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< TSeqPos >	CMappingRange::TRange
typedef CRef< CInt_fuzz >	CMappingRange::TFuzz
typedef pair< TFuzz, TFuzz >	CMappingRange::TRangeFuzz
typedef CMappingRange::TRange	CMappingRanges::TRange
typedef CRangeMultimap< CRef< CMappingRange >, TSeqPos >	CMappingRanges::TRangeMap
typedef TRangeMap::const_iterator	CMappingRanges::TRangeIterator
typedef map< CSeq_id_Handle, TRangeMap >	CMappingRanges::TIdMap
typedef TIdMap::const_iterator	CMappingRanges::TIdIterator
typedef vector< CRef< CMappingRange > >	CMappingRanges::TSortedMappings
typedef CRange< TSeqPos >	CGraphRanges::TRange
typedef vector< TRange >	CGraphRanges::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_Handle >	CSeq_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< TRange >	CSeq_loc_Mapper_Base::TDstRanges
typedef map< CSeq_id_Handle, TDstRanges >	CSeq_loc_Mapper_Base::TDstIdMap
typedef vector< TDstIdMap >	CSeq_loc_Mapper_Base::TDstStrandMap
typedef CRef< CInt_fuzz >	CSeq_loc_Mapper_Base::TFuzz
typedef pair< TFuzz, TFuzz >	CSeq_loc_Mapper_Base::TRangeFuzz
typedef list< SMappedRange >	CSeq_loc_Mapper_Base::TMappedRanges
typedef vector< TMappedRanges >	CSeq_loc_Mapper_Base::TRangesByStrand
typedef map< CSeq_id_Handle, TRangesByStrand >	CSeq_loc_Mapper_Base::TRangesById
typedef map< CSeq_id_Handle, ESeqType >	CSeq_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_Handle >	CSeq_loc_Mapper_Base::TSynonymMap
typedef map< CSeq_id_Handle, TSeqPos >	CSeq_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< int >	CBlobIdInt
typedef CBlobIdFor< const void * >	CBlobIdPtr
typedef CBlobIdFor< string >	CBlobIdString
typedef CBlobIdFor< CSeq_id_Handle >	CBlobIdSeq_id
typedef CRange< TSeqPos >	SRequestDetails::TRange
typedef set< SAnnotTypeSelector >	SRequestDetails::TAnnotTypesSet
typedef map< CAnnotName, TAnnotTypesSet >	SRequestDetails::TAnnotSet
typedef int	SRequestDetails::TAnnotBlobType
typedef SRegisterLoaderInfo< CDataLoader >	CLoaderMaker_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_Lock >	CDataLoader::TTSE_LockSet
typedef CRef< CTSE_Chunk_Info >	CDataLoader::TChunk
typedef vector< TChunk >	CDataLoader::TChunkSet
typedef set< string >	CDataLoader::TProcessedNAs
typedef set< CSeq_id_Handle >	CDataLoader::TSeq_idSet
typedef vector< CSeq_id_Handle >	CDataLoader::TIds
typedef vector< bool >	CDataLoader::TLoaded
	Bulk loading interface for a small pieces of information per id. More...
typedef vector< TIds >	CDataLoader::TBulkIds
typedef vector< TGi >	CDataLoader::TGis
typedef vector< string >	CDataLoader::TLabels
typedef vector< TTaxId >	CDataLoader::TTaxIds
typedef vector< TSeqPos >	CDataLoader::TSequenceLengths
typedef vector< CSeq_inst::TMol >	CDataLoader::TSequenceTypes
typedef vector< int >	CDataLoader::TSequenceStates
typedef vector< int >	CDataLoader::TSequenceHashes
typedef vector< bool >	CDataLoader::THashKnown
typedef map< CSeq_id_Handle, TTSE_LockSet >	CDataLoader::TTSE_LockSets
typedef vector< vector< CSeq_id_Handle > >	CDataLoader::TSeqIdSets
typedef vector< CTSE_Lock >	CDataLoader::TCDD_Locks
typedef CBlobIdKey	CDataLoader::TBlobId
typedef int	CDataLoader::TBlobVersion
typedef CRef< IEditSaver >	CDataLoader::TEditSaver
typedef int	CGC_Assembly_Parser::TParserFlags
typedef set< CSeq_id_Handle >	CGC_Assembly_Parser::TSeqIds
typedef unsigned int	CPrefetchManager_Impl::TPriority
typedef CRef< CDataSource >	CObjectManager::TDataSourceLock
typedef int	CObjectManager::TPriority
typedef vector< string >	CObjectManager::TRegisteredNames
typedef SRegisterLoaderInfo< CDataLoader >	CObjectManager::TRegisterLoaderInfo
typedef set< TDataSourceLock >	CObjectManager::TDataSourcesLock
typedef CPluginManager< CDataLoader >	CObjectManager::TPluginManager
typedef set< TDataSourceLock >	CObjectManager::TSetDefaultSource
typedef map< string, CDataLoader * >	CObjectManager::TMapNameToLoader
typedef map< const CObject *, TDataSourceLock >	CObjectManager::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< TObject >	CPrefetchComplete< Handle >::TResult
typedef CBioseq_Handle	CPrefetchComplete< CBioseq_Handle >::THandle
typedef THandle::TObject	CPrefetchComplete< CBioseq_Handle >::TObject
typedef CConstRef< TObject >	CPrefetchComplete< CBioseq_Handle >::TResult
typedef Container	CStdSeq_idSource< Container >::TContainer
typedef TContainer::const_iterator	CStdSeq_idSource< Container >::TIterator
typedef vector< CSeq_id_Handle >	CPrefetchBioseqActionSource::TIds
typedef vector< CSeq_id_Handle >	CPrefetchFeat_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_Handle >	CScope::TIds
typedef vector< CBioseq_Handle >	CScope::TBioseqHandles
typedef vector< CTSE_Handle >	CScope::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_Handle >	CScope::TSeq_id_Handles
	Bulk retrieval methods Common argument typedef - vector of requested ids. More...
typedef vector< TIds >	CScope::TBulkIds
	Get all ids of sequences Returns empty ids if the sequence is not found. More...
typedef vector< TGi >	CScope::TGIs
	Get GI of a sequence Returns ZERO_GI for sequence that aren't found or don't have GI. More...
typedef vector< string >	CScope::TLabels
	Get short descriptions of sequences, usually "accession.version" Returns empty strings for sequences that aren't found. More...
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. More...
typedef vector< TSeqPos >	CScope::TSequenceLengths
	Get lengths of sequences Return kInvalidSeqPos for sequences that aren't found. More...
typedef vector< CSeq_inst::TMol >	CScope::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::TBioseqStateFlags >	CScope::TSequenceStates
	Get GenBank states of sequences Return (fState_not_found|fState_no_data) for sequences that aren't found. More...
typedef vector< TSequenceHash >	CScope::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_Handle >	CScope::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_id >	CMappingRange::GetDstId (void) const
const CSeq_id_Handle &	CMappingRange::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 TIdMap &	CMappingRanges::GetIdMap () const
void	CMappingRanges::AddConversion (CRef< CMappingRange > cvt)
	Add new mapping range to the proper place. More...
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)
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 TGraphRanges &	CGraphRanges::GetRanges (void) const
void	CGraphRanges::AddRange (const TRange &rg)
const TRange &	CGraphRanges::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_Info *	CSeq_loc_Mapper_Options::GetMapperSequenceInfo (void) const
	Sequence type, length etc. More...
CSeq_loc_Mapper_Options &	CSeq_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_Options &	CSeq_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_Options &	CSeq_loc_Mapper_Options::SetAlign_Sparse_ToFirst (bool value=true)
CSeq_loc_Mapper_Options &	CSeq_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_Options &	CSeq_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_Options &	CSeq_loc_Mapper_Options::SetTrimMappedLocation (bool value=true)
IMapper_Sequence_Info &	CSeq_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_Base &	CSeq_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_Base &	CSeq_loc_Mapper_Base::SetMergeAbutting (void)
	Merge only abutting intervals, keep overlapping. More...
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::SetMergeBySeg (void)
	Merge only intervals from the same group. More...
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::SetMergeContained (void)
	Merge intervals only if one is completely covered by another. More...
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::SetMergeAll (void)
	Merge any abutting or overlapping intervals. More...
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::SetGapPreserve (void)
	Whether to preserve or remove NULL sub-locations (usually indicating gaps) from the result. More...
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::SetGapRemove (void)
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::SetTrimSplicedSeg (bool trim)
	For mapping spliced-segs only: preserve or trim starting/ending indels. More...
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::KeepNonmappingRanges (void)
	Keep ranges which can not be mapped. More...
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::TruncateNonmappingRanges (void)
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::SetCheckStrand (bool value=true)
	Check strands before mapping a range. More...
CSeq_loc_Mapper_Base &	CSeq_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_Base &	CSeq_loc_Mapper_Base::IncludeSourceLocs (bool value=true)
	Include source ranges in the mapped location. More...
CSeq_loc_Mapper_Base &	CSeq_loc_Mapper_Base::SetErrorOnPartial (bool value=true)
	Report source range trimming as an error. More...
CRef< CSeq_loc >	CSeq_loc_Mapper_Base::Map (const CSeq_loc &src_loc)
	Map seq-loc. More...
CRef< CSeq_loc >	CSeq_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_align >	CSeq_loc_Mapper_Base::Map (const CSeq_align &src_align)
	Map the whole alignment. More...
CRef< CSeq_align >	CSeq_loc_Mapper_Base::Map (const CSeq_align &src_align, size_t row)
	Map a single row of the alignment. More...
CRef< CSeq_graph >	CSeq_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_Handle &	CSeq_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_Base *	CSeq_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_Base &	CSeq_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_align >	CSeq_loc_Mapper_Base::x_MapSeq_align (const CSeq_align &src_align, size_t *row)
TMappedRanges &	CSeq_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_loc >	CSeq_loc_Mapper_Base::x_RangeToSeq_loc (const CSeq_id_Handle &idh, TSeqPos from, TSeqPos to, size_t strand_idx, TRangeFuzz rg_fuzz)
CRef< CSeq_loc >	CSeq_loc_Mapper_Base::x_GetMappedSeq_loc (void)
void	CSeq_loc_Mapper_Base::x_StripExtraneousFuzz (CRef< CSeq_loc > &loc) const
CConstRef< CSeq_loc >	CSeq_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_Handle &	CSeq_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 CMappingRanges &	CSeq_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_Message *	CSeq_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_loc *	CSeq_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_feat *	CSeq_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_align *	CSeq_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_graph *	CSeq_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 string &	PConvertToString< 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_type &	CBlobIdFor< 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 CBlobId &	CBlobIdKey::operator* (void) const
const CBlobId *	CBlobIdKey::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
CNcbiOstream &	operator<< (CNcbiOstream &out, const CBlobId &id)
CNcbiOstream &	operator<< (CNcbiOstream &out, const CBlobIdKey &id)
	SRequestDetails::SRequestDetails (void)
virtual CDataLoader *	CLoaderMaker_Base::CreateLoader (void) const =0
virtual	CLoaderMaker_Base::~CLoaderMaker_Base (void)
	CSimpleLoaderMaker< TDataLoader >::CSimpleLoaderMaker (void)
virtual	CSimpleLoaderMaker< TDataLoader >::~CSimpleLoaderMaker (void)
virtual CDataLoader *	CSimpleLoaderMaker< TDataLoader >::CreateLoader (void) const
TRegisterInfo	CSimpleLoaderMaker< TDataLoader >::GetRegisterInfo (void)
	CParamLoaderMaker< TDataLoader, TParam >::CParamLoaderMaker (TParam param)
virtual	CParamLoaderMaker< TDataLoader, TParam >::~CParamLoaderMaker (void)
virtual CDataLoader *	CParamLoaderMaker< 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)
CDataSource *	CDataLoader::GetDataSource (void) const
	CDataLoader::CDataLoader (const CDataLoader &)
CDataLoader &	CDataLoader::operator= (const CDataLoader &)
	NCBI_DECLARE_INTERFACE_VERSION (objects::CDataLoader, "xloader", 9, 0, 0)
CPluginManager_DllResolver *	CDllResolver_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_entry >	CGC_Assembly_Parser::GetTSE (void) const
	Create seq-entry with all parsed sequences, annotations etc. More...
const TSeqIds &	CGC_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< CPrefetchRequest >	CPrefetchManager_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< CObjectManager >	CObjectManager::GetInstance (void)
	Return the existing object manager or create one. More...
virtual	CObjectManager::~CObjectManager (void)
CDataLoader *	CObjectManager::RegisterDataLoader (TPluginManagerParamTree *params=0, const string &driver_name=kEmptyStr)
	Add data loader using plugin manager. More...
CDataLoader *	CObjectManager::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)
CDataLoader *	CObjectManager::x_GetLoaderByName (const string &loader_name) const
TDataSourceLock	CObjectManager::x_FindDataSource (const CObject *key)
TDataSourceLock	CObjectManager::x_RevokeDataLoader (CDataLoader *loader)
TPluginManager &	CObjectManager::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 CException *	CBlobStateException::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)
CPrefetchTokenOld &	CPrefetchTokenOld::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)
CScope &	CScopeSource::GetScope (void)
	CPrefetchBioseq::CPrefetchBioseq (const CScopeSource &scope, const CSeq_id_Handle &id)
virtual bool	CPrefetchBioseq::Execute (CRef< CPrefetchRequest > token)
const CSeq_id_Handle &	CPrefetchBioseq::GetSeq_id (void) const
const CBioseq_Handle &	CPrefetchBioseq::GetBioseqHandle (void) const
const CBioseq_Handle &	CPrefetchBioseq::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 SAnnotSelector &	CPrefetchFeat_CI::GetSelector (void) const
const CFeat_CI &	CPrefetchFeat_CI::GetFeat_CI (void) const
const CFeat_CI &	CPrefetchFeat_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< IPrefetchAction >	CPrefetchBioseqActionSource::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< IPrefetchAction >	CPrefetchFeat_CIActionSource::GetNextAction (void)
static void	CStdPrefetch::Wait (CRef< CPrefetchRequest > token)
static CRef< CPrefetchRequest >	CStdPrefetch::GetBioseqHandle (CPrefetchManager &manager, const CScopeSource &scope, const CSeq_id_Handle &id)
static CBioseq_Handle	CStdPrefetch::GetBioseqHandle (CRef< CPrefetchRequest > token)
static CRef< CPrefetchRequest >	CStdPrefetch::GetFeat_CI (CPrefetchManager &manager, const CBioseq_Handle &bioseq, const CRange< TSeqPos > &range, ENa_strand strand, const SAnnotSelector &sel)
static CRef< CPrefetchRequest >	CStdPrefetch::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< CPrefetchRequest >	CStdPrefetch::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< IPrefetchAction >	IPrefetchActionSource::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< CPrefetchRequest >	CPrefetchManager::AddAction (TPriority priority, IPrefetchAction *action, IPrefetchListener *listener=0)
CRef< CPrefetchRequest >	CPrefetchManager::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< CPrefetchRequest >	CPrefetchSequence::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)
IPrefetchAction *	CPrefetchRequest::GetAction (void) const
IPrefetchListener *	CPrefetchRequest::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)
CObjectManager &	CScope::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< CSynonymsSet >	CScope::GetSynonyms (const CSeq_id &id)
	Get bioseq synonyms, resolving to the bioseq in this scope. More...
CConstRef< CSynonymsSet >	CScope::GetSynonyms (const CSeq_id_Handle &id)
	Get bioseq synonyms, resolving to the bioseq in this scope. More...
CConstRef< CSynonymsSet >	CScope::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_Impl &	CScope::GetImpl (void)
	CScope::CScope (const CScope &)
CScope &	CScope::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_Base *	CSeq_loc_Mapper::InitAlignMapper (const CSeq_align &src_align)
	CSeq_loc_Mapper::CSeq_loc_Mapper (const CSeq_loc_Mapper &)
CSeq_loc_Mapper &	CSeq_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_Info >	CSeq_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_loc >	CSeq_loc_Mapper_Base::m_SrcLocs
CRef< CGraphRanges >	CSeq_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< CMappingRanges >	CSeq_loc_Mapper_Base::m_Mappings
CRef< CSeq_loc >	CSeq_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< CObject >	CSeq_loc_Mapper_Message::m_Obj
pair_base_member< convert_to_string_type, value_type >	CBlobIdFor< Value, Converter >::m_Value
CConstRef< CBlobId >	CBlobIdKey::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
CDataSource *	CDataLoader::m_DataSource
TParserFlags	CGC_Assembly_Parser::m_Flags
CRef< CSeq_entry >	CGC_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_Mapper >	CObjectManager::m_Seq_id_Mapper
unique_ptr< TPluginManager >	CObjectManager::m_PluginManager
string	CLoaderException::m_FailedCall
TBlobState	CBlobStateException::m_BlobState
CRef< CPrefetchTokenOld_Impl >	CPrefetchTokenOld::m_Impl
CHeapScope	CScopeSource::m_Scope
CHeapScope	CScopeSource::m_BaseScope
CSeq_id_Handle	CPrefetchBioseq::m_Seq_id
TResult	CPrefetchBioseq::m_Result
CConstRef< CSeq_loc >	CPrefetchFeat_CI::m_Loc
CRange< TSeqPos >	CPrefetchFeat_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_idSource >	CPrefetchBioseqActionSource::m_Ids
CScopeSource	CPrefetchFeat_CIActionSource::m_Scope
CIRef< ISeq_idSource >	CPrefetchFeat_CIActionSource::m_Ids
SAnnotSelector	CPrefetchFeat_CIActionSource::m_Selector
CRef< CPrefetchManager_Impl >	CPrefetchManager::m_Impl
CRef< CPrefetchManager >	CPrefetchSequence::m_Manager
CIRef< IPrefetchActionSource >	CPrefetchSequence::m_Source
CMutex	CPrefetchSequence::m_Mutex
list< CRef< CPrefetchRequest > >	CPrefetchSequence::m_ActiveTokens
CRef< CObjectFor< CMutex > >	CPrefetchRequest::m_StateMutex
CIRef< IPrefetchAction >	CPrefetchRequest::m_Action
CIRef< IPrefetchListener >	CPrefetchRequest::m_Listener
TProgress	CPrefetchRequest::m_Progress
CRef< CScope >	CScope::m_HeapScope
CRef< CScope_Impl >	CScope::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

typedef CBlobIdFor<int> 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

typedef CBlobIdFor<CSeq_id_Handle> CBlobIdSeq_id

Definition at line 154 of file blob_id.hpp.

CBlobIdString

typedef CBlobIdFor<string> 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

typedef EState SPrefetchTypes::EEvent

Definition at line 67 of file prefetch_manager.hpp.

TAnnotBlobType

typedef int SRequestDetails::TAnnotBlobType

Definition at line 86 of file data_loader.hpp.

TAnnotMapFlags

typedef int CSeq_loc_Mapper_Base::TAnnotMapFlags

Definition at line 554 of file seq_loc_mapper_base.hpp.

TAnnotSet

typedef map<CAnnotName, TAnnotTypesSet> SRequestDetails::TAnnotSet

Definition at line 76 of file data_loader.hpp.

TAnnotTypesSet

typedef set<SAnnotTypeSelector> SRequestDetails::TAnnotTypesSet

Definition at line 75 of file data_loader.hpp.

TBioseqHandles

typedef vector<CBioseq_Handle> CScope::TBioseqHandles

Definition at line 144 of file scope.hpp.

TBlobId [1/2]

typedef CBlobIdKey CDataLoader::TBlobId

Definition at line 429 of file data_loader.hpp.

TBlobId [2/2]

typedef CBlobIdKey CScope::TBlobId

Definition at line 161 of file scope.hpp.

TBlobState

typedef int CBlobStateException::TBlobState

Definition at line 162 of file objmgr_exception.hpp.

TBlobVersion

typedef int CDataLoader::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

typedef vector<CTSE_Handle> CScope::TCDD_Entries

Get CDD annotations for all ids.

Definition at line 150 of file scope.hpp.

TCDD_Locks

typedef vector<CTSE_Lock> CDataLoader::TCDD_Locks

Definition at line 397 of file data_loader.hpp.

TChunk

typedef CRef<CTSE_Chunk_Info> CDataLoader::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

typedef CRef<CDataSource> CObjectManager::TDataSourceLock

Definition at line 134 of file object_manager.hpp.

TDataSourcesLock

typedef set<TDataSourceLock> CObjectManager::TDataSourcesLock

protected

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

typedef map<CSeq_id_Handle, TDstRanges> CSeq_loc_Mapper_Base::TDstIdMap

protected

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

typedef vector<TDstIdMap> CSeq_loc_Mapper_Base::TDstStrandMap

protected

Definition at line 692 of file seq_loc_mapper_base.hpp.

TEditSaver

typedef CRef<IEditSaver> CDataLoader::TEditSaver

Definition at line 461 of file data_loader.hpp.

TErrCode

typedef int CBlobStateException::TErrCode

Definition at line 186 of file objmgr_exception.hpp.

TFuzz [1/2]

typedef CRef<CInt_fuzz> CMappingRange::TFuzz

Definition at line 95 of file seq_loc_mapper_base.hpp.

TFuzz [2/2]

typedef CRef<CInt_fuzz> CSeq_loc_Mapper_Base::TFuzz

protected

Definition at line 695 of file seq_loc_mapper_base.hpp.

TFuzzOption

typedef int CSeq_loc_Mapper_Base::TFuzzOption

Definition at line 391 of file seq_loc_mapper_base.hpp.

TGetFlags

typedef int CScope::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

typedef vector<TRange> CGraphRanges::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]

typedef CBioseq_Handle CPrefetchComplete< CBioseq_Handle >::THandle

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

typedef TIdMap::const_iterator CMappingRanges::TIdIterator

Definition at line 189 of file seq_loc_mapper_base.hpp.

TIdMap

typedef map<CSeq_id_Handle, TRangeMap> CMappingRanges::TIdMap

Definition at line 188 of file seq_loc_mapper_base.hpp.

TIds [1/5]

typedef vector<CSeq_id_Handle> CDataLoader::TIds

Definition at line 283 of file data_loader.hpp.

TIds [2/5]

typedef CPrefetchTokenOld_Impl::TIds CPrefetchTokenOld::TIds

Definition at line 64 of file prefetch.hpp.

TIds [3/5]

typedef vector<CSeq_id_Handle> CPrefetchBioseqActionSource::TIds

Definition at line 275 of file prefetch_actions.hpp.

TIds [4/5]

typedef vector<CSeq_id_Handle> CPrefetchFeat_CIActionSource::TIds

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

typedef map<CSeq_id_Handle, TSeqPos> CSeq_loc_Mapper_Base::TLengthMap

private

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

typedef map< string, CDataLoader* > CObjectManager::TMapNameToLoader

private

Definition at line 258 of file object_manager.hpp.

TMapOptions [1/2]

typedef int CSeq_loc_Mapper_Options::TMapOptions

Definition at line 285 of file seq_loc_mapper_base.hpp.

TMapOptions [2/2]

typedef int CSeq_loc_Mapper_Base::TMapOptions

Definition at line 374 of file seq_loc_mapper_base.hpp.

TMappedRanges

typedef list<SMappedRange> CSeq_loc_Mapper_Base::TMappedRanges

protected

Definition at line 716 of file seq_loc_mapper_base.hpp.

TMapToSource

typedef map< const CObject* , TDataSourceLock > CObjectManager::TMapToSource

private

Definition at line 259 of file object_manager.hpp.

TMiscFlags

typedef int CSeq_loc_Mapper_Base::TMiscFlags

private

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]

typedef THandle::TObject CPrefetchComplete< CBioseq_Handle >::TObject

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

typedef int CGC_Assembly_Parser::TParserFlags

Definition at line 83 of file gc_assembly_parser.hpp.

TPluginManager

typedef CPluginManager<CDataLoader> CObjectManager::TPluginManager

private

Definition at line 252 of file object_manager.hpp.

TPriority [1/4]

typedef unsigned int CPrefetchManager_Impl::TPriority

Definition at line 65 of file prefetch_manager_impl.hpp.

TPriority [2/4]

typedef int CObjectManager::TPriority

Definition at line 151 of file object_manager.hpp.

TPriority [3/4]

typedef int SPrefetchTypes::TPriority

Definition at line 69 of file prefetch_manager.hpp.

TPriority [4/4]

typedef int CScope::TPriority

priority type and special value for added objects

Definition at line 98 of file scope.hpp.

TProcessedNAs

typedef set<string> CDataLoader::TProcessedNAs

Definition at line 233 of file data_loader.hpp.

TProgress

typedef int SPrefetchTypes::TProgress

Definition at line 70 of file prefetch_manager.hpp.

TRange [1/5]

typedef CRange<TSeqPos> CMappingRange::TRange

Definition at line 94 of file seq_loc_mapper_base.hpp.

TRange [2/5]

typedef CMappingRange::TRange CMappingRanges::TRange

Definition at line 185 of file seq_loc_mapper_base.hpp.

TRange [3/5]

typedef CRange<TSeqPos> CGraphRanges::TRange

Definition at line 239 of file seq_loc_mapper_base.hpp.

TRange [4/5]

typedef CMappingRange::TRange CSeq_loc_Mapper_Base::TRange

protected

Definition at line 684 of file seq_loc_mapper_base.hpp.

TRange [5/5]

typedef CRange<TSeqPos> SRequestDetails::TRange

Definition at line 74 of file data_loader.hpp.

TRangeFuzz [1/2]

typedef pair<TFuzz, TFuzz> CMappingRange::TRangeFuzz

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]

typedef TRangeMap::const_iterator CMappingRanges::TRangeIterator

Definition at line 187 of file seq_loc_mapper_base.hpp.

TRangeIterator [2/2]

typedef CMappingRanges::TRangeIterator CSeq_loc_Mapper_Base::TRangeIterator

protected

Definition at line 686 of file seq_loc_mapper_base.hpp.

TRangeMap [1/2]

typedef CRangeMultimap<CRef<CMappingRange>, TSeqPos> CMappingRanges::TRangeMap

Definition at line 186 of file seq_loc_mapper_base.hpp.

TRangeMap [2/2]

typedef CMappingRanges::TRangeMap CSeq_loc_Mapper_Base::TRangeMap

protected

Definition at line 685 of file seq_loc_mapper_base.hpp.

TRangesById

typedef map<CSeq_id_Handle, TRangesByStrand> CSeq_loc_Mapper_Base::TRangesById

protected

Definition at line 720 of file seq_loc_mapper_base.hpp.

TRangesByStrand

typedef vector<TMappedRanges> CSeq_loc_Mapper_Base::TRangesByStrand

protected

Definition at line 719 of file seq_loc_mapper_base.hpp.

TReadLockGuard

typedef CMutexGuard CObjectManager::TReadLockGuard

private

Definition at line 268 of file object_manager.hpp.

TRegisteredNames

typedef vector<string> CObjectManager::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

typedef SRegisterLoaderInfo<CDataLoader> CLoaderMaker_Base::TRegisterInfo_Base

protected

Definition at line 113 of file data_loader.hpp.

TRegisterLoaderInfo

typedef SRegisterLoaderInfo<CDataLoader> CObjectManager::TRegisterLoaderInfo

Definition at line 213 of file object_manager.hpp.

TResult [1/4]

typedef CBioseq_Handle CPrefetchBioseq::TResult

Definition at line 83 of file prefetch_actions.hpp.

TResult [2/4]

typedef CFeat_CI CPrefetchFeat_CI::TResult

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]

typedef CConstRef<TObject> CPrefetchComplete< CBioseq_Handle >::TResult

Definition at line 206 of file prefetch_actions.hpp.

TRWLock

typedef CMutex CObjectManager::TRWLock

private

Definition at line 267 of file object_manager.hpp.

TSeq_id_Handles

typedef vector<CSeq_id_Handle> CScope::TSeq_id_Handles

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

Definition at line 518 of file scope.hpp.

TSeq_idSet

typedef set<CSeq_id_Handle> CDataLoader::TSeq_idSet

Definition at line 268 of file data_loader.hpp.

TSeqIds

typedef set<CSeq_id_Handle> CGC_Assembly_Parser::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

typedef CSeq_loc_Mapper_Base::ESeqType IMapper_Sequence_Info::TSeqType

Definition at line 1022 of file seq_loc_mapper_base.hpp.

TSeqTypeById

typedef map<CSeq_id_Handle, ESeqType> CSeq_loc_Mapper_Base::TSeqTypeById

protected

Definition at line 721 of file seq_loc_mapper_base.hpp.

TSequenceHash

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.

See also

EGetflags

Definition at line 512 of file scope.hpp.

TSequenceHashes [1/2]

typedef vector<int> CDataLoader::TSequenceHashes

Definition at line 393 of file data_loader.hpp.

TSequenceHashes [2/2]

typedef vector<TSequenceHash> CScope::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.

See also

EGetflags

Definition at line 611 of file scope.hpp.

TSequenceLengths [1/2]

typedef vector<TSeqPos> CDataLoader::TSequenceLengths

Definition at line 390 of file data_loader.hpp.

TSequenceLengths [2/2]

typedef vector<TSeqPos> CScope::TSequenceLengths

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]

typedef vector<int> CDataLoader::TSequenceStates

Definition at line 392 of file data_loader.hpp.

TSequenceStates [2/2]

typedef vector<CBioseq_Handle::TBioseqStateFlags> CScope::TSequenceStates

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]

typedef vector<CSeq_inst::TMol> CDataLoader::TSequenceTypes

Definition at line 391 of file data_loader.hpp.

TSequenceTypes [2/2]

typedef vector<CSeq_inst::TMol> CScope::TSequenceTypes

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

typedef set< TDataSourceLock > CObjectManager::TSetDefaultSource

private

Definition at line 257 of file object_manager.hpp.

TSetScope

typedef set< CScope_Impl* > CObjectManager::TSetScope

private

Definition at line 260 of file object_manager.hpp.

TSortedMappings [1/2]

typedef vector< CRef<CMappingRange> > CMappingRanges::TSortedMappings

Definition at line 190 of file seq_loc_mapper_base.hpp.

TSortedMappings [2/2]

typedef CMappingRanges::TSortedMappings CSeq_loc_Mapper_Base::TSortedMappings

protected

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

typedef map<CSeq_id_Handle, CSeq_id_Handle> CSeq_loc_Mapper_Base::TSynonymMap

private

Definition at line 904 of file seq_loc_mapper_base.hpp.

TSynonyms [1/2]

typedef set<CSeq_id_Handle> CSeq_loc_Mapper_Base::TSynonyms

Definition at line 575 of file seq_loc_mapper_base.hpp.

TSynonyms [2/2]

typedef CSeq_loc_Mapper_Base::TSynonyms IMapper_Sequence_Info::TSynonyms

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

typedef vector<CSeq_entry_Handle> CScope::TTSE_Handles

Definition at line 645 of file scope.hpp.

TTSE_Lock

typedef CTSE_Lock CDataLoader::TTSE_Lock

Definition at line 228 of file data_loader.hpp.

TTSE_LockSet

typedef set<TTSE_Lock> CDataLoader::TTSE_LockSet

Definition at line 229 of file data_loader.hpp.

TTSE_LockSets

typedef map<CSeq_id_Handle, TTSE_LockSet> CDataLoader::TTSE_LockSets

Definition at line 395 of file data_loader.hpp.

TWriteLockGuard

typedef CMutexGuard CObjectManager::TWriteLockGuard

private

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

enum CScope::EActionIfLocked

Enumerator
eKeepIfLocked
eThrowIfLocked
eRemoveIfLocked

Definition at line 342 of file scope.hpp.

EChoice

enum CDataLoader::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]

enum CAnnotMapperException::EErrCode

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]

enum CSeqTableException::EErrCode

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]

enum CAssemblyParserException::EErrCode

Enumerator
eUnsupported	Unsupported type/flag.
eOtherError

Definition at line 126 of file gc_assembly_parser.hpp.

EErrCode [4/13]

enum CObjMgrException::EErrCode

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]

enum CSeqMapException::EErrCode

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]

enum CSeqVectorException::EErrCode

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]

enum CAnnotException::EErrCode

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]

enum CLoaderException::EErrCode

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

Definition at line 125 of file objmgr_exception.hpp.

EErrCode [9/13]

enum CBlobStateException::EErrCode

Enumerator
eBlobStateError
eLoaderError
eOtherError

Definition at line 157 of file objmgr_exception.hpp.

EErrCode [10/13]

enum CObjmgrUtilException::EErrCode

Enumerator
eNotImplemented
eBadSequenceType
eBadLocation
eNotUnique
eUnknownLength
eBadFeature
eBadResidue
eBadAlignment

Definition at line 212 of file objmgr_exception.hpp.

EErrCode [11/13]

enum CAnnotSearchLimitException::EErrCode

Enumerator
eTimeLimitExceded
eSegmentsLimitExceded

Definition at line 237 of file objmgr_exception.hpp.

EErrCode [12/13]

enum CPrefetchFailed::EErrCode

Enumerator
eFailed

Definition at line 140 of file prefetch_manager.hpp.

EErrCode [13/13]

enum CPrefetchCanceled::EErrCode

Enumerator
eCanceled

Definition at line 152 of file prefetch_manager.hpp.

EExist

enum CScope::EExist

AddXxx() control values.

Enumerator
eExist_Throw
eExist_Get
eExist_Default

Definition at line 258 of file scope.hpp.

EFeatMapDirection

enum CSeq_loc_Mapper_Base::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

enum CScope::EForceLabelLoad

obsolete enum

See also

EGetFlags

Enumerator
eNoForceLabelLoad
eForceLabelLoad

Definition at line 443 of file scope.hpp.

EForceLoad

enum CScope::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

enum CSeq_loc_Mapper_Base::EGapFlags

private

Enumerator
eGapPreserve
eGapRemove

Definition at line 739 of file seq_loc_mapper_base.hpp.

EGCAssemblyAlias

enum CSeq_loc_Mapper::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

enum CScope::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

enum CScope::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

enum CObjectManager::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

enum CSeq_loc_Mapper_Base::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

enum CSeq_loc_Mapper_Base::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

enum CSeq_loc_Mapper_Base::EMergeFlags

private

Enumerator
eMergeNone
eMergeAbutting
eMergeContained
eMergeBySeg
eMergeAll

Definition at line 732 of file seq_loc_mapper_base.hpp.

EMiscFlags

enum CSeq_loc_Mapper_Base::EMiscFlags

private

Enumerator
fTrimSplicedSegs
fKeepNonmapping
fCheckStrand
fIncludeSrcLocs
fMixedAlignsAsSpliced
fErrorOnPartial

Definition at line 915 of file seq_loc_mapper_base.hpp.

EMissing

enum CScope::EMissing

GetXxxHandle control values.

Enumerator
eMissing_Throw
eMissing_Null
eMissing_Default

Definition at line 155 of file scope.hpp.

ENon_locking_prefetch

enum CPrefetchTokenOld::ENon_locking_prefetch

Enumerator
eNon_locking_prefetch

Definition at line 66 of file prefetch.hpp.

EObjectType

enum CSeq_loc_Mapper_Message::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]

enum CObjectManager::EPriority

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]

enum CScope::EPriority

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

enum CScope::ERemoveDataLoaders

Clear all information in the scope including data loaders.

Enumerator
eRemoveDataLoaders

Definition at line 356 of file scope.hpp.

EScopeFlag

enum CSeq_loc_Mapper::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

enum CSeq_loc_Mapper::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

enum CSeq_loc_Mapper_Base::ESeqType

Enumerator
eSeq_unknown
eSeq_nuc
eSeq_prot

Definition at line 583 of file seq_loc_mapper_base.hpp.

ESplicedRow

enum CSeq_loc_Mapper_Base::ESplicedRow

Spliced-seg row indexing constants.

Enumerator
eSplicedRow_Prod
eSplicedRow_Gen

Definition at line 377 of file seq_loc_mapper_base.hpp.

EState

enum SPrefetchTypes::EState

Enumerator
eInvalid
eQueued
eStarted
eAdvanced
eCompleted
eCanceled
eFailed

Definition at line 58 of file prefetch_manager.hpp.

ETSEKind

enum CScope::ETSEKind

Enumerator
eManualTSEs
eAllTSEs

Definition at line 641 of file scope.hpp.

FAnnotBlobType

enum SRequestDetails::FAnnotBlobType

Enumerator
fAnnotBlobNone
fAnnotBlobInternal
fAnnotBlobExternal
fAnnotBlobOrphan
fAnnotBlobAll

Definition at line 77 of file data_loader.hpp.

FAnnotMapFlag

enum CSeq_loc_Mapper_Base::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

enum CSeq_loc_Mapper_Base::FFuzzOption

Enumerator
fFuzzOption_CStyle
fFuzzOption_RemoveLimTlOrTr

Definition at line 382 of file seq_loc_mapper_base.hpp.

FParserFlags

enum CGC_Assembly_Parser::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

Definition at line 369 of file object_manager.cpp.

References CObjectManager::eNonDefault, CObjectManager::kPriority_Default, CObjectManager::m_OM_Lock, CGuard< Resource, Lock, Unlock, ReportExceptions >::Release(), CObjectManager::x_FindDataSource(), and CObjectManager::x_RegisterLoader().

Referenced by CScope_Impl::AddDataLoader(), and CScope_Impl::RemoveDataLoader().

AcquireDataLoader() [2/2]

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

protected

Definition at line 383 of file object_manager.cpp.

References _ASSERT, CObjectManager::m_OM_Lock, NCBI_THROW, CObjectManager::x_FindDataSource(), and CObjectManager::x_GetLoaderByName().

AcquireDefaultDataSources()

void CObjectManager::AcquireDefaultDataSources ( TDataSourcesLock &  sources )

protected

Definition at line 361 of file object_manager.cpp.

References CObjectManager::m_OM_Lock, and CObjectManager::m_setDefaultSource.

Referenced by CScope_Impl::AddDefaults().

AcquireSharedBioseq()

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

protected

Definition at line 418 of file object_manager.cpp.

References _ASSERT, CObjectManager::CDataSource, map_checker< Container >::insert(), CObjectManager::m_mapToSource, CObjectManager::m_OM_Lock, CGuard< Resource, Lock, Unlock, ReportExceptions >::Release(), CSeq_entry_Base::SetSeq(), rapidjson::source, and CObjectManager::x_FindDataSource().

Referenced by CScope_Impl::AddSharedBioseq().

AcquireSharedSeq_annot()

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

protected

Definition at line 440 of file object_manager.cpp.

References _ASSERT, CObjectManager::CDataSource, map_checker< Container >::insert(), CObjectManager::m_mapToSource, CObjectManager::m_OM_Lock, Ref(), CGuard< Resource, Lock, Unlock, ReportExceptions >::Release(), CBioseq_set_Base::SetAnnot(), CBioseq_set_Base::SetSeq_set(), CSeq_entry_Base::SetSet(), rapidjson::source, and CObjectManager::x_FindDataSource().

Referenced by CScope_Impl::AddSharedSeq_annot().

AcquireSharedSeq_entry()

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

protected

Definition at line 398 of file object_manager.cpp.

References _ASSERT, CObjectManager::CDataSource, map_checker< Container >::insert(), CObjectManager::m_mapToSource, CObjectManager::m_OM_Lock, CGuard< Resource, Lock, Unlock, ReportExceptions >::Release(), rapidjson::source, and CObjectManager::x_FindDataSource().

Referenced by CScope_Impl::AddSharedSeq_entry().

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
	)

Definition at line 235 of file prefetch_manager_impl.cpp.

References CThreadPool::AddTask(), CPrefetchManager_Impl::CPrefetchRequest, CObjectFor< T >::GetData(), CThreadPool::IsAborted(), CPrefetchManager_Impl::m_StateMutex, and CPrefetchManager_Impl::m_ThreadPool.

Referenced by CPrefetchManager::AddAction().

AddAction() [3/3]

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

Definition at line 78 of file prefetch_manager.cpp.

References CPrefetchManager_Impl::AddAction(), CPrefetchManager::m_Impl, and NCBI_THROW.

Referenced by CPrefetchManager::AddAction(), CPrefetchSequence::EnqueNextAction(), CStdPrefetch::GetBioseqHandle(), CStdPrefetch::GetFeat_CI(), and CDemoApp::Run().

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

)

Add new mapping range to the proper place.

Definition at line 446 of file seq_loc_mapper_base.cpp.

References map_checker< Container >::insert(), and CMappingRanges::m_IdMap.

Referenced by CMappingRanges::AddConversion(), s_DumpSequences_wRange(), CSeq_loc_Mapper_Base::x_AddConversion(), CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt(), CFeatureGraph::x_CreateMapRanges(), CBLASTSeqToolJob::x_CreateProjectItems(), and CSeq_loc_Mapper_Base::x_PreserveDestinationLocs().

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
	)

Add data loader by name.

The loader (or its factory) must be known to Object Manager.

Definition at line 510 of file scope.cpp.

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

Referenced by CGBDocument::AttachDataLoader(), BOOST_AUTO_TEST_CASE(), CHugeFileProcess::ForEachEntry(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), CGeneFinder::GetFeatViaSubsetThenExtremesIfPossible_Helper(), CDUpdater::getSequencesFromGB(), GetVDBScope(), CAlnMrgApp::LoadBlastDb(), CDLTestThread::Main(), CDLTest2Thread::Main(), TestUtil::CBlastOM::NewScope(), RemoteFetchLongNucleotideBioseq(), CDeltaBlastApp::Run(), CSeedTopApp::Run(), CGBProjectTool::Run(), CVectorScreen::Run(), CXcompareAnnotsApplication::Run(), CAsnCacheTestApplication::Run(), CDemoApp::Run(), CAsnvalThreadState::ValidateAsync(), and COligoSpecificityCheck::x_SequencesMappedToSameTarget().

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(), GetDeleteAllFeaturesCommand_Ex(), 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(), CTable2AsnValidator::Validate(), 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()

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.

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

Definition at line 255 of file seq_loc_mapper_base.hpp.

References COpenRange< Position >::CombineWith(), COpenRange< Position >::Empty(), CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< Position >::IsWhole(), CGraphRanges::m_Offset, CGraphRanges::m_Ranges, and CGraphRanges::m_TotalRange.

Referenced by CSeq_loc_Conversion::ConvertInterval(), CSeq_loc_Conversion::ConvertPoint(), and CSeq_loc_Mapper_Base::x_MapNextRange().

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(), GetDeleteAllFeaturesCommand_Ex(), GetGoodSeqEntryWithFeatureIds(), GetScope(), CEditSequence::GetSequence(), CGbScopeLoader::HandleSeqEntry(), CCleanupApp::HandleSeqEntry(), CAsn2FastaApp::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(), CTable2AsnValidator::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
	)

Definition at line 617 of file scope.cpp.

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

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

Get mapping ranges iterator for the given seq-id and range.

Definition at line 477 of file seq_loc_mapper_base.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), and CMappingRanges::m_IdMap.

Referenced by CReportEntry::x_GetAdjustment(), CSeq_loc_Mapper_Base::x_MapInterval(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().

CancelAllTasks()

void CPrefetchManager::CancelAllTasks

(

void

)

Definition at line 97 of file prefetch_manager.cpp.

References CThreadPool::CancelTasks(), CThreadPool::fCancelExecutingTasks, CThreadPool::fCancelQueuedTasks, CPrefetchManager::m_Impl, and CPrefetchManager_Impl::m_ThreadPool.

CanGetBlobById()

bool CDataLoader::CanGetBlobById ( void  ) const

virtual

Reimplemented in CVDBGraphDataLoader, CSNPDataLoader, CHugeAsnDataLoader, CPSGDataLoader, CGBDataLoader_Native, CSplitDataLoader, CWGSDataLoader, CSRADataLoader, CCSRADataLoader, CBAMDataLoader, CDataLoaderPatcher, CLDS2_DataLoader, CBuffer_DataLoader, CBlastDbDataLoader, and CAsnCache_DataLoader.

Definition at line 282 of file data_loader.cpp.

Referenced by CDataLoaderPatcher::CanGetBlobById(), and CDataLoader::GetExternalAnnotRecords().

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

Definition at line 198 of file objmgr_exception.hpp.

Referenced by CBlobStateException::GetErrCode(), and CBlobStateException::x_Clone().

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

Definition at line 849 of file data_loader.cpp.

References CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, CSeq_annot_Base::C_Data::e_not_set, CDataLoader::eAlign, CDataLoader::eAll, CDataLoader::eAnnot, CDataLoader::eBioseq, CDataLoader::eBioseqCore, CDataLoader::eBlob, CDataLoader::eExtAlign, CDataLoader::eExtAnnot, CDataLoader::eExtFeatures, CDataLoader::eExtGraph, CDataLoader::eFeatures, CDataLoader::eGraph, CDataLoader::eOrphanAnnot, CDataLoader::eSequence, SRequestDetails::fAnnotBlobAll, SRequestDetails::fAnnotBlobExternal, SRequestDetails::fAnnotBlobInternal, SRequestDetails::fAnnotBlobNone, SRequestDetails::fAnnotBlobOrphan, COpenRange< TSeqPos >::GetWhole(), map_checker< Container >::insert(), SRequestDetails::m_AnnotBlobType, SRequestDetails::m_NeedAnnots, SRequestDetails::m_NeedSeqData, and SRequestDetails::m_NeedSeqMap.

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

Definition at line 2259 of file seq_loc_mapper_base.cpp.

References IMapper_Sequence_Info::CollectSynonyms(), map_checker< Container >::end(), map_checker< Container >::find(), CSeq_id::GetMatchingIds(), CSeq_loc_Mapper_Options::GetSeqInfo(), ITERATE, CSeq_loc_Mapper_Base::m_MapOptions, and CSeq_loc_Mapper_Base::m_SynonymMap.

Referenced by CSeq_loc_Mapper_Base::GetSeqTypeById(), CSeq_loc_Mapper_Base::GetSequenceLength(), s_GetBestSynonym(), CSeq_loc_Mapper_Base::SetSeqTypeById(), CSeq_loc_Mapper_Base::x_AddConversion(), CSeq_loc_Mapper_Base::x_ForceSeqTypes(), CSeq_loc_Mapper_Base::x_InitializeAlign(), and CSeq_loc_Mapper_Base::x_PreserveDestinationLocs().

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]

CPrefetchComplete< CBioseq_Handle >::CPrefetchComplete	(	const CScopeSource &	scope,
		const CSeq_id_Handle &	seq_id
	)

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]

CPrefetchComplete< CBioseq_Handle >::CPrefetchComplete ( const THandle &  handle )

explicit

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