMapException::eUnimplemented , CSeqMapException::eIteratorTooBig , CSeqMapException::eSegmentTypeError , CSeqMapException::eDataError ,
  CSeqMapException::eOutOfRange , CSeqMapException::eInvalidIndex , CSeqMapException::eNullPointer , CSeqMapException::eSelfReference ,
  CSeqMapException::eFail
}
 
enum  CSeqVectorException::EErrCode { CSeqVectorException::eCodingError , CSeqVectorException::eDataError , CSeqVectorException::eOutOfRange }
 
enum  CAnnotException::EErrCode {
  CAnnotException::eBadLocation , CAnnotException::eFindFailed , CAnnotException::eLimitError , CAnnotException::eIncomatibleType ,
  CAnnotException::eOtherError
}
 
enum  CLoaderException::EErrCode {
  CLoaderException::eNotImplemented , CLoaderException::eNoData , CLoaderException::ePrivateData , CLoaderException::eConnectionFailed ,
  CLoaderException::eCompressionError , CLoaderException::eLoaderFailed , CLoaderException::eNoConnection , CLoaderException::eOtherError ,
  CLoaderException::eRepeatAgain , CLoaderException::eBadConfig , CLoaderException::eNotFound
}
 
enum  CBlobStateException::EErrCode { CBlobStateException::eBlobStateError , CBlobStateException::eLoaderError , CBlobStateException::eOtherError }
 
enum  CObjmgrUtilException::EErrCode {
  CObjmgrUtilException::eNotImplemented , CObjmgrUtilException::eBadSequenceType , CObjmgrUtilException::eBadLocation , CObjmgrUtilException::eNotUnique ,
  CObjmgrUtilException::eUnknownLength , CObjmgrUtilException::eBadFeature , CObjmgrUtilException::eBadResidue , CObjmgrUtilException::eBadAlignment
}
 
enum  CAnnotSearchLimitException::EErrCode { CAnnotSearchLimitException::eTimeLimitExceded = CObjMgrException::eOtherError + 1 , CAnnotSearchLimitException::eSegmentsLimitExceded }
 
enum  CPrefetchTokenOld::ENon_locking_prefetch { CPrefetchTokenOld::eNon_locking_prefetch }
 
enum  SPrefetchTypes::EState {
  SPrefetchTypes::eInvalid , SPrefetchTypes::eQueued , SPrefetchTypes::eStarted , SPrefetchTypes::eAdvanced ,
  SPrefetchTypes::eCompleted , SPrefetchTypes::eCanceled , SPrefetchTypes::eFailed
}
 
enum  CPrefetchFailed::EErrCode { CPrefetchFailed::eFailed }
 
enum  CPrefetchCanceled::EErrCode { CPrefetchCanceled::eCanceled }
 
enum  CScope::EPriority { CScope::kPriority_Default = -1 , CScope::kPriority_NotSet = -1 }
 
enum  CScope::EGetBioseqFlag { CScope::eGetBioseq_Resolved , CScope::eGetBioseq_Loaded , CScope::eGetBioseq_All }
 
enum  CScope::EMissing { CScope::eMissing_Throw , CScope::eMissing_Null , CScope::eMissing_Default = eMissing_Throw }
 GetXxxHandle control values. More...
 
enum  CScope::EExist { CScope::eExist_Throw , CScope::eExist_Get , CScope::eExist_Default = eExist_Throw }
 AddXxx() control values. More...
 
enum  CScope::EActionIfLocked { CScope::eKeepIfLocked , CScope::eThrowIfLocked , CScope::eRemoveIfLocked }
 
enum  CScope::ERemoveDataLoaders { CScope::eRemoveDataLoaders }
 Clear all information in the scope including data loaders. More...
 
enum  CScope::EForceLoad { CScope::eNoForceLoad , CScope::eForceLoad }
 EForceLoad flag instruct scope to ignore already loaded information and always request data loader for data. More...
 
enum  CScope::EGetFlags {
  CScope::fForceLoad = (1 << 0) , CScope::fThrowOnMissingSequence = (1 << 1) , CScope::fThrowOnMissingData = (1 << 2) , CScope::fThrowOnMissing = fThrowOnMissingSequence|fThrowOnMissingData ,
  CScope::fDoNotRecalculate = (1 << 3)
}
 Flags to control behavior of various meta-data getters fForceLoad instructs scope to ignore already loaded information and alway request data loader for data fThrowOnMissing instructs to throw an exeption if the requested data is missing - either sequence id cannot be found in any data loader or the sequence doesn't have the requested meta-data without the flag getter will return special value. More...
 
enum  CScope::EForceLabelLoad { CScope::eNoForceLabelLoad = eNoForceLoad , CScope::eForceLabelLoad = eForceLoad }
 obsolete enum More...
 
enum  CScope::ETSEKind { CScope::eManualTSEs , CScope::eAllTSEs }
 
enum  CSeq_loc_Mapper::ESeqMapDirection { CSeq_loc_Mapper::eSeqMap_Up , CSeq_loc_Mapper::eSeqMap_Down }
 
enum  CSeq_loc_Mapper::EGCAssemblyAlias {
  CSeq_loc_Mapper::eGCA_Genbank , CSeq_loc_Mapper::eGCA_GenbankAcc , CSeq_loc_Mapper::eGCA_Refseq , CSeq_loc_Mapper::eGCA_RefseqAcc ,
  CSeq_loc_Mapper::eGCA_UCSC , CSeq_loc_Mapper::eGCA_Other
}
 Destination of seq-id mapping through a GC-Assembly. More...
 
enum  CSeq_loc_Mapper::EScopeFlag { CSeq_loc_Mapper::eOriginalScope , CSeq_loc_Mapper::eCopyScope }
 Using CScope for virtual bioseqs created from GC-Assemblies. More...
 

Functions

virtual const char * CAnnotMapperException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CAnnotMapperException::NCBI_EXCEPTION_DEFAULT (CAnnotMapperException, CException)
 
 CMappingRange::CMappingRange (CSeq_id_Handle src_id, TSeqPos src_from, TSeqPos src_length, ENa_strand src_strand, CSeq_id_Handle dst_id, TSeqPos dst_from, ENa_strand dst_strand, bool ext_to=false, int frame=0, TSeqPos src_bioseq_len=kInvalidSeqPos, TSeqPos dst_len=kInvalidSeqPos)
 
bool CMappingRange::GoodSrcId (const CSeq_id &id) const
 Check if the id is on the source sequence. More...
 
CRef< CSeq_idCMappingRange::GetDstId (void) const
 
const CSeq_id_HandleCMappingRange::GetDstIdHandle (void) const
 
bool CMappingRange::CanMap (TSeqPos from, TSeqPos to, bool is_set_strand, ENa_strand strand) const
 Check if the interval can be mapped through this mapping range. More...
 
TSeqPos CMappingRange::Map_Pos (TSeqPos pos) const
 Map a single point. More...
 
TRange CMappingRange::Map_Range (TSeqPos from, TSeqPos to, const TRangeFuzz *fuzz=0) const
 Map an interval, set fuzz when the mapping truncates the original range. More...
 
bool CMappingRange::Map_Strand (bool is_set_strand, ENa_strand src, ENa_strand *dst) const
 Map the strand, return true if the destination strand should be set (even if it's eNa_strand_unknown – this may happen if the source strand is set to unknown). More...
 
TRangeFuzz CMappingRange::Map_Fuzz (const TRangeFuzz &fuzz) const
 Map fuzz if one is set in the original location. More...
 
CInt_fuzz::ELim CMappingRange::x_ReverseFuzzLim (CInt_fuzz::ELim lim) const
 
void CMappingRange::x_Map_Fuzz (TFuzz &fuzz) const
 
TSeqPos CMappingRange::GetSrc_from (void) const
 
TSeqPos CMappingRange::GetDst_from (void) const
 
TSeqPos CMappingRange::GetLength (void) const
 
bool CMappingRange::GetReverse (void) const
 
int CMappingRange::GetGroup (void) const
 
void CMappingRange::SetGroup (int grp)
 
 CMappingRanges::CMappingRanges (void)
 
const TIdMapCMappingRanges::GetIdMap () const
 
void CMappingRanges::AddConversion (CRef< CMappingRange > cvt)
 Add new mapping range to the proper place. More...
 
CRef< CMappingRangeCMappingRanges::AddConversion (CSeq_id_Handle src_id, TSeqPos src_from, TSeqPos src_length, ENa_strand src_strand, CSeq_id_Handle dst_id, TSeqPos dst_from, ENa_strand dst_strand, bool ext_to=false, int frame=0, TSeqPos dst_total_len=kInvalidSeqPos, TSeqPos src_bioseq_len=kInvalidSeqPos, TSeqPos dst_len=kInvalidSeqPos)
 
TRangeIterator CMappingRanges::BeginMappingRanges (CSeq_id_Handle id, TSeqPos from, TSeqPos to) const
 Get mapping ranges iterator for the given seq-id and range. More...
 
void CMappingRanges::SetReverseSrc (bool value=true)
 
bool CMappingRanges::GetReverseSrc (void) const
 
void CMappingRanges::SetReverseDst (bool value=true)
 
bool CMappingRanges::GetReverseDst (void) const
 
 CGraphRanges::CGraphRanges (void)
 
TSeqPos CGraphRanges::GetOffset (void) const
 
void CGraphRanges::SetOffset (TSeqPos offset)
 
void CGraphRanges::IncOffset (TSeqPos inc)
 
const TGraphRangesCGraphRanges::GetRanges (void) const
 
void CGraphRanges::AddRange (const TRange &rg)
 
const TRangeCGraphRanges::GetTotalRange (void) const
 
 CSeq_loc_Mapper_Options::CSeq_loc_Mapper_Options (void)
 
 CSeq_loc_Mapper_Options::CSeq_loc_Mapper_Options (IMapper_Sequence_Info *seq_info, TMapOptions opts=0)
 
 CSeq_loc_Mapper_Options::CSeq_loc_Mapper_Options (TMapOptions opts)
 
IMapper_Sequence_InfoCSeq_loc_Mapper_Options::GetMapperSequenceInfo (void) const
 Sequence type, length etc. More...
 
CSeq_loc_Mapper_OptionsCSeq_loc_Mapper_Options::SetMapperSequenceInfo (IMapper_Sequence_Info *seq_info)
 
bool CSeq_loc_Mapper_Options::GetAlign_Dense_seg_TotalRange (void) const
 Dense-seg mapping option. More...
 
CSeq_loc_Mapper_OptionsCSeq_loc_Mapper_Options::SetAlign_Dense_seg_TotalRange (bool value=true)
 
bool CSeq_loc_Mapper_Options::GetAlign_Sparse_ToFirst (void) const
 Mapping direction when mapping through a sparse-seg. More...
 
bool CSeq_loc_Mapper_Options::GetAlign_Sparse_ToSecond (void) const
 
CSeq_loc_Mapper_OptionsCSeq_loc_Mapper_Options::SetAlign_Sparse_ToFirst (bool value=true)
 
CSeq_loc_Mapper_OptionsCSeq_loc_Mapper_Options::SetAlign_Sparse_ToSecond (bool value=true)
 
bool CSeq_loc_Mapper_Options::GetMapSingleLevel (void) const
 Mapping depth when using a seq-map, a bioseq or a GC-assembly. More...
 
CSeq_loc_Mapper_OptionsCSeq_loc_Mapper_Options::SetMapSingleLevel (bool value=true)
 
bool CSeq_loc_Mapper_Options::GetTrimMappedLocation (void) const
 Mapped location trimming at sequence end. More...
 
CSeq_loc_Mapper_OptionsCSeq_loc_Mapper_Options::SetTrimMappedLocation (bool value=true)
 
IMapper_Sequence_InfoCSeq_loc_Mapper_Options::GetSeqInfo (void) const
 CSeq_loc_Mapper_Options –. More...
 
bool CSeq_loc_Mapper_Options::x_IsSetOption (int opt) const
 
void CSeq_loc_Mapper_Options::x_SetOption (int opt, bool enable)
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (CMappingRanges *mapping_ranges, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through a pre-filled CMappipngRanges. More...
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (const CSeq_feat &map_feat, EFeatMapDirection dir, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through a feature, both location and product must be set. More...
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (const CSeq_loc &source, const CSeq_loc &target, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping between two seq_locs. More...
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (const CSeq_align &map_align, const CSeq_id &to_id, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through an alignment. More...
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (const CSeq_id &from_id, const CSeq_id &to_id, const CSeq_align &map_align, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through an alignment using specific source and target ids. More...
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (const CSeq_align &map_align, const CSeq_id &to_id, TMapOptions opts, IMapper_Sequence_Info *seq_info)
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (const CSeq_align &map_align, size_t to_row, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Sparse alignments require special row indexing since each row contains two seq-ids. More...
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (size_t from_row, size_t to_row, const CSeq_align &map_align, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through an alignment using specific source and target row numbers. More...
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (const CSeq_align &map_align, size_t to_row, TMapOptions opts, IMapper_Sequence_Info *seq_info)
 
 CSeq_loc_Mapper_Base::~CSeq_loc_Mapper_Base (void)
 
void CSeq_loc_Mapper_Base::SetFuzzOption (TFuzzOption newOption)
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetMergeNone (void)
 Intervals' merging mode MergeNone and MergeAbutting do not change the order of ranges in the destination seq-loc. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetMergeAbutting (void)
 Merge only abutting intervals, keep overlapping. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetMergeBySeg (void)
 Merge only intervals from the same group. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetMergeContained (void)
 Merge intervals only if one is completely covered by another. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetMergeAll (void)
 Merge any abutting or overlapping intervals. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetGapPreserve (void)
 Whether to preserve or remove NULL sub-locations (usually indicating gaps) from the result. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetGapRemove (void)
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetTrimSplicedSeg (bool trim)
 For mapping spliced-segs only: preserve or trim starting/ending indels. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::KeepNonmappingRanges (void)
 Keep ranges which can not be mapped. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::TruncateNonmappingRanges (void)
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetCheckStrand (bool value=true)
 Check strands before mapping a range. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::MixedAlignsAsSpliced (bool value=true)
 When set to 'true' if mapped alignment has exactly one genomic and one protein row, convert it to spliced-seg. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::IncludeSourceLocs (bool value=true)
 Include source ranges in the mapped location. More...
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::SetErrorOnPartial (bool value=true)
 Report source range trimming as an error. More...
 
CRef< CSeq_locCSeq_loc_Mapper_Base::Map (const CSeq_loc &src_loc)
 Map seq-loc. More...
 
CRef< CSeq_locCSeq_loc_Mapper_Base::MapTotalRange (const CSeq_loc &seq_loc)
 Take the total range from the location and run it through the mapper. More...
 
CRef< CSeq_alignCSeq_loc_Mapper_Base::Map (const CSeq_align &src_align)
 Map the whole alignment. More...
 
CRef< CSeq_alignCSeq_loc_Mapper_Base::Map (const CSeq_align &src_align, size_t row)
 Map a single row of the alignment. More...
 
CRef< CSeq_graphCSeq_loc_Mapper_Base::Map (const CSeq_graph &src_graph)
 Map seq-graph. More...
 
EMapResult CSeq_loc_Mapper_Base::Map (CSeq_annot &annot, TAnnotMapFlags flags=fAnnotMap_Default)
 Map each object from the Seq-annot and replace the original with the mapped one. More...
 
bool CSeq_loc_Mapper_Base::LastIsPartial (void)
 Check if the last mapping resulted in partial location (not all ranges from the original location could be mapped to the target). More...
 
const CSeq_id_HandleCSeq_loc_Mapper_Base::CollectSynonyms (const CSeq_id_Handle &id) const
 
ESeqType CSeq_loc_Mapper_Base::GetSeqType (const CSeq_id_Handle &idh) const
 
TSeqPos CSeq_loc_Mapper_Base::GetSequenceLength (const CSeq_id &id)
 
virtual CSeq_align_Mapper_BaseCSeq_loc_Mapper_Base::InitAlignMapper (const CSeq_align &src_align)
 
void CSeq_loc_Mapper_Base::x_InitializeFeat (const CSeq_feat &map_feat, EFeatMapDirection dir)
 
void CSeq_loc_Mapper_Base::x_InitializeLocs (const CSeq_loc &source, const CSeq_loc &target, int src_frame=0, int dst_frame=0)
 
void CSeq_loc_Mapper_Base::x_InitializeAlign (const CSeq_align &map_align, const CSeq_id &to_id, const CSeq_id *from_id=nullptr)
 
void CSeq_loc_Mapper_Base::x_InitializeAlign (const CSeq_align &map_align, const TSynonyms &to_ids, const TSynonyms *from_ids=nullptr)
 
void CSeq_loc_Mapper_Base::x_InitializeAlign (const CSeq_align &map_align, size_t to_row, size_t from_row=size_t(-1))
 
void CSeq_loc_Mapper_Base::x_PreserveDestinationLocs (void)
 
void CSeq_loc_Mapper_Base::x_NextMappingRange (const CSeq_id &src_id, TSeqPos &src_start, TSeqPos &src_len, ENa_strand src_strand, const CSeq_id &dst_id, TSeqPos &dst_start, TSeqPos &dst_len, ENa_strand dst_strand, const CInt_fuzz *fuzz_from=0, const CInt_fuzz *fuzz_to=0, int frame=0, TSeqPos src_bioseq_len=kInvalidSeqPos)
 
void CSeq_loc_Mapper_Base::x_AddConversion (const CSeq_id &src_id, TSeqPos src_start, ENa_strand src_strand, const CSeq_id &dst_id, TSeqPos dst_start, ENa_strand dst_strand, TSeqPos length, bool ext_right, int frame, TSeqPos src_bioseq_len, TSeqPos dst_length)
 
void CSeq_loc_Mapper_Base::x_MapSeq_loc (const CSeq_loc &src_loc)
 
void CSeq_loc_Mapper_Base::x_PushRangesToDstMix (void)
 
 CSeq_loc_Mapper_Base::SMappedRange::SMappedRange (void)
 
 CSeq_loc_Mapper_Base::SMappedRange::SMappedRange (const TRange &rg, const TRangeFuzz &fz, int grp=0)
 
bool CSeq_loc_Mapper_Base::SMappedRange::operator< (const SMappedRange &rg) const
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (const CSeq_loc_Mapper_Base &)
 
CSeq_loc_Mapper_BaseCSeq_loc_Mapper_Base::operator= (const CSeq_loc_Mapper_Base &)
 
bool CSeq_loc_Mapper_Base::x_CheckSeqTypes (const CSeq_loc &loc, ESeqType &seqtype, TSeqPos &len)
 
ESeqType CSeq_loc_Mapper_Base::x_ForceSeqTypes (const CSeq_loc &loc) const
 
void CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt (const CSeq_id_Handle &idh)
 
TSeqPos CSeq_loc_Mapper_Base::x_GetRangeLength (const CSeq_loc_CI &it)
 
void CSeq_loc_Mapper_Base::x_InitAlign (const CDense_diag &diag, size_t to_row, size_t from_row)
 
void CSeq_loc_Mapper_Base::x_InitAlign (const CDense_seg &denseg, size_t to_row, size_t from_row)
 
void CSeq_loc_Mapper_Base::x_InitAlign (const CStd_seg &sseg, size_t to_row)
 
void CSeq_loc_Mapper_Base::x_InitAlign (const CPacked_seg &pseg, size_t to_row, size_t from_row)
 
void CSeq_loc_Mapper_Base::x_InitSpliced (const CSpliced_seg &spliced, const TSynonyms &to_ids)
 
void CSeq_loc_Mapper_Base::x_InitSpliced (const CSpliced_seg &spliced, ESplicedRow to_row)
 
void CSeq_loc_Mapper_Base::x_InitSparse (const CSparse_seg &sparse, size_t to_row)
 
void CSeq_loc_Mapper_Base::x_IterateExonParts (const CSpliced_exon::TParts &parts, ESplicedRow to_row, const CSeq_id &gen_id, TSeqPos &gen_start, TSeqPos &gen_len, ENa_strand gen_strand, const CSeq_id &prod_id, TSeqPos &prod_start, TSeqPos &prod_len, ENa_strand prod_strand)
 
void CSeq_loc_Mapper_Base::x_AddExonPartsMapping (TSeqPos &mapping_len, ESplicedRow to_row, const CSeq_id &gen_id, TSeqPos &gen_start, TSeqPos &gen_len, ENa_strand gen_strand, const CSeq_id &prod_id, TSeqPos &prod_start, TSeqPos &prod_len, ENa_strand prod_strand)
 
static TSeqPos CSeq_loc_Mapper_Base::sx_GetExonPartLength (const CSpliced_exon_chunk &part)
 
bool CSeq_loc_Mapper_Base::x_MapNextRange (const TRange &src_rg, bool is_set_strand, ENa_strand src_strand, const TRangeFuzz &src_fuzz, TSortedMappings &mappings, size_t cvt_idx, TSeqPos *last_src_to)
 
bool CSeq_loc_Mapper_Base::x_MapInterval (const CSeq_id &src_id, TRange src_rg, bool is_set_strand, ENa_strand src_strand, TRangeFuzz orig_fuzz)
 
void CSeq_loc_Mapper_Base::x_SetLastTruncated (void)
 
void CSeq_loc_Mapper_Base::x_PushLocToDstMix (CRef< CSeq_loc > loc)
 
void CSeq_loc_Mapper_Base::x_PushNullLoc (void)
 
CRef< CSeq_alignCSeq_loc_Mapper_Base::x_MapSeq_align (const CSeq_align &src_align, size_t *row)
 
TMappedRangesCSeq_loc_Mapper_Base::x_GetMappedRanges (const CSeq_id_Handle &id, size_t strand_idx) const
 
void CSeq_loc_Mapper_Base::x_PushMappedRange (const CSeq_id_Handle &id, size_t strand_idx, const TRange &range, const TRangeFuzz &fuzz, bool push_reverse, int group)
 
void CSeq_loc_Mapper_Base::x_PushSourceRange (const CSeq_id_Handle &idh, size_t src_strand, size_t dst_strand, const TRange &range, bool push_reverse)
 
CRef< CSeq_locCSeq_loc_Mapper_Base::x_RangeToSeq_loc (const CSeq_id_Handle &idh, TSeqPos from, TSeqPos to, size_t strand_idx, TRangeFuzz rg_fuzz)
 
CRef< CSeq_locCSeq_loc_Mapper_Base::x_GetMappedSeq_loc (void)
 
void CSeq_loc_Mapper_Base::x_StripExtraneousFuzz (CRef< CSeq_loc > &loc) const
 
CConstRef< CSeq_locCSeq_loc_Mapper_Base::x_FixNonsenseFuzz (CConstRef< CSeq_loc > loc_piece) const
 
void CSeq_loc_Mapper_Base::x_OptimizeSeq_loc (CRef< CSeq_loc > &loc) const
 
bool CSeq_loc_Mapper_Base::x_ReverseRangeOrder (int str) const
 
void CSeq_loc_Mapper_Base::x_Map_PackedInt_Element (const CSeq_interval &si)
 
void CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element (const CPacked_seqpnt &pp, TSeqPos p)
 
const CSeq_id_HandleCSeq_loc_Mapper_Base::x_GetPrimaryId (const CSeq_id_Handle &synonym) const
 
bool CSeq_loc_Mapper_Base::x_IsSynonym (const CSeq_id &id, const TSynonyms &synonyms) const
 
bool CSeq_loc_Mapper_Base::x_IsSetMiscFlag (EMiscFlags flag) const
 
void CSeq_loc_Mapper_Base::x_SetMiscFlag (EMiscFlags flag, bool value)
 
 CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base (CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 
ESeqType CSeq_loc_Mapper_Base::GetSeqTypeById (const CSeq_id_Handle &idh) const
 Methods for getting sequence types, use cached types (m_SeqTypes) if possible. More...
 
ESeqType CSeq_loc_Mapper_Base::GetSeqTypeById (const CSeq_id &id) const
 
void CSeq_loc_Mapper_Base::SetSeqTypeById (const CSeq_id_Handle &idh, ESeqType seqtype) const
 Methods for setting sequence types. More...
 
void CSeq_loc_Mapper_Base::SetSeqTypeById (const CSeq_id &id, ESeqType seqtype) const
 
int CSeq_loc_Mapper_Base::GetWidthById (const CSeq_id_Handle &idh) const
 Get sequence width. More...
 
int CSeq_loc_Mapper_Base::GetWidthById (const CSeq_id &id) const
 
const CMappingRangesCSeq_loc_Mapper_Base::GetMappingRanges (void) const
 Get mapping ranges. More...
 
void CSeq_loc_Mapper_Base::CollectSynonyms (const CSeq_id_Handle &id, TSynonyms &synonyms) const
 NOTE: In most cases CollectSynonyms(const CSeq_id_Handle& id) should be used instead, since it takes care of synonym storage and mapping. More...
 
static bool CSeq_loc_Mapper_Base::GetNonMappingAsNull (void)
 
virtual TSeqType IMapper_Sequence_Info::GetSequenceType (const CSeq_id_Handle &idh)=0
 Get information about sequence type (nuc or prot). More...
 
virtual TSeqPos IMapper_Sequence_Info::GetSequenceLength (const CSeq_id_Handle &idh)=0
 Get sequence length or kInvalidSeqPos. More...
 
virtual void IMapper_Sequence_Info::CollectSynonyms (const CSeq_id_Handle &id, TSynonyms &synonyms)=0
 Collect all synonyms for the id including the id itself. More...
 
 CSeq_loc_Mapper_Message::CSeq_loc_Mapper_Message (const string &msg, EDiagSev sev, int err_code=0, int sub_code=0)
 
virtual CSeq_loc_Mapper_Message::~CSeq_loc_Mapper_Message (void)
 
virtual CSeq_loc_Mapper_MessageCSeq_loc_Mapper_Message::Clone (void) const
 Create a copy of the message. More...
 
virtual void CSeq_loc_Mapper_Message::Write (CNcbiOstream &out) const
 Print the message and any additional information to the stream. More...
 
EObjectType CSeq_loc_Mapper_Message::Which (void) const
 Check type of the object stored in the message. More...
 
void CSeq_loc_Mapper_Message::SetLoc (const CSeq_loc &loc)
 Set seq-loc object (copy into the message). More...
 
const CSeq_locCSeq_loc_Mapper_Message::GetLoc (void) const
 Get seq-loc object or null. More...
 
void CSeq_loc_Mapper_Message::SetFeat (const CSeq_feat &feat)
 Set seq-feat object (copy into the message). More...
 
const CSeq_featCSeq_loc_Mapper_Message::GetFeat (void) const
 Get seq-feat object or null. More...
 
void CSeq_loc_Mapper_Message::SetAlign (const CSeq_align &align)
 Set seq-align object (copy into the message). More...
 
const CSeq_alignCSeq_loc_Mapper_Message::GetAlign (void) const
 Get seq-align object or null. More...
 
void CSeq_loc_Mapper_Message::SetGraph (const CSeq_graph &graph)
 Set seq-graph object (copy into the message). More...
 
const CSeq_graphCSeq_loc_Mapper_Message::GetGraph (void) const
 Get seq-graph object or null. More...
 
void CSeq_loc_Mapper_Message::ResetObject (void)
 Set the stored object to null. More...
 
bool CMappingRangeRef_Less::operator() (const CRef< CMappingRange > &x, const CRef< CMappingRange > &y) const
 
bool CMappingRangeRef_LessRev::operator() (const CRef< CMappingRange > &x, const CRef< CMappingRange > &y) const
 
virtual const char * CSeqTableException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CSeqTableException::NCBI_EXCEPTION_DEFAULT (CSeqTableException, CException)
 
string PConvertToString< int >::operator() (int v) const
 
string PConvertToString< const void * >::operator() (const void *v) const
 
const stringPConvertToString< string >::operator() (const string &v) const
 
string PConvertToString< CSeq_id_Handle >::operator() (const CSeq_id_Handle &v) const
 
virtual CBlobId::~CBlobId (void)
 
virtual string CBlobId::ToString (void) const =0
 Get string representation of blob id. More...
 
virtual bool CBlobId::operator< (const CBlobId &id) const =0
 
virtual bool CBlobId::operator== (const CBlobId &id) const
 
bool CBlobId::LessByTypeId (const CBlobId &id2) const
 
 CBlobIdFor< Value, Converter >::CBlobIdFor (const value_type &v)
 
const value_typeCBlobIdFor< Value, Converter >::GetValue (void) const
 
string CBlobIdFor< Value, Converter >::ToString (void) const
 Get string representation of blob id. More...
 
bool CBlobIdFor< Value, Converter >::operator== (const CBlobId &id_ref) const
 
bool CBlobIdFor< Value, Converter >::operator< (const CBlobId &id_ref) const
 
 CBlobIdKey::CBlobIdKey (const CBlobId *id=0)
 
 CBlobIdKey::DECLARE_OPERATOR_BOOL_REF (m_Id)
 
const CBlobIdCBlobIdKey::operator* (void) const
 
const CBlobIdCBlobIdKey::operator-> (void) const
 
string CBlobIdKey::ToString (void) const
 
bool CBlobIdKey::operator< (const CBlobIdKey &id) const
 
bool CBlobIdKey::operator== (const CBlobIdKey &id) const
 
bool CBlobIdKey::operator!= (const CBlobIdKey &id) const
 
CNcbiOstreamoperator<< (CNcbiOstream &out, const CBlobId &id)
 
CNcbiOstreamoperator<< (CNcbiOstream &out, const CBlobIdKey &id)
 
 SRequestDetails::SRequestDetails (void)
 
virtual CDataLoaderCLoaderMaker_Base::CreateLoader (void) const =0
 
virtual CLoaderMaker_Base::~CLoaderMaker_Base (void)
 
 CSimpleLoaderMaker< TDataLoader >::CSimpleLoaderMaker (void)
 
virtual CSimpleLoaderMaker< TDataLoader >::~CSimpleLoaderMaker (void)
 
virtual CDataLoaderCSimpleLoaderMaker< TDataLoader >::CreateLoader (void) const
 
TRegisterInfo CSimpleLoaderMaker< TDataLoader >::GetRegisterInfo (void)
 
 CParamLoaderMaker< TDataLoader, TParam >::CParamLoaderMaker (TParam param)
 
virtual CParamLoaderMaker< TDataLoader, TParam >::~CParamLoaderMaker (void)
 
virtual CDataLoaderCParamLoaderMaker< TDataLoader, TParam >::CreateLoader (void) const
 
TRegisterInfo CParamLoaderMaker< TDataLoader, TParam >::GetRegisterInfo (void)
 
 CDataLoader::CDataLoader (void)
 
 CDataLoader::CDataLoader (const string &loader_name)
 
virtual CDataLoader::~CDataLoader (void)
 
static bool CDataLoader::IsRequestedAnyNA (const SAnnotSelector *sel)
 
static bool CDataLoader::IsRequestedNA (const string &na, const SAnnotSelector *sel)
 
static bool CDataLoader::IsProcessedNA (const string &na, const TProcessedNAs *processed_nas)
 
static void CDataLoader::SetProcessedNA (const string &na, TProcessedNAs *processed_nas)
 
virtual TTSE_LockSet CDataLoader::GetRecords (const CSeq_id_Handle &idh, EChoice choice)
 Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call will be added to the tse_set. More...
 
TTSE_LockSet CDataLoader::GetRecordsNoBlobState (const CSeq_id_Handle &idh, EChoice choice)
 The same as GetRecords() but always returns empty TSE lock set instead of throwing CBlobStateException. More...
 
virtual TTSE_LockSet CDataLoader::GetDetailedRecords (const CSeq_id_Handle &idh, const SRequestDetails &details)
 Request from a datasource using handles and ranges instead of seq-loc The TSEs loaded in this call will be added to the tse_set. More...
 
virtual TTSE_LockSet CDataLoader::GetExternalRecords (const CBioseq_Info &bioseq)
 Request from a datasource set of blobs with external annotations. More...
 
virtual TTSE_LockSet CDataLoader::GetOrphanAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)
 old Get*AnnotRecords() methods More...
 
virtual TTSE_LockSet CDataLoader::GetExternalAnnotRecords (const CSeq_id_Handle &idh, const SAnnotSelector *sel)
 
virtual TTSE_LockSet CDataLoader::GetExternalAnnotRecords (const CBioseq_Info &bioseq, const SAnnotSelector *sel)
 
virtual TTSE_LockSet CDataLoader::GetOrphanAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
 new Get*AnnotRecords() methods More...
 
virtual TTSE_LockSet CDataLoader::GetOrphanAnnotRecordsNA (const TSeq_idSet &ids, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
 
virtual TTSE_LockSet CDataLoader::GetExternalAnnotRecordsNA (const CSeq_id_Handle &idh, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
 
virtual TTSE_LockSet CDataLoader::GetExternalAnnotRecordsNA (const CBioseq_Info &bioseq, const SAnnotSelector *sel, TProcessedNAs *processed_nas)
 
virtual void CDataLoader::GetIds (const CSeq_id_Handle &idh, TIds &ids)
 Request for a list of all Seq-ids of a sequence. More...
 
bool CDataLoader::SequenceExists (const CSeq_id_Handle &idh)
 helper function to check if sequence exists, uses GetIds() More...
 
virtual CSeq_id_Handle CDataLoader::GetAccVer (const CSeq_id_Handle &idh)
 Request for a accession.version Seq-id of a sequence. More...
 
 CDataLoader::SAccVerFound::SAccVerFound ()
 
virtual SAccVerFound CDataLoader::GetAccVerFound (const CSeq_id_Handle &idh)
 
virtual TGi CDataLoader::GetGi (const CSeq_id_Handle &idh)
 Request for a gi of a sequence. More...
 
 CDataLoader::SGiFound::SGiFound ()
 
virtual SGiFound CDataLoader::GetGiFound (const CSeq_id_Handle &idh)
 
virtual string CDataLoader::GetLabel (const CSeq_id_Handle &idh)
 Request for a label string of a sequence. More...
 
virtual TTaxId CDataLoader::GetTaxId (const CSeq_id_Handle &idh)
 Request for a taxonomy id of a sequence. More...
 
virtual TSeqPos CDataLoader::GetSequenceLength (const CSeq_id_Handle &idh)
 Request for a length of a sequence. More...
 
virtual CSeq_inst::TMol CDataLoader::GetSequenceType (const CSeq_id_Handle &idh)
 Request for a type of a sequence Returns CSeq_inst::eMol_not_set if sequence is not known. More...
 
 CDataLoader::STypeFound::STypeFound ()
 
virtual STypeFound CDataLoader::GetSequenceTypeFound (const CSeq_id_Handle &idh)
 
virtual int CDataLoader::GetSequenceState (const CSeq_id_Handle &idh)
 Request for a state of a sequence. More...
 
virtual int CDataLoader::GetSequenceHash (const CSeq_id_Handle &idh)
 Request for a sequence hash. More...
 
 CDataLoader::SHashFound::SHashFound ()
 
virtual SHashFound CDataLoader::GetSequenceHashFound (const CSeq_id_Handle &idh)
 
virtual void CDataLoader::GetBulkIds (const TIds &ids, TLoaded &loaded, TBulkIds &ret)
 Bulk request for all Seq-ids of a set of sequences. More...
 
virtual void CDataLoader::GetAccVers (const TIds &ids, TLoaded &loaded, TIds &ret)
 Bulk request for accession.version Seq-ids of a set of sequences. More...
 
virtual void CDataLoader::GetGis (const TIds &ids, TLoaded &loaded, TGis &ret)
 Bulk request for gis of a set of sequences. More...
 
virtual void CDataLoader::GetLabels (const TIds &ids, TLoaded &loaded, TLabels &ret)
 Bulk request for label strings of a set of sequences. More...
 
virtual void CDataLoader::GetTaxIds (const TIds &ids, TLoaded &loaded, TTaxIds &ret)
 Bulk request for taxonomy ids of a set of sequences. More...
 
virtual void CDataLoader::GetSequenceLengths (const TIds &ids, TLoaded &loaded, TSequenceLengths &ret)
 Bulk request for lengths of a set of sequences. More...
 
virtual void CDataLoader::GetSequenceTypes (const TIds &ids, TLoaded &loaded, TSequenceTypes &ret)
 Bulk request for types of a set of sequences. More...
 
virtual void CDataLoader::GetSequenceStates (const TIds &ids, TLoaded &loaded, TSequenceStates &ret)
 Bulk request for states of a set of sequences. More...
 
virtual void CDataLoader::GetSequenceHashes (const TIds &ids, TLoaded &loaded, TSequenceHashes &ret, THashKnown &known)
 Bulk request for hashes of a set of sequences. More...
 
virtual void CDataLoader::GetCDDAnnots (const TSeqIdSets &id_sets, TLoaded &loaded, TCDD_Locks &ret)
 
virtual void CDataLoader::GetBlobs (TTSE_LockSets &tse_sets)
 
virtual TBlobId CDataLoader::GetBlobId (const CSeq_id_Handle &idh)
 
virtual TBlobId CDataLoader::GetBlobIdFromString (const string &str) const
 
virtual TBlobVersion CDataLoader::GetBlobVersion (const TBlobId &id)
 
virtual bool CDataLoader::CanGetBlobById (void) const
 
virtual TTSE_Lock CDataLoader::GetBlobById (const TBlobId &blob_id)
 
virtual SRequestDetails CDataLoader::ChoiceToDetails (EChoice choice) const
 
virtual EChoice CDataLoader::DetailsToChoice (const SRequestDetails::TAnnotSet &annots) const
 
virtual EChoice CDataLoader::DetailsToChoice (const SRequestDetails &details) const
 
virtual void CDataLoader::GetChunk (TChunk chunk_info)
 
virtual void CDataLoader::GetChunks (const TChunkSet &chunks)
 
virtual void CDataLoader::DropTSE (CRef< CTSE_Info > tse_info)
 
void CDataLoader::SetTargetDataSource (CDataSource &data_source)
 Specify datasource to send loaded data to. More...
 
string CDataLoader::GetName (void) const
 
virtual TTSE_Lock CDataLoader::ResolveConflict (const CSeq_id_Handle &id, const TTSE_LockSet &tse_set)
 Resolve TSE conflict *select the best TSE from the set of dead TSEs. More...
 
virtual void CDataLoader::GC (void)
 
virtual TEditSaver CDataLoader::GetEditSaver () const
 
virtual CObjectManager::TPriority CDataLoader::GetDefaultPriority (void) const
 
virtual Uint4 CDataLoader::EstimateLoadBytes (const CTSE_Chunk_Info &chunk) const
 
virtual double CDataLoader::EstimateLoadSeconds (const CTSE_Chunk_Info &chunk, Uint4 bytes) const
 
virtual unsigned CDataLoader::GetDefaultBlobCacheSizeLimit () const
 
virtual bool CDataLoader::GetTrackSplitSeq () const
 
static void CDataLoader::RegisterInObjectManager (CObjectManager &om, CLoaderMaker_Base &loader_maker, CObjectManager::EIsDefault is_default, CObjectManager::TPriority priority)
 Register the loader only if the name is not yet registered in the object manager. More...
 
void CDataLoader::SetName (const string &loader_name)
 
CDataSourceCDataLoader::GetDataSource (void) const
 
 CDataLoader::CDataLoader (const CDataLoader &)
 
CDataLoaderCDataLoader::operator= (const CDataLoader &)
 
 NCBI_DECLARE_INTERFACE_VERSION (objects::CDataLoader, "xloader", 9, 0, 0)
 
CPluginManager_DllResolverCDllResolver_Getter< objects::CDataLoader >::operator() (void)
 
 CGC_Assembly_Parser::CGC_Assembly_Parser (const CGC_Assembly &assembly, TParserFlags flags=fDefault)
 Parse the assembly, convert it to seq-entry, collect additional information (top-level sequences etc). More...
 
virtual CGC_Assembly_Parser::~CGC_Assembly_Parser (void)
 
CRef< CSeq_entryCGC_Assembly_Parser::GetTSE (void) const
 Create seq-entry with all parsed sequences, annotations etc. More...
 
const TSeqIdsCGC_Assembly_Parser::GetTopLevelSequences (void) const
 Get seq-ids for all top-level sequences in the assembly. More...
 
void CGC_Assembly_Parser::x_ParseGCAssembly (const CGC_Assembly &gc_assembly, CRef< CSeq_entry > parent_entry)
 
void CGC_Assembly_Parser::x_ParseGCSequence (const CGC_Sequence &gc_seq, const CGC_Sequence *parent_seq, CRef< CSeq_entry > parent_entry, CRef< CSeq_id > override_id)
 
void CGC_Assembly_Parser::x_AddBioseq (CRef< CSeq_entry > parent_entry, const TSeqIds &synonyms, const CGC_Sequence &gc_seq)
 
void CGC_Assembly_Parser::x_InitSeq_entry (CRef< CSeq_entry > entry, CRef< CSeq_entry > parent)
 
void CGC_Assembly_Parser::x_CopyData (const CGC_AssemblyDesc &assm_desc, CSeq_entry &entry)
 
virtual const char * CAssemblyParserException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CAssemblyParserException::NCBI_EXCEPTION_DEFAULT (CAssemblyParserException, CException)
 
 CPrefetchManager_Impl::CPrefetchManager_Impl (unsigned max_threads, CThread::TRunMode threads_mode)
 
 CPrefetchManager_Impl::~CPrefetchManager_Impl (void)
 
CRef< CPrefetchRequestCPrefetchManager_Impl::AddAction (TPriority priority, IPrefetchAction *action, IPrefetchListener *listener)
 
 CPrefetchManager_Impl::CPrefetchManager_Impl (const CPrefetchManager_Impl &)=delete
 
void CPrefetchManager_Impl::operator= (const CPrefetchManager_Impl &)=delete
 
TLoader * SRegisterLoaderInfo< TLoader >::GetLoader (void) const
 Get pointer to the loader. More...
 
bool SRegisterLoaderInfo< TLoader >::IsCreated (void) const
 Return true if the loader was just created, false if already registered or if the operation failed. More...
 
 SRegisterLoaderInfo< TLoader >::SRegisterLoaderInfo ()
 
void SRegisterLoaderInfo< TLoader >::Set (CDataLoader *loader, bool created)
 
static CRef< CObjectManagerCObjectManager::GetInstance (void)
 Return the existing object manager or create one. More...
 
virtual CObjectManager::~CObjectManager (void)
 
CDataLoaderCObjectManager::RegisterDataLoader (TPluginManagerParamTree *params=0, const string &driver_name=kEmptyStr)
 Add data loader using plugin manager. More...
 
CDataLoaderCObjectManager::FindDataLoader (const string &loader_name) const
 Try to find a registered data loader by name. More...
 
void CObjectManager::GetRegisteredNames (TRegisteredNames &names)
 Get names of all registered data loaders. More...
 
void CObjectManager::SetLoaderOptions (const string &loader_name, EIsDefault is_default, TPriority priority=kPriority_Default)
 Update loader's default-ness and priority. More...
 
bool CObjectManager::RevokeDataLoader (CDataLoader &loader)
 Revoke previously registered data loader. More...
 
bool CObjectManager::RevokeDataLoader (const string &loader_name)
 
void CObjectManager::RevokeAllDataLoaders (void)
 Revoke all registered data loaders, even if they were still used. More...
 
virtual CObjectManager::IDataLoaderFilter::~IDataLoaderFilter ()
 
virtual bool CObjectManager::IDataLoaderFilter::IsDataLoaderMatches (CDataLoader &loader) const =0
 
void CObjectManager::RevokeDataLoaders (IDataLoaderFilter &filter)
 Revoke data loaders by filter, even if they were still used. More...
 
void CObjectManager::ReleaseDataSource (TDataSourceLock &data_source)
 
void CObjectManager::RegisterDataLoader (CLoaderMaker_Base &loader_maker, EIsDefault is_default=eNonDefault, TPriority priority=kPriority_Default)
 
void CObjectManager::RegisterScope (CScope_Impl &scope)
 
void CObjectManager::RevokeScope (CScope_Impl &scope)
 
TDataSourceLock CObjectManager::AcquireDataLoader (CDataLoader &loader)
 
TDataSourceLock CObjectManager::AcquireDataLoader (const string &loader_name)
 
TDataSourceLock CObjectManager::AcquireSharedSeq_entry (const CSeq_entry &object)
 
TDataSourceLock CObjectManager::AcquireSharedBioseq (const CBioseq &object)
 
TDataSourceLock CObjectManager::AcquireSharedSeq_annot (const CSeq_annot &object)
 
void CObjectManager::AcquireDefaultDataSources (TDataSourcesLock &sources)
 
 CObjectManager::CObjectManager (void)
 
TDataSourceLock CObjectManager::x_RegisterLoader (CDataLoader &loader, TPriority priority, EIsDefault is_default=eNonDefault, bool no_warning=false)
 
CDataLoaderCObjectManager::x_GetLoaderByName (const string &loader_name) const
 
TDataSourceLock CObjectManager::x_FindDataSource (const CObject *key)
 
TDataSourceLock CObjectManager::x_RevokeDataLoader (CDataLoader *loader)
 
TPluginManagerCObjectManager::x_GetPluginManager (void)
 
virtual const char * CObjMgrException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CObjMgrException::NCBI_EXCEPTION_DEFAULT (CObjMgrException, CException)
 
virtual const char * CSeqMapException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CSeqMapException::NCBI_EXCEPTION_DEFAULT (CSeqMapException, CObjMgrException)
 
virtual const char * CSeqVectorException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CSeqVectorException::NCBI_EXCEPTION_DEFAULT (CSeqVectorException, CObjMgrException)
 
virtual const char * CAnnotException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CAnnotException::NCBI_EXCEPTION_DEFAULT (CAnnotException, CObjMgrException)
 
virtual const char * CLoaderException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CLoaderException::NCBI_EXCEPTION_DEFAULT (CLoaderException, CObjMgrException)
 
void CLoaderException::SetFailedCall (const string &call)
 
virtual void CLoaderException::ReportExtra (ostream &out) const override
 Report "non-standard" attributes. More...
 
virtual const char * CBlobStateException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CBlobStateException::CBlobStateException (const CDiagCompileInfo &info, const CException *prev_exception, EErrCode err_code, const string &message, TBlobState state, EDiagSev severity=eDiag_Error)
 
 CBlobStateException::CBlobStateException (const CBlobStateException &other)
 
virtual CBlobStateException::~CBlobStateException (void) noexcept
 
const char * CBlobStateException::GetType (void) const override
 Get class name as a string. More...
 
TErrCode CBlobStateException::GetErrCode (void) const
 
TBlobState CBlobStateException::GetBlobState (void)
 
 CBlobStateException::CBlobStateException (void)
 
virtual const CExceptionCBlobStateException::x_Clone (void) const override
 Helper method for cloning the exception. More...
 
virtual const char * CObjmgrUtilException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CObjmgrUtilException::NCBI_EXCEPTION_DEFAULT (CObjmgrUtilException, CObjMgrException)
 
virtual const char * CAnnotSearchLimitException::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CAnnotSearchLimitException::NCBI_EXCEPTION_DEFAULT (CAnnotSearchLimitException, CObjMgrException)
 
 CPrefetchTokenOld::CPrefetchTokenOld (void)
 
 CPrefetchTokenOld::CPrefetchTokenOld (CScope &scope, const TIds &ids, unsigned int depth=2)
 Find the first loader in the scope, request prefetching from this loader. More...
 
 CPrefetchTokenOld::CPrefetchTokenOld (CScope &scope, const TIds &ids, ENon_locking_prefetch)
 Do not lock prefetched TSEs, prefetch depth is ignored. More...
 
 CPrefetchTokenOld::~CPrefetchTokenOld (void)
 
 CPrefetchTokenOld::CPrefetchTokenOld (const CPrefetchTokenOld &token)
 
CPrefetchTokenOldCPrefetchTokenOld::operator= (const CPrefetchTokenOld &token)
 
 CPrefetchTokenOld::DECLARE_OPERATOR_BOOL (m_Impl &&*m_Impl)
 
CBioseq_Handle CPrefetchTokenOld::NextBioseqHandle (CScope &scope)
 Get bioseq handle and move to the next requested id Scope must contain the loader used for prefetching. More...
 
 CScopeSource::CScopeSource (void)
 
 CScopeSource::CScopeSource (CScope &scope)
 
static CScopeSource CScopeSource::New (CScope &scope)
 
CScopeCScopeSource::GetScope (void)
 
 CPrefetchBioseq::CPrefetchBioseq (const CScopeSource &scope, const CSeq_id_Handle &id)
 
virtual bool CPrefetchBioseq::Execute (CRef< CPrefetchRequest > token)
 
const CSeq_id_HandleCPrefetchBioseq::GetSeq_id (void) const
 
const CBioseq_HandleCPrefetchBioseq::GetBioseqHandle (void) const
 
const CBioseq_HandleCPrefetchBioseq::GetResult (void) const
 
 CPrefetchBioseq::CPrefetchBioseq (const CScopeSource &scope)
 
 CPrefetchBioseq::CPrefetchBioseq (const CBioseq_Handle &bioseq)
 
 CPrefetchFeat_CI::CPrefetchFeat_CI (const CScopeSource &scope, CConstRef< CSeq_loc > loc, const SAnnotSelector &selector)
 
 CPrefetchFeat_CI::CPrefetchFeat_CI (const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &selector)
 
 CPrefetchFeat_CI::CPrefetchFeat_CI (const CScopeSource &scope, const CSeq_id_Handle &seq_id, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &selector)
 
virtual bool CPrefetchFeat_CI::Execute (CRef< CPrefetchRequest > token)
 
const SAnnotSelectorCPrefetchFeat_CI::GetSelector (void) const
 
const CFeat_CICPrefetchFeat_CI::GetFeat_CI (void) const
 
const CFeat_CICPrefetchFeat_CI::GetResult (void) const
 
 CPrefetchComplete< Handle >::CPrefetchComplete (const THandle &handle)
 
virtual bool CPrefetchComplete< Handle >::Execute (CRef< CPrefetchRequest > token)
 
const THandle CPrefetchComplete< Handle >::GetHandle (void) const
 
const CConstRef< TObject > & CPrefetchComplete< Handle >::GetResult (void) const
 
 CPrefetchComplete< CBioseq_Handle >::CPrefetchComplete (const THandle &handle)
 
 CPrefetchComplete< CBioseq_Handle >::CPrefetchComplete (const CScopeSource &scope, const CSeq_id_Handle &seq_id)
 
virtual bool CPrefetchComplete< CBioseq_Handle >::Execute (CRef< CPrefetchRequest > token)
 
const THandle CPrefetchComplete< CBioseq_Handle >::GetHandle (void) const
 
const CConstRef< TObject > & CPrefetchComplete< CBioseq_Handle >::GetComplete (void) const
 
const CConstRef< TObject > & CPrefetchComplete< CBioseq_Handle >::GetResult (void) const
 
virtual ISeq_idSource::~ISeq_idSource (void)
 
virtual CSeq_id_Handle ISeq_idSource::GetNextSeq_id (void)=0
 
 CStdSeq_idSource< Container >::CStdSeq_idSource (const TContainer &cont)
 
virtual CSeq_id_Handle CStdSeq_idSource< Container >::GetNextSeq_id (void)
 
 CPrefetchBioseqActionSource::CPrefetchBioseqActionSource (const CScopeSource &scope, ISeq_idSource *ids)
 
 CPrefetchBioseqActionSource::CPrefetchBioseqActionSource (const CScopeSource &scope, const TIds &ids)
 
virtual CIRef< IPrefetchActionCPrefetchBioseqActionSource::GetNextAction (void)
 
 CPrefetchFeat_CIActionSource::CPrefetchFeat_CIActionSource (const CScopeSource &scope, ISeq_idSource *ids, const SAnnotSelector &sel)
 
 CPrefetchFeat_CIActionSource::CPrefetchFeat_CIActionSource (const CScopeSource &scope, const TIds &ids, const SAnnotSelector &sel)
 
virtual CIRef< IPrefetchActionCPrefetchFeat_CIActionSource::GetNextAction (void)
 
static void CStdPrefetch::Wait (CRef< CPrefetchRequest > token)
 
static CRef< CPrefetchRequestCStdPrefetch::GetBioseqHandle (CPrefetchManager &manager, const CScopeSource &scope, const CSeq_id_Handle &id)
 
static CBioseq_Handle CStdPrefetch::GetBioseqHandle (CRef< CPrefetchRequest > token)
 
static CRef< CPrefetchRequestCStdPrefetch::GetFeat_CI (CPrefetchManager &manager, const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)
 
static CRef< CPrefetchRequestCStdPrefetch::GetFeat_CI (CPrefetchManager &manager, const CScopeSource &scope, const CSeq_id_Handle &seq_id, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)
 
static CRef< CPrefetchRequestCStdPrefetch::GetFeat_CI (CPrefetchManager &manager, const CScopeSource &scope, CConstRef< CSeq_loc > loc, const SAnnotSelector &sel)
 
static CFeat_CI CStdPrefetch::GetFeat_CI (CRef< CPrefetchRequest > token)
 
virtual IPrefetchAction::~IPrefetchAction (void)
 
virtual bool IPrefetchAction::Execute (CRef< CPrefetchRequest > token)=0
 
virtual IPrefetchActionSource::~IPrefetchActionSource (void)
 
virtual CIRef< IPrefetchActionIPrefetchActionSource::GetNextAction (void)=0
 
virtual IPrefetchListener::~IPrefetchListener (void)
 
virtual void IPrefetchListener::PrefetchNotify (CRef< CPrefetchRequest > token, EEvent event)=0
 
 CPrefetchManager::CPrefetchManager (void)
 
 CPrefetchManager::CPrefetchManager (unsigned max_threads, CThread::TRunMode threads_mode=CThread::fRunDefault)
 
 CPrefetchManager::~CPrefetchManager (void)
 
CRef< CPrefetchRequestCPrefetchManager::AddAction (TPriority priority, IPrefetchAction *action, IPrefetchListener *listener=0)
 
CRef< CPrefetchRequestCPrefetchManager::AddAction (IPrefetchAction *action, IPrefetchListener *listener=0)
 
static bool CPrefetchManager::IsActive (void)
 
void CPrefetchManager::CancelAllTasks (void)
 
void CPrefetchManager::Shutdown (void)
 
 CPrefetchManager::CPrefetchManager (const CPrefetchManager &)
 
void CPrefetchManager::operator= (const CPrefetchManager &)
 
virtual const char * CPrefetchFailed::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CPrefetchFailed::NCBI_EXCEPTION_DEFAULT (CPrefetchFailed, CException)
 
virtual const char * CPrefetchCanceled::GetErrCodeString (void) const override
 Get error code interpreted as text. More...
 
 CPrefetchCanceled::NCBI_EXCEPTION_DEFAULT (CPrefetchCanceled, CException)
 
 CPrefetchSequence::CPrefetchSequence (CPrefetchManager &manager, IPrefetchActionSource *source, size_t active_size=10)
 
 CPrefetchSequence::~CPrefetchSequence (void)
 
CRef< CPrefetchRequestCPrefetchSequence::GetNextToken (void)
 Returns next action waiting for its result if necessary. More...
 
void CPrefetchSequence::EnqueNextAction (void)
 
 CPrefetchRequest::CPrefetchRequest (CObjectFor< CMutex > *state_mutex, IPrefetchAction *action, IPrefetchListener *listener, unsigned int priority)
 
 CPrefetchRequest::~CPrefetchRequest (void)
 
IPrefetchActionCPrefetchRequest::GetAction (void) const
 
IPrefetchListenerCPrefetchRequest::GetListener (void) const
 
void CPrefetchRequest::SetListener (IPrefetchListener *listener)
 
EState CPrefetchRequest::GetState (void) const
 
bool CPrefetchRequest::IsDone (void) const
 
TProgress CPrefetchRequest::GetProgress (void) const
 
TProgress CPrefetchRequest::SetProgress (TProgress progress)
 
virtual EStatus CPrefetchRequest::Execute (void)
 Do the actual job. More...
 
virtual void CPrefetchRequest::OnStatusChange (EStatus)
 Callback to notify on changes in the task status. More...
 
 CScope::CScope (CObjectManager &objmgr)
 
virtual CScope::~CScope (void)
 
CObjectManagerCScope::GetObjectManager (void)
 Get object manager controlling this scope. More...
 
CBioseq_Handle CScope::GetBioseqHandle (const CSeq_id &id)
 Get bioseq handle by seq-id. More...
 
CBioseq_Handle CScope::GetBioseqHandle (const CSeq_id_Handle &id)
 Get bioseq handle by seq-id handle. More...
 
CBioseq_Handle CScope::GetBioseqHandle (const CSeq_loc &loc)
 Get bioseq handle by seq-loc. More...
 
CBioseq_Handle CScope::GetBioseqHandle (const CSeq_id &id, EGetBioseqFlag get_flag)
 Get bioseq handle without loading new data. More...
 
CBioseq_Handle CScope::GetBioseqHandle (const CSeq_id_Handle &id, EGetBioseqFlag get_flag)
 Get bioseq handle without loading new data. More...
 
bool CScope::IsSameBioseq (const CSeq_id_Handle &id1, const CSeq_id_Handle &id2, EGetBioseqFlag get_flag)
 Check if two seq-ids are resolved to the same Bioseq. More...
 
TBioseqHandles CScope::GetBioseqHandles (const TIds &ids)
 Get bioseq handles for all ids. More...
 
TCDD_Entries CScope::GetCDDAnnots (const TIds &idhs)
 
TCDD_Entries CScope::GetCDDAnnots (const TBioseqHandles &bhs)
 
CSeq_entry_Handle CScope::GetSeq_entryHandle (CDataLoader *loader, const TBlobId &blob_id, EMissing action=eMissing_Default)
 Get Seq-entry handle by its blob-id, with possible loading. More...
 
CTSE_Handle CScope::GetTSE_Handle (const CSeq_entry &tse, EMissing action=eMissing_Default)
 Find object in scope If object is not found GetXxxHandle() methods will either throw an exception or return null handle depending on argument. More...
 
CBioseq_Handle CScope::GetBioseqHandle (const CBioseq &bioseq, EMissing action=eMissing_Default)
 
CBioseq_set_Handle CScope::GetBioseq_setHandle (const CBioseq_set &seqset, EMissing action=eMissing_Default)
 
CSeq_entry_Handle CScope::GetSeq_entryHandle (const CSeq_entry &entry, EMissing action=eMissing_Default)
 
CSeq_annot_Handle CScope::GetSeq_annotHandle (const CSeq_annot &annot, EMissing action=eMissing_Default)
 
CSeq_feat_Handle CScope::GetSeq_featHandle (const CSeq_feat &feat, EMissing action=eMissing_Default)
 
CBioseq_Handle CScope::GetObjectHandle (const CBioseq &bioseq, EMissing action=eMissing_Default)
 
CBioseq_set_Handle CScope::GetObjectHandle (const CBioseq_set &seqset, EMissing action=eMissing_Default)
 
CSeq_entry_Handle CScope::GetObjectHandle (const CSeq_entry &entry, EMissing action=eMissing_Default)
 
CSeq_annot_Handle CScope::GetObjectHandle (const CSeq_annot &annot, EMissing action=eMissing_Default)
 
CSeq_feat_Handle CScope::GetObjectHandle (const CSeq_feat &feat, EMissing action=eMissing_Default)
 
CBioseq_EditHandle CScope::GetBioseqEditHandle (const CBioseq &bioseq)
 Get edit handle for the specified object Throw an exception if object is not found, or non-editable. More...
 
CSeq_entry_EditHandle CScope::GetSeq_entryEditHandle (const CSeq_entry &entry)
 
CSeq_annot_EditHandle CScope::GetSeq_annotEditHandle (const CSeq_annot &annot)
 
CBioseq_set_EditHandle CScope::GetBioseq_setEditHandle (const CBioseq_set &seqset)
 
CBioseq_EditHandle CScope::GetObjectEditHandle (const CBioseq &bioseq)
 
CBioseq_set_EditHandle CScope::GetObjectEditHandle (const CBioseq_set &seqset)
 
CSeq_entry_EditHandle CScope::GetObjectEditHandle (const CSeq_entry &entry)
 
CSeq_annot_EditHandle CScope::GetObjectEditHandle (const CSeq_annot &annot)
 
CBioseq_Handle CScope::GetBioseqHandleFromTSE (const CSeq_id &id, const CTSE_Handle &tse)
 Get bioseq handle for sequence withing one TSE. More...
 
CBioseq_Handle CScope::GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CTSE_Handle &tse)
 
CBioseq_Handle CScope::GetBioseqHandleFromTSE (const CSeq_id &id, const CBioseq_Handle &bh)
 
CBioseq_Handle CScope::GetBioseqHandleFromTSE (const CSeq_id &id, const CSeq_entry_Handle &seh)
 Get bioseq handle for sequence withing one TSE. More...
 
CBioseq_Handle CScope::GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CBioseq_Handle &bh)
 Get bioseq handle for sequence withing one TSE. More...
 
CBioseq_Handle CScope::GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CSeq_entry_Handle &seh)
 Get bioseq handle for sequence withing one TSE. More...
 
void CScope::AddDefaults (TPriority pri=kPriority_Default)
 Add default data loaders from object manager. More...
 
void CScope::AddDataLoader (const string &loader_name, TPriority pri=kPriority_Default)
 Add data loader by name. More...
 
void CScope::AddScope (CScope &scope, TPriority pri=kPriority_Default)
 Add the scope's datasources as a single group with the given priority All data sources (data loaders and explicitly added data) have priorities. More...
 
CSeq_entry_Handle CScope::AddTopLevelSeqEntry (CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)
 Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with possibility to edit it directly. More...
 
CSeq_entry_Handle CScope::AddTopLevelSeqEntry (const CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
 Add shared Seq-entry, scope will not modify it. More...
 
CBioseq_Handle CScope::AddBioseq (CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
 Add bioseq, return bioseq handle. More...
 
CBioseq_Handle CScope::AddBioseq (const CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
 Add shared Bioseq, scope will not modify it. More...
 
CSeq_entry_Handle CScope::AddGC_Assembly (const CGC_Assembly &gc_assembly, CGC_Assembly_Parser::FParserFlags flags=CGC_Assembly_Parser::fDefault, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
 Add GC-Assembly. More...
 
CSeq_annot_Handle CScope::AddSeq_annot (CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
 Add Seq-annot, return its CSeq_annot_Handle. More...
 
CSeq_annot_Handle CScope::AddSeq_annot (const CSeq_annot &annot, TPriority pri=kPriority_Default, EExist action=eExist_Throw)
 Add shared Seq-annot, scope will not modify it. More...
 
CSeq_entry_Handle CScope::AddSeq_submit (CSeq_submit &submit, TPriority pri=kPriority_Default)
 Add Seq-submit, return its CSeq_entry_Handle. More...
 
CBioseq_EditHandle CScope::GetEditHandle (const CBioseq_Handle &seq)
 Get editable Biosec handle by regular one. More...
 
CSeq_entry_EditHandle CScope::GetEditHandle (const CSeq_entry_Handle &entry)
 Get editable SeqEntry handle by regular one. More...
 
CSeq_annot_EditHandle CScope::GetEditHandle (const CSeq_annot_Handle &annot)
 Get editable Seq-annot handle by regular one. More...
 
CBioseq_set_EditHandle CScope::GetEditHandle (const CBioseq_set_Handle &seqset)
 Get editable Biosec-set handle by regular one. More...
 
void CScope::ResetHistory (EActionIfLocked action=eKeepIfLocked)
 Clean all unused TSEs from the scope's cache and release the memory. More...
 
void CScope::ResetDataAndHistory (void)
 Clear all information in the scope except added data loaders. More...
 
void CScope::ResetDataAndHistory (ERemoveDataLoaders remove_data_loaders)
 
void CScope::RemoveFromHistory (const CTSE_Handle &tse, EActionIfLocked action=eKeepIfLocked)
 Remove single TSE from the scope's history. More...
 
void CScope::RemoveFromHistory (const CBioseq_Handle &bioseq, EActionIfLocked action=eKeepIfLocked)
 Remove the bioseq's TSE from the scope's history. More...
 
void CScope::RemoveFromHistory (const CSeq_id_Handle &seq_id)
 Remove the Seq-id failed resolution from the scope's history. More...
 
void CScope::RemoveFromHistory (const CSeq_id &seq_id)
 Remove the Seq-id failed resolution from the scope's history. More...
 
void CScope::RemoveDataLoader (const string &loader_name, EActionIfLocked action=eThrowIfLocked)
 Revoke data loader from the scope. More...
 
void CScope::RemoveTopLevelSeqEntry (const CTSE_Handle &entry)
 Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq(). More...
 
void CScope::RemoveTopLevelSeqEntry (const CSeq_entry_Handle &entry)
 
void CScope::RemoveBioseq (const CBioseq_Handle &seq)
 Revoke Bioseq previously added using AddBioseq(). More...
 
void CScope::RemoveSeq_annot (const CSeq_annot_Handle &annot)
 Revoke Seq-annot previously added using AddSeq_annot(). More...
 
bool CScope::Exists (const CSeq_id &id)
 Check existence of sequence with this id. More...
 
bool CScope::Exists (const CSeq_id_Handle &id)
 
TIds CScope::GetIds (const CSeq_id &id, TGetFlags flags=0)
 Get "native" bioseq ids without filtering and matching. More...
 
TIds CScope::GetIds (const CSeq_id_Handle &idh, TGetFlags flags=0)
 
CSeq_id_Handle CScope::GetAccVer (const CSeq_id_Handle &idh, TGetFlags flags=0)
 Get accession.version Seq-id Returns null CSeq_id_Handle if the sequence is not found or if it doesn't have accession. More...
 
TGi CScope::GetGi (const CSeq_id_Handle &idh, TGetFlags flags=0)
 Get GI of a sequence Returns ZERO_GI if the sequence is not found or if it doesn't have GI. More...
 
static CSeq_id_Handle CScope::x_GetAccVer (const TIds &ids)
 
static TGi CScope::x_GetGi (const TIds &ids)
 
string CScope::GetLabel (const CSeq_id &id, TGetFlags flags=0)
 Get short description of bioseq, usually "accession.version" Returns empty string if the sequence is not found. More...
 
string CScope::GetLabel (const CSeq_id_Handle &idh, TGetFlags flags=0)
 
TTaxId CScope::GetTaxId (const CSeq_id &id, TGetFlags flags=0)
 Get taxonomy id of bioseq Return -1 if sequence is not found Return 0 if sequence doesn't have taxonomy id. More...
 
TTaxId CScope::GetTaxId (const CSeq_id_Handle &idh, TGetFlags flags=0)
 
TSeqPos CScope::GetSequenceLength (const CSeq_id &id, TGetFlags flags=0)
 Get sequence length Return kInvalidSeqPos if sequence is not found. More...
 
TSeqPos CScope::GetSequenceLength (const CSeq_id_Handle &id, TGetFlags flags=0)
 
CSeq_inst::TMol CScope::GetSequenceType (const CSeq_id &id, TGetFlags flags=0)
 Get molecular type of sequence (protein/dna/rna) Return CSeq_inst::eMol_not_set if sequence is not found. More...
 
CSeq_inst::TMol CScope::GetSequenceType (const CSeq_id_Handle &id, TGetFlags flags=0)
 
CBioseq_Handle::TBioseqStateFlags CScope::GetSequenceState (const CSeq_id &id, TGetFlags flags=0)
 Get sequence GenBank state Return (fState_not_found|fState_no_data) if sequence is not found. More...
 
CBioseq_Handle::TBioseqStateFlags CScope::GetSequenceState (const CSeq_id_Handle &id, TGetFlags flags=0)
 
TSequenceHash CScope::GetSequenceHash (const CSeq_id &id, TGetFlags flags=0)
 
TSequenceHash CScope::GetSequenceHash (const CSeq_id_Handle &id, TGetFlags flags=0)
 
TBulkIds CScope::GetBulkIds (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
void CScope::GetBulkIds (TBulkIds *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
TSeq_id_Handles CScope::GetAccVers (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 Get accession.version Seq-id Returns null CSeq_id_Handles for sequences that aren't found or don't have accession id. More...
 
void CScope::GetAccVers (TSeq_id_Handles *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
TGIs CScope::GetGis (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
void CScope::GetGis (TGIs *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
TLabels CScope::GetLabels (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
void CScope::GetLabels (TLabels *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
TTaxIds CScope::GetTaxIds (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
void CScope::GetTaxIds (TTaxIds *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
TSequenceLengths CScope::GetSequenceLengths (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
void CScope::GetSequenceLengths (TSequenceLengths *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
TSequenceTypes CScope::GetSequenceTypes (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
void CScope::GetSequenceTypes (TSequenceTypes *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
TSequenceStates CScope::GetSequenceStates (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
void CScope::GetSequenceStates (TSequenceStates *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
TSequenceHashes CScope::GetSequenceHashes (const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
void CScope::GetSequenceHashes (TSequenceHashes *results, const TSeq_id_Handles &idhs, TGetFlags flags=0)
 
CConstRef< CSynonymsSetCScope::GetSynonyms (const CSeq_id &id)
 Get bioseq synonyms, resolving to the bioseq in this scope. More...
 
CConstRef< CSynonymsSetCScope::GetSynonyms (const CSeq_id_Handle &id)
 Get bioseq synonyms, resolving to the bioseq in this scope. More...
 
CConstRef< CSynonymsSetCScope::GetSynonyms (const CBioseq_Handle &bh)
 Get bioseq synonyms, resolving to the bioseq in this scope. More...
 
void CScope::AttachEntry (CSeq_entry &parent, CSeq_entry &entry)
 
void CScope::RemoveEntry (CSeq_entry &entry)
 
void CScope::AttachAnnot (CSeq_entry &parent, CSeq_annot &annot)
 
void CScope::RemoveAnnot (CSeq_entry &parent, CSeq_annot &annot)
 
void CScope::ReplaceAnnot (CSeq_entry &entry, CSeq_annot &old_annot, CSeq_annot &new_annot)
 
CBioseq_Handle CScope::GetBioseqHandleFromTSE (const CSeq_id &id, const CSeq_entry &tse)
 
CBioseq_Handle CScope::GetBioseqHandleFromTSE (const CSeq_id_Handle &id, const CSeq_entry &tse)
 
void CScope::GetAllTSEs (TTSE_Handles &tses, enum ETSEKind kind=eManualTSEs)
 
CScopeTransaction CScope::GetTransaction ()
 
void CScope::UpdateAnnotIndex (void)
 
static bool CScope::GetDefaultKeepExternalAnnotsForEdit ()
 Return current application-wide KeepExternalAnnotsForEdit flag. More...
 
static void CScope::SetDefaultKeepExternalAnnotsForEdit (bool keep=true)
 Set new application-wide KeepExternalAnnotsForEdit flag. More...
 
bool CScope::GetKeepExternalAnnotsForEdit () const
 Return this scope's KeepExternalAnnotsForEdit flag. More...
 
void CScope::SetKeepExternalAnnotsForEdit (bool keep=true)
 Change this scope's KeepExternalAnnotsForEdit flag. More...
 
CScope_ImplCScope::GetImpl (void)
 
 CScope::CScope (const CScope &)
 
CScopeCScope::operator= (const CScope &)
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (CMappingRanges *mapping_ranges, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through a pre-filled CMappipngRanges. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeq_feat &map_feat, EFeatMapDirection dir, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through a feature, both location and product must be set. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeq_loc &source, const CSeq_loc &target, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping between two seq_locs. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeq_align &map_align, const CSeq_id &to_id, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through an alignment. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeq_align &map_align, size_t to_row, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeq_id &from_id, const CSeq_id &to_id, const CSeq_align &map_align, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through an alignment using specific source and target ids. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (size_t from_row, size_t to_row, const CSeq_align &map_align, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through an alignment using specific source and target row numbers. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (CBioseq_Handle target_seq, ESeqMapDirection direction, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping between segments and the top level sequence. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (CBioseq_Handle target_seq, ESeqMapDirection direction, SSeqMapSelector selector, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping between segments and the top level sequence. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeqMap &seq_map, ESeqMapDirection direction, const CSeq_id *top_level_id=0, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through a seq-map. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeqMap &seq_map, ESeqMapDirection direction, SSeqMapSelector selector, const CSeq_id *top_level_id=0, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping through a seq-map. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (size_t depth, const CBioseq_Handle &top_level_seq, ESeqMapDirection direction, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Mapping between segments and the top level sequence limited by depth. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (size_t depth, const CSeqMap &top_level_seq, ESeqMapDirection direction, const CSeq_id *top_level_id=0, CScope *scope=0, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Depth-limited mapping through a seq-map. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CGC_Assembly &gc_assembly, EGCAssemblyAlias to_alias, CScope *scope=0, EScopeFlag scope_flag=eCopyScope)
 Initialize the mapper to map through a GC-Assembly to the selected alias type. More...
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CGC_Assembly &gc_assembly, ESeqMapDirection direction, SSeqMapSelector selector, CScope *scope=0, EScopeFlag scope_flag=eCopyScope, CSeq_loc_Mapper_Options options=CSeq_loc_Mapper_Options())
 Initialize the mapper to map through deltas from a GC-Assembly. More...
 
 CSeq_loc_Mapper::~CSeq_loc_Mapper (void)
 
virtual CSeq_align_Mapper_BaseCSeq_loc_Mapper::InitAlignMapper (const CSeq_align &src_align)
 
 CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeq_loc_Mapper &)
 
CSeq_loc_MapperCSeq_loc_Mapper::operator= (const CSeq_loc_Mapper &)
 
void CSeq_loc_Mapper::x_InitializeSeqMap (const CSeqMap &seq_map, const CSeq_id *top_id, ESeqMapDirection direction)
 
void CSeq_loc_Mapper::x_InitializeSeqMap (const CSeqMap &seq_map, size_t depth, const CSeq_id *top_id, ESeqMapDirection direction)
 
void CSeq_loc_Mapper::x_InitializeSeqMap (const CSeqMap &seq_map, SSeqMapSelector selector, const CSeq_id *top_id, ESeqMapDirection direction)
 
void CSeq_loc_Mapper::x_InitializeSeqMap (CSeqMap_CI seg_it, const CSeq_id *top_id, ESeqMapDirection direction)
 
void CSeq_loc_Mapper::x_InitializeSeqMapUp (CSeqMap_CI seg_it, const CSeq_id *top_id)
 
void CSeq_loc_Mapper::x_InitializeSeqMapDown (CSeqMap_CI seg_it, const CSeq_id *top_id)
 
void CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel (CSeqMap_CI seg_it, const CSeq_id *top_id, ESeqMapDirection direction)
 
void CSeq_loc_Mapper::x_InitGCAssembly (const CGC_Assembly &gc_assembly, EGCAssemblyAlias to_alias)
 
void CSeq_loc_Mapper::x_InitGCSequence (const CGC_Sequence &gc_seq, EGCAssemblyAlias to_alias)
 
CBioseq_Handle CSeq_loc_Mapper::x_AddVirtualBioseq (const TSynonyms &synonyms, const CGC_Sequence &gc_seq)
 
bool CSeq_loc_Mapper::x_IsUCSCRandomChr (const CGC_Sequence &gc_seq, CConstRef< CSeq_id > &chr_id, TSynonyms &synonyms) const
 

Variables

CSeq_id_Handle CMappingRange::m_Src_id_Handle
 
TSeqPos CMappingRange::m_Src_from
 
TSeqPos CMappingRange::m_Src_to
 
ENa_strand CMappingRange::m_Src_strand
 
CSeq_id_Handle CMappingRange::m_Dst_id_Handle
 
TSeqPos CMappingRange::m_Dst_from
 
ENa_strand CMappingRange::m_Dst_strand
 
bool CMappingRange::m_Reverse
 
bool CMappingRange::m_ExtTo
 
int CMappingRange::m_Frame
 
TSeqPos CMappingRange::m_Src_bioseq_len
 
TSeqPos CMappingRange::m_Dst_len
 
int CMappingRange::m_Group
 
TIdMap CMappingRanges::m_IdMap
 
bool CMappingRanges::m_ReverseSrc
 
bool CMappingRanges::m_ReverseDst
 
TSeqPos CGraphRanges::m_Offset
 
TGraphRanges CGraphRanges::m_Ranges
 
TRange CGraphRanges::m_TotalRange
 
CRef< IMapper_Sequence_InfoCSeq_loc_Mapper_Options::m_SeqInfo
 
TMapOptions CSeq_loc_Mapper_Options::m_Options
 
TRange CSeq_loc_Mapper_Base::SMappedRange::range
 
TRangeFuzz CSeq_loc_Mapper_Base::SMappedRange::fuzz
 
int CSeq_loc_Mapper_Base::SMappedRange::group
 
EMergeFlags CSeq_loc_Mapper_Base::m_MergeFlag
 
EGapFlags CSeq_loc_Mapper_Base::m_GapFlag
 
TMiscFlags CSeq_loc_Mapper_Base::m_MiscFlags
 
TRangesById CSeq_loc_Mapper_Base::m_MappedLocs
 
CRef< CSeq_locCSeq_loc_Mapper_Base::m_SrcLocs
 
CRef< CGraphRangesCSeq_loc_Mapper_Base::m_GraphRanges
 
TSynonymMap CSeq_loc_Mapper_Base::m_SynonymMap
 
TLengthMap CSeq_loc_Mapper_Base::m_LengthMap
 
TSeqTypeById CSeq_loc_Mapper_Base::m_SeqTypes
 
bool CSeq_loc_Mapper_Base::m_Partial
 
bool CSeq_loc_Mapper_Base::m_LastTruncated
 
CRef< CMappingRangesCSeq_loc_Mapper_Base::m_Mappings
 
CRef< CSeq_locCSeq_loc_Mapper_Base::m_Dst_loc
 
TDstStrandMap CSeq_loc_Mapper_Base::m_DstRanges
 
int CSeq_loc_Mapper_Base::m_CurrentGroup
 
TFuzzOption CSeq_loc_Mapper_Base::m_FuzzOption
 
CSeq_loc_Mapper_Options CSeq_loc_Mapper_Base::m_MapOptions
 
EObjectType CSeq_loc_Mapper_Message::m_ObjType
 
CRef< CObjectCSeq_loc_Mapper_Message::m_Obj
 
pair_base_member< convert_to_string_type, value_typeCBlobIdFor< Value, Converter >::m_Value
 
CConstRef< CBlobIdCBlobIdKey::m_Id
 
TRange SRequestDetails::m_NeedSeqMap
 
TRange SRequestDetails::m_NeedSeqData
 
TAnnotSet SRequestDetails::m_NeedAnnots
 
TAnnotBlobType SRequestDetails::m_AnnotBlobType
 
string CLoaderMaker_Base::m_Name
 
TRegisterInfo_Base CLoaderMaker_Base::m_RegisterInfo
 
TParam CParamLoaderMaker< TDataLoader, TParam >::m_Param
 
bool CDataLoader::SAccVerFound::sequence_found
 
CSeq_id_Handle CDataLoader::SAccVerFound::acc_ver
 
bool CDataLoader::SGiFound::sequence_found
 
TGi CDataLoader::SGiFound::gi
 
bool CDataLoader::STypeFound::sequence_found
 
CSeq_inst::TMol CDataLoader::STypeFound::type
 
bool CDataLoader::SHashFound::sequence_found
 
bool CDataLoader::SHashFound::hash_known
 
int CDataLoader::SHashFound::hash
 
string CDataLoader::m_Name
 
CDataSourceCDataLoader::m_DataSource
 
TParserFlags CGC_Assembly_Parser::m_Flags
 
CRef< CSeq_entryCGC_Assembly_Parser::m_TSE
 
TSeqIds CGC_Assembly_Parser::m_TopSeqs
 
TSeqIds CGC_Assembly_Parser::m_AllSeqs
 
CRef< CObjectFor< CMutex > > CPrefetchManager_Impl::m_StateMutex
 
CThreadPool CPrefetchManager_Impl::m_ThreadPool
 
TLoader * SRegisterLoaderInfo< TLoader >::m_Loader
 
bool SRegisterLoaderInfo< TLoader >::m_Created
 
TSetDefaultSource CObjectManager::m_setDefaultSource
 
TMapNameToLoader CObjectManager::m_mapNameToLoader
 
TMapToSource CObjectManager::m_mapToSource
 
TSetScope CObjectManager::m_setScope
 
TRWLock CObjectManager::m_OM_Lock
 
TRWLock CObjectManager::m_OM_ScopeLock
 
CRef< CSeq_id_MapperCObjectManager::m_Seq_id_Mapper
 
unique_ptr< TPluginManagerCObjectManager::m_PluginManager
 
string CLoaderException::m_FailedCall
 
TBlobState CBlobStateException::m_BlobState
 
CRef< CPrefetchTokenOld_ImplCPrefetchTokenOld::m_Impl
 
CHeapScope CScopeSource::m_Scope
 
CHeapScope CScopeSource::m_BaseScope
 
CSeq_id_Handle CPrefetchBioseq::m_Seq_id
 
TResult CPrefetchBioseq::m_Result
 
CConstRef< CSeq_locCPrefetchFeat_CI::m_Loc
 
CRange< TSeqPosCPrefetchFeat_CI::m_Range
 
ENa_strand CPrefetchFeat_CI::m_Strand
 
SAnnotSelector CPrefetchFeat_CI::m_Selector
 
TResult CPrefetchFeat_CI::m_Result
 
THandle CPrefetchComplete< Handle >::m_Handle
 
TResult CPrefetchComplete< Handle >::m_Result
 
TResult CPrefetchComplete< CBioseq_Handle >::m_Result
 
TContainer CStdSeq_idSource< Container >::m_Container
 
TIterator CStdSeq_idSource< Container >::m_Iterator
 
CScopeSource CPrefetchBioseqActionSource::m_Scope
 
CIRef< ISeq_idSourceCPrefetchBioseqActionSource::m_Ids
 
CScopeSource CPrefetchFeat_CIActionSource::m_Scope
 
CIRef< ISeq_idSourceCPrefetchFeat_CIActionSource::m_Ids
 
SAnnotSelector CPrefetchFeat_CIActionSource::m_Selector
 
CRef< CPrefetchManager_ImplCPrefetchManager::m_Impl
 
CRef< CPrefetchManagerCPrefetchSequence::m_Manager
 
CIRef< IPrefetchActionSourceCPrefetchSequence::m_Source
 
CMutex CPrefetchSequence::m_Mutex
 
list< CRef< CPrefetchRequest > > CPrefetchSequence::m_ActiveTokens
 
CRef< CObjectFor< CMutex > > CPrefetchRequest::m_StateMutex
 
CIRef< IPrefetchActionCPrefetchRequest::m_Action
 
CIRef< IPrefetchListenerCPrefetchRequest::m_Listener
 
TProgress CPrefetchRequest::m_Progress
 
CRef< CScopeCScope::m_HeapScope
 
CRef< CScope_ImplCScope::m_Impl
 
CHeapScope CSeq_loc_Mapper::m_Scope
 

Friends

class CMappingRange::CSeq_loc_Mapper_Base
 
class CMappingRange::CMappingRanges
 
class CMappingRange::CSeq_align_Mapper_Base
 
struct CMappingRange::CMappingRangeRef_Less
 
struct CMappingRange::CMappingRangeRef_LessRev
 
class CSeq_loc_Mapper_Options::CSeq_loc_Mapper_Base
 
class CSeq_loc_Mapper_Base::CSeq_align_Mapper_Base
 
class CSeq_loc_Mapper_Base::CTotalRangeSynonymMapper
 
class CLoaderMaker_Base::CObjectManager
 
class CDataLoader::CGBReaderRequestResult
 
class CDataLoader::CScope_Impl
 
class CDataLoader::CObjectManager
 
class CPrefetchManager_Impl::CPrefetchRequest
 
class CPrefetchManager_Impl::CPrefetchManager
 
class CObjectManager::CSafeStatic_Allocator< CObjectManager >
 
class CObjectManager::CScope_Impl
 
class CObjectManager::CDataSource
 
class CObjectManager::CDataLoader
 
class CPrefetchRequest::CPrefetchManager
 
class CPrefetchRequest::CPrefetchManager_Impl
 
class CScope::CSeqMap_CI
 
class CScope::CSeq_annot_CI
 
class CScope::CAnnot_Collector
 
class CScope::CBioseq_CI
 
class CScope::CHeapScope
 
class CScope::CPrefetchTokenOld_Impl
 
class CScope::CScopeTransaction
 

Detailed Description

Typedef Documentation

◆ CBlobIdInt

Definition at line 151 of file blob_id.hpp.

◆ CBlobIdPtr

typedef CBlobIdFor<const void*> CBlobIdPtr

Definition at line 152 of file blob_id.hpp.

◆ CBlobIdSeq_id

Definition at line 154 of file blob_id.hpp.

◆ CBlobIdString

Definition at line 153 of file blob_id.hpp.

◆ convert_to_string_type

template<typename Value , class Converter = PConvertToString<Value>>
typedef Converter CBlobIdFor< Value, Converter >::convert_to_string_type

Definition at line 114 of file blob_id.hpp.

◆ EEvent

Definition at line 67 of file prefetch_manager.hpp.

◆ TAnnotBlobType

Definition at line 86 of file data_loader.hpp.

◆ TAnnotMapFlags

Definition at line 554 of file seq_loc_mapper_base.hpp.

◆ TAnnotSet

Definition at line 76 of file data_loader.hpp.

◆ TAnnotTypesSet

Definition at line 75 of file data_loader.hpp.

◆ TBioseqHandles

Definition at line 144 of file scope.hpp.

◆ TBlobId [1/2]

Definition at line 429 of file data_loader.hpp.

◆ TBlobId [2/2]

Definition at line 161 of file scope.hpp.

◆ TBlobState

Definition at line 162 of file objmgr_exception.hpp.

◆ TBlobVersion

Definition at line 430 of file data_loader.hpp.

◆ TBulkIds [1/2]

typedef vector<TIds> CDataLoader::TBulkIds

Definition at line 386 of file data_loader.hpp.

◆ TBulkIds [2/2]

typedef vector<TIds> CScope::TBulkIds

Get all ids of sequences Returns empty ids if the sequence is not found.

See also
EGetflags

Definition at line 523 of file scope.hpp.

◆ TCDD_Entries

Get CDD annotations for all ids.

Definition at line 150 of file scope.hpp.

◆ TCDD_Locks

Definition at line 397 of file data_loader.hpp.

◆ TChunk

Definition at line 230 of file data_loader.hpp.

◆ TChunkSet

typedef vector<TChunk> CDataLoader::TChunkSet

Definition at line 231 of file data_loader.hpp.

◆ TContainer

template<class Container >
typedef Container CStdSeq_idSource< Container >::TContainer

Definition at line 246 of file prefetch_actions.hpp.

◆ TDataSourceLock

Definition at line 134 of file object_manager.hpp.

◆ TDataSourcesLock

Definition at line 229 of file object_manager.hpp.

◆ TDendiag

typedef CSeq_align::C_Segs::TDendiag CSeq_loc_Mapper_Base::TDendiag
protected

Definition at line 723 of file seq_loc_mapper_base.hpp.

◆ TDstIdMap

Definition at line 691 of file seq_loc_mapper_base.hpp.

◆ TDstRanges

typedef list<TRange> CSeq_loc_Mapper_Base::TDstRanges
protected

Definition at line 690 of file seq_loc_mapper_base.hpp.

◆ TDstStrandMap

Definition at line 692 of file seq_loc_mapper_base.hpp.

◆ TEditSaver

Definition at line 461 of file data_loader.hpp.

◆ TErrCode

Definition at line 186 of file objmgr_exception.hpp.

◆ TFuzz [1/2]

Definition at line 95 of file seq_loc_mapper_base.hpp.

◆ TFuzz [2/2]

Definition at line 695 of file seq_loc_mapper_base.hpp.

◆ TFuzzOption

Definition at line 391 of file seq_loc_mapper_base.hpp.

◆ TGetFlags

Definition at line 440 of file scope.hpp.

◆ TGis

typedef vector<TGi> CDataLoader::TGis

Definition at line 387 of file data_loader.hpp.

◆ TGIs

typedef vector<TGi> CScope::TGIs

Get GI of a sequence Returns ZERO_GI for sequence that aren't found or don't have GI.

See also
GetGi
EGetflags

Definition at line 545 of file scope.hpp.

◆ TGraphRanges

Definition at line 240 of file seq_loc_mapper_base.hpp.

◆ THandle [1/2]

template<class Handle >
typedef Handle CPrefetchComplete< Handle >::THandle

Definition at line 168 of file prefetch_actions.hpp.

◆ THandle [2/2]

Definition at line 204 of file prefetch_actions.hpp.

◆ THashKnown

typedef vector<bool> CDataLoader::THashKnown

Definition at line 394 of file data_loader.hpp.

◆ TIdIterator

Definition at line 189 of file seq_loc_mapper_base.hpp.

◆ TIdMap

Definition at line 188 of file seq_loc_mapper_base.hpp.

◆ TIds [1/5]

Definition at line 283 of file data_loader.hpp.

◆ TIds [2/5]

Definition at line 64 of file prefetch.hpp.

◆ TIds [3/5]

Definition at line 275 of file prefetch_actions.hpp.

◆ TIds [4/5]

Definition at line 295 of file prefetch_actions.hpp.

◆ TIds [5/5]

typedef vector<CSeq_id_Handle> CScope::TIds

Definition at line 143 of file scope.hpp.

◆ TIterator

template<class Container >
typedef TContainer::const_iterator CStdSeq_idSource< Container >::TIterator

Definition at line 247 of file prefetch_actions.hpp.

◆ TLabels [1/2]

typedef vector<string> CDataLoader::TLabels

Definition at line 388 of file data_loader.hpp.

◆ TLabels [2/2]

typedef vector<string> CScope::TLabels

Get short descriptions of sequences, usually "accession.version" Returns empty strings for sequences that aren't found.

See also
GetLabel
EGetflags

Definition at line 556 of file scope.hpp.

◆ TLengthMap

Definition at line 905 of file seq_loc_mapper_base.hpp.

◆ TLoaded

typedef vector<bool> CDataLoader::TLoaded

Bulk loading interface for a small pieces of information per id.

The 'loaded' bit set (in/out) marks ids that already processed. If an element in 'loaded' is set on input then bulk methods should skip corresponding id, as it's already processed. Othewise, if the id is known and processed, the 'loaded' element will be set to true. Othewise, the 'loaded' element will remain false.

Definition at line 385 of file data_loader.hpp.

◆ TMapNameToLoader

Definition at line 258 of file object_manager.hpp.

◆ TMapOptions [1/2]

Definition at line 285 of file seq_loc_mapper_base.hpp.

◆ TMapOptions [2/2]

Definition at line 374 of file seq_loc_mapper_base.hpp.

◆ TMappedRanges

Definition at line 716 of file seq_loc_mapper_base.hpp.

◆ TMapToSource

Definition at line 259 of file object_manager.hpp.

◆ TMiscFlags

Definition at line 931 of file seq_loc_mapper_base.hpp.

◆ TObject [1/2]

template<class Handle >
typedef THandle::TObject CPrefetchComplete< Handle >::TObject

Definition at line 169 of file prefetch_actions.hpp.

◆ TObject [2/2]

Definition at line 205 of file prefetch_actions.hpp.

◆ TParamType

template<class TDataLoader , class TParam >
typedef TParam CParamLoaderMaker< TDataLoader, TParam >::TParamType

Definition at line 153 of file data_loader.hpp.

◆ TParserFlags

Definition at line 83 of file gc_assembly_parser.hpp.

◆ TPluginManager

Definition at line 252 of file object_manager.hpp.

◆ TPriority [1/4]

Definition at line 65 of file prefetch_manager_impl.hpp.

◆ TPriority [2/4]

Definition at line 151 of file object_manager.hpp.

◆ TPriority [3/4]

Definition at line 69 of file prefetch_manager.hpp.

◆ TPriority [4/4]

priority type and special value for added objects

Definition at line 98 of file scope.hpp.

◆ TProcessedNAs

Definition at line 233 of file data_loader.hpp.

◆ TProgress

Definition at line 70 of file prefetch_manager.hpp.

◆ TRange [1/5]

Definition at line 94 of file seq_loc_mapper_base.hpp.

◆ TRange [2/5]

Definition at line 185 of file seq_loc_mapper_base.hpp.

◆ TRange [3/5]

Definition at line 239 of file seq_loc_mapper_base.hpp.

◆ TRange [4/5]

Definition at line 684 of file seq_loc_mapper_base.hpp.

◆ TRange [5/5]

Definition at line 74 of file data_loader.hpp.

◆ TRangeFuzz [1/2]

Definition at line 96 of file seq_loc_mapper_base.hpp.

◆ TRangeFuzz [2/2]

typedef pair<TFuzz, TFuzz> CSeq_loc_Mapper_Base::TRangeFuzz
protected

Definition at line 696 of file seq_loc_mapper_base.hpp.

◆ TRangeIterator [1/2]

Definition at line 187 of file seq_loc_mapper_base.hpp.

◆ TRangeIterator [2/2]

Definition at line 686 of file seq_loc_mapper_base.hpp.

◆ TRangeMap [1/2]

Definition at line 186 of file seq_loc_mapper_base.hpp.

◆ TRangeMap [2/2]

Definition at line 685 of file seq_loc_mapper_base.hpp.

◆ TRangesById

Definition at line 720 of file seq_loc_mapper_base.hpp.

◆ TRangesByStrand

Definition at line 719 of file seq_loc_mapper_base.hpp.

◆ TReadLockGuard

Definition at line 268 of file object_manager.hpp.

◆ TRegisteredNames

Definition at line 178 of file object_manager.hpp.

◆ TRegisterInfo [1/2]

template<class TDataLoader >
typedef SRegisterLoaderInfo<TDataLoader> CSimpleLoaderMaker< TDataLoader >::TRegisterInfo

Definition at line 137 of file data_loader.hpp.

◆ TRegisterInfo [2/2]

template<class TDataLoader , class TParam >
typedef SRegisterLoaderInfo<TDataLoader> CParamLoaderMaker< TDataLoader, TParam >::TRegisterInfo

Definition at line 168 of file data_loader.hpp.

◆ TRegisterInfo_Base

Definition at line 113 of file data_loader.hpp.

◆ TRegisterLoaderInfo

Definition at line 213 of file object_manager.hpp.

◆ TResult [1/4]

Definition at line 83 of file prefetch_actions.hpp.

◆ TResult [2/4]

Definition at line 117 of file prefetch_actions.hpp.

◆ TResult [3/4]

template<class Handle >
typedef CConstRef<TObject> CPrefetchComplete< Handle >::TResult

Definition at line 170 of file prefetch_actions.hpp.

◆ TResult [4/4]

Definition at line 206 of file prefetch_actions.hpp.

◆ TRWLock

Definition at line 267 of file object_manager.hpp.

◆ TSeq_id_Handles

Bulk retrieval methods Common argument typedef - vector of requested ids.

Definition at line 518 of file scope.hpp.

◆ TSeq_idSet

Definition at line 268 of file data_loader.hpp.

◆ TSeqIds

Definition at line 95 of file gc_assembly_parser.hpp.

◆ TSeqIdSets

typedef vector<vector<CSeq_id_Handle> > CDataLoader::TSeqIdSets

Definition at line 396 of file data_loader.hpp.

◆ TSeqType

Definition at line 1022 of file seq_loc_mapper_base.hpp.

◆ TSeqTypeById

Definition at line 721 of file seq_loc_mapper_base.hpp.

◆ TSequenceHash

Get sequence data hash value Return 0 if sequence is not found or if its hash is not known Note: 0 can be a real hash value, use flags to distinguish these cases.

See also
EGetflags

Definition at line 512 of file scope.hpp.

◆ TSequenceHashes [1/2]

Definition at line 393 of file data_loader.hpp.

◆ TSequenceHashes [2/2]

Get data hashes of sequences Return 0 for sequences that aren't found or they don't have hash Note: 0 can be a real hash value, use flags to distinguish these cases.

See also
EGetflags

Definition at line 611 of file scope.hpp.

◆ TSequenceLengths [1/2]

Definition at line 390 of file data_loader.hpp.

◆ TSequenceLengths [2/2]

Get lengths of sequences Return kInvalidSeqPos for sequences that aren't found.

See also
EGetflags

Definition at line 577 of file scope.hpp.

◆ TSequenceStates [1/2]

Definition at line 392 of file data_loader.hpp.

◆ TSequenceStates [2/2]

Get GenBank states of sequences Return (fState_not_found|fState_no_data) for sequences that aren't found.

See also
EGetflags
CBioseq_Handle::EBioseqStateFlags

Definition at line 600 of file scope.hpp.

◆ TSequenceTypes [1/2]

Definition at line 391 of file data_loader.hpp.

◆ TSequenceTypes [2/2]

Get molecular types of sequences (protein/dna/rna) Return CSeq_inst::eMol_not_set for sequences that aren't found.

See also
EGetflags
CSeq_inst::EMol

Definition at line 588 of file scope.hpp.

◆ TSetDefaultSource

Definition at line 257 of file object_manager.hpp.

◆ TSetScope

Definition at line 260 of file object_manager.hpp.

◆ TSortedMappings [1/2]

Definition at line 190 of file seq_loc_mapper_base.hpp.

◆ TSortedMappings [2/2]

Definition at line 687 of file seq_loc_mapper_base.hpp.

◆ TStd

typedef CSeq_align::C_Segs::TStd CSeq_loc_Mapper_Base::TStd
protected

Definition at line 724 of file seq_loc_mapper_base.hpp.

◆ TSynonymMap

Definition at line 904 of file seq_loc_mapper_base.hpp.

◆ TSynonyms [1/2]

Definition at line 575 of file seq_loc_mapper_base.hpp.

◆ TSynonyms [2/2]

Definition at line 1023 of file seq_loc_mapper_base.hpp.

◆ TTaxIds [1/2]

typedef vector<TTaxId> CDataLoader::TTaxIds

Definition at line 389 of file data_loader.hpp.

◆ TTaxIds [2/2]

typedef vector<TTaxId> CScope::TTaxIds

Get taxonomy ids of sequences Return -1 for sequences that aren't found Return 0 for sequences that don't have taxonomy id.

See also
EGetflags

Definition at line 567 of file scope.hpp.

◆ TThisType

template<typename Value , class Converter = PConvertToString<Value>>
typedef CBlobIdFor<Value, Converter> CBlobIdFor< Value, Converter >::TThisType

Definition at line 115 of file blob_id.hpp.

◆ TTSE_Handles

Definition at line 645 of file scope.hpp.

◆ TTSE_Lock

Definition at line 228 of file data_loader.hpp.

◆ TTSE_LockSet

Definition at line 229 of file data_loader.hpp.

◆ TTSE_LockSets

Definition at line 395 of file data_loader.hpp.

◆ TWriteLockGuard

Definition at line 269 of file object_manager.hpp.

◆ value_type

template<typename Value , class Converter = PConvertToString<Value>>
typedef Value CBlobIdFor< Value, Converter >::value_type

Definition at line 113 of file blob_id.hpp.

Enumeration Type Documentation

◆ EActionIfLocked

Enumerator
eKeepIfLocked 
eThrowIfLocked 
eRemoveIfLocked 

Definition at line 342 of file scope.hpp.

◆ EChoice

main blob is blob with sequence all other blobs are external and contain external annotations

Enumerator
eBlob 

whole main

eBioseq 

main blob with complete bioseq

eCore 

?only seq-entry core?

eBioseqCore 

main blob with bioseq core (no seqdata and annots)

eSequence 

seq data

eFeatures 

features from main blob

eGraph 

graph annotations from main blob

eAlign 

aligns from main blob

eAnnot 

all annotations from main blob

eExtFeatures 

external features

eExtGraph 

external graph annotations

eExtAlign 

external aligns

eExtAnnot 

all external annotations

eOrphanAnnot 

all external annotations if no Bioseq exists

eAll 

all blobs (main and external)

Definition at line 210 of file data_loader.hpp.

◆ EErrCode [1/13]

Enumerator
eBadLocation 

Attempt to map from/to invalid seq-loc.

eUnknownLength 

Can not resolve sequence length.

eBadAlignment 

Unsuported or invalid alignment.

eBadFeature 

Feature can not be used for mapping.

eCanNotMap 

An object can not be mapped - thrown by Map(CSeq_annot&).

eOtherError 

Definition at line 60 of file annot_mapper_exception.hpp.

◆ EErrCode [2/13]

Enumerator
eColumnNotFound 

Requested column is missing.

eRowNotFound 

Requested row is missing.

eIncompatibleValueType 

Data cannot be converted to asked type.

eOtherError 

Definition at line 53 of file seq_table_exception.hpp.

◆ EErrCode [3/13]

Enumerator
eUnsupported 

Unsupported type/flag.

eOtherError 

Definition at line 126 of file gc_assembly_parser.hpp.

◆ EErrCode [4/13]

Enumerator
eNotImplemented 

The method is not implemented.

eRegisterError 

Error while registering a data source/loader.

eFindConflict 

Conflicting data found.

eFindFailed 

The data requested can not be found.

eAddDataError 

Error while adding new data.

eModifyDataError 

Error while modifying data.

eInvalidHandle 

Attempt to use an invalid handle.

eLockedData 

Attempt to remove locked data.

eTransaction 

Transaction violation.

eMissingData 

The sequence doesn't have the data requested.

eOtherError 

Definition at line 53 of file objmgr_exception.hpp.

◆ EErrCode [5/13]

Enumerator
eUnimplemented 

The method is not implemented.

eIteratorTooBig 

Bad internal iterator in delta map.

eSegmentTypeError 

Wrong segment type.

eDataError 

SeqMap data error.

eOutOfRange 

Iterator is out of range.

eInvalidIndex 

Invalid segment index.

eNullPointer 

Attempt to access non-existing object.

eSelfReference 

Self-reference in seq map is detected.

eFail 

Operation failed.

Definition at line 75 of file objmgr_exception.hpp.

◆ EErrCode [6/13]

Enumerator
eCodingError 

Incompatible coding selected.

eDataError 

Sequence data error.

eOutOfRange 

Attempt to access out-of-range iterator.

Definition at line 95 of file objmgr_exception.hpp.

◆ EErrCode [7/13]

Enumerator
eBadLocation 

Wrong location type while mapping annotations.

eFindFailed 

Seq-id can not be resolved.

eLimitError 

Invalid or unknown limit object.

eIncomatibleType 

Incompatible annotation type (feat/graph/align)

eOtherError 

Definition at line 109 of file objmgr_exception.hpp.

◆ EErrCode [8/13]

Enumerator
eNotImplemented 
eNoData 
ePrivateData 
eConnectionFailed 
eCompressionError 
eLoaderFailed 
eNoConnection 
eOtherError 
eRepeatAgain 
eBadConfig 
eNotFound 

Definition at line 125 of file objmgr_exception.hpp.

◆ EErrCode [9/13]

Enumerator
eBlobStateError 
eLoaderError 
eOtherError 

Definition at line 157 of file objmgr_exception.hpp.

◆ EErrCode [10/13]

Enumerator
eNotImplemented 
eBadSequenceType 
eBadLocation 
eNotUnique 
eUnknownLength 
eBadFeature 
eBadResidue 
eBadAlignment 

Definition at line 212 of file objmgr_exception.hpp.

◆ EErrCode [11/13]

Enumerator
eTimeLimitExceded 
eSegmentsLimitExceded 

Definition at line 237 of file objmgr_exception.hpp.

◆ EErrCode [12/13]

Enumerator
eFailed 

Definition at line 140 of file prefetch_manager.hpp.

◆ EErrCode [13/13]

Enumerator
eCanceled 

Definition at line 152 of file prefetch_manager.hpp.

◆ EExist

AddXxx() control values.

Enumerator
eExist_Throw 
eExist_Get 
eExist_Default 

Definition at line 258 of file scope.hpp.

◆ EFeatMapDirection

Mapping direction used when initializing the mapper with a feature.

Enumerator
eLocationToProduct 

Map from the feature's location to product.

eProductToLocation 

Map from the feature's product to location.

Definition at line 345 of file seq_loc_mapper_base.hpp.

◆ EForceLabelLoad

obsolete enum

See also
EGetFlags
Enumerator
eNoForceLabelLoad 
eForceLabelLoad 

Definition at line 443 of file scope.hpp.

◆ EForceLoad

EForceLoad flag instruct scope to ignore already loaded information and always request data loader for data.

Enumerator
eNoForceLoad 
eForceLoad 

Definition at line 404 of file scope.hpp.

◆ EGapFlags

Enumerator
eGapPreserve 
eGapRemove 

Definition at line 739 of file seq_loc_mapper_base.hpp.

◆ EGCAssemblyAlias

Destination of seq-id mapping through a GC-Assembly.

Enumerator
eGCA_Genbank 

Map to GenBank alias, prefer GI.

eGCA_GenbankAcc 

Map to GenBank alias, prefer acc.ver.

eGCA_Refseq 

Map to RefSeq alias, prefer GI.

eGCA_RefseqAcc 

Map to RefSeq alias, prefer acc.ver.

eGCA_UCSC 

Map to UCSC alias.

eGCA_Other 

Map to 'private' seq-id.

Definition at line 228 of file seq_loc_mapper.hpp.

◆ EGetBioseqFlag

Enumerator
eGetBioseq_Resolved 

Search only in already resolved ids.

eGetBioseq_Loaded 

Search in all loaded TSEs in the scope.

eGetBioseq_All 

Search bioseq, load if not loaded yet.

Definition at line 125 of file scope.hpp.

◆ EGetFlags

Flags to control behavior of various meta-data getters fForceLoad instructs scope to ignore already loaded information and alway request data loader for data fThrowOnMissing instructs to throw an exeption if the requested data is missing - either sequence id cannot be found in any data loader or the sequence doesn't have the requested meta-data without the flag getter will return special value.

Enumerator
fForceLoad 

ignore already loaded information and alway request data loader

fThrowOnMissingSequence 

fThrowOnMissingSequence will cause exception to be thrown if sequence not found.

The exception type/code: CObjMgrException/eFindFailed

See also
CObjMgrException
fThrowOnMissingData 

fThrowOnMissingData will cause exception to be thrown if sequence is found but doesn't have the data The exception type/code: CObjMgrException/eMissingData

See also
CObjMgrException
fThrowOnMissing 

throw exception if sequence or requested data aren't found

See also
fThrowOnMissingSequence
fThrowOnMissingData
CObjMgrException
fDoNotRecalculate 

avoid time-consuming recalculation of missing data

Definition at line 415 of file scope.hpp.

◆ EIsDefault

Flag defining if the data loader is included in the "default" group.

Default data loaders can be added to a scope using CScope::AddDefaults().

See also
CScope::AddDefaults()
Enumerator
eDefault 
eNonDefault 

Definition at line 146 of file object_manager.hpp.

◆ EMapOptions

Options for interpretations of locations.

Enumerator
fAlign_Dense_seg_TotalRange 

Ignore internal dense-seg structure - map each dense-seg according to the total ranges involved.

fAlign_Sparse_ToFirst 

Flags used to indicate mapping direction when mapping through a sparse-seg.

Map to first-id

fAlign_Sparse_ToSecond 

Map to second-id.

fMapSingleLevel 

Flag used when mapping through a seq-map (this includes mapping through a bioseq or a GC-assembly).

If set, each call to Map() goes only one level up or down, unlike normal mode which maps from any level as far up/down as possible. The result of mapping can be mapped further by making another call to Map().

fTrimMappedLocation 

Enable trimming of source/destination ranges at sequence end.

By default locations can stretch beyond sequence end. With trimming enabled the mapper will truncate ranges to fit sequence lengths.

Definition at line 351 of file seq_loc_mapper_base.hpp.

◆ EMapResult

Result of seq-annot mapping.

Enumerator
eMapped_None 

No annotation was mapped, the input seq-annot is unchanged.

eMapped_Some 

Some (not all) annotations were mapped.

eMapped_All 

All annotations were mapped, none was removed.

Definition at line 557 of file seq_loc_mapper_base.hpp.

◆ EMergeFlags

Enumerator
eMergeNone 
eMergeAbutting 
eMergeContained 
eMergeBySeg 
eMergeAll 

Definition at line 732 of file seq_loc_mapper_base.hpp.

◆ EMiscFlags

Enumerator
fTrimSplicedSegs 
fKeepNonmapping 
fCheckStrand 
fIncludeSrcLocs 
fMixedAlignsAsSpliced 
fErrorOnPartial 

Definition at line 915 of file seq_loc_mapper_base.hpp.

◆ EMissing

GetXxxHandle control values.

Enumerator
eMissing_Throw 
eMissing_Null 
eMissing_Default 

Definition at line 155 of file scope.hpp.

◆ ENon_locking_prefetch

Enumerator
eNon_locking_prefetch 

Definition at line 66 of file prefetch.hpp.

◆ EObjectType

Enumerator
eNot_set 
eSeq_loc 
eSeq_feat 
eSeq_align 
eSeq_graph 

Definition at line 1056 of file seq_loc_mapper_base.hpp.

◆ EPriority [1/2]

Default data source priority.

Enumerator
kPriority_Entry 

Default priority for explicit entries.

kPriority_Local 

Default priority for local data storage.

kPriority_Replace 

Default priority for replacement loaders.

kPriority_Loader 

Default priority for main loaders.

kPriority_Extra 

Default priority for extra annot loaders.

kPriority_Default 

Use default priority for added data.

kPriority_NotSet 

Deprecated: use kPriority_Default instead.

Definition at line 153 of file object_manager.hpp.

◆ EPriority [2/2]

Enumerator
kPriority_Default 

Use default priority for added data.

kPriority_NotSet 

Deprecated: use kPriority_Default instead.

Definition at line 99 of file scope.hpp.

◆ ERemoveDataLoaders

Clear all information in the scope including data loaders.

Enumerator
eRemoveDataLoaders 

Definition at line 356 of file scope.hpp.

◆ EScopeFlag

Using CScope for virtual bioseqs created from GC-Assemblies.

Enumerator
eOriginalScope 

Put the generated bioseqs into the original scope.

eCopyScope 

Create a new scope for virtual bioseqs.

This keeps The original scope clean, but any changes made to it after creating the mapper will not be picked up by the mapper.

Definition at line 238 of file seq_loc_mapper.hpp.

◆ ESeqMapDirection

Enumerator
eSeqMap_Up 

map from segments to the top level bioseq

eSeqMap_Down 

map from a segmented bioseq to segments

Definition at line 78 of file seq_loc_mapper.hpp.

◆ ESeqType

Enumerator
eSeq_unknown 
eSeq_nuc 
eSeq_prot 

Definition at line 583 of file seq_loc_mapper_base.hpp.

◆ ESplicedRow

Spliced-seg row indexing constants.

Enumerator
eSplicedRow_Prod 
eSplicedRow_Gen 

Definition at line 377 of file seq_loc_mapper_base.hpp.

◆ EState

Enumerator
eInvalid 
eQueued 
eStarted 
eAdvanced 
eCompleted 
eCanceled 
eFailed 

Definition at line 58 of file prefetch_manager.hpp.

◆ ETSEKind

Enumerator
eManualTSEs 
eAllTSEs 

Definition at line 641 of file scope.hpp.

◆ FAnnotBlobType

Enumerator
fAnnotBlobNone 
fAnnotBlobInternal 
fAnnotBlobExternal 
fAnnotBlobOrphan 
fAnnotBlobAll 

Definition at line 77 of file data_loader.hpp.

◆ FAnnotMapFlag

Flags defining seq-annot mapping options.

Enumerator
fAnnotMap_Location 

Map seq-feat locations.

fAnnotMap_Product 

Map seq-feat products.

fAnnotMap_Both 
fAnnotMap_RemoveNonMapping 

Remove annotations which can not be mapped with this mapper.

If the flag is not set, the original annotation is stored in the seq-annot.

fAnnotMap_ThrowOnFailure 

Throw exception if an annotation can not be mapped.

fAnnotMap_Default 

Definition at line 539 of file seq_loc_mapper_base.hpp.

◆ FFuzzOption

Enumerator
fFuzzOption_CStyle 
fFuzzOption_RemoveLimTlOrTr 

Definition at line 382 of file seq_loc_mapper_base.hpp.

◆ FParserFlags

Parser options.

Enumerator
fIgnoreLocalIds 

Do not add local private and external ids to bioseqs.

fIgnoreExternalIds 

Do not add external ids to bioseqs.

fIgnoreAnnots 

Do not add annotations to seq-entries and bioseqs.

fIgnoreDescr 

Do not add descriptions to seq-entries and bioseqs.

fSkipDuplicates 

Skip duplicate sequences (all synonyms are checked).

fDefault 

Definition at line 69 of file gc_assembly_parser.hpp.

Function Documentation

◆ AcquireDataLoader() [1/2]

CObjectManager::TDataSourceLock CObjectManager::AcquireDataLoader ( CDataLoader loader)
protected

◆ AcquireDataLoader() [2/2]

CObjectManager::TDataSourceLock CObjectManager::AcquireDataLoader ( const string loader_name)
protected

◆ AcquireDefaultDataSources()

void CObjectManager::AcquireDefaultDataSources ( TDataSourcesLock sources)
protected

◆ AcquireSharedBioseq()

CObjectManager::TDataSourceLock CObjectManager::AcquireSharedBioseq ( const CBioseq object)
protected

◆ AcquireSharedSeq_annot()

CObjectManager::TDataSourceLock CObjectManager::AcquireSharedSeq_annot ( const CSeq_annot object)
protected

◆ AcquireSharedSeq_entry()

CObjectManager::TDataSourceLock CObjectManager::AcquireSharedSeq_entry ( const CSeq_entry object)
protected

◆ AddAction() [1/3]

CRef< CPrefetchRequest > CPrefetchManager::AddAction ( IPrefetchAction action,
IPrefetchListener listener = 0 
)

Definition at line 90 of file prefetch_manager.cpp.

References CPrefetchManager::AddAction().

◆ AddAction() [2/3]

CRef< CPrefetchRequest > CPrefetchManager_Impl::AddAction ( TPriority  priority,
IPrefetchAction action,
IPrefetchListener listener 
)

◆ AddAction() [3/3]

CRef< CPrefetchRequest > CPrefetchManager::AddAction ( TPriority  priority,
IPrefetchAction action,
IPrefetchListener listener = 0 
)

◆ AddBioseq() [1/2]

CBioseq_Handle CScope::AddBioseq ( CBioseq bioseq,
TPriority  pri = kPriority_Default,
EExist  action = eExist_Throw 
)

Add bioseq, return bioseq handle.

Try to use unresolved seq-id from the bioseq, fail if all ids are already resolved to other sequences. Add object to the score with possibility to edit it directly. If the object is already in the scope the AddXxx() methods will throw an exception or return handle to existent object depending on the action argument.

Definition at line 530 of file scope.cpp.

References CScope_Impl::AddBioseq(), and CScope::m_Impl.

Referenced by CVDBBlastUtil::AddSubjectsToScope(), CProjectFileWriter::AddToScope(), CTrimN::apply(), CdBlaster::blast(), BOOST_AUTO_TEST_CASE(), CkCdRegion(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CSeqEntryGetSource::CSeqEntryGetSource(), CSimpleB2SWrapper::DoBlast2Seqs(), CReadBlastApp::dump_fasta_for_pretty_blast(), CSeqFormatter::DumpAll(), EmblAscii(), CBlastDBExtractor::ExtractFasta(), GenBankAscii(), GenBankAsciiOrig(), CDeflineGenerator::GenerateDefline(), LoadSequencesToScope(), CAsn2FastaApp::ObtainSeqEntryFromBioseq(), CSelectFeatureDlg::OnButtonLoadFile(), CFlatFileDemoDlg::OnLoadFileClick(), CdBlaster::psiBlast(), CGffExportJob::Run(), CGtfExportJob::Run(), CDemoApp::Run(), s_ConvertBioseqs2TSeqLocVector(), s_ConvertSubjects2TSeqLocVector(), s_CreateKmerCounts(), s_GetSequencesIntoScope(), CPsiBlastTestFixture::s_SetupSubject(), CClippedScorer::ScoreAlignments(), SpPrepareEntry(), sRunTest(), sUpdateCase(), CTestAction::TestOID(), CMacroFunction_TrimTerminalNs::TheFunction(), TrimSeqData(), CFastaOstream::Write(), CBlastDB_FastaFormatter::Write(), CIdMapperGCAssembly::x_AddAliasMappings(), CSeq_loc_Mapper::x_AddVirtualBioseq(), CIgBlast::x_AnnotateDomain(), CFlatGatherer::x_GatherFeaturesOnRange(), CBuffer_DataLoader::x_LoadData(), CPromote::x_MakeNewBioseq(), CBlastFormatterApp::x_QueryBioseqToSSeqLoc(), CBlastFormatterVdbApp::x_QueryBioseqToSSeqLoc(), CBlastFormat::x_ReverseQuery(), CBioseqContext::x_SetMapper(), CVectorTrimPanel::x_SetSeqData(), CPsiBl2SeqTestFixture::x_SetupSubject(), CFastaOstreamEx::x_WriteTranslatedCds(), XMLAscii(), and CAnnotWriterApp::xProcessInputObject().

◆ AddBioseq() [2/2]

CBioseq_Handle CScope::AddBioseq ( const CBioseq bioseq,
TPriority  pri = kPriority_Default,
EExist  action = eExist_Throw 
)

Add shared Bioseq, scope will not modify it.

If edit handle is requested, scope will create a copy object. If the object is already in the scope the AddXxx() methods will throw an exception or return handle to existent object depending on the action argument.

Definition at line 554 of file scope.cpp.

References CScope_Impl::AddSharedBioseq(), and CScope::m_Impl.

◆ AddConversion() [1/2]

void CMappingRanges::AddConversion ( CRef< CMappingRange cvt)

◆ AddConversion() [2/2]

CRef< CMappingRange > CMappingRanges::AddConversion ( CSeq_id_Handle  src_id,
TSeqPos  src_from,
TSeqPos  src_length,
ENa_strand  src_strand,
CSeq_id_Handle  dst_id,
TSeqPos  dst_from,
ENa_strand  dst_strand,
bool  ext_to = false,
int  frame = 0,
TSeqPos  dst_total_len = kInvalidSeqPos,
TSeqPos  src_bioseq_len = kInvalidSeqPos,
TSeqPos  dst_len = kInvalidSeqPos 
)

Definition at line 454 of file seq_loc_mapper_base.cpp.

References CMappingRanges::AddConversion().

◆ AddDataLoader()

void CScope::AddDataLoader ( const string loader_name,
TPriority  pri = kPriority_Default 
)

◆ AddDefaults()

void CScope::AddDefaults ( TPriority  pri = kPriority_Default)

Add default data loaders from object manager.

Definition at line 504 of file scope.cpp.

References CScope_Impl::AddDefaults(), and CScope::m_Impl.

Referenced by CTableAnnotDataSource::AddSeqLoc(), CTableAnnotDataSource::AddSnpSeqLoc(), AutofixCommand(), AutofixCommandHugeMode(), BOOST_AUTO_TEST_CASE(), CAsnvalThreadState::BuildScope(), CBiosampleChkApp::BuildScope(), CTLSHandler::BuildScope(), BuildScope(), CFeatTableEdit::CFeatTableEdit(), CFlatFileParser::CFlatFileParser(), CGff2Writer::CGff2Writer(), CheckOneSpecificHost(), CIdMapperNumAssembly::CIdMapperNumAssembly(), CAnnotationASN1::CImplementationData::CImplementationData(), CleanupCommand(), CleanupHugeFileCommand(), CTestObjMgr::CreateBlastSearchQuery(), CTestObjMgr::CreateEmptySSeqLoc(), CTableAnnotDataSource::CreateFeature(), CGBDocument::CreateProjectScope(), CTableAnnotDataSource::CreateSnpFeature(), CTableAnnotDataSource::CreateSnps(), CTestObjMgr::CreateWholeSSeqLoc(), CAgpObjectLoader::Execute(), CAssemblyObjectLoader::Execute(), CBedObjectLoader::Execute(), CGBObjectLoader::Execute(), CGffObjectLoader::Execute(), CLBLASTObjectLoader::Execute(), CPhyObjectLoader::Execute(), CRMObjectLoader::Execute(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CSequenceEditingEventHandler::FixNonReciprocalLinks(), fta_parse_buf(), CGeneFinder::GetFeatViaSubsetThenExtremesIfPossible_Helper(), GetGIForSeqId(), CSeqFetchQueue::GetInstance(), GetResolveOrder(), GetScope(), CAlnBuildApp::GetScope(), CAlnTestApp::GetScope(), CAlnMrgApp::GetScope(), CPairwiseAlnApp::GetScope(), GetSeqIdsForGI(), CDUpdater::getSequencesFromGB(), TaxClient::GetTaxIDForSeqId(), CCleanupApp::HandleSeqID(), ImportFeatTblTesting(), CAltValidator::Init(), CCrossAlnDemoDlg::Init(), CAlignMultipleDemoDlg::Init(), CwxDemoAlignTableFrame::Init(), CSelectFeatureDlg::Init(), CHitMatrixDemoDlg::Init(), CFlatFileDemoDlg::Init(), CSeqGraphicDemoDlg::Init(), CSeqTextDemoDlg::Init(), IsSequenceFetchable(), CwxDemoAlignTableFrame::LoadAccession(), CwxDemoFeatureTableFrame::LoadAccession(), CAlnVwrApp::LoadDenseg(), CwxDemoAlignTableFrame::LoadFile(), CwxDemoFeatureTableFrame::LoadFile(), CSimpleOM::NewScope(), CSeqTextDemoDlg::OnFileClick(), CWinMaskUtil::CInputBioseq_CI::operator++(), OverlapsSameAccessionAlignment::OverlapsSameAccessionAlignment(), CBiosampleChkApp::ProcessFileList(), CBiosampleChkApp::ProcessList(), CHgvsReader::ReadSeqAnnot(), CSeqTestApplication::Render(), IEditingActionFeat::ResetScope(), RetrieveGi555WithTimeOut(), RetrieveLargeChromosomeWithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), RetrievePartsOfLargeChromosome(), CGffExportJob::Run(), CGtfExportJob::Run(), CDemoContigAssemblyApp::Run(), CNgAlignApp::Run(), CProSplignApp::Run(), CIdMapperTestApp::Run(), CDemoSeqQaApp::Run(), CSplignApp::Run(), CSrcChkApp::Run(), CSeqDescrRetrievalJob::Run(), CAnalyzeShiftApp::Run(), CAnnotWriterApp::Run(), CAsn2FastaApp::Run(), CDiscRepApp::Run(), CAlignCleanupApplication::Run(), CTestCompartApplication::Run(), CDemoScoreBuilderApp::Run(), CCpGDemoApp::Run(), CGeneModelDemoApp::Run(), CRegexpLocApp::Run(), CAsnSubCacheCreateApplication::Run(), CGuideTreeApplication::Run(), CConversionApp::Run(), CHgvsToSeqfeatConverter::Run(), CId1FetchApp::Run(), CIdfetchApplication::Run(), CDemoApp::Run(), CMytestApplication::Run(), CObjConvProfile::Run(), CTestBMApp::Run(), CSampleAlnmgrApplication::Run(), VSRunSampleApplication::Run(), CSampleLds2Application::Run(), CFeatTreeSampleApp::Run(), CSampleObjmgrApplication::Run(), s_CreateScope(), s_MakeNewMasterSeq(), s_SetupWithMultipleQueriesAndSubjects(), SCoverageData::SCoverageData(), CScopedProcess::SeqEntryInitialize(), CChainer::CChainerImpl::SetFlagsForChains(), CChainer::CChainerImpl::SetGenomicRange(), CValidError_imp::SetScope(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), CSplitCacheApp::SetupCache(), BlastEngineTestFixture::setupQueryAndSubject(), setupQueryInfoForOffsetTranslation(), sParseFlatfile(), sRunTest(), sUpdateCase(), TestDataNotFound(), CSplitCacheApp::TestSplit(), CMacroFunction_RemoveSingleItemSet::TheFunction(), CMacroFunction_RenormalizeNucProtSet::TheFunction(), CTable2AsnValidator::ValCollect(), CValidError_bioseq::ValidateBioseq(), CValidError_annot::ValidateSeqAnnot(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CCmdCleanup::x_CreateActionCmd(), CCmdPlaceProteinFeats::x_CreateActionCmd(), CMappingObjectLoader::x_CreateMapper(), CGBankLoadingJob::x_CreateProjectItems(), CEditBioseqSampleApp::x_CreateScope(), CSNPSearchJob::x_DoSearch(), CEntrezSearchJob::x_DoSearch(), CAsnSubCacheCreateApplication::x_EliminateIdsAlreadyInCache(), CCreateGeneModelTask::x_GetCommand(), CGapStatsApplication::x_GetScope(), x_GetSeqLocFromStream(), CSeqMasterIndex::x_Init(), CBlastHitMatrix::x_InitObjectManager(), CMultiAlignerFixture::x_InitScope(), CAppHitFilter::x_LoadConstraints(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CAgpconvertApplication::x_LoadTemplate(), CSplitQueryTestFixture::x_PrepareBlastQueryStructures(), CAlnMultiCGIApplication::x_PreProcess(), CGenBankLoadOptionPanel::x_ProccessText(), CPrimeCacheApplication::x_Process_Ids(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CCleanupApp::x_ProcessOneFile(), CClustererApplication::x_RunBinary(), CClustererApplication::x_RunSparse(), CMappingObjectLoader::x_ShowMappingDlg(), CSelectProjectOptions::x_ShowSelectProjectDialog(), CAssemblyListPanel::x_UpdateSearchTerm(), CGenbankIdResolve::xGetDefaultScope(), and CFeatureTableReader::xParseCdregions().

◆ AddGC_Assembly()

Add GC-Assembly.

Sequences from the assembly are converted to bioseqs and added to the scope as a new top level seq-entry.

Definition at line 569 of file scope.cpp.

References CScope::AddTopLevelSeqEntry(), flags, and CGC_Assembly_Parser::GetTSE().

◆ AddRange()

void CGraphRanges::AddRange ( const TRange rg)
inline

◆ AddScope()

void CScope::AddScope ( CScope scope,
TPriority  pri = kPriority_Default 
)

Add the scope's datasources as a single group with the given priority All data sources (data loaders and explicitly added data) have priorities.

The scope scans data sources in order of increasing priorities to find the sequence you've requested. By default, explicitly added data have priority 9, and data loaders - priority 99, so the scope will first look in explicit data, then in data loaders. If you have conflicting data or loaders (e.g. GenBank and BLAST), you may need different priorities to make scope first look, for example, in BLAST, and then if sequence is not found - in GenBank. Note, that the priority you've specified for a data loader at registration time (RegisterInObjectManager()) is a new default for it, and can be overridden when you add the data loader to a scope.

Definition at line 516 of file scope.cpp.

References CScope_Impl::AddScope(), and CScope::m_Impl.

Referenced by CCleanup::CCleanup(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CBlastFormatterApp::PrintFormattedOutput(), CBlastFormatterVdbApp::PrintFormattedOutput(), CVectorScreen::Run(), CXcompareAnnotsApplication::Run(), CCleanup::SetScope(), and CFindOverlapJob::x_CreateProjectItems().

◆ AddSeq_annot() [1/2]

CSeq_annot_Handle CScope::AddSeq_annot ( const CSeq_annot annot,
TPriority  pri = kPriority_Default,
EExist  action = eExist_Throw 
)

Add shared Seq-annot, scope will not modify it.

If edit handle is requested, scope will create a copy object. If the object is already in the scope the AddXxx() methods will throw an exception or return handle to existent object depending on the action argument.

Definition at line 579 of file scope.cpp.

References CScope_Impl::AddSharedSeq_annot(), and CScope::m_Impl.

◆ AddSeq_annot() [2/2]

CSeq_annot_Handle CScope::AddSeq_annot ( CSeq_annot annot,
TPriority  pri = kPriority_Default,
EExist  action = eExist_Throw 
)

Add Seq-annot, return its CSeq_annot_Handle.

Add object to the score with possibility to edit it directly. If the object is already in the scope the AddXxx() methods will throw an exception or return handle to existent object depending on the action argument.

Definition at line 538 of file scope.cpp.

References CScope_Impl::AddSeq_annot(), and CScope::m_Impl.

Referenced by AddSpanningSentinelFeat(), CProjectFileWriter::AddToScope(), CNewCleanup_imp::BasicCleanupSeqAnnotHandle(), BOOST_AUTO_TEST_CASE(), CFeatTableEdit::CFeatTableEdit(), CSourceFeatureItem::CSourceFeatureItem(), LoadScope(), CAsnvalThreadState::ProcessSeqAnnot(), CFeatureGenerator::SImplementation::RecomputePartialFlags(), CDemoApp::Run(), s_AttachAnnotToScope(), s_GetMappedFeat(), CBedWriter::WriteAnnot(), CVcfWriter::WriteAnnot(), and CGff2Writer::x_WriteAnnot().

◆ AddSeq_submit()

CSeq_entry_Handle CScope::AddSeq_submit ( CSeq_submit submit,
TPriority  pri = kPriority_Default 
)

Add Seq-submit, return its CSeq_entry_Handle.

Add object to the score with possibility to edit it directly.

Definition at line 562 of file scope.cpp.

References CScope_Impl::AddSeq_submit(), and CScope::m_Impl.

Referenced by CDemoApp::Run().

◆ AddTopLevelSeqEntry() [1/2]

CSeq_entry_Handle CScope::AddTopLevelSeqEntry ( const CSeq_entry top_entry,
TPriority  pri = kPriority_Default,
EExist  action = eExist_Throw 
)

Add shared Seq-entry, scope will not modify it.

If edit handle is requested, scope will create a copy object. If the object is already in the scope the AddXxx() methods will throw an exception or return handle to existent object depending on the action argument.

Definition at line 546 of file scope.cpp.

References CScope_Impl::AddSharedSeq_entry(), and CScope::m_Impl.

◆ AddTopLevelSeqEntry() [2/2]

CSeq_entry_Handle CScope::AddTopLevelSeqEntry ( CSeq_entry top_entry,
TPriority  pri = kPriority_Default,
EExist  action = eExist_Default 
)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with possibility to edit it directly.

If the object is already in the scope the AddXxx() methods will throw an exception or return handle to existent object depending on the action argument.

Definition at line 522 of file scope.cpp.

References CScope_Impl::AddSeq_entry(), and CScope::m_Impl.

Referenced by AddBioseqsToScope(), AddFastaToScope(), CScope::AddGC_Assembly(), CFeatureTableReader::AddProteins(), AddSentinelRNASeq(), CProjectFileWriter::AddToScope(), CAlignmentAssistant::AdjustBioseq(), AutofixCommand(), AutofixCommandHugeMode(), BOOST_AUTO_TEST_CASE(), CheckDeflineMatches(), CheckOneSpecificHost(), CheckPropagatedCDSLocation(), CheckRegulatoryFeatures(), CheckTargetedLocusEntry(), CleanupCommand(), CleanupHugeFileCommand(), CTable2AsnContext::CopyFeatureIdsToComments(), CAlnVec::CreateConsensus(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSeqEntrySource::CSeqEntrySource(), CNewCleanup_imp::EnteringEntry(), CAnnotationASN1::ExtractModels(), IEditingActionFeat::FindOrCreateProtFeat(), CEditingActionFeatGeneLocus::FindRelated(), CSequenceEditingEventHandler::FixNonReciprocalLinks(), CFlatFileGenerator::Generate(), CScore_CdsInternalStops::Get(), CBiosampleChkApp::GetBiosampleDescriptorsFromSeqEntry(), CEditSequenceEnds::GetCommand(), CEditSeqEndsWithAlign::GetCommand(), GetGoodSeqEntryWithFeatureIds(), GetScope(), CEditSequence::GetSequence(), CGbScopeLoader::HandleSeqEntry(), CAsn2FastaApp::HandleSeqEntry(), CCleanupApp::HandleSeqEntry(), ImportFeatTblTesting(), CwxDemoAlignTableFrame::LoadAccession(), CwxDemoFeatureTableFrame::LoadAccession(), CAlnVwrApp::LoadDenseg(), CAlnMrgApp::LoadFasta(), CwxDemoAlignTableFrame::LoadFile(), CwxDemoFeatureTableFrame::LoadFile(), LoadScope(), CAlnMrgApp::LoadSeqEntry(), CId1FetchApp::LookUpGI(), CTblastnNode::Main(), MakeRegulatoryFeatureTest(), MakeTrnaWithAnticodon(), CAsn2FastaApp::ObtainSeqEntryFromBioseqSet(), CAsn2FastaApp::ObtainSeqEntryFromSeqEntry(), CAsn2FastaApp::ObtainSeqEntryFromSeqSubmit(), CFlatFileDemoDlg::OnLoadFileClick(), CPrimeCacheApplication::CCacheBioseq::operator()(), SBlobCopier::operator()(), CWinMaskUtil::CInputBioseq_CI::operator++(), CMytestApplication::PlayAroundWithSuggestIntervals(), CTabularFormatter_StopCodonChanges::Print(), CSplitCacheApp::ProcessEntry(), CAsnvalThreadState::ProcessSeqDesc(), CBiosampleChkApp::ProcessSeqEntry(), CTLSHandler::ProcessSeqEntry(), CAsnvalThreadState::ProcessSeqEntry(), CAsnvalThreadState::ProcessSeqSubmit(), CAlnAsnReader::Read(), ReadBioSeqs(), CAsnvalThreadState::ReadClassMember(), ReadEntry(), ReadFromFile(), ReadMsa(), CGffExportJob::Run(), CGtfExportJob::Run(), CPsiBlastApp::Run(), CLocalFinderApp::Run(), CWinMaskDemoApplication::Run(), CVDBTblastnApp::Run(), CConversionApp::Run(), CDustMaskApplication::Run(), CDemoApp::Run(), SegMaskerApplication::Run(), CMytestApplication::Run(), CWinMaskApplication::Run(), s_AttachEntryToScope(), s_CreateScope(), s_GatherSources(), s_GetScope(), s_HasUnprocessedCdregions(), s_MakeNewMasterSeq(), CScopedProcess::SeqEntryInitialize(), CValidError_imp::SetScope(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), CValidError_imp::Setup(), CTable2AsnContext::SmartFeatureAnnotation(), CBlobSplitterImpl::Split(), sRunTest(), sUpdateCase(), TestFeatInsideGap(), TestForRecomb(), TestOneGapSeq(), TestRepeatRegion(), TestTrimForFrame(), CMacroFunction_RemoveSingleItemSet::TheFunction(), CMacroFunction_RenormalizeNucProtSet::TheFunction(), TryMiscWithNs(), TryOneCase(), TryOneCaseMixLoc(), TryOneCDSCase(), CTable2AsnValidator::ValCollect(), CValidError_imp::Validate(), CValidError_bioseq::ValidateBioseq(), CValidError_annot::ValidateSeqAnnot(), CFastaOstream::Write(), CSrcWriter::WriteSeqEntry(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CLocalFileRestorer::x_AttachNewObject(), CPrimeCacheApplication::x_CacheSeqEntry(), CCmdCleanup::x_CreateActionCmd(), CCmdPlaceProteinFeats::x_CreateActionCmd(), CBlastFastaInputSource::x_FastaToSeqLoc(), CSraInputSource::x_GetNextSeq_loc(), x_GetSeqLocFromStream(), CSeqMasterIndex::x_Init(), CDeltaBlastTestFixture::x_InitScope(), CNgAlignApp::x_LoadExternalSequences(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CAlnPrinterFixture::x_LoadSequences(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CGapStatsApplication::x_ReadFileOrAccn(), CNgAlignApp::x_RecurseSeqEntry(), CTblastnApp::x_RunMTBySplitDB(), CCDSTranslationPanel::x_SetLocationForProtein(), CFeatureTableReader::xAddProteinToSeqEntry(), CFeatureTableReader::xParseCdregions(), CAnnotWriterApp::xProcessInputObject(), and CAnnotWriterApp::xTryProcessInputId().

◆ AttachAnnot()

void CScope::AttachAnnot ( CSeq_entry parent,
CSeq_annot annot 
)

◆ AttachEntry()

void CScope::AttachEntry ( CSeq_entry parent,
CSeq_entry entry 
)

Definition at line 603 of file scope.cpp.

References CScope::GetSeq_entryEditHandle(), and CSeq_entry_EditHandle::SetSet().

◆ BeginMappingRanges()

CMappingRanges::TRangeIterator CMappingRanges::BeginMappingRanges ( CSeq_id_Handle  id,
TSeqPos  from,
TSeqPos  to 
) const

◆ CancelAllTasks()

void CPrefetchManager::CancelAllTasks ( void  )

◆ CanGetBlobById()

bool CDataLoader::CanGetBlobById ( void  ) const
virtual

◆ CanMap()

bool CMappingRange::CanMap ( TSeqPos  from,
TSeqPos  to,
bool  is_set_strand,
ENa_strand  strand 
) const

Check if the interval can be mapped through this mapping range.

Strand direction is checked only if is_set_strand is true.

Definition at line 216 of file seq_loc_mapper_base.cpp.

References IsReverse(), CMappingRange::m_Src_from, and CMappingRange::m_Src_strand.

Referenced by CMappingRange::x_Map_Fuzz(), and CSeq_loc_Mapper_Base::x_MapNextRange().

◆ CBlobIdFor()

template<typename Value , class Converter = PConvertToString<Value>>
CBlobIdFor< Value, Converter >::CBlobIdFor ( const value_type v)
inline

Definition at line 117 of file blob_id.hpp.

◆ CBlobIdKey()

CBlobIdKey::CBlobIdKey ( const CBlobId id = 0)
inline

Definition at line 160 of file blob_id.hpp.

◆ CBlobStateException() [1/3]

CBlobStateException::CBlobStateException ( const CBlobStateException other)
inline

Definition at line 178 of file objmgr_exception.hpp.

References CException::x_Assign().

◆ CBlobStateException() [2/3]

CBlobStateException::CBlobStateException ( const CDiagCompileInfo info,
const CException prev_exception,
EErrCode  err_code,
const string message,
TBlobState  state,
EDiagSev  severity = eDiag_Error 
)
inline

Definition at line 165 of file objmgr_exception.hpp.

References info, CException::x_Init(), and CException::x_InitErrCode().

◆ CBlobStateException() [3/3]

CBlobStateException::CBlobStateException ( void  )
inlineprotected

◆ CDataLoader() [1/3]

CDataLoader::CDataLoader ( const CDataLoader )
private

◆ CDataLoader() [2/3]

CDataLoader::CDataLoader ( const string loader_name)
protected

Definition at line 70 of file data_loader.cpp.

References CDataLoader::m_Name, and NStr::PtrToString().

◆ CDataLoader() [3/3]

CDataLoader::CDataLoader ( void  )
protected

Definition at line 63 of file data_loader.cpp.

References CDataLoader::m_Name, and NStr::PtrToString().

◆ CGC_Assembly_Parser()

CGC_Assembly_Parser::CGC_Assembly_Parser ( const CGC_Assembly assembly,
TParserFlags  flags = fDefault 
)

Parse the assembly, convert it to seq-entry, collect additional information (top-level sequences etc).

Definition at line 68 of file gc_assembly_parser.cpp.

References CGC_Assembly_Parser::m_TSE, CRef< C, Locker >::Reset(), CGC_Assembly_Parser::x_InitSeq_entry(), and CGC_Assembly_Parser::x_ParseGCAssembly().

◆ CGraphRanges()

CGraphRanges::CGraphRanges ( void  )
inline

Definition at line 237 of file seq_loc_mapper_base.hpp.

◆ ChoiceToDetails()

SRequestDetails CDataLoader::ChoiceToDetails ( EChoice  choice) const
virtual

◆ Clone()

CSeq_loc_Mapper_Message * CSeq_loc_Mapper_Message::Clone ( void  ) const
virtual

Create a copy of the message.

The caller is responsible for destroying the copy.

Reimplemented from CMessage_Basic.

Definition at line 512 of file seq_loc_mapper_base.cpp.

References CSeq_loc_Mapper_Message::CSeq_loc_Mapper_Message().

◆ CMappingRange()

CMappingRange::CMappingRange ( CSeq_id_Handle  src_id,
TSeqPos  src_from,
TSeqPos  src_length,
ENa_strand  src_strand,
CSeq_id_Handle  dst_id,
TSeqPos  dst_from,
ENa_strand  dst_strand,
bool  ext_to = false,
int  frame = 0,
TSeqPos  src_bioseq_len = kInvalidSeqPos,
TSeqPos  dst_len = kInvalidSeqPos 
)

Definition at line 187 of file seq_loc_mapper_base.cpp.

◆ CMappingRanges()

CMappingRanges::CMappingRanges ( void  )

Definition at line 439 of file seq_loc_mapper_base.cpp.

◆ CObjectManager()

CObjectManager::CObjectManager ( void  )
private

Definition at line 111 of file object_manager.cpp.

◆ CollectSynonyms() [1/3]

const CSeq_id_Handle & CSeq_loc_Mapper_Base::CollectSynonyms ( const CSeq_id_Handle id) const

◆ CollectSynonyms() [2/3]

void CSeq_loc_Mapper_Base::CollectSynonyms ( const CSeq_id_Handle id,
TSynonyms synonyms 
) const

NOTE: In most cases CollectSynonyms(const CSeq_id_Handle& id) should be used instead, since it takes care of synonym storage and mapping.

This method does nothing but storing synonyms in the container.

Definition at line 2248 of file seq_loc_mapper_base.cpp.

References IMapper_Sequence_Info::CollectSynonyms(), set< Key, Compare >::empty(), CSeq_loc_Mapper_Options::GetSeqInfo(), set< Key, Compare >::insert(), and CSeq_loc_Mapper_Base::m_MapOptions.

◆ CollectSynonyms() [3/3]

virtual void IMapper_Sequence_Info::CollectSynonyms ( const CSeq_id_Handle id,
TSynonyms synonyms 
)
pure virtual

Collect all synonyms for the id including the id itself.

Any derived class must add at least the original id to the collection.

Implemented in CScope_Mapper_Sequence_Info, CTestMapperSeqInfo, CDefault_Mapper_Sequence_Info, and CExplicit_Mapper_Sequence_Info.

Referenced by CSeq_loc_Mapper_Base::CollectSynonyms().

◆ CParamLoaderMaker()

template<class TDataLoader , class TParam >
CParamLoaderMaker< TDataLoader, TParam >::CParamLoaderMaker ( TParam  param)
inline

Definition at line 156 of file data_loader.hpp.

References CLoaderMaker_Base::m_Name.

◆ CPrefetchBioseq() [1/3]

CPrefetchBioseq::CPrefetchBioseq ( const CBioseq_Handle bioseq)
protected

Definition at line 67 of file prefetch_actions.cpp.

References NCBI_THROW.

◆ CPrefetchBioseq() [2/3]

CPrefetchBioseq::CPrefetchBioseq ( const CScopeSource scope)
protected

Definition at line 61 of file prefetch_actions.cpp.

◆ CPrefetchBioseq() [3/3]

CPrefetchBioseq::CPrefetchBioseq ( const CScopeSource scope,
const CSeq_id_Handle id 
)

Definition at line 78 of file prefetch_actions.cpp.

References NCBI_THROW.

◆ CPrefetchBioseqActionSource() [1/2]

CPrefetchBioseqActionSource::CPrefetchBioseqActionSource ( const CScopeSource scope,
const TIds ids 
)

Definition at line 329 of file prefetch_actions.cpp.

◆ CPrefetchBioseqActionSource() [2/2]

CPrefetchBioseqActionSource::CPrefetchBioseqActionSource ( const CScopeSource scope,
ISeq_idSource ids 
)

Definition at line 321 of file prefetch_actions.cpp.

◆ CPrefetchComplete() [1/3]

Definition at line 165 of file prefetch_actions.cpp.

◆ CPrefetchComplete() [2/3]

template<class Handle >
CPrefetchComplete< Handle >::CPrefetchComplete ( const THandle handle)
inlineexplicit

Definition at line 173 of file prefetch_actions.hpp.

◆ CPrefetchComplete() [3/3]

Definition at line 159 of file prefetch_actions.cpp.

◆ CPrefetchFeat_CI() [1/3]

CPrefetchFeat_CI::CPrefetchFeat_CI ( const CBioseq_Handle bioseq,
const CRange< TSeqPos > &  range,
ENa_strand  strand,
const SAnnotSelector selector 
)

Definition at line 116 of file prefetch_actions.cpp.

◆ CPrefetchFeat_CI() [2/3]

CPrefetchFeat_CI::CPrefetchFeat_CI ( const CScopeSource scope,
CConstRef< CSeq_loc loc,
const SAnnotSelector selector 
)

Definition at line 102 of file prefetch_actions.cpp.

References NCBI_THROW.

◆ CPrefetchFeat_CI() [3/3]

CPrefetchFeat_CI::CPrefetchFeat_CI ( const CScopeSource scope,
const CSeq_id_Handle seq_id,
const CRange< TSeqPos > &  range,
ENa_strand  strand,
const SAnnotSelector selector 
)

Definition at line 128 of file prefetch_actions.cpp.

◆ CPrefetchFeat_CIActionSource() [1/2]

CPrefetchFeat_CIActionSource::CPrefetchFeat_CIActionSource ( const CScopeSource scope,
const TIds ids,
const SAnnotSelector sel 
)

Definition at line 348 of file prefetch_actions.cpp.

◆ CPrefetchFeat_CIActionSource() [2/2]

CPrefetchFeat_CIActionSource::CPrefetchFeat_CIActionSource ( const CScopeSource scope,
ISeq_idSource ids,
const SAnnotSelector sel 
)

Definition at line 358 of file prefetch_actions.cpp.

◆ CPrefetchManager() [1/3]

CPrefetchManager::CPrefetchManager ( const CPrefetchManager )
private

◆ CPrefetchManager() [2/3]

CPrefetchManager::CPrefetchManager ( unsigned  max_threads,
CThread::TRunMode  threads_mode = CThread::fRunDefault 
)
explicit

Definition at line 66 of file prefetch_manager.cpp.

◆ CPrefetchManager() [3/3]

CPrefetchManager::CPrefetchManager ( void  )

Definition at line 60 of file prefetch_manager.cpp.

◆ CPrefetchManager_Impl() [1/2]

CPrefetchManager_Impl::CPrefetchManager_Impl ( const CPrefetchManager_Impl )
privatedelete

◆ CPrefetchManager_Impl() [2/2]

CPrefetchManager_Impl::CPrefetchManager_Impl ( unsigned  max_threads,
CThread::TRunMode  threads_mode 
)

Definition at line 222 of file prefetch_manager_impl.cpp.

◆ CPrefetchRequest()

CPrefetchRequest::CPrefetchRequest ( CObjectFor< CMutex > *  state_mutex,
IPrefetchAction action,
IPrefetchListener listener,
unsigned int  priority 
)

Definition at line 121 of file prefetch_manager_impl.cpp.

◆ CPrefetchSequence()

CPrefetchSequence::CPrefetchSequence ( CPrefetchManager manager,
IPrefetchActionSource source,
size_t  active_size = 10 
)

Definition at line 132 of file prefetch_manager.cpp.

References CPrefetchSequence::EnqueNextAction(), and i.

◆ CPrefetchTokenOld() [1/4]

CPrefetchTokenOld::CPrefetchTokenOld ( const CPrefetchTokenOld token)
inline

Definition at line 149 of file prefetch.hpp.

◆ CPrefetchTokenOld() [2/4]

CPrefetchTokenOld::CPrefetchTokenOld ( CScope scope,
const TIds ids,