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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/group__ObjectManagerCore.html below:

NCBI C++ ToolKit: Object Manager Core 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...
  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   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...
  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...
  TBioseqHandles  CScope::GetBioseqHandlesFromTSE (const TIds &ids, const CTSE_Handle &tse)   Bulk get bioseq handles for sequence withing one TSE. More...
  TBioseqHandles  CScope::GetBioseqHandlesFromTSE (const TIds &ids, const CBioseq_Handle &bh)   TBioseqHandles  CScope::GetBioseqHandlesFromTSE (const TIds &ids, const CSeq_entry_Handle &seh)   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   ◆ CBlobIdInt ◆ CBlobIdPtr ◆ CBlobIdSeq_id ◆ CBlobIdString ◆ convert_to_string_type

template<typename Value , class Converter = PConvertToString<Value>>

Definition at line 114 of file blob_id.hpp.

◆ EEvent ◆ TAnnotBlobType ◆ TAnnotMapFlags ◆ TAnnotSet ◆ TAnnotTypesSet ◆ TBioseqHandles ◆ TBlobId [1/2] ◆ TBlobId [2/2] ◆ TBlobState ◆ TBlobVersion ◆ TBulkIds [1/2] ◆ TBulkIds [2/2]

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

See also
EGetflags

Definition at line 531 of file scope.hpp.

◆ TCDD_Entries

Get CDD annotations for all ids.

Definition at line 150 of file scope.hpp.

◆ TCDD_Locks ◆ TChunk ◆ TChunkSet ◆ TContainer ◆ TDataSourceLock ◆ TDataSourcesLock ◆ TDendiag ◆ TDstIdMap ◆ TDstRanges ◆ TDstStrandMap ◆ TEditSaver ◆ TErrCode ◆ TFuzz [1/2] ◆ TFuzz [2/2] ◆ TFuzzOption ◆ TGetFlags ◆ TGis ◆ 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 553 of file scope.hpp.

◆ TGraphRanges ◆ THandle [1/2] ◆ THandle [2/2] ◆ THashKnown ◆ TIdIterator ◆ TIdMap ◆ TIds [1/5] ◆ TIds [2/5] ◆ TIds [3/5] ◆ TIds [4/5] ◆ TIds [5/5] ◆ TIterator ◆ TLabels [1/2] ◆ TLabels [2/2]

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

See also
GetLabel
EGetflags

Definition at line 564 of file scope.hpp.

◆ TLengthMap ◆ 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 ◆ TMapOptions [1/2] ◆ TMapOptions [2/2] ◆ TMappedRanges ◆ TMapToSource ◆ TMiscFlags ◆ TObject [1/2] ◆ TObject [2/2] ◆ TParamType

template<class TDataLoader , class TParam >

Definition at line 153 of file data_loader.hpp.

◆ TParserFlags ◆ TPluginManager ◆ TPriority [1/4] ◆ TPriority [2/4] ◆ TPriority [3/4] ◆ TPriority [4/4]

priority type and special value for added objects

Definition at line 98 of file scope.hpp.

◆ TProcessedNAs ◆ TProgress ◆ TRange [1/5] ◆ TRange [2/5] ◆ TRange [3/5] ◆ TRange [4/5] ◆ TRange [5/5] ◆ TRangeFuzz [1/2] ◆ TRangeFuzz [2/2] ◆ TRangeIterator [1/2] ◆ TRangeIterator [2/2] ◆ TRangeMap [1/2] ◆ TRangeMap [2/2] ◆ TRangesById ◆ TRangesByStrand ◆ TReadLockGuard ◆ TRegisteredNames ◆ TRegisterInfo [1/2] ◆ TRegisterInfo [2/2]

template<class TDataLoader , class TParam >

Definition at line 168 of file data_loader.hpp.

◆ TRegisterInfo_Base ◆ TRegisterLoaderInfo ◆ TResult [1/4] ◆ TResult [2/4] ◆ TResult [3/4] ◆ TResult [4/4] ◆ TRWLock ◆ TSeq_id_Handles

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

Definition at line 526 of file scope.hpp.

◆ TSeq_idSet ◆ TSeqIds ◆ TSeqIdSets ◆ TSeqType ◆ TSeqTypeById ◆ 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 520 of file scope.hpp.

◆ TSequenceHashes [1/2] ◆ TSequenceHashes [2/2]

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

See also
EGetflags

Definition at line 619 of file scope.hpp.

◆ TSequenceLengths [1/2] ◆ TSequenceLengths [2/2]

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

See also
EGetflags

Definition at line 585 of file scope.hpp.

◆ TSequenceStates [1/2] ◆ TSequenceStates [2/2] ◆ TSequenceTypes [1/2] ◆ TSequenceTypes [2/2] ◆ TSetDefaultSource ◆ TSetScope ◆ TSortedMappings [1/2] ◆ TSortedMappings [2/2] ◆ TStd ◆ TSynonymMap ◆ TSynonyms [1/2] ◆ TSynonyms [2/2] ◆ TTaxIds [1/2] ◆ TTaxIds [2/2]

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 575 of file scope.hpp.

◆ TThisType

template<typename Value , class Converter = PConvertToString<Value>>

Definition at line 115 of file blob_id.hpp.

◆ TTSE_Handles ◆ TTSE_Lock ◆ TTSE_LockSet ◆ TTSE_LockSets ◆ TWriteLockGuard ◆ value_type

template<typename Value , class Converter = PConvertToString<Value>>

Definition at line 113 of file blob_id.hpp.

◆ EActionIfLocked Enumerator eKeepIfLocked  eThrowIfLocked  eRemoveIfLocked 

Definition at line 350 of file scope.hpp.

◆ EChoice

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

Enumerator eBlob 

whole main

eBioseq 

main blob with complete bioseq

eCore 

?only seq-entry core?

eBioseqCore 

main blob with bioseq core (no seqdata and annots)

eSequence 

seq data

eFeatures 

features from main blob

eGraph 

graph annotations from main blob

eAlign 

aligns from main blob

eAnnot 

all annotations from main blob

eExtFeatures 

external features

eExtGraph 

external graph annotations

eExtAlign 

external aligns

eExtAnnot 

all external annotations

eOrphanAnnot 

all external annotations if no Bioseq exists

eAll 

all blobs (main and external)

Definition at line 210 of file data_loader.hpp.

◆ EErrCode [1/13] Enumerator eBadLocation 

Attempt to map from/to invalid seq-loc.

eUnknownLength 

Can not resolve sequence length.

eBadAlignment 

Unsuported or invalid alignment.

eBadFeature 

Feature can not be used for mapping.

eCanNotMap 

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

eOtherError 

Definition at line 60 of file annot_mapper_exception.hpp.

◆ EErrCode [2/13] Enumerator eColumnNotFound 

Requested column is missing.

eRowNotFound 

Requested row is missing.

eIncompatibleValueType 

Data cannot be converted to asked type.

eOtherError 

Definition at line 53 of file seq_table_exception.hpp.

◆ EErrCode [3/13] ◆ EErrCode [4/13] Enumerator eNotImplemented 

The method is not implemented.

eRegisterError 

Error while registering a data source/loader.

eFindConflict 

Conflicting data found.

eFindFailed 

The data requested can not be found.

eAddDataError 

Error while adding new data.

eModifyDataError 

Error while modifying data.

eInvalidHandle 

Attempt to use an invalid handle.

eLockedData 

Attempt to remove locked data.

eTransaction 

Transaction violation.

eMissingData 

The sequence doesn't have the data requested.

eOtherError 

Definition at line 53 of file objmgr_exception.hpp.

◆ EErrCode [5/13] Enumerator eUnimplemented 

The method is not implemented.

eIteratorTooBig 

Bad internal iterator in delta map.

eSegmentTypeError 

Wrong segment type.

eDataError 

SeqMap data error.

eOutOfRange 

Iterator is out of range.

eInvalidIndex 

Invalid segment index.

eNullPointer 

Attempt to access non-existing object.

eSelfReference 

Self-reference in seq map is detected.

eFail 

Operation failed.

Definition at line 75 of file objmgr_exception.hpp.

◆ EErrCode [6/13] Enumerator eCodingError 

Incompatible coding selected.

eDataError 

Sequence data error.

eOutOfRange 

Attempt to access out-of-range iterator.

Definition at line 95 of file objmgr_exception.hpp.

◆ EErrCode [7/13] Enumerator eBadLocation 

Wrong location type while mapping annotations.

eFindFailed 

Seq-id can not be resolved.

eLimitError 

Invalid or unknown limit object.

eIncomatibleType 

Incompatible annotation type (feat/graph/align)

eOtherError 

Definition at line 109 of file objmgr_exception.hpp.

◆ EErrCode [8/13] Enumerator eNotImplemented  eNoData  ePrivateData  eConnectionFailed  eCompressionError  eLoaderFailed  eNoConnection  eOtherError  eRepeatAgain  eBadConfig  eNotFound 

Definition at line 125 of file objmgr_exception.hpp.

◆ EErrCode [9/13] ◆ EErrCode [10/13] Enumerator eNotImplemented  eBadSequenceType  eBadLocation  eNotUnique  eUnknownLength  eBadFeature  eBadResidue  eBadAlignment 

Definition at line 212 of file objmgr_exception.hpp.

◆ EErrCode [11/13] ◆ EErrCode [12/13] ◆ EErrCode [13/13] ◆ EExist

AddXxx() control values.

Enumerator eExist_Throw  eExist_Get  eExist_Default 

Definition at line 266 of file scope.hpp.

◆ EFeatMapDirection

Mapping direction used when initializing the mapper with a feature.

Enumerator eLocationToProduct 

Map from the feature's location to product.

eProductToLocation 

Map from the feature's product to location.

Definition at line 345 of file seq_loc_mapper_base.hpp.

◆ EForceLabelLoad

obsolete enum

See also
EGetFlags
Enumerator eNoForceLabelLoad  eForceLabelLoad 

Definition at line 451 of file scope.hpp.

◆ EForceLoad

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

Enumerator eNoForceLoad  eForceLoad 

Definition at line 412 of file scope.hpp.

◆ EGapFlags ◆ EGCAssemblyAlias

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

Enumerator eGCA_Genbank 

Map to GenBank alias, prefer GI.

eGCA_GenbankAcc 

Map to GenBank alias, prefer acc.ver.

eGCA_Refseq 

Map to RefSeq alias, prefer GI.

eGCA_RefseqAcc 

Map to RefSeq alias, prefer acc.ver.

eGCA_UCSC 

Map to UCSC alias.

eGCA_Other 

Map to 'private' seq-id.

Definition at line 228 of file seq_loc_mapper.hpp.

◆ EGetBioseqFlag Enumerator eGetBioseq_Resolved 

Search only in already resolved ids.

eGetBioseq_Loaded 

Search in all loaded TSEs in the scope.

eGetBioseq_All 

Search bioseq, load if not loaded yet.

Definition at line 125 of file scope.hpp.

◆ EGetFlags

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

Enumerator fForceLoad 

ignore already loaded information and alway request data loader

fThrowOnMissingSequence 

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

The exception type/code: CObjMgrException/eFindFailed

See also
CObjMgrException
fThrowOnMissingData 

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

See also
CObjMgrException
fThrowOnMissing 

throw exception if sequence or requested data aren't found

See also
fThrowOnMissingSequence
fThrowOnMissingData
CObjMgrException
fDoNotRecalculate 

avoid time-consuming recalculation of missing data

Definition at line 423 of file scope.hpp.

◆ EIsDefault ◆ EMapOptions

Options for interpretations of locations.

Enumerator fAlign_Dense_seg_TotalRange 

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

fAlign_Sparse_ToFirst 

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

Map to first-id

fAlign_Sparse_ToSecond 

Map to second-id.

fMapSingleLevel 

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

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

fTrimMappedLocation 

Enable trimming of source/destination ranges at sequence end.

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

Definition at line 351 of file seq_loc_mapper_base.hpp.

◆ EMapResult

Result of seq-annot mapping.

Enumerator eMapped_None 

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

eMapped_Some 

Some (not all) annotations were mapped.

eMapped_All 

All annotations were mapped, none was removed.

Definition at line 557 of file seq_loc_mapper_base.hpp.

◆ EMergeFlags Enumerator eMergeNone  eMergeAbutting  eMergeContained  eMergeBySeg  eMergeAll 

Definition at line 732 of file seq_loc_mapper_base.hpp.

◆ EMiscFlags Enumerator fTrimSplicedSegs  fKeepNonmapping  fCheckStrand  fIncludeSrcLocs  fMixedAlignsAsSpliced  fErrorOnPartial 

Definition at line 915 of file seq_loc_mapper_base.hpp.

◆ EMissing

GetXxxHandle control values.

Enumerator eMissing_Throw  eMissing_Null  eMissing_Default 

Definition at line 155 of file scope.hpp.

◆ ENon_locking_prefetch Enumerator eNon_locking_prefetch 

Definition at line 66 of file prefetch.hpp.

◆ EObjectType ◆ EPriority [1/2]

Default data source priority.

Enumerator kPriority_Entry 

Default priority for explicit entries.

kPriority_Local 

Default priority for local data storage.

kPriority_Replace 

Default priority for replacement loaders.

kPriority_Loader 

Default priority for main loaders.

kPriority_Extra 

Default priority for extra annot loaders.

kPriority_Default 

Use default priority for added data.

kPriority_NotSet 

Deprecated: use kPriority_Default instead.

Definition at line 153 of file object_manager.hpp.

◆ EPriority [2/2] Enumerator kPriority_Default 

Use default priority for added data.

kPriority_NotSet 

Deprecated: use kPriority_Default instead.

Definition at line 99 of file scope.hpp.

◆ ERemoveDataLoaders

Clear all information in the scope including data loaders.

Enumerator eRemoveDataLoaders 

Definition at line 364 of file scope.hpp.

◆ EScopeFlag

Using CScope for virtual bioseqs created from GC-Assemblies.

Enumerator eOriginalScope 

Put the generated bioseqs into the original scope.

eCopyScope 

Create a new scope for virtual bioseqs.

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

Definition at line 238 of file seq_loc_mapper.hpp.

◆ ESeqMapDirection Enumerator eSeqMap_Up 

map from segments to the top level bioseq

eSeqMap_Down 

map from a segmented bioseq to segments

Definition at line 78 of file seq_loc_mapper.hpp.

◆ ESeqType ◆ ESplicedRow

Spliced-seg row indexing constants.

Enumerator eSplicedRow_Prod  eSplicedRow_Gen 

Definition at line 377 of file seq_loc_mapper_base.hpp.

◆ EState Enumerator eInvalid  eQueued  eStarted  eAdvanced  eCompleted  eCanceled  eFailed 

Definition at line 58 of file prefetch_manager.hpp.

◆ ETSEKind Enumerator eManualTSEs  eAllTSEs 

Definition at line 649 of file scope.hpp.

◆ FAnnotBlobType Enumerator fAnnotBlobNone  fAnnotBlobInternal  fAnnotBlobExternal  fAnnotBlobOrphan  fAnnotBlobAll 

Definition at line 77 of file data_loader.hpp.

◆ FAnnotMapFlag

Flags defining seq-annot mapping options.

Enumerator fAnnotMap_Location 

Map seq-feat locations.

fAnnotMap_Product 

Map seq-feat products.

fAnnotMap_Both  fAnnotMap_RemoveNonMapping 

Remove annotations which can not be mapped with this mapper.

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

fAnnotMap_ThrowOnFailure 

Throw exception if an annotation can not be mapped.

fAnnotMap_Default 

Definition at line 539 of file seq_loc_mapper_base.hpp.

◆ FFuzzOption ◆ 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.

◆ AcquireDataLoader() [1/2] ◆ AcquireDataLoader() [2/2] ◆ AcquireDefaultDataSources() ◆ AcquireSharedBioseq()

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()

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()

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] ◆ AddAction() [2/3] ◆ AddAction() [3/3] ◆ AddBioseq() [1/2]

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(), CBlastDBExtractor::ExtractFasta(), 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(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CXml2Asn::xGetEntry(), and CAnnotWriterApp::xProcessInputObject().

◆ AddBioseq() [2/2]

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] ◆ 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  ) ◆ AddDataLoader()

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()

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() ◆ AddRange() ◆ AddScope()

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]

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]

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() ◆ AddTopLevelSeqEntry() [1/2]

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]

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() ◆ AttachEntry() ◆ BeginMappingRanges() ◆ CancelAllTasks() void CPrefetchManager::CancelAllTasks ( void  ) ◆ 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() ◆ CBlobIdFor()

template<typename Value , class Converter = PConvertToString<Value>>

Definition at line 117 of file blob_id.hpp.

◆ CBlobIdKey() ◆ CBlobStateException() [1/3] ◆ CBlobStateException() [2/3] ◆ CBlobStateException() [3/3] CBlobStateException::CBlobStateException ( void  ) inlineprotected ◆ CDataLoader() [1/3] ◆ CDataLoader() [2/3] CDataLoader::CDataLoader ( const string &  loader_name ) protected ◆ CDataLoader() [3/3] CDataLoader::CDataLoader ( void  ) protected ◆ CGC_Assembly_Parser() ◆ CGraphRanges() ◆ ChoiceToDetails()

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() ◆ 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() ◆ CObjectManager() ◆ CollectSynonyms() [1/3]

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] ◆ CollectSynonyms() [3/3] ◆ CParamLoaderMaker()

template<class TDataLoader , class TParam >

◆ CPrefetchBioseq() [1/3] ◆ CPrefetchBioseq() [2/3] ◆ CPrefetchBioseq() [3/3] ◆ CPrefetchBioseqActionSource() [1/2] ◆ CPrefetchBioseqActionSource() [2/2] ◆ CPrefetchComplete() [1/3] ◆ CPrefetchComplete() [2/3] ◆ CPrefetchComplete() [3/3] ◆ CPrefetchFeat_CI() [1/3] ◆ CPrefetchFeat_CI() [2/3] ◆ CPrefetchFeat_CI() [3/3] ◆ CPrefetchFeat_CIActionSource() [1/2] ◆ CPrefetchFeat_CIActionSource() [2/2] ◆ CPrefetchManager() [1/3] ◆ CPrefetchManager() [2/3] ◆ CPrefetchManager() [3/3] ◆ CPrefetchManager_Impl() [1/2] ◆ CPrefetchManager_Impl() [2/2] ◆ CPrefetchRequest() ◆ CPrefetchSequence() ◆ CPrefetchTokenOld() [1/4] ◆ CPrefetchTokenOld() [2/4] ◆ CPrefetchTokenOld() [3/4] CPrefetchTokenOld::CPrefetchTokenOld ( CScope &  scope, const TIds &  ids, unsigned int  depth = 2  ) inline ◆ CPrefetchTokenOld() [4/4] CPrefetchTokenOld::CPrefetchTokenOld ( void  ) inline

Definition at line 107 of file prefetch.hpp.

◆ CreateLoader() [1/3]

template<class TDataLoader >

◆ CreateLoader() [2/3]

template<class TDataLoader , class TParam >

◆ CreateLoader() [3/3] virtual CDataLoader* CLoaderMaker_Base::CreateLoader ( void  ) const pure virtual ◆ CScope() [1/2] ◆ CScope() [2/2] ◆ CScopeSource() [1/2] ◆ CScopeSource() [2/2] ◆ CSeq_loc_Mapper() [1/16]

Mapping between segments and the top level sequence.

Parameters
target_seq Top level bioseq direction Direction of mapping: up (from segments to master) or down.

Definition at line 250 of file seq_loc_mapper.cpp.

References CSeq_loc_Mapper::eSeqMap_Up, CSeq_id_Handle::GetHandle(), CConstRef< C, Locker >::GetPointerOrNull(), CBioseq_Handle::GetSeqId(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetSynonyms(), COpenRange< TSeqPos >::GetWhole(), CSeq_loc_Mapper_Base::m_DstRanges, CSeq_loc_Mapper::x_InitializeSeqMap(), and CSeq_loc_Mapper_Base::x_PreserveDestinationLocs().

◆ CSeq_loc_Mapper() [2/16]

Mapping between segments and the top level sequence.

Parameters
target_seq Top level bioseq direction Direction of mapping: up (from segments to master) or down. selector Seq-map selector with additional restrictions (range, strand etc.). Some properties of the selector are always adjusted by the mapper.

Definition at line 292 of file seq_loc_mapper.cpp.

References CSeq_loc_Mapper::eSeqMap_Up, CSeq_id_Handle::GetHandle(), CBioseq_Handle::GetSeqId(), CBioseq_Handle::GetSeqMap(), CBioseq_Handle::GetSynonyms(), CBioseq_Handle::GetTSE_Handle(), COpenRange< TSeqPos >::GetWhole(), CSeq_loc_Mapper_Base::m_DstRanges, SSeqMapSelector::SetLinkUsedTSE(), CSeq_loc_Mapper::x_InitializeSeqMap(), and CSeq_loc_Mapper_Base::x_PreserveDestinationLocs().

◆ CSeq_loc_Mapper() [3/16]

Mapping through a pre-filled CMappipngRanges.

Source(s) and destination(s) are considered as having the same width.

Parameters
mapping_ranges CMappingRanges filled with the desired source and destination ranges. Must be a heap object (will be stored in a CRef<>). NOTE: If the mapper is used with mixed sequence types, the ranges must use genomic coordinates (for ranges on proteins multiply all coordinates by 3). scope Optional scope (required only for mapping alignments). If any ids from the mapping ranges are not available through this object, they must be registered using SetSeqTypeById.
See also
SetSeqTypeById

Definition at line 173 of file seq_loc_mapper.cpp.

◆ CSeq_loc_Mapper() [4/16] ◆ CSeq_loc_Mapper() [5/16]

Initialize the mapper to map through deltas from a GC-Assembly.

Definition at line 407 of file seq_loc_mapper.cpp.

References CScope::AddScope(), CScope::AddTopLevelSeqEntry(), CSeq_loc_Mapper::eCopyScope, CSeq_loc_Mapper::eSeqMap_Up, CScope::GetBioseqHandle(), CObjectManager::GetInstance(), CHeapScope::GetScope(), CBioseq_Handle::GetSeqMap(), CGC_Assembly_Parser::GetTopLevelSequences(), CGC_Assembly_Parser::GetTSE(), COpenRange< TSeqPos >::GetWhole(), ITERATE, CSeq_loc_Mapper_Base::m_DstRanges, CSeq_loc_Mapper_Base::m_MapOptions, CSeq_loc_Mapper::m_Scope, CSeq_loc_Mapper_Options::SetMapperSequenceInfo(), CSeq_loc_Mapper::x_InitializeSeqMap(), and CSeq_loc_Mapper_Base::x_PreserveDestinationLocs().

◆ CSeq_loc_Mapper() [6/16]

Mapping through an alignment.

Need to specify target ID or target row of the alignment. Any other ID is mapped to the target one. If scope is set, synonyms are resolved for each source ID. Only the first row matching target ID is used, all other rows are considered source.

Definition at line 204 of file seq_loc_mapper.cpp.

References CSeq_loc_Mapper_Base::x_InitializeAlign().

◆ CSeq_loc_Mapper() [7/16] ◆ CSeq_loc_Mapper() [8/16] ◆ CSeq_loc_Mapper() [9/16] ◆ CSeq_loc_Mapper() [10/16] ◆ CSeq_loc_Mapper() [11/16] ◆ CSeq_loc_Mapper() [12/16] ◆ CSeq_loc_Mapper() [13/16]

Mapping through a seq-map.

Parameters
seq_map Sequence map defining the mapping direction Direction of mapping: up (from segments to master) or down. selector Seq-map selector with additional restrictions (range, strand etc.). Some properties of the selector are always adjusted by the mapper. top_level_id Explicit destination id when mapping up, may be used with seq-maps constructed from a seq-loc with multiple ids.

Definition at line 321 of file seq_loc_mapper.cpp.

References CSeq_loc_Mapper::x_InitializeSeqMap(), and CSeq_loc_Mapper_Base::x_PreserveDestinationLocs().

◆ CSeq_loc_Mapper() [14/16]

Mapping between segments and the top level sequence limited by depth.

Parameters
depth Mapping depth. Depth of 0 converts synonyms. top_level_seq Top level bioseq direction Direction of mapping: up (from segments to master) or down.

Definition at line 338 of file seq_loc_mapper.cpp.

References depth, CSeq_loc_Mapper::eSeqMap_Up, CSeq_id_Handle::GetHandle(), CConstRef< C, Locker >::GetPointer(), CBioseq_Handle::GetSeqId(), CBioseq_Handle::GetSeqMap(), COpenRange< TSeqPos >::GetWhole(), CSeq_loc_Mapper_Base::m_DstRanges, CSeq_loc_Mapper::x_InitializeSeqMap(), and CSeq_loc_Mapper_Base::x_PreserveDestinationLocs().

◆ CSeq_loc_Mapper() [15/16] ◆ CSeq_loc_Mapper() [16/16] ◆ CSeq_loc_Mapper_Base() [1/11]

Mapping through a pre-filled CMappipngRanges.

Parameters
mapping_ranges CMappingRanges filled with the desired source and destination ranges. Must be a heap object (will be stored in a CRef<>). NOTE: If the mapper is used with mixed sequence types, the ranges must use genomic coordinates (for ranges on proteins multiply all coordinates by 3). options Mapping options which need to be set during mapper initialization.
See also
CSeq_loc_Mapper_Options

Definition at line 670 of file seq_loc_mapper_base.cpp.

◆ CSeq_loc_Mapper_Base() [2/11] ◆ CSeq_loc_Mapper_Base() [3/11] ◆ CSeq_loc_Mapper_Base() [4/11] ◆ CSeq_loc_Mapper_Base() [5/11] ◆ CSeq_loc_Mapper_Base() [6/11] ◆ CSeq_loc_Mapper_Base() [7/11] ◆ CSeq_loc_Mapper_Base() [8/11] ◆ CSeq_loc_Mapper_Base() [9/11] ◆ CSeq_loc_Mapper_Base() [10/11] ◆ CSeq_loc_Mapper_Base() [11/11] ◆ CSeq_loc_Mapper_Message() ◆ CSeq_loc_Mapper_Options() [1/3] ◆ CSeq_loc_Mapper_Options() [2/3] ◆ CSeq_loc_Mapper_Options() [3/3] ◆ CSimpleLoaderMaker()

template<class TDataLoader >

◆ CStdSeq_idSource() ◆ DECLARE_OPERATOR_BOOL() CPrefetchTokenOld::DECLARE_OPERATOR_BOOL ( m_Impl &&*  m_Impl ) ◆ DECLARE_OPERATOR_BOOL_REF() CBlobIdKey::DECLARE_OPERATOR_BOOL_REF ( m_Id  ) ◆ DetailsToChoice() [1/2]

Definition at line 805 of file data_loader.cpp.

References _ASSERT, CDataLoader::DetailsToChoice(), CDataLoader::eAll, CDataLoader::eAnnot, CDataLoader::eBlob, CDataLoader::eCore, CDataLoader::eExtAnnot, CDataLoader::eExtFeatures, CDataLoader::eFeatures, COpenRange< Position >::Empty(), CDataLoader::eOrphanAnnot, CDataLoader::eSequence, SRequestDetails::fAnnotBlobExternal, SRequestDetails::fAnnotBlobInternal, SRequestDetails::fAnnotBlobNone, SRequestDetails::fAnnotBlobOrphan, SRequestDetails::m_AnnotBlobType, SRequestDetails::m_NeedAnnots, SRequestDetails::m_NeedSeqData, and SRequestDetails::m_NeedSeqMap.

◆ DetailsToChoice() [2/2]

Definition at line 773 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::eAnnot, CDataLoader::eCore, CDataLoader::eFeatures, CDataLoader::eGraph, i, and ITERATE.

Referenced by CDataLoader::DetailsToChoice(), CDataLoader::GetDetailedRecords(), and CGBDataLoader_Native::x_MakeContentMask().

◆ DropTSE() ◆ EnqueNextAction() void CPrefetchSequence::EnqueNextAction ( void  ) protected ◆ EstimateLoadBytes() ◆ EstimateLoadSeconds() ◆ Execute() [1/6] ◆ Execute() [2/6] ◆ Execute() [3/6] ◆ Execute() [4/6] ◆ Execute() [5/6] ◆ Execute() [6/6]

Do the actual job.

Called by whichever thread handles this task.

Returns
Result of task execution (the status will be set accordingly)
Note
Only 3 values are allowed: eCompleted, eFailed, eCanceled.

Implements CThreadPool_Task.

Definition at line 198 of file prefetch_manager_impl.cpp.

References CThreadPool_Task::eCanceled, CThreadPool_Task::eCompleted, CThreadPool_Task::eFailed, CPrefetchRequest::GetAction(), CThreadPool_Task::IsCancelRequested(), CPrefetchRequest::m_Action, CRef< C, Locker >::NotNull(), Ref(), and result.

◆ Exists() [1/2] ◆ Exists() [2/2] ◆ FindDataLoader() ◆ GC() void CDataLoader::GC ( void  ) virtual ◆ GetAccVer() [1/2] ◆ GetAccVer() [2/2] ◆ GetAccVerFound()

Reimplemented in CPSGDataLoader, CGBDataLoader_Native, CWGSDataLoader, CCSRADataLoader, and CBAMDataLoader.

Definition at line 342 of file data_loader.cpp.

References CDataLoader::SAccVerFound::acc_ver, CLoaderException::eNoData, CLoaderException::eNotFound, CDataLoader::GetAccVer(), CException::GetErrCode(), CDataLoader::SAccVerFound::sequence_found, and CDataLoader::SequenceExists().

Referenced by CDataSource::GetAccVer(), and CDataLoader::GetAccVers().

◆ GetAccVers() [1/3] ◆ GetAccVers() [2/3]

Get accession.version Seq-id Returns null CSeq_id_Handles for sequences that aren't found or don't have accession id.

See also
GetAccVer
EGetflags

Referenced by s_ReplaceGIs().

◆ GetAccVers() [3/3] ◆ GetAction() ◆ GetAlign() ◆ GetAlign_Dense_seg_TotalRange() bool CSeq_loc_Mapper_Options::GetAlign_Dense_seg_TotalRange ( void  ) const inline ◆ GetAlign_Sparse_ToFirst() bool CSeq_loc_Mapper_Options::GetAlign_Sparse_ToFirst ( void  ) const inline ◆ GetAlign_Sparse_ToSecond() bool CSeq_loc_Mapper_Options::GetAlign_Sparse_ToSecond ( void  ) const inline ◆ GetAllTSEs()

Definition at line 295 of file scope.cpp.

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

Referenced by CBlkEdtFeatLocationPanel::AddCommand(), CGroupExplode::apply(), CollectBioseqForSeqdesc(), CollectBioseqForSeqFeat(), CSequenceEditingEventHandler::Duplicate(), GetBioseqForSeqdesc(), GetDefaultTopLevelSeqEntry(), GetProductToCDSMap(), GetSeqEntryForPubdesc(), GetSeqEntryForSeqdesc(), GetSeqFeatHandleForBadLocFeature(), IsManualScope(), CClickableSortUniqueCount::OnListItemActivated(), CEditSequence::OnRetranslate(), s_AreThereOtherCDSForThisProduct(), CSimpleProjectView::x_ActivateTextView(), CSequenceEditingEventHandler::x_CacheSelectedLocations(), CProjectFileWriter::x_FindParent(), and CNewCleanup_imp::x_MoveCdregionXrefsToProt().

◆ GetBioseq_setEditHandle() ◆ GetBioseq_setHandle()

Definition at line 176 of file scope.cpp.

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

Referenced by CScope::GetObjectHandle(), CPropagateDescriptors::GetPropagateDownCommand(), CPropagateDescriptors::GetPropagateUpCommand(), GetSeqEntryHandle(), CSUCDataGenerator::GetSUCResults(), GetTextObjectDescription(), CRemoveSet::remove_set(), CRemoveSet::remove_sets_from_set(), CMacroBioData_SeqSetIter::RunDeleteCommand(), CMacroBioData_SeqSetIter::RunEditCommand(), s_HasAlignment(), sGetValidateObject(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_annot::ValidateSeqAnnotContext(), CValidError_bioseqset::ValidateSetElements(), CSeqMasterIndex::x_InitSeqs(), CNewCleanup_imp::x_MoveNPTitle(), CNewCleanup_imp::x_SingleSeqSetToSeq(), and CValidError_bioseqset::x_ValidateSetDescriptors().

◆ GetBioseqEditHandle() ◆ GetBioseqHandle() [1/9] ◆ GetBioseqHandle() [2/9]

Get bioseq handle by seq-id.

Definition at line 95 of file scope.cpp.

References CScope::eGetBioseq_All.

Referenced by CSequenceEditingEventHandler::AddAssemblyStructuredComment(), CValidError_imp::AddBioseqWithNoPub(), CLinkUtils::AddBlastProductLink(), CExportTableDlg::AddCdsGeneMrnaTable(), AddColumnsToFeatureTable(), CStrandPanel::AddCommand(), AddDefaultSentinelFeats(), AddExceptionsToShortIntron(), CExportTableDlg::AddFeaturesToTable(), AddFeatureToBioseq(), CSequenceEditingEventHandler::AddGenomeAssemblyStructuredComment(), AddMiscColumnsToTable(), CCleanup::AddProtein(), CNewCleanup_imp::AddProteinTitles(), CExportTableDlg::AddRnaToTable(), CSAM_CIGAR_Formatter::AddRow(), CSequenceEditingEventHandler::AddSecondary(), CLinkUtils::AddSequenceLinks(), CClickableSortUniqueCount::AddToBulkEditList(), AdjustFeatureEnd3(), AdjustFeatureEnd5(), AdjustForCDSPartials(), CFeatGapInfo::AdjustForRelevantGapIntervals(), AdjustMappedStop(), CEditSequence::AdjustProtFeatureLocations(), AdjustSingleFeature(), CPaintAlignment::AlignPosToSeqPos(), CFeaturePropagator::AlignPosToSeqPos(), CAlnGraphic::AlnGraphicDisplay(), CPackageFeaturesOnParts::apply(), CConvertFeatToDescComment::apply(), CConvertFeatToDescSource::apply(), CConvertFeatToDescPub::apply(), CRecomputeIntervals::apply(), CAdjustFeatsForIntrons::apply(), CCreateLocusTagGene::apply(), CGroupExplode::apply(), CRemoveUnindexedFeatures::apply(), CLoadSecondaryAccessions::apply(), CConvertBadCdsAndRnaToMiscFeat::apply(), CConvertSelectedGaps::apply_impl(), CEditSelectedGaps::apply_impl(), CApplyObject::ApplyChange(), ApplyFeatureSeqTableToSeqEntry(), CRemoveFeaturesDlg::ApplyToCSeq_entry(), CCorrectIntervalOrder::ApplyToCSeq_entry(), CProSplign::AssignGeneticCode(), CSequenceEditingEventHandler::Autodef(), CDiscrepancyVisitorImpl< _Name >::Autofix(), BadSeqLocSortOrder(), CContigAssembly::BandedGlobalAlignment(), CAutogeneratedCleanup::BasicCleanupSeqEntry(), BioseqHandleFromLocation(), BlastXML_FormatReport(), BOOST_AUTO_TEST_CASE(), CNewCleanup_imp::CdRegionEC(), CdsTrnaOverlapStr(), CGapInfo< CBlastTabular >::CGapInfo(), CGeneFinder::CGeneSearchPlugin::CGeneSearchPlugin(), ChangeFeat(), ChangeSeqId(), CAddIdChecker::Check(), CRemoveIdChecker::Check(), CResetIdChecker::Check(), CRemoveBioseqChecker::Check(), CAddBioseqChecker::Check(), CRemoveFeatChecker::Check(), CAddFeatChecker::Check(), variation::CVariationUtil::CheckExonBoundary(), CValidError_bioseq::CheckForMultipleStructuredComments(), variation::CVariationUtil::CheckPlacement(), CVisibleRange::Clamp(), COligoSpecificityTemplate::COligoSpecificityTemplate(), CollectNucProtBioseqs(), CFixForTransSplicing::CollectProteinNames(), CChain::CollectTrustedmRNAsProts(), CFixForTransSplicing::CombineFeatures(), CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes(), CScoreBuilderBase::ComputeScore(), CFeaturePropagator::ConstructProteinFeatureForPropagatedCodingRegion(), CBioseq_Handle::ContainsSegment(), CConvertProtToImp::Convert(), CConvertCDSToProt::Convert(), CConvertCDSToGene::Convert(), CConvertCDSToPseudoGene::Convert(), Convert_Seq_entry_Seq_align(), Convert_Seq_entry_Seq_annot(), Convert_Seq_id_Bioseq(), Convert_Seq_id_Bioseq_set(), Convert_Seq_id_Seq_entry(), CCdsToMatPeptide::ConvertInner(), CNewCleanup_imp::ConvertSeqLocWholeToInt(), CBlobSplitterImpl::CopySkeleton(), CRemoveFeaturesDlg::CountOrphanedProteins(), CCreateProteinId::create_protein_ids(), CBlastBioseqMaker::CreateBioseqFromId(), CSequenceEditingEventHandler::CreateDescriptor(), CAlignmentAssistant::CreateFeature(), CSequenceEditingEventHandler::CreateFeature(), variation_ref::CVariationUtil::CreateFlankLocs(), variation::CVariationUtil::CreateFlankLocs(), CFeatureGenerator::CreateMicroIntrons(), CNewCleanup_imp::CreateMissingMolInfo(), CTextItemSeq_loc::CreateObject(), CSequenceEditingEventHandler::CreateRegulatory(), CSeqMap::CreateSeqMapForSeq_loc(), CSequenceEditingEventHandler::CreateSpecificStructuredComment(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSeqVector::CSeqVector(), CSGSequenceDS::CSGSequenceDS(), DeleteProteinAndRenormalizeNucProtSet(), CAlignmentAssistant::DeleteSelection(), CAddIdChecker::Do(), CRemoveIdChecker::Do(), CResetIdChecker::Do(), CRemoveBioseqChecker::Do(), CAddBioseqChecker::Do(), CRemoveFeatChecker::Do(), CAddFeatChecker::Do(), CValidError_feat::DoesCDSHaveShortIntrons(), DoesCodingRegionHaveUnnecessaryException(), DoesFeatureHaveUnnecessaryException(), DoesmRNAHaveUnnecessaryException(), CSequenceEditingEventHandler::EditHistory(), CEditingBtnsPanel::EditSequence(), CSequenceEditingEventHandler::EditSequence(), EndAdded(), CPrefetchBioseq::Execute(), CGBObjectLoader::Execute(), CLocationEditPolicy::Extend3(), CLocationEditPolicy::Extend5(), CExtendPartialFeatDlg::ExtendCDS(), ExtendCDSToStopCodon(), ExtendLocationForTranslExcept(), ExtendToGapsOrEnds(), ExtendToStopCodon(), FinalCleanup(), CSelectTargetDlg::FindBioseq(), FindCitInFeats(), CProSplign::CImplementation::FindGlobalAlignment_stage1(), variation::CVariationUtil::FindLocationProperties(), CSeqIdGuesser::FindMatches(), FindNewLocations(), IEditingActionFeat::FindOrCreateProtFeat(), IEditingActionFeat::FindRelated(), CEditingActionFeatGeneLocus::FindRelated(), IEditingActionFeat::FindRelatedOrCreateProtFeat(), CFeaturePropagator::FindRow(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), variation::FindSSRLoc(), CInternalStopFinder::FindStartStopRanges(), CHugeFileProcess::ForEachEntry(), CHTMLFormatterEx::FormatLocation(), CHTMLFormatterEx::FormatProteinId(), CHTMLFormatterEx::FormatTranscriptId(), CValidError_bioseq::GapByGapInst(), CFlatFileGenerator::Generate(), CScore_FrameShifts::Get(), CScore_3PrimeUnaligned::Get(), CScore_Polya::Get(), CScore_SequenceLength::Get(), CScore_SymmetricOverlap::Get(), CScore_StartStopCodon::Get(), CScore_CdsScore::Get(), CScore_GeneID::Get(), CScore_RibosomalSlippage::Get(), CScore_SegPct::Get(), CScore_Entropy::Get(), CDiscrepancyPanel::GetAccessionForObject(), GetAccessionFromObjects(), CSparseMultiDataSource::GetAlignType(), CSGAlignmentJob::GetAlignType(), CDataTrackUtils::GetAlignType(), CProjectedMappingInfo::GetAnchorSequence(), CProductColumn::GetApplyObjects(), CCodonStartColumn::GetApplyObjects(), CFieldHandler::GetApplyObjectsFromRelatedObjects(), GetBestCdsForMrna(), GetBestMrnaForCds(), GetBioseqForSeqFeat(), GetBioseqFromSeqLoc(), CSplitCacheApp::GetBioseqHandle(), CSimpleOM::GetBioseqHandle(), CScope::GetBioseqHandle(), CAlnVec::GetBioseqHandle(), GetBioseqHandleForMultihomeLocation(), CSeqMasterIndex::GetBioseqIndex(), CScoreBuilder::GetBlastScoreProtToNucl(), CScoreBuilder::GetBlastScoreStd(), GetCDSForProduct(), CValidError_imp::GetCDSGivenProduct(), CSeqUtils::GetCdsMappingInfoFromRna(), GetCdsOnMrna(), GetCDSProductSeq(), GetCDSProductSequence(), CAlignCollapser::GetCollapsedAlgnments(), CAddGlobalCodeBreak::GetCommand(), CBulkEditFeatDlg::GetCommand(), CCdsFromGeneMrnaExon::GetCommand(), CConvertCdsToMiscFeat::GetCommand(), CConvertFeatDlg::GetCommand(), CCorrectGenesDialog::GetCommand(), CExtendCDSToStop::GetCommand(), CExtendPartialFeatDlg::GetCommand(), CFarPointerSeq::GetCommand(), CFixForTransSplicing::GetCommand(), CFuseFeaturesDlg::GetCommand(), CGeneFeatFromOtherFeatDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), CGeneFeatFromXrefs::GetCommand(), CBulkCDS::GetCommandFromValuesTable(), CCreateSeqHistForTpa::GetCreateSeqHistFromTpaCommand(), CAlignFormatUtil::GetDbType(), GetDeleteAllFeaturesCommand_Ex(), GetDeleteFeatureCommand(), GetDNASequence(), CValidator::CCacheImpl::GetFeatStrKeyToFeats(), CGeneCache::GetFeatTreeFromCache(), CValidErrorFormat::GetFeatureBioseqLabel(), CBioseqIndex::GetFeatureForProduct(), CAlignmentAssistant::GetFeatures(), CEditSequence::GetFeatures(), GetGIForSeqId(), CDefaultLengthGetter::GetLength(), CBlobSplitterImpl::GetLength(), GetLoc(), CValidError_imp::GetLocalBioseqHandle(), NMacroUtil::GetLocusTagFromProtRef(), CFarPointerSeq::GetMessageForId(), variation::CVariationUtil::GetMolType(), GetmRNAforCDS(), GetmRNAForProduct(), CValidError_imp::GetmRNAGivenProduct(), GetNewGeneralProtId(), GetNewLocalProtId(), GetNucleotideParent(), CScope::GetObjectHandle(), CValidErrorFormat::GetObjectLabel(), CFeatureSeqTableColumnBase::GetObjects(), CAlignCollapser::GetOnlyOtherAlignments(), GetOverlappingFeatures(), CRemoveFeaturesDlg::GetProductId(), CProductStringBuilder::GetProductString(), GetProductToCDSMap(), GetProtAndRnaForCDS(), CCleanup::GetProteinLocationFromNucleotideLocation(), GetProteinString(), GetProteinWeight(), GetPROTForProduct(), GetProtRefSeqId(), GetRelatedFeatureApplyObjects(), GetRelatedFeatures(), CDBLinkField::GetRelatedObjects(), CPubField::GetRelatedObjects(), CStructuredCommentField::GetRelatedObjects(), CTextDescriptorField::GetRelatedObjects(), GetReportableSeqIdForAlignment(), GetResolveOrder(), GetRetranslateCDSCommand(), CCodingPropensity::GetScore(), CPaintAlignment::GetSegments(), GetSeqEntryHandle(), CSeqMap::GetSeqMapForSeq_loc(), CEditSequence::GetSequence(), CScope_Mapper_Sequence_Info::GetSequenceLength(), CDUpdater::getSequencesFromGB(), CSUCDataGenerator::GetSUCResults(), GetSynchronizeProductMolInfoCommand(), GetSynchronizeProteinPartialsCommand(), GetTargetedLocusName(), CAlignFormatUtil::GetTaxidForSeqid(), CMacroBioData_FeatIterBase::GetTaxnames(), CBlastQuerySourceOM::GetTitle(), CFeatGlyph::GetTooltip(), CValidError_imp::GetTSACDSOnMinusStrandErrors(), CValidError_feat::GetTSACDSOnMinusStrandErrors(), CValidError_bioseq::GetTSANStretchErrors(), IEditingAction::GetUpdateMRNAProductNameCmd(), GetValidatorLocationLabel(), CBankITCommentField::GetVals(), CGeneralCommentField::GetVals(), CEditingActionFeatTranslation::GetValue(), CBulkCDS::GetValuesTableFromSeqEntry(), IEditingActionFeat::GoToProtFeature(), CAsn2FastaApp::HandleSeqID(), CCleanupApp::HandleSeqID(), HasBadProteinStart(), HasNoStop(), CBlastBioseqMaker::HasSequence(), HasStopInProtein(), CNewCleanup_imp::ImpFeatBC(), CAlnGraphic::Init(), CAlignCollapser::InitContig(), InitSplicedsegFromPairwiseAln(), CViewGraphic::InitView(), CVcfTableView::InitView(), CDiscrepancyPanel::InvalidObject(), CLocationEditPolicy::Is3AtEndOfSeq(), CLocationEditPolicy::Is5AtEndOfSeq(), CContigAssembly::IsAtLeastHalfDovetail(), IsBioseqTSA(), CValidError_bioseqset::IsCDSProductInGPS(), IsExtendable(), CValidError_bioseq::IsHistAssemblyMissing(), IsInOrganelleSmallGenomeSet(), CSequenceEditingEventHandler::IsLocationSelected(), CEditingBtnsPanel::IsLocationSelectedAa(), CEditingBtnsPanel::IsLocationSelectedNa(), CValidError_bioseqset::IsMrnaProductInGPS(), CMRnaForCDS::IsOrganelle(), CValidError_bioseq::IsPartial(), CBlastBioseqMaker::IsProtein(), CValidator::IsSeqLocCorrectlyOrdered(), IsSequenceFetchable(), CEditingActionFeatTranslation::IsSetValue(), CSeqUtils::isTopLevel(), CValidError_align::IsTpaAlignment(), CValidError_bioseq::IsWGSMaster(), LaunchDescEditorForSeq(), CmRNACDSLinker::LinkByProduct(), ListOrphanProteins(), CwxDemoAlignTableFrame::LoadAccession(), CwxDemoFeatureTableFrame::LoadAccession(), CLoadStructComments::LoadWithAccessions(), CId1FetchApp::LookUpGI(), CDLTestThread::Main(), CDLTest2Thread::Main(), MakeMailReportPostReport(), MakemRNAforCDS(), MakeSubjectScores(), CMakeBadSpecificHostTable::MakeTable(), MapSeq_feat(), CLocationConstraintMatcher::Match(), IEditingActionFeat::MatchBioseqConstraintForFeatHandle(), CNewCleanup_imp::MoveCitationQuals(), CCleanup::MoveFeatToProtein(), CPrefetchTokenOld_Impl::NextBioseqHandle(), CCrossAlnDemoDlg::OnAccClick(), CAlignMultipleDemoDlg::OnAccClick(), CHitMatrixDemoDlg::OnAccClick(), CSeqTextDemoDlg::OnAccClick(), CCompareWithBiosample::OnClickOk(), CDiscrepancyPanel::OnDblClk(), CDiscrepancyPanel::OnListClk(), CClickableSortUniqueCount::OnListItemActivated(), CClickableSortUniqueCount::OnListItemSelected(), CSelectFeatureDlg::OnLoadAccession(), CBioseqEditor::OnPropagateAllFeatures(), CAlignmentAssistant::OnPropagateFeatures(), CAlignmentAssistant::OnReverseStrand(), CClickableSortUniqueCount::OnTreeSelectionChanged(), CScopeAlnSeqIdConverter< TAlnSeqId >::operator()(), SBlobCopier::operator()(), CSeqIdBioseqHandleComp< TSeqIdPtr >::operator()(), CWinMaskUtil::CInputBioseq_CI::operator++(), CRemoveProteins::OrphanedProteins(), OverrideLenIfAccession(), PackSeqPntCheckCpp(), PatchTargetSequence(), CValidError_imp::PostErr(), CSeqVectorCache::PrefetchSequence(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintPhiResult(), CBlastFormat::PrintReport(), CResolveRequest::Process(), ProcessForTrimAndSplitUpdates(), CBiosampleChkApp::ProcessList(), CAlnWriter::ProcessSeqId(), PromoteCDSToNucProtSet(), CGlimmerReader::Read(), CConversionApp::Read(), variation::CVariationUtil::RemapToAnnotatedTarget(), RemoteFetchLongNucleotideBioseq(), CNewCleanup_imp::RemoveBadProteinTitle(), CRemoveFeaturesDlg::RemoveOrphansRenormalizeNucProtSets(), CCleanup::RemovePseudoProduct(), CSeqTestApplication::Render(), CAlignmentAssistant::ReportUnresolvedBioseqs(), RestoreModelFromInternalGnomonFeature(), RestoreModelFromPublicMrnaFeature(), CNewCleanup_imp::ResynchPeptidePartials(), CNewCleanup_imp::ResynchProteinPartials(), RetranslateCdregion(), RetranslateCDS(), CRetranslateCDS::RetranslateCDSCommand(), CAddGlobalCodeBreak::RetranslateCDSCommand(), CExtendCDSToStop::RetranslateCDSCommand(), RetrieveGi555WithTimeOut(), RetrieveLargeChromosomeWithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), RetrievePartsOfLargeChromosome(), ReverseComplementLocation(), CAsnExportJob::Run(), CAlignTabExportJob::Run(), C5ColExportJob::Run(), CAgpExportJob::Run(), CFastaExportJob::Run(), CFlatFileExportJob::Run(), CGffExportJob::Run(), CGtfExportJob::Run(), CDiscrepancyReportJob::Run(), CDemoSeqQaApp::Run(), CSeedTopApp::Run(), CFeatCompareJob_Align::Run(), CFeatureRetrievalJob::Run(), CXcompareAnnotsApplication::Run(), CAsnCacheTestApplication::Run(), CIdfetchApplication::Run(), CDemoApp::Run(), CSampleLds2Application::Run(), CFeatTreeSampleApp::Run(), CSampleObjmgrApplication::Run(), CTestBlastp_All::RunTest(), CTestSingleAln_All::RunTest(), s_AddSeqDataToPssm(), s_AddSeqTitleToPssm(), s_AreFullLengthCodingRegionsWithDifferentFrames(), s_BlastXMLAddIteration(), s_CheckDataStatus(), s_CollectCollidingIDs_Entry(), ScorePositionSort::s_CompareSeqAlignByScoreAndPosition(), s_ConvertWholeToInt(), s_Create5ColFeatTable(), s_DetermineComponentType(), s_DivvyUpAlignments_ProcessAnnot_Dendiag(), s_DivvyUpAlignments_ProcessAnnot_Denseg(), s_DumpSequences_wRange(), s_ExtendEntriesFromAlignments(), ApplyCDSFrame::s_FindMatchingFrame(), CMacroFunction_ApplyCDSFrame::s_FindMatchingFrame(), s_GetCdregionContentLabel(), s_GetCdregionLabel(), s_GetCDSformRNA(), s_GetCdsSequence(), s_GetCigarString(), s_GetClipLoc(), s_GetDefline(), CMacroFunction_NumberOfFeatures::s_GetFeatTypeCount(), s_GetFeatureKeyLinkLocation(), s_GetFrame(), s_GetGeneticCode(), s_GetMaskLoc(), s_GetmRNAForCDS(), s_GetPercentCoverage(), s_GetPolyA_genomic_priming(), CDesktopFeatItem::s_GetProteinName(), s_GetQueryBioseq(), s_GetSplicedSegIdentityMismatch(), s_GetTaxid(), s_GetTopology(), s_GetUngapLoc(), CMiscSeqTable::s_GetValueToSehMap(), s_GuessId(), s_ImportQueries(), s_IsFarLocation(), s_IsNucLocation(), s_IsVirtualId(), s_MakeBioseqs(), s_MatchSeqIds(), s_ModifySeqAlnWithFilteredSeqIDs(), s_MoveProteinSpecificFeats(), s_ParseTRnaFromAnticodonString(), s_PartialAtGapOrNs(), s_QueryVectorToBioseqSet(), s_Render_SeqFeat(), s_SeqAlignSetToXMLHsps(), s_SeqAlignToXMLHit(), s_SequenceIsProtein(), s_SetBlastXMLSearch(), ScanForCpGs(), CWeightedIdentityScorer::ScoreAlignments(), CHangScorer::ScoreAlignments(), COverlapScorer::ScoreAlignments(), CClippedScorer::ScoreAlignments(), CGeneOverlapProcess::SeqEntryProcess(), CGeneFeatTreeProcess::SeqEntryProcess(), CInvertProcess::SeqEntryProcess(), CSeqVectorProcess::SeqEntryProcess(), CTitleProcess::SeqEntryProcess(), SeqIntCheckCpp(), SeqIntPartialCheck(), CNewCleanup_imp::SeqLocBC(), SeqLocPartialCheck(), CSeqUtils::SeqLocToBioseq(), SeqPntCheckCpp(), CPaintAlignment::SeqPosToAlignPos(), CFeaturePropagator::SeqPosToAlignPos(), CIgBlastTabularInfo::SetAirrFormatData(), CReportEntry::SetAlignment(), CSameConstraintMatcher::SetFeat(), CBlastTabularInfo::SetFields(), CCleanup::SetGenePartialByLongestContainedFeature(), CNewCleanup_imp::SetGeneticCode(), CMultAlign::SetGenomic(), CChainer::CChainerImpl::SetGenomicRange(), variation::CHgvsParser::CContext::SetId(), variation_ref::CHgvsParser::CContext::SetId(), CIgBlastTabularInfo::SetIgAnnotation(), variation::CVariationUtil::SetPlacementProperties(), CCleanup::SetProteinName(), CRBSubpanel::SetSubsets(), variation_ref::CVariationUtil::SetVariantProperties(), sGenerateFields(), sGetValidateObject(), CFeatureGenerator::SImplementation::SMapper::SMapper(), CAlignFormatUtil::SplitSeqalignByMolecularType(), StartAbutsGap(), StopAbutsGap(), TestDataNotFound(), CSequenceEditingEventHandler::TestHupIdEnabled(), CSplitCacheApp::TestSplitBlob(), TestUpdateCDS(), CMacroFunction_SwapRelFeatQual::TheFunction(), CMacroFunction_SetRelFeatQual::TheFunction(), CMacroFunction_ConvertFeatQual::TheFunction(), CMacroFunction_ConvertRNARelQual::TheFunction(), CMacroFunction_ParseFeatQual::TheFunction(), CMacroFunction_ParseRNARelQual::TheFunction(), CMacroFunction_AddParsedToFeatQual::TheFunction(), CMacroFunction_CopyFeatQual::TheFunction(), CMacroFunction_CopyRNARelQual::TheFunction(), CMacroFunction_RemoveAllFeatures::TheFunction(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), CMacroFunction_ApplyCDS::TheFunction(), CMacroFunction_ApplyRNA::TheFunction(), CMacroFunction_ApplyGene::TheFunction(), CMacroFunction_ApplyOtherFeature::TheFunction(), CMacroFunction_LocationDistConstraint::TheFunction(), CMacroFunction_ApplyPublication::TheFunction(), CMacroFunction_FeatStrandednessConstraint::TheFunction(), CCdregion_translate::TranslateCdregion(), TranslateCDSCommand(), TranslateCodingRegionForValidation(), CAlignmentAssistant::TranslateLocations(), TrimStopsFromCompleteCDS(), UpdatemRNAProduct(), UpdateToBestId(), UpgradeSeqLocId(), CValidError_imp::Validate(), CAsnvalThreadState::ValidateAsync(), CValidError_bioseq::ValidateBioseq(), CValidError_bioseq::ValidateBioseqContext(), CValidError_bioseq::ValidateDelta(), CValidError_bioseq::ValidateDeltaLoc(), CValidError_bioseqset::ValidateGenProdSet(), CValidError_bioseq::ValidateNsAndGaps(), CValidError_bioseqset::ValidateNucProtSet(), CValidError_bioseqset::ValidatePopSet(), CValidError_bioseq::ValidateRawConst(), CValidError_bioseq::ValidateSecondaryAccConflict(), CValidError_bioseq::ValidateSegRef(), CValidError_annot::ValidateSeqAnnotContext(), CValidError_bioseq::ValidateSeqDescContext(), CValidError_graph::ValidateSeqGraphContext(), CValidError_bioseq::ValidateSeqId(), CSpliceProblems::ValidateSpliceCdregion(), CSpliceProblems::ValidateSpliceExon(), CSpliceProblems::ValidateSpliceMrna(), CValidError_bioseq::ValidateTwintrons(), CCleanup::WGSCleanup(), CVcfWriter::WriteAnnot(), CFastaOstreamEx::WriteFeature(), CAlnWriter::WriteSplicedExons(), CAnnotGetter::x_AddAnnotations(), CFastaOstreamEx::x_AddLocationAttribute(), CFastaOstreamEx::x_AddProteinNameAttribute(), CFeatureItem::x_AddQualSeqfeatNote(), CSeq_loc_Mapper::x_AddVirtualBioseq(), CSequenceUpdater::x_AdjustOldCDSProduct(), CIgBlast::x_AnnotateC(), CCountryFixup::x_ApplyToDescriptors(), CCountryFixup::x_ApplyToSeqAndFeat(), variation::CHgvsParser::x_AsHgvsInstExpression(), variation::CVariationUtil::CCdregionIndex::x_CacheSeqData(), CSingleFeatValidator::x_CalculateLocationGaps(), CNewCleanup_imp::x_ChangePopToPhy(), CSeqdesc_CI::x_CheckRef(), CMRnaForCDS::x_ChkAndMakeMRna(), CNewCleanup_imp::x_CleanupGenbankBlock(), CConvertFeatureBase::x_ConvertToCDS(), CFlatGatherer::x_CopyCDSFromCDNA(), CSeq_id_Resolver__LRG::x_Create(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CHitMatrixDataSource::x_CreateIds(), CBLASTSeqToolJob::x_CreateProjectItems(), CTaxTreeToolJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CCleanupJob::x_CreateProjectItems(), CWindowMaskerJob::x_CreateProjectItems(), CBlastFormat::x_CreateSubjectBioseq(), CVectorTrimPanel::x_DeleteSelected(), CAdjustFeaturesForGaps::x_DoOne(), CComponentSearchJob::x_DoSearch(), CCpgSearchJob::x_DoSearch(), COrfSearchJob::x_DoSearch(), CCdsGlyph::x_DrawProjectedProtSeq(), CCdsGlyph::x_DrawProtSeqWithMapping(), CFeatGlyph::x_DrawRNAProductSequence(), CIgBlast::x_ExtendAlign3end(), CIgBlast::x_ExtendAlign5end(), CNewCleanup_imp::x_ExtendProteinFeatureOnProteinSeq(), CNewCleanup_imp::x_ExtendSingleGeneOnMrna(), CIgBlast::x_FillJDomain(), CVectorTrimPanel::x_FindCompleteDeletions(), CCorrectGenesDialog::x_FindExactMatches(), IEditingActionFeat::x_FindGeneForFeature(), x_FindLatestSequence(), CCorrectGenesDialog::x_FindNonExactMatches(), CUpdateSeq_Input::x_FixCollidingIDs_Bioseq(), CSequenceUpdater::x_FuseProtFeatsForCDS(), CFlatGatherer::x_GatherCDSReferences(), CDeflineItem::x_GatherInfo(), CFlatGatherer::x_GatherReferences(), CAlnGraphic::x_GetAlnInfo(), CTableDataAlnSummary::x_GetAlnSummary(), CFeatureItem::x_GetAssociatedProtInfo(), CFeatureItem::x_GetAssociatedProtInfoIdx(), CSeqMap_CI::x_GetBioseq(), CSingleFeatValidator::x_GetBioseqByLocation(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CSeqMap::x_GetBioseqInfo(), CNaSeqlocHelper::x_GetCDS(), CConvertFeatureBase::x_GetCDSProduct(), CCreateGeneModelTask::x_GetCommand(), CCommonComponentScorer::x_GetCompList(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CDisplaySeqalign::x_GetFeatureInfo(), CSingleFeatValidator::x_GetFeatureProduct(), CProjectFileWriter::x_GetGi(), CVecscreenRun::CFormatter::x_GetIdsAndTitlesForSeqAlign(), variation::CVariationUtil::x_GetLiteralAtLoc(), CScore_BlastRatio::x_GetPerfectScore(), CAutoDefFeatureClause::x_GetProductName(), CConvertCDSToMiscFeat::x_GetProteinDesc(), CEditingBtnsPanel::x_GetSelectedSeq(), CCdregionValidator::x_GetShortIntrons(), CVectorTrimPanel::x_GetSortedCuts(), CMacroFunction_ParsedText::x_GetSpecialField(), CAlignGroup::x_GetTaxId(), CVectorTrimPanel::x_GetTrimCoordinates(), CCreateGeneModelTask::x_GetUpdatedGeneCommand(), CFastaExportJob::x_GetWholeLoc(), CBioseqEditor::x_HasAlignment(), CAlnMixSequences::x_IdentifyAlnMixSeq(), CSequenceUpdater::x_ImportCDSProduct(), variation::CVariationUtil::CCdregionIndex::x_Index(), variation::CVariationUtil::CVariantPropertiesIndex::x_Index(), CNewCleanup_imp::x_InGpsGenomic(), CIdMapperScope::x_Init(), CAnnotTypes_CI::x_Init(), CSeqMasterIndex::x_InitSeqs(), CPhyTreeFormatter::x_InitTreeFeatures(), CCDSTranslationProblems::x_Is5AtEndSpliceSiteOrGap(), CNewCleanup_imp::x_IsCommentRedundantWithEC(), CSingleFeatValidator::x_IsMostlyNs(), CCdregionValidator::x_IsProductMisplaced(), CReportTrim::x_IsProtLocation(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CAgpconvertApplication::x_LoadTemplate(), CNewCleanup_imp::x_MoveNPTitle(), COligoSpecificityCheck::x_NW_alignment(), CValidError_bioseq::x_ParentAndComponentLocationsDiffer(), CValidError_bioseq::x_PartialAdjacentToIntron(), variation::CHgvsParser::x_PlacementCoordsToStr(), CAlnMultiCGIApplication::x_PreProcess(), CBlastFormat::x_PrintAirrRearrangement(), CMultiAlnPrinter::x_PrintFastaPlusGaps(), CBlastFormat::x_PrintIgTabularReport(), CMultiAlnPrinter::x_PrintPhylipInterleaved(), CMultiAlnPrinter::x_PrintPhylipSequential(), CBlastFormat::x_PrintTabularReport(), CBlastFormat::x_PrintTaxReport(), CPrimeCacheApplication::x_Process_Ids(), CSplignApp::x_ProcessPair(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), CPromote::x_PromoteFeatures(), CGapStatsApplication::x_ReadFileOrAccn(), CNewCleanup_imp::x_RemoveOldFeatures(), CNewCleanup_imp::x_RemovePopPhyMolInfo(), CValidError_imp::x_ReportInvalidFuzz(), CValidError_bioseq::x_ReportOverlappingPeptidePair(), CVectorTrimPanel::x_RetranslateCDS(), CReportTrim::x_RetranslateCDS(), CSequenceUpdater::x_RetranslateImportedCDSProduct(), CSequenceUpdater::x_RetranslateOldCDSProduct(), CSGAlnQualityScore::x_RetrieveQualityMap(), CBlastFormat::x_ReverseQuery(), CClustererApplication::x_RunBinary(), CInstancedAligner::x_RunMMGlobal(), CClustererApplication::x_RunSparse(), COligoSpecificityCheck::x_SavePrimerInfo(), CNewCleanup_imp::x_SeqFeatCDSGBQualBC(), variation_ref::CHgvsParser::x_SeqIdToHgvsHeader(), variation_ref::CHgvsParser::x_SeqLocToStr(), COligoSpecificityCheck::x_SequencesMappedToSameTarget(), CMacroFunction_MakeLocation::x_SetCurrentBioseq(), CReportEntry::x_SetFeature(), CReportEntry::x_SetId(), CCDSTranslationPanel::x_SetLocationForProtein(), CNewCleanup_imp::x_SetPartialsForProtein(), CReportEntry::x_SetSequence(), variation_ref::CVariationUtil::x_SetVariantProperties(), CValidError_bioseq::x_ShowBioProjectWarning(), CConvertFeatureBase::x_SimpleConversion(), CPrimeCacheApplication::x_StripSeqEntry(), CValidError_bioseq::x_TranscriptIDsMatch(), CVectorTrimPanel::x_TrimSelected(), CNewCleanup_imp::x_tRNACodonEC(), CIdResolver::x_TryProcessLRG(), CAssemblyListPanel::x_UpdateSearchTerm(), CValidError_bioseq::x_ValidateBarcode(), CCdregionValidator::x_ValidateCDSPeptides(), CCdregionValidator::x_ValidateCommonProduct(), CValidError_align::x_ValidateDim(), CCdregionValidator::x_ValidateFarProducts(), CValidError_align::x_ValidateFastaLike(), CSingleFeatValidator::x_ValidateGeneXRef(), CValidError_graph::x_ValidateGraphOnDeltaBioseq(), CValidError_align::x_ValidateSeqId(), CValidError_align::x_ValidateSeqLength(), CValidError_bioseq::x_ValidateTitle(), CRNAValidator::x_ValidateTrnaType(), CVcfWriter::x_WriteFeature(), CProjectFileWriter::x_WriteGtf(), CGff3Writer::xAssignAlignmentDensegGap(), CGff3Writer::xAssignAlignmentDensegMethod(), CGff3Writer::xAssignAlignmentDensegSeqId(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentDensegType(), CGff2Writer::xAssignFeatureAttributeProduct(), CGtfWriter::xAssignFeatureMethod(), CEditObjectFeaturePropagate::xInit(), CPslRecord::xInitializeSequenceInfo(), CFeatureTableReader::xTranslateProtein(), CSrcChkApp::xTryProcessIdFile(), CAnnotWriterApp::xTryProcessInputId(), CNewCleanup_imp::xUpdateSeqfeatCitPub(), and CGff3Writer::xWriteAlignDenseg().

◆ GetBioseqHandle() [3/9] ◆ GetBioseqHandle() [4/9] ◆ GetBioseqHandle() [5/9] ◆ GetBioseqHandle() [6/9]

Get bioseq handle by seq-loc.

If the seq-loc contains no seq-ids or there's a single seq-id which can not be resolved, returns empty handle. If the seq-loc references only parts of a segmented set, the method returns bioseq handle for the master bioseq. If the seq-loc contains a single seq-id, the bioseq handle for this id is returned. If there are multiple seq-ids not belonging to the same seg-set, the method throws CObjMgrException.

Definition at line 107 of file scope.cpp.

References CScope::eGetBioseq_All, CScope_Impl::GetBioseqHandle(), and CScope::m_Impl.

◆ GetBioseqHandle() [7/9] ◆ GetBioseqHandle() [8/9] ◆ GetBioseqHandle() [9/9] ◆ GetBioseqHandleFromTSE() [1/8] ◆ GetBioseqHandleFromTSE() [2/8] ◆ GetBioseqHandleFromTSE() [3/8] ◆ GetBioseqHandleFromTSE() [4/8]

Get bioseq handle for sequence withing one TSE.

Definition at line 253 of file scope.cpp.

References CSeq_id_Handle::GetHandle().

Referenced by CBioseq_Handle::GetAccessSeq_id_Handle(), CValidError_imp::GetBioseqHandleFromTSE(), CScope::GetBioseqHandleFromTSE(), GetCDSProductSequence(), CMasterContext::GetPartNumber(), IsFarLocation(), CValidError_annot::IsLocationUnindexed(), CRemoveUnindexedFeatures::IsLocationUnindexed(), CBioseqContext::IsSeqIdInSameTopLevelSeqEntry(), CId1FetchApp::LookUpGI(), CDemoApp::Run(), s_CheckQuals_cdregion(), s_HasLocalBioseq(), s_HasOneIntervalInSet(), s_LocIdType(), CCleanup::WGSCleanup(), CFeatureItem::x_AddQualsRna(), CFlatGatherer::x_CollectSourceDescriptors(), CFlatGatherer::x_DoMultipleSections(), x_GetDivisionProc(), x_GetDivisionProcIdx(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CSingleFeatValidator::x_GetFeatureProduct(), CNewCleanup_imp::x_MoveCdregionXrefsToProt(), CPromote::x_PromoteCdregion(), CMasterContext::x_SetBaseName(), CMasterContext::x_SetNumParts(), CCdregionValidator::x_ValidateFarProducts(), and CGff3Writer::xWriteFeatureCds().

◆ GetBioseqHandleFromTSE() [5/8] ◆ GetBioseqHandleFromTSE() [6/8] ◆ GetBioseqHandleFromTSE() [7/8] ◆ GetBioseqHandleFromTSE() [8/8] ◆ GetBioseqHandles() ◆ GetBioseqHandlesFromTSE() [1/3] ◆ GetBioseqHandlesFromTSE() [2/3] ◆ GetBioseqHandlesFromTSE() [3/3] ◆ GetBlobById()

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

Definition at line 288 of file data_loader.cpp.

References NCBI_THROW.

Referenced by CDataLoaderPatcher::GetBlobById(), CDataLoaderPatcher::GetDetailedRecords(), CDataLoaderPatcher::GetRecords(), CDataSource::GetSeq_entry_Lock(), and CSplitCacheApp::ProcessBlob().

◆ GetBlobId()

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

Definition at line 949 of file data_loader.cpp.

Referenced by CDataLoaderPatcher::GetBlobId(), CDataLoader::GetExternalAnnotRecords(), CDataLoader::GetExternalRecords(), CGBDataLoader::GetSatSatkey(), CSplitCacheApp::ProcessBlob(), and CDemoApp::Run().

◆ GetBlobIdFromString()

Reimplemented in CVDBGraphDataLoader, CSNPDataLoader, CPSGDataLoader, CGBDataLoader_Native, CWGSDataLoader, CSRADataLoader, CCSRADataLoader, CBAMDataLoader, and CDataLoaderPatcher.

Definition at line 294 of file data_loader.cpp.

References NCBI_THROW.

Referenced by CDataLoaderPatcher::GetBlobId(), CDataLoaderPatcher::GetBlobIdFromString(), CDataLoaderPatcher::GetDetailedRecords(), and CDataLoaderPatcher::GetRecords().

◆ GetBlobs() ◆ GetBlobState() TBlobState CBlobStateException::GetBlobState ( void  ) inline ◆ GetBlobVersion() ◆ GetBulkIds() [1/3] ◆ GetBulkIds() [2/3] ◆ GetBulkIds() [3/3] ◆ GetCDDAnnots() [1/3] ◆ GetCDDAnnots() [2/3] ◆ GetCDDAnnots() [3/3] ◆ GetChunk() void CDataLoader::GetChunk ( TChunk  chunk_info ) virtual

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

Definition at line 926 of file data_loader.cpp.

References NCBI_THROW.

Referenced by CDataLoaderPatcher::GetChunk(), CDataLoader::GetChunks(), and CTSE_Chunk_Info::Load().

◆ GetChunks()

Reimplemented in CVDBGraphDataLoader, CSNPDataLoader, CPSGDataLoader, CGBDataLoader_Native, CWGSDataLoader, CCSRADataLoader, CBAMDataLoader, CDataLoaderPatcher, and CRemoteBlastDbDataLoader.

Definition at line 933 of file data_loader.cpp.

References CDataLoader::GetChunk(), and ITERATE.

Referenced by CSeqMap::CanResolveRange(), CDataLoaderPatcher::GetChunks(), and CTSE_Split_Info::x_LoadChunks().

◆ GetComplete() ◆ GetDataSource() CDataSource * CDataLoader::GetDataSource ( void  ) const protected

Definition at line 92 of file data_loader.cpp.

References CDataLoader::m_DataSource.

Referenced by CAsnCache_DataLoader::GetBlobById(), CBlastDbDataLoader::GetBlobById(), CRemoteBlastDbDataLoader::GetBlobById(), CLDS2_DataLoader::GetBlobById(), CBAMDataLoader::GetBlobById(), CCSRADataLoader::GetBlobById(), CSRADataLoader::GetBlobById(), CWGSDataLoader::GetBlobById(), CSplitDataLoader::GetBlobById(), CBuffer_DataLoader::GetBlobById(), CPSGDataLoader::GetBlobById(), CHugeAsnDataLoader::GetBlobById(), CSNPDataLoader::GetBlobById(), CVDBGraphDataLoader::GetBlobById(), CPSGDataLoader::GetBlobs(), CPSGDataLoader::GetCDDAnnots(), CPSGDataLoader::GetChunk(), CPSGDataLoader::GetChunks(), CPSGDataLoader::GetExternalAnnotRecordsNA(), CGBReaderRequestResult::GetLoadedBlob_ids(), CSNPDataLoader::GetOrphanAnnotRecordsNA(), CVDBGraphDataLoader::GetOrphanAnnotRecordsNA(), CCDDDataLoader::GetOrphanAnnotRecordsNA(), CPSGDataLoader::GetOrphanAnnotRecordsNA(), CGBDataLoader::GetRealBlobId(), CCSRADataLoader::GetRecords(), CWGSDataLoader::GetRecords(), CPSGDataLoader::GetRecords(), CSNPDataLoader::GetRecords(), CVDBGraphDataLoader::GetRecords(), CScope_Impl::GetSeq_entryHandle(), CPSGDataLoader::GetSequenceState(), CPSGDataLoader::GetSequenceStates(), CGBReaderRequestResult::GetTSE_LoadLock(), CGBReaderRequestResult::GetTSE_LoadLockIfLoaded(), CLDS2_DataLoader::x_LoadBlobs(), and CDataLoaderPatcher::x_PatchLock().

◆ GetDefaultBlobCacheSizeLimit() unsigned CDataLoader::GetDefaultBlobCacheSizeLimit ( void  ) const virtual ◆ GetDefaultKeepExternalAnnotsForEdit() bool CScope::GetDefaultKeepExternalAnnotsForEdit ( ) static ◆ GetDefaultPriority() ◆ GetDetailedRecords() ◆ GetDst_from() TSeqPos CMappingRange::GetDst_from ( void  ) const inline ◆ GetDstId() ◆ GetDstIdHandle() ◆ GetEditHandle() [1/4] ◆ GetEditHandle() [2/4] ◆ GetEditHandle() [3/4] ◆ GetEditHandle() [4/4] ◆ GetEditSaver() ◆ GetErrCode() TErrCode CBlobStateException::GetErrCode ( void  ) const inline ◆ GetErrCodeString() [1/13] const char * CAnnotMapperException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [2/13] const char * CSeqTableException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [3/13] const char * CAssemblyParserException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [4/13] const char * CObjMgrException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [5/13] const char * CSeqMapException::GetErrCodeString ( void  ) const overridevirtual

Get error code interpreted as text.

Reimplemented from CObjMgrException.

Definition at line 61 of file objmgr_exception.cpp.

References CSeqMapException::eDataError, CSeqMapException::eFail, CSeqMapException::eInvalidIndex, CSeqMapException::eIteratorTooBig, CSeqMapException::eNullPointer, CSeqMapException::eOutOfRange, CSeqMapException::eSegmentTypeError, CSeqMapException::eSelfReference, CSeqMapException::eUnimplemented, CException::GetErrCode(), and CException::GetErrCodeString().

◆ GetErrCodeString() [6/13] const char * CSeqVectorException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [7/13] const char * CAnnotException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [8/13] const char * CLoaderException::GetErrCodeString ( void  ) const overridevirtual

Get error code interpreted as text.

Reimplemented from CObjMgrException.

Definition at line 102 of file objmgr_exception.cpp.

References CLoaderException::eBadConfig, CLoaderException::eCompressionError, CLoaderException::eConnectionFailed, CLoaderException::eLoaderFailed, CLoaderException::eNoConnection, CLoaderException::eNoData, CLoaderException::eNotFound, CLoaderException::eNotImplemented, CLoaderException::eOtherError, CLoaderException::ePrivateData, CLoaderException::eRepeatAgain, CException::GetErrCode(), and CException::GetErrCodeString().

◆ GetErrCodeString() [9/13] const char * CBlobStateException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [10/13] const char * CObjmgrUtilException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [11/13] const char * CAnnotSearchLimitException::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [12/13] const char * CPrefetchFailed::GetErrCodeString ( void  ) const overridevirtual ◆ GetErrCodeString() [13/13] const char * CPrefetchCanceled::GetErrCodeString ( void  ) const overridevirtual ◆ GetExternalAnnotRecords() [1/2] ◆ GetExternalAnnotRecords() [2/2] ◆ GetExternalAnnotRecordsNA() [1/2] ◆ GetExternalAnnotRecordsNA() [2/2] ◆ GetExternalRecords() ◆ GetFeat() ◆ GetFeat_CI() [1/5] ◆ GetFeat_CI() [2/5] ◆ GetFeat_CI() [3/5] ◆ GetFeat_CI() [4/5] ◆ GetFeat_CI() [5/5] ◆ GetGi() [1/2] ◆ GetGi() [2/2] ◆ GetGiFound()

Reimplemented in CPSGDataLoader, CGBDataLoader_Native, CWGSDataLoader, CCSRADataLoader, and CBAMDataLoader.

Definition at line 385 of file data_loader.cpp.

References CLoaderException::eNoData, CLoaderException::eNotFound, CException::GetErrCode(), CDataLoader::GetGi(), CDataLoader::SGiFound::gi, CDataLoader::SGiFound::sequence_found, CDataLoader::SequenceExists(), and ZERO_GI.

Referenced by CDataSource::GetGi(), and CDataLoader::GetGis().

◆ GetGis() [1/3] ◆ GetGis() [2/3] ◆ GetGis() [3/3] ◆ GetGraph() ◆ GetGroup() int CMappingRange::GetGroup ( void  ) const inline ◆ GetHandle() [1/2] ◆ GetHandle() [2/2] ◆ GetIdMap() ◆ GetIds() [1/3]

Get "native" bioseq ids without filtering and matching.

Returns empty ids if the sequence is not found

See also
EGetflags

Definition at line 401 of file scope.cpp.

References flags, and CSeq_id_Handle::GetHandle().

Referenced by CSeq_id_Descr::Assign(), CAddIdChecker::Check(), CAddIdChecker::Do(), CRemoveIdChecker::Do(), CResetIdChecker::Do(), GetBestCdsForMrna(), GetBestMrnaForCds(), GetId(), CDemoApp::GetIds(), GetSeqIdsForGI(), TaxClient::GetTaxIDForSeqId(), IsSequenceFetchable(), CSelectionEvent::MatchIdWithId(), CResolveRequest::Process(), CSampleLds2Application::Run(), CSampleObjmgrApplication::Run(), s_FindBestChoiceForDbsource(), and s_GetDeflineIdString().

◆ GetIds() [2/3] ◆ GetIds() [3/3]

Request for a list of all Seq-ids of a sequence.

The result container should not change if sequence with requested id is not known. The result must be non-empty for existing sequences

Definition at line 301 of file data_loader.cpp.

References CDataLoader::eBioseqCore, CBioseq_Info::GetId(), CDataLoader::GetRecordsNoBlobState(), and ITERATE.

Referenced by CDataLoader::GetAccVer(), CDataLoader::GetBulkIds(), CDataLoader::GetGi(), CDataSource::GetIds(), CDataLoader::GetLabel(), CWGSResolver_DL::GetPrefixes(), CAsnCacheTestApplication::Run(), and CDataLoader::SequenceExists().

◆ GetImpl() ◆ GetInstance()

Return the existing object manager or create one.

Definition at line 102 of file object_manager.cpp.

References CSafeStaticLifeSpan::eLifeLevel_AppMain, CSafeStaticLifeSpan::eLifeSpan_Longest, Ref(), and s_Instance.

Referenced by AddBioseqsToScope(), CBamUIDataSource::AddDataLoader(), CLBLASTObjectLoader::AddDataLoader(), CGBProjectHelper::AddProjectItemsFromRID(), CFeatureTableReader::AddProteins(), CTableAnnotDataSource::AddSeqLoc(), CTableAnnotDataSource::AddSnpSeqLoc(), CAlignmentAssistant::AdjustBioseq(), CTrimN::apply(), CChangeStructuredCommentKeyword::ApplyToCSeq_entry_user(), AutofixCommand(), AutofixCommandHugeMode(), CdBlaster::blast(), BOOST_AUTO_TEST_CASE(), BuildScope(), CGraphUtils::CalcGraphLevels(), CAsnvalThreadState::CAsnvalThreadState(), CAutoRegistrar::CAutoRegistrar(), CBlastScopeSource::CBlastScopeSource(), CBsDiffApp::CBsDiffApp(), CCleanup::CCleanup(), CFeatTableEdit::CFeatTableEdit(), CFlatFileParser::CFlatFileParser(), CGenBankFixture::CGenBankFixture(), CGff2Writer::CGff2Writer(), CheckDeflineMatches(), CheckDuplicates(), CheckOneSpecificHost(), CheckPropagatedCDSLocation(), CheckRegulatoryFeatures(), CheckTargetedLocusEntry(), CIdMapperNumAssembly::CIdMapperNumAssembly(), CAnnotationASN1::CImplementationData::CImplementationData(), CleanupCommand(), CleanupHugeFileCommand(), CNewCleanup_imp::CNewCleanup_imp(), CTable2AsnContext::CopyFeatureIdsToComments(), CTableAnnotDataSource::CreateFeature(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CGBDocument::CreateProjectScope(), CTableAnnotDataSource::CreateSnpFeature(), CTableAnnotDataSource::CreateSnps(), CSeq_loc_Mapper::CSeq_loc_Mapper(), CSourceFeatureItem::CSourceFeatureItem(), CTableColumnTypeGuesser::CTableColumnTypeGuesser(), CTestObjMgr::CTestObjMgr(), CTLSHandler::CTLSHandler(), CSimpleB2SWrapper::DoBlast2Seqs(), CReadBlastApp::dump_fasta_for_pretty_blast(), CSeqFormatter::DumpAll(), CAgpObjectLoader::Execute(), CAssemblyObjectLoader::Execute(), CBedObjectLoader::Execute(), CGBObjectLoader::Execute(), CGffObjectLoader::Execute(), CLBLASTObjectLoader::Execute(), CPhyObjectLoader::Execute(), CRMObjectLoader::Execute(), CIgBlastArgs::ExtractAlgorithmOptions(), CBlastDBExtractor::ExtractFasta(), CAnnotationASN1::ExtractModels(), CChainer::FindSelenoproteinsClipProteinsToStartStop(), CSequenceEditingEventHandler::FixNonReciprocalLinks(), CHugeFileProcess::ForEachEntry(), fta_init_gbdataloader(), fta_parse_buf(), CScore_CdsInternalStops::Get(), CEditSequenceEnds::GetCommand(), CEditSeqEndsWithAlign::GetCommand(), GetDeleteAllFeaturesCommand_Ex(), CGeneFinder::GetFeatViaSubsetThenExtremesIfPossible_Helper(), GetGIForSeqId(), GetGoodSeqEntryWithFeatureIds(), CSeqFetchQueue::GetInstance(), GetResolveOrder(), GetScope(), CAlnBuildApp::GetScope(), CAlnTestApp::GetScope(), CAlnMrgApp::GetScope(), CPairwiseAlnApp::GetScope(), CScoreLookup::GetScore(), GetSeqIdsForGI(), CEditSequence::GetSequence(), CDUpdater::getSequencesFromGB(), TaxClient::GetTaxIDForSeqId(), GetVDBScope(), ImportFeatTblTesting(), CAsnObjectLoader::Init(), CFastaObjectLoader::Init(), CGBFlatFileObjectLoader::Init(), CTextAlignObjectLoader::Init(), CAltValidator::Init(), CSplignApp::Init(), CCrossAlnDemoDlg::Init(), CAlignMultipleDemoDlg::Init(), CwxDemoAlignTableFrame::Init(), CSelectFeatureDlg::Init(), CHitMatrixDemoDlg::Init(), CTableXformPanel::Init(), CwxDemoFeatureTableFrame::Init(), CFlatFileDemoDlg::Init(), CSeqGraphicDemoDlg::Init(), CSeqTextDemoDlg::Init(), InitializeSubject(), IsSequenceFetchable(), CAlnVwrApp::LoadDenseg(), CDLTestThread::Main(), CDLTest2Thread::Main(), CTblastnNode::Main(), CIgBlastnApp::CIgWorker::Main(), CMagicBlastThread::Main(), MakeRegulatoryFeatureTest(), MakeTrnaWithAnticodon(), CFeatureTableReader::MoveRegionsToProteins(), NCBITEST_AUTO_INIT(), CSeqTextDemoDlg::OnFileClick(), CTaxTreeTestDlg::OnSubmitClick(), CAlignmentAssistant::OnValidate(), CGenBankUIDataSource::Open(), CWinMaskUtil::CInputBioseq_CI::operator++(), OverlapsSameAccessionAlignment::OverlapsSameAccessionAlignment(), CTabularFormatter_StopCodonChanges::Print(), CWinMaskCountsGenerator::process(), CBiosampleChkApp::ProcessFileList(), CScopedProcess::ProcessInitialize(), CBiosampleChkApp::ProcessList(), CdBlaster::psiBlast(), ReadEntry(), CHgvsReader::ReadSeqAnnot(), ReadSequencesToBlast(), CFeatureGenerator::SImplementation::RecomputePartialFlags(), CAutoRegistrar::RegisterGenbankDataLoader(), RegisterOMDataLoader(), RemoteFetchLongNucleotideBioseq(), CdBlaster::RemoveAllDataLoaders(), CSimpleB2SWrapper::RemoveAllDataLoaders(), RemoveAllDataLoaders(), CAutoRegistrar::RemoveAllDataLoaders(), IEditingActionFeat::ResetScope(), RetrieveGi555WithTimeOut(), RetrieveLargeChromosomeWithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), RetrievePartsOfLargeChromosome(), CBlastScopeSource::RevokeBlastDbDataLoader(), TestUtil::CBlastOM::RevokeBlastDbDataLoader(), CGffExportJob::Run(), CGtfExportJob::Run(), CDemoContigAssemblyApp::Run(), CMergeyApp::Run(), CNgAlignApp::Run(), CProSplignApp::Run(), CIdMapperTestApp::Run(), CDemoSeqQaApp::Run(), CPsiBlastApp::Run(), CSeedTopApp::Run(), CCompartApp::Run(), CIgBlastnApp::Run(), CIgBlastpApp::Run(), CSrcChkApp::Run(), CGBProjectTool::Run(), CSeqDescrRetrievalJob::Run(), CHugeFileDemoApp::Run(), CAnalyzeShiftApp::Run(), CAnnotWriterApp::Run(), CAsn2FastaApp::Run(), CAsn2FlatApp::Run(), CCleanupApp::Run(), CDiscRepApp::Run(), CAgpFastaComparator::Run(), CVectorScreen::Run(), CAlignCleanupApplication::Run(), CTestCompartApplication::Run(), CDemoScoreBuilderApp::Run(), CMultiApplication::Run(), CLocalFinderApp::Run(), CCpGDemoApp::Run(), CGeneModelDemoApp::Run(), CRegexpLocApp::Run(), CXcompareAnnotsApplication::Run(), CWinMaskDemoApplication::Run(), CAsnCacheTestApplication::Run(), CPrimeCacheApplication::Run(), CAsnSubCacheCreateApplication::Run(), CGuideTreeApplication::Run(), CConversionApp::Run(), CDustMaskApplication::Run(), CHgvsToSeqfeatConverter::Run(), CId1FetchApp::Run(), CIdfetchApplication::Run(), CDemoApp::Run(), SegMaskerApplication::Run(), CMytestApplication::Run(), CWinMaskApplication::Run(), CObjConvProfile::Run(), CTestBMApp::Run(), CSampleAlnmgrApplication::Run(), CBlastDemoApplication::Run(), VSRunSampleApplication::Run(), CSampleLds2Application::Run(), CFeatTreeSampleApp::Run(), CSampleObjmgrApplication::Run(), s_ConvertBioseqs2TSeqLocVector(), s_ConvertSubjects2TSeqLocVector(), s_CountBlastDbDataLoaders(), s_CreateKmerCounts(), s_CreateScope(), s_GatherSources(), s_GetScope(), s_HasUnprocessedCdregions(), s_InitializeSubject(), s_IsUsingRemoteBlastDbDataLoader(), s_MakeNewMasterSeq(), s_MoveProteinSpecificFeats(), s_MTDataLoaderTest2(), s_ReadAndTestQueryFromString(), s_RegisterOMDataLoader(), CPsiBlastTestFixture::s_SetupSubject(), s_UnregisterDataLoader(), SCoverageData::SCoverageData(), CScopedProcess::SeqEntryInitialize(), CAlignFilter::SetFilter(), CChainer::CChainerImpl::SetFlagsForChains(), CChainer::CChainerImpl::SetGenomicRange(), CBamRefSequencesPanel::SetReferenceSeqIds(), CVcfRefSequencesPanel::SetReferenceSeqIds(), CCleanup::SetScope(), CSequenceEditingEventHandler::SetTopLevelBioseqSetClass(), CAsnvalApp::Setup(), CBiosampleChkApp::Setup(), CTbl2AsnApp::Setup(), CSplitCacheApp::SetupCache(), CTable2AsnContext::SmartFeatureAnnotation(), CBlobSplitterImpl::Split(), sRunTest(), sUpdateCase(), TestDataNotFound(), TestFeatInsideGap(), TestForRecomb(), CTestAction::TestOID(), TestOneGapSeq(), TestRepeatRegion(), TestTrimForFrame(), CMacroFunction_RemoveSingleItemSet::TheFunction(), CMacroFunction_RenormalizeNucProtSet::TheFunction(), TryMiscWithNs(), TryOneCase(), TryOneCaseMixLoc(), TryOneCDSCase(), CTable2AsnValidator::ValCollect(), CTable2AsnValidator::Validate(), CValidError_bioseq::ValidateBioseq(), CValidError_annot::ValidateSeqAnnot(), CFastaOstream::Write(), CBlastDB_FastaFormatter::Write(), CSequenceUpdater::x_AddCitSubToUpdatedSequence(), CIgBlast::x_AnnotateDomain(), CSequenceUpdater::x_AttachFeaturesToNewSeq(), CBlastFormatterApp::x_BuildQueryFromPssm(), CBlastFormatterVdbApp::x_BuildQueryFromPssm(), CPrimeCacheApplication::x_CacheSeqEntry(), CSubPrep_panel::x_CheckValidation(), CIgBlastnApp::x_CountUserBatches(), CCmdCleanup::x_CreateActionCmd(), CCmdPlaceProteinFeats::x_CreateActionCmd(), CMappingObjectLoader::x_CreateMapper(), CGBankLoadingJob::x_CreateProjectItems(), CFindOverlapJob::x_CreateProjectItems(), CNetBlastLoadingJob::x_CreateProjectItemsFromBlastResult(), CEditBioseqSampleApp::x_CreateScope(), CSNPSearchJob::x_DoSearch(), CEntrezSearchJob::x_DoSearch(), CAsnSubCacheCreateApplication::x_EliminateIdsAlreadyInCache(), CBlastFormatterApp::x_ExtractQueries(), CBlastFormatterVdbApp::x_ExtractQueries(), CTableDataValidateJob::x_FetchAll(), CCreateGeneModelTask::x_GetCommand(), CDataLoaderFactory::x_GetObjectManager(), CSimpleOM::x_GetOM(), CBuildDatabase::x_GetScope(), CGapStatsApplication::x_GetScope(), CSeqMasterIndex::x_Init(), CDisplaySeqalign::x_InitAlignParams(), CSeqMasterIndex::x_Initialize(), CWGSFileInfo::x_InitMasterDescr(), CBlastHitMatrix::x_InitObjectManager(), CDeltaBlastTestFixture::x_InitScope(), CMultiAlignerFixture::x_InitScope(), CAlnPrinterFixture::x_InitScope(), CAppHitFilter::x_LoadConstraints(), seqmasks_io_fixture::x_LoadMaskedBioseq(), CAgpconvertApplication::x_LoadTemplate(), CAlnMultiCGIApplication::x_PreProcess(), CGenBankLoadOptionPanel::x_ProccessText(), CPrimeCacheApplication::x_Process_Fasta(), CPrimeCacheApplication::x_Process_Ids(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CClustererApplication::x_RunBinary(), CTblastnApp::x_RunMTBySplitDB(), CClustererApplication::x_RunSparse(), COligoSpecificityCheck::x_SequencesMappedToSameTarget(), CPsiBl2SeqTestFixture::x_SetupSubject(), CMappingObjectLoader::x_ShowMappingDlg(), CSelectProjectOptions::x_ShowSelectProjectDialog(), CAssemblyListPanel::x_UpdateSearchTerm(), CGenbankIdResolve::xGetDefaultScope(), CGenbank2Asn::xGetEntry(), CFeatureTableReader::xParseCdregions(), CAutoRegistrar::~CAutoRegistrar(), CGenBankFixture::~CGenBankFixture(), and CRevoker::~CRevoker().

◆ GetKeepExternalAnnotsForEdit() bool CScope::GetKeepExternalAnnotsForEdit ( ) const ◆ GetLabel() [1/3] ◆ GetLabel() [2/3] ◆ GetLabel() [3/3] ◆ GetLabels() [1/3] ◆ GetLabels() [2/3] ◆ GetLabels() [3/3] ◆ GetLength() TSeqPos CMappingRange::GetLength ( void  ) const inline ◆ GetListener() ◆ GetLoader()

Get pointer to the loader.

The loader can be just created or already registered in the object manager. NULL if the operation failed.

Definition at line 90 of file object_manager.hpp.

Referenced by BOOST_AUTO_TEST_CASE(), CAutoRegistrar::CAutoRegistrar(), CGenBankFixture::CGenBankFixture(), CAsnCache_DataLoaderCF::CreateAndRegister(), CBlastDb_DataLoaderCF::CreateAndRegister(), CRmtBlastDb_DataLoaderCF::CreateAndRegister(), CCDD_DataLoaderCF::CreateAndRegister(), CGB_DataLoaderCF::CreateAndRegister(), CPSG_DataLoaderCF::CreateAndRegister(), CLDS2_DataLoaderCF::CreateAndRegister(), CDLPatcher_DataLoaderCF::CreateAndRegister(), CBAM_DataLoaderCF::CreateAndRegister(), CCSRA_DataLoaderCF::CreateAndRegister(), CSNP_DataLoaderCF::CreateAndRegister(), CSRA_DataLoaderCF::CreateAndRegister(), CVDBGraph_DataLoaderCF::CreateAndRegister(), CWGS_DataLoaderCF::CreateAndRegister(), CSimpleLoaderMaker< TDataLoader >::GetRegisterInfo(), CParamLoaderMaker< TDataLoader, TParam >::GetRegisterInfo(), CGBDataLoader::CGBLoaderMaker< TDataLoader >::GetRegisterInfo(), CDUpdater::getSequencesFromGB(), GetVDBScope(), CAlnMrgApp::LoadBlastDb(), CAutoRegistrar::RegisterGenbankDataLoader(), CAsn2FlatApp::Run(), CVectorScreen::Run(), CDemoApp::Run(), s_InitializeSubject(), sRunTest(), sUpdateCase(), TestUtil::CBlastOM::x_InitBlastDatabaseDataLoader(), CBlastScopeSource::x_InitBlastDatabaseDataLoader(), CBlastScopeSource::x_InitGenbankDataLoader(), and TestUtil::CBlastOM::x_InitGenbankDataLoader().

◆ GetLoc() ◆ GetMapperSequenceInfo() ◆ GetMappingRanges() ◆ GetMapSingleLevel() bool CSeq_loc_Mapper_Options::GetMapSingleLevel ( void  ) const inline ◆ GetName() string CDataLoader::GetName ( void  ) const

Definition at line 104 of file data_loader.cpp.

References CDataLoader::m_Name.

Referenced by CSGAlignmentDS::GetDataLoader(), CDataLoaderPatcher::GetLoaderNameFromArgs(), CDataSource::GetName(), CAlnMrgApp::LoadBlastDb(), CGenBankUIDataSource::Open(), CObjectManager::RevokeDataLoader(), CObjectManager::RevokeDataLoaders(), CVectorScreen::Run(), CAsnCacheTestApplication::Run(), CDemoApp::Run(), CSplitCacheApp::TestSplit(), CObjectManager::x_RegisterLoader(), and CObjectManager::x_RevokeDataLoader().

◆ GetNextAction() [1/3] ◆ GetNextAction() [2/3] ◆ GetNextAction() [3/3] ◆ GetNextSeq_id() [1/2]

template<class Container >

◆ GetNextSeq_id() [2/2] ◆ GetNextToken() ◆ GetNonMappingAsNull() bool CSeq_loc_Mapper_Base::GetNonMappingAsNull ( void  ) static

Definition at line 4485 of file seq_loc_mapper_base.cpp.

Referenced by CSeq_loc_Conversion::ConvertEquiv(), CSeq_loc_Conversion_Set::ConvertEquiv(), CSeq_loc_Conversion::ConvertMix(), CSeq_loc_Conversion_Set::ConvertMix(), CSeq_loc_Conversion::ConvertPacked_int(), CSeq_loc_Conversion_Set::ConvertPacked_int(), CSeq_loc_Conversion::ConvertPacked_pnt(), CSeq_loc_Conversion_Set::ConvertPacked_pnt(), CSeq_loc_Mapper_Base::x_MapNextRange(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), and CSeq_loc_Mapper_Base::x_SetLastTruncated().

◆ GetObjectEditHandle() [1/4] ◆ GetObjectEditHandle() [2/4] ◆ GetObjectEditHandle() [3/4] ◆ GetObjectEditHandle() [4/4] ◆ GetObjectHandle() [1/5]

Definition at line 734 of file scope.hpp.

References CScope::GetBioseqHandle().

Referenced by CFeatTableEdit::EliminateBadQualifiers(), CFeatTableEdit::GenerateLocusTags(), GetSeq_entry_Handle(), CFeatTableEdit::InferPartials(), CFeatTableEdit::ProcessCodonRecognized(), CGff3Writer::x_WriteBioseqHandle(), CFeatTableEdit::xAdjustExistingParentGene(), CFeatTableEdit::xCreateMissingParentGene(), CFeatTableEdit::xFeatureAddQualifier(), CFeatTableEdit::xFeatureRemoveQualifier(), CFeatTableEdit::xFeatureSetProduct(), CFeatTableEdit::xGenerateMissingMrnaForCds(), and CGff2Writer::xGenerateMissingTranscript().

◆ GetObjectHandle() [2/5] ◆ GetObjectHandle() [3/5] ◆ GetObjectHandle() [4/5] ◆ GetObjectHandle() [5/5] ◆ GetObjectManager() ◆ GetOffset() TSeqPos CGraphRanges::GetOffset ( void  ) const inline ◆ GetOrphanAnnotRecords() ◆ GetOrphanAnnotRecordsNA() [1/2] ◆ GetOrphanAnnotRecordsNA() [2/2]

Reimplemented in CPSGDataLoader, and CCDDDataLoader.

Definition at line 241 of file data_loader.cpp.

References set< Key, Compare >::begin(), set< Key, Compare >::empty(), set< Key, Compare >::end(), CDataLoader::GetOrphanAnnotRecordsNA(), set< Key, Compare >::insert(), ITERATE, and set< Key, Compare >::swap().

◆ GetProgress() TProgress CPrefetchRequest::GetProgress ( void  ) const inline ◆ GetRanges() ◆ GetRecords()

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.

The GetRecords() may throw CBlobStateException if the sequence is not available (not known or disabled), and blob state is different from minimal fState_no_data. The actual blob state can be read from the exception in this case.

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

Definition at line 121 of file data_loader.cpp.

References NCBI_THROW.

Referenced by CDataLoader::GetBlobs(), CDataLoader::GetDetailedRecords(), CDataLoader::GetExternalAnnotRecords(), CDataLoader::GetExternalRecords(), CDataLoader::GetOrphanAnnotRecords(), CDataLoaderPatcher::GetRecords(), CDataLoader::GetRecordsNoBlobState(), CDataLoader::GetSequenceState(), CAsnCacheTestApplication::Run(), and CDataSource::x_GetRecords().

◆ GetRecordsNoBlobState() ◆ GetRegisteredNames() ◆ GetRegisterInfo() [1/2]

template<class TDataLoader >

◆ GetRegisterInfo() [2/2]

template<class TDataLoader , class TParam >

Definition at line 169 of file data_loader.hpp.

References SRegisterLoaderInfo< TLoader >::GetLoader(), info, SRegisterLoaderInfo< TLoader >::IsCreated(), and CLoaderMaker_Base::m_RegisterInfo.

Referenced by CCDDDataLoader::RegisterInObjectManager(), CSRADataLoader::RegisterInObjectManager(), CVDBGraphDataLoader::RegisterInObjectManager(), CBAMDataLoader::RegisterInObjectManager(), CCSRADataLoader::RegisterInObjectManager(), CSNPDataLoader::RegisterInObjectManager(), CWGSDataLoader::RegisterInObjectManager(), CSplitDataLoader::RegisterInObjectManager(), CAsnCache_DataLoader::RegisterInObjectManager(), CBlastDbDataLoader::RegisterInObjectManager(), CRemoteBlastDbDataLoader::RegisterInObjectManager(), CDataLoaderPatcher::RegisterInObjectManager(), and CBuffer_DataLoader::RegisterInObjectManager().

◆ GetResult() [1/4] ◆ GetResult() [2/4] ◆ GetResult() [3/4] ◆ GetResult() [4/4] ◆ GetReverse() bool CMappingRange::GetReverse ( void  ) const inline ◆ GetReverseDst() bool CMappingRanges::GetReverseDst ( void  ) const inline ◆ GetReverseSrc() bool CMappingRanges::GetReverseSrc ( void  ) const inline ◆ GetScope() CScope & CScopeSource::GetScope ( void  ) ◆ GetSelector() ◆ GetSeq_annotEditHandle() ◆ GetSeq_annotHandle()

Definition at line 192 of file scope.cpp.

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

Referenced by AddFeatureToBioseq(), CAnnotationASN1::ExtractModels(), GetAccessionFromObjects(), CScope::GetObjectHandle(), CCleanup::MoveFeatToProtein(), CFeatureRetrievalJob::Run(), CValidError_annot::ValidateSeqAnnot(), CNewCleanup_imp::x_CollapseSet(), CNewCleanup_imp::x_RemoveEmptyFeatureTables(), CVcfWriter::x_WriteData(), and CProjectFileWriter::x_WriteGtf().

◆ GetSeq_entryEditHandle()

Definition at line 207 of file scope.cpp.

References CTSE_Handle::CanBeEdited(), CScope::eMissing_Throw, CScope_Impl::GetEditHandle(), CScope_Impl::GetSeq_entryHandle(), CSeq_entry_Handle::GetTSE_Handle(), CScope::m_Impl, and NCBI_THROW.

Referenced by CCleanup::AddProtein(), CScope::AttachAnnot(), CScope::AttachEntry(), CCmdAddSeqEntry::Execute(), CScope::GetObjectEditHandle(), CScope::RemoveAnnot(), CScope::RemoveEntry(), CScope::ReplaceAnnot(), s_DoSmartProcessing(), and CCmdAddSeqEntry::Unexecute().

◆ GetSeq_entryHandle() [1/2]

Get Seq-entry handle by its blob-id, with possible loading.

The blob-id can be obtained from CTSE_Handle::GetBlobId() or from specific data loader (see CGBDataLoader::GetBlobId()).

Definition at line 113 of file scope.cpp.

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

Referenced by CRemoveBankitComment::ApplyToCSeq_entry(), CRemoveGenomeProjectsDB::ApplyToCSeq_entry(), CRemoveStructuredComment::ApplyToCSeq_entry(), CRemoveSeqAnnot::ApplyToCSeq_entry(), CConvertComment::ApplyToCSeq_entry(), CModifyStructuredComment::ApplyToCSeq_entry(), CRemoveUnverified::ApplyToCSeq_entry(), CRemoveStructuredCommentKeyword::ApplyToCSeq_entry_genbank(), CAddStructuredCommentKeyword::ApplyToCSeq_entry_genbank(), CReorderStructuredComment::ApplyToCSeq_entry_user(), CachedTaxonomyLookupCommand(), CBioseq_CI::CBioseq_CI(), CSequenceEditingEventHandler::CreateSeqSubmit(), CSeq_annot_CI::CSeq_annot_CI(), CNewCleanup_imp::EnteringEntry(), CNewCleanup_imp::ExtendedCleanupSeqEntry(), CNewCleanup_imp::ExtendedCleanupSeqSubmit(), CFlatFileGenerator::Generate(), GetAccessionFromObjects(), CScope::GetBioseqHandleFromTSE(), CValidError_imp::GetCDSGivenProduct(), GetChangeStrainForwardingCommand(), CValidError_imp::GetmRNAGivenProduct(), CScope::GetObjectHandle(), GetRmCultureNotesCommand(), GetSeqEntryHandle(), CSUCDataGenerator::GetSUCResults(), CScope::GetTSE_Handle(), CMytestApplication::PlayAroundWithSuggestIntervals(), CSequenceEditingEventHandler::PrepareSeqSubmit(), CSplitCacheApp::ProcessBlob(), PropagateDescriptor(), RemoveTitlesSeqEntry(), CCleanup::RenormalizeNucProtSets(), CValidError_imp::ReportMissingPubs(), CDemoApp::Run(), CMacroFunction_RenormalizeNucProtSet::s_RenormalizeNucProtSets(), CRemoveSeqFromAlignDlg::SearchSeq_entry(), sGetValidateObject(), SpecificHostCleanupCommand(), TaxonomyLookupCommand(), CValidError_imp::Validate(), CConversionApp::Write(), CDescPlacementPanel::x_AddToStrings(), CApplyGCode::x_ApplyToDescriptors(), CCountryFixup::x_ApplyToDescriptors(), CLatLonTool::x_ApplyToDescriptors(), CRemoveUnreviewed::x_ApplyToSeq_entry(), CRemoveDescDlg::x_ApplyToSeq_entry(), CNewCleanup_imp::x_CollapseSet(), CLocalFileRestorer::x_DetachOrigObject(), CAsnSubCacheCreateApplication::x_GetBioseqHandle(), CSubmissionWizard::x_LoadProjectItemData(), CAutodefJob::x_MakeChanges(), CNewCleanup_imp::x_MoveCDSFromNucAnnotToSetAnnot(), CNewCleanup_imp::x_MoveNpPub(), and CCmdInsertBioseqSet::x_TransferSeqSet().

◆ GetSeq_entryHandle() [2/2] ◆ GetSeq_featHandle()

Definition at line 200 of file scope.cpp.

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

Referenced by CStrandPanel::AddCommand(), CResyncPanel::AddCommand(), CPseudoPanel::AddCommand(), CExceptionPanel::AddCommand(), CExperimentPanel::AddCommand(), CEditInferencePanel::AddCommand(), AddException(), AddExceptionsToShortIntron(), CClickableSortUniqueCount::AddToBulkEditList(), AdjustGene(), CRecomputeIntervals::apply(), CCreateLocusTagGene::apply(), CGroupExplode::apply(), CConvertBadCdsAndRnaToMiscFeat::apply(), CApplyObject::ApplyChange(), ApplyFeatureSeqTableToSeqEntry(), ApplyPolicyToFeature(), CReverseAuthorNames::ApplyToPubdesc(), CCdsMatchInfo::AssignMatch(), CDiscrepancyVisitorImpl< _Name >::Autofix(), CAutogeneratedCleanup::BasicCleanupSeqFeat(), BOOST_AUTO_TEST_CASE(), CachedTaxonomyLookupCommand(), CNewCleanup_imp::CdRegionEC(), CMiscSeqTableColumn::ClearValCmd(), CSequenceEditingEventHandler::CombineSelectedGenesIntoPseudogenes(), CConvertProtToImp::Convert(), CConvertCDSToPseudoGene::Convert(), CCdsToMatPeptide::ConvertInner(), CTaxValidationAndCleanup::DoTaxonomyUpdate(), CSequenceEditingEventHandler::Duplicate(), CAutogeneratedExtendedCleanup::ExtendedCleanupSeqFeat(), ExtendToGapsOrEnds(), IEditingActionFeat::FindRelated(), GetChangeStrainForwardingCommand(), CCdsFromGeneMrnaExon::GetCommand(), CCorrectGenesDialog::GetCommand(), CExtendPartialFeatDlg::GetCommand(), CFuseFeaturesDlg::GetCommand(), CmRNAFromGeneCdsExon::GetCommand(), CResolveIntersectingFeats::GetCommand(), CtRNAFromGene::GetCommand(), CTruncateCDS::GetCommand(), CRetranslateCDS::GetCommand(), GetCommandFromApplyObject(), GetEditLocationCommand(), CGeneCache::GetGeneFromCache(), CScope::GetObjectHandle(), CCleanup::GetProteinLocationFromNucleotideLocation(), GetRelatedFeatures(), GetReplacementCommand(), CMiscSeqTableColumn::GetReplacementCommand(), GetRetranslateCDSCommand(), GetReverseComplimentSequenceCommand(), GetRmCultureNotesCommand(), IEditingAction::GetUpdateMRNAProductNameCmd(), CBulkCDS::GetUpdateMRNAProductNameCmd(), CDiscrepancyPanel::InvalidObject(), CmRNACDSLinker::LinkSelectedFeatures(), MakemRNAforCDS(), CDiscrepancyPanel::OnDblClk(), CHugeFileDemoApp::ProcessHugeSeqEntry(), CmRNACDSLinker::ReplaceExistingXrefs(), CSequenceEditingEventHandler::ResynchronizePartials(), CDemoApp::Run(), s_Create5ColFeatTable(), s_GetCdsByLocation(), s_GetMappedFeat(), s_IsLocalFeature(), s_MoveProteinSpecificFeats(), CmRNACDSLinker::SetReciprocalXrefs(), SetTranslExcept(), SpecificHostCleanupCommand(), CCleanup::TaxonomyLookup(), TaxonomyLookupCommand(), CMacroFunction_SwapRelFeatQual::TheFunction(), CMacroFunction_SetRelFeatQual::TheFunction(), CMacroFunction_EditRelFeatQual::TheFunction(), CMacroFunction_ConvertFeatQual::TheFunction(), CMacroFunction_ConvertRNARelQual::TheFunction(), CMacroFunction_ParseFeatQual::TheFunction(), CMacroFunction_ParseRNARelQual::TheFunction(), CMacroFunction_AddParsedToFeatQual::TheFunction(), CMacroFunction_ParsedTextFrom::TheFunction(), CMacroFunction_CopyFeatQual::TheFunction(), CMacroFunction_CopyRNARelQual::TheFunction(), CMacroFunction_RmvOutsideRelFeatQual::TheFunction(), CMacroFunction_UpdateProteinSeqs::TheFunction(), CMacroFunction_ConvertLocStrand::TheFunction(), CMacroFunction_ConvertLocType::TheFunction(), UpdatemRNAProduct(), CCleanup::WGSCleanup(), CConvertFeatureBase::x_ConvertToCDS(), CCmdFeatIdXrefsFromQualifiers::x_CreateActionCmd(), CNewCleanup_imp::x_ExtendSingleGeneOnMrna(), CCleanupApp::x_FixCDS(), CCdregionValidator::x_HasGoodParent(), CNewCleanup_imp::x_MergeAdjacentFeatureTables(), CHugeFileDemoApp::x_ProcessFileTraditionally(), CNewCleanup_imp::x_RemoveEmptyFeatures(), CConvertFeatureBase::x_SimpleConversion(), CCdregionValidator::x_ValidateFarProducts(), CSingleFeatValidator::x_ValidateGeneId(), CPeptideValidator::x_ValidatePeptideOnCodonBoundary(), CFeatTableEdit::xGetLinkedFeature(), CFeatTableEdit::xMakeGeneForFeature(), and CNewCleanup_imp::xUpdateSeqfeatCitPub().

◆ GetSeq_id() ◆ GetSeqInfo() ◆ GetSeqType() ◆ GetSeqTypeById() [1/2] ◆ GetSeqTypeById() [2/2]

Methods for getting sequence types, use cached types (m_SeqTypes) if possible.

Definition at line 1295 of file seq_loc_mapper_base.hpp.

References CSeq_loc_Mapper_Base::CollectSynonyms(), map_checker< Container >::end(), map_checker< Container >::find(), CSeq_loc_Mapper_Base::GetSeqType(), and CSeq_loc_Mapper_Base::m_SeqTypes.

Referenced by CSeq_align_Mapper_Base::GetDstAlign(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CSeq_loc_Mapper_Base::GetWidthById(), CSeq_loc_Mapper_Base::Map(), CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt(), CSeq_loc_Mapper_Base::x_CheckSeqTypes(), CSeq_align_Mapper_Base::x_GetDstDendiag(), CSeq_align_Mapper_Base::x_GetDstDenseg(), CSeq_align_Mapper_Base::x_GetDstExon(), CSeq_align_Mapper_Base::x_GetDstPacked(), CSeq_align_Mapper_Base::x_GetDstSparse(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CSeq_align_Mapper_Base::x_GetDstStd(), CSeq_align_Mapper_Base::x_GetPartialDenseg(), CSeq_align_Mapper_Base::x_HaveMixedSeqTypes(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitAlign(), CSeq_loc_Mapper_Base::x_InitSparse(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_NextMappingRange(), CSeq_loc_Mapper_Base::x_PreserveDestinationLocs(), CSeq_loc_Mapper_Base::x_PushSourceRange(), and CSeq_loc_Mapper_Base::x_RangeToSeq_loc().

◆ GetSequenceHash() [1/3] ◆ GetSequenceHash() [2/3] ◆ GetSequenceHash() [3/3] ◆ GetSequenceHashes() [1/3] ◆ GetSequenceHashes() [2/3] ◆ GetSequenceHashes() [3/3] ◆ GetSequenceHashFound()

Reimplemented in CPSGDataLoader, CGBDataLoader_Native, and CWGSDataLoader.

Definition at line 527 of file data_loader.cpp.

References CLoaderException::eNoData, CLoaderException::eNotFound, CException::GetErrCode(), CDataLoader::GetSequenceHash(), CDataLoader::SHashFound::hash, CDataLoader::SHashFound::hash_known, CDataLoader::SHashFound::sequence_found, and CDataLoader::SequenceExists().

Referenced by CDataSource::GetSequenceHash(), and CDataLoader::GetSequenceHashes().

◆ GetSequenceLength() [1/5]

Definition at line 2283 of file seq_loc_mapper_base.cpp.

References CSeq_loc_Mapper_Base::CollectSynonyms(), map_checker< Container >::end(), map_checker< Container >::find(), CSeq_id_Handle::GetHandle(), CSeq_loc_Mapper_Options::GetSeqInfo(), IMapper_Sequence_Info::GetSequenceLength(), len, CSeq_loc_Mapper_Base::m_LengthMap, and CSeq_loc_Mapper_Base::m_MapOptions.

Referenced by CSeq_loc_Mapper_Base::x_AddConversion(), CSeq_loc_Mapper_Base::x_CheckSeqTypes(), CSeq_loc_Mapper_Base::x_GetRangeLength(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

◆ GetSequenceLength() [2/5]

Get sequence length Return kInvalidSeqPos if sequence is not found.

See also
EGetflags

Definition at line 790 of file scope.cpp.

References flags, and CSeq_id_Handle::GetHandle().

Referenced by CSparseGraph::CreateCompoundID(), CScore_Coverage::Get(), CBedCoverageGraph::GetCacheKey(), CVcfHeatmap::GetCacheKey(), CFeatureGenerator::SImplementation::GetExonStructure(), CValidError_annot::IsLocationUnindexed(), RetrieveGi555WithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), and RetrievePartsOfLargeChromosome().

◆ GetSequenceLength() [3/5] ◆ GetSequenceLength() [4/5]

Request for a length of a sequence.

Returns kInvalidSeqPos if sequence with requested id is not known. The result must not be kInvalidSeqPos for existing sequences

Reimplemented in CGBDataLoader_Native, CHugeAsnDataLoader, CPSGDataLoader, CWGSDataLoader, CSRADataLoader, CCSRADataLoader, CBlastDbDataLoader, and CAsnCache_DataLoader.

Definition at line 436 of file data_loader.cpp.

References CDataLoader::eBioseqCore, CBioseq_Info::GetBioseqLength(), CDataLoader::GetRecordsNoBlobState(), ITERATE, and kInvalidSeqPos.

Referenced by CDataSource::GetSequenceLength(), and CDataLoader::GetSequenceLengths().

◆ GetSequenceLength() [5/5] ◆ GetSequenceLengths() [1/3] ◆ GetSequenceLengths() [2/3] ◆ GetSequenceLengths() [3/3] ◆ GetSequenceState() [1/3] ◆ GetSequenceState() [2/3] ◆ GetSequenceState() [3/3] ◆ GetSequenceStates() [1/3] ◆ GetSequenceStates() [2/3] ◆ GetSequenceStates() [3/3] ◆ GetSequenceType() [1/4]

Get molecular type of sequence (protein/dna/rna) Return CSeq_inst::eMol_not_set if sequence is not found.

See also
EGetflags
CSeq_inst::EMol

Definition at line 825 of file scope.cpp.

References flags, and CSeq_id_Handle::GetHandle().

Referenced by BOOST_AUTO_TEST_CASE(), CScope_Mapper_Sequence_Info::GetSequenceType(), RemoteFetchLongNucleotideBioseq(), RetrieveGi555WithTimeOut(), RetrieveLargeNuclSequence(), RetrieveLargeProteinWithTimeOut(), RetrievePartsOfLargeChromosome(), s_SequenceIsProtein(), CBlastTabularInfo::SetFields(), CFastaOstreamEx::x_GetOtherIdString(), CNewCleanup_imp::x_SeqIntervalBC(), and CNewCleanup_imp::x_SeqPointBC().

◆ GetSequenceType() [2/4] ◆ GetSequenceType() [3/4] ◆ GetSequenceType() [4/4] ◆ GetSequenceTypeFound()

Reimplemented in CGBDataLoader_Native, CHugeAsnDataLoader, CPSGDataLoader, CWGSDataLoader, CSRADataLoader, and CCSRADataLoader.

Definition at line 471 of file data_loader.cpp.

References CSeq_inst_Base::eMol_not_set, CLoaderException::eNoData, CLoaderException::eNotFound, CException::GetErrCode(), CDataLoader::GetSequenceType(), CDataLoader::STypeFound::sequence_found, CDataLoader::SequenceExists(), and CDataLoader::STypeFound::type.

Referenced by CDataSource::GetSequenceType(), and CDataLoader::GetSequenceTypes().

◆ GetSequenceTypes() [1/3] ◆ GetSequenceTypes() [2/3] ◆ GetSequenceTypes() [3/3] ◆ GetSrc_from() TSeqPos CMappingRange::GetSrc_from ( void  ) const inline ◆ GetState()

Definition at line 139 of file prefetch_manager_impl.cpp.

References SPrefetchTypes::eCanceled, CThreadPool_Task::eCanceled, SPrefetchTypes::eCompleted, CThreadPool_Task::eCompleted, CThreadPool_Task::eExecuting, SPrefetchTypes::eFailed, CThreadPool_Task::eFailed, CThreadPool_Task::eIdle, SPrefetchTypes::eInvalid, SPrefetchTypes::eQueued, CThreadPool_Task::eQueued, SPrefetchTypes::eStarted, and CThreadPool_Task::GetStatus().

Referenced by CPrefetchRequest::OnStatusChange().

◆ GetSynonyms() [1/3] ◆ GetSynonyms() [2/3] ◆ GetSynonyms() [3/3] ◆ GetTaxId() [1/3] ◆ GetTaxId() [2/3]

Request for a taxonomy id of a sequence.

Returns -1 if sequence with requested id is not known. Returns 0 if existing sequence doesn't have TaxID

Reimplemented in CHugeAsnDataLoader, CPSGDataLoader, CGBDataLoader_Native, CWGSDataLoader, CCSRADataLoader, CBAMDataLoader, CBlastDbDataLoader, and CAsnCache_DataLoader.

Definition at line 422 of file data_loader.cpp.

References CDataLoader::eBioseqCore, CDataLoader::GetRecordsNoBlobState(), CBioseq_Info::GetTaxId(), INVALID_TAX_ID, and ITERATE.

Referenced by CDataSource::GetTaxId(), CGBDataLoader_Native::GetTaxId(), CPSGDataLoader::GetTaxId(), and CDataLoader::GetTaxIds().

◆ GetTaxId() [3/3] ◆ GetTaxIds() [1/3] ◆ GetTaxIds() [2/3] ◆ GetTaxIds() [3/3] ◆ GetTopLevelSequences() const TSeqIds& CGC_Assembly_Parser::GetTopLevelSequences ( void  ) const inline ◆ GetTotalRange() const TRange& CGraphRanges::GetTotalRange ( void  ) const inline ◆ GetTrackSplitSeq() bool CDataLoader::GetTrackSplitSeq ( ) const virtual ◆ GetTransaction() ◆ GetTrimMappedLocation() bool CSeq_loc_Mapper_Options::GetTrimMappedLocation ( void  ) const inline ◆ GetTSE() ◆ GetTSE_Handle() ◆ GetType() const char* CBlobStateException::GetType ( void  ) const inlineoverridevirtual ◆ GetValue()

template<typename Value , class Converter = PConvertToString<Value>>

Definition at line 122 of file blob_id.hpp.

References CBlobIdFor< Value, Converter >::m_Value, and pair_base_member< Base, Member >::second().

Referenced by CAsnCache_DataLoader::GetBlobById(), CBlastDbDataLoader::GetBlobById(), CRemoteBlastDbDataLoader::GetBlobById(), CBuffer_DataLoader::GetBlobById(), CBlobIdFor< Value, Converter >::operator<(), CBlobIdFor< Value, Converter >::operator==(), CLDS2_DataLoader::ResolveConflict(), and CBlastDbDataLoader::x_GetOid().

◆ GetWidthById() [1/2] ◆ GetWidthById() [2/2] ◆ GoodSrcId() ◆ IncludeSourceLocs() ◆ IncOffset() void CGraphRanges::IncOffset ( TSeqPos  inc ) inline ◆ InitAlignMapper() [1/2] ◆ InitAlignMapper() [2/2] ◆ IsActive() bool CPrefetchManager::IsActive ( void  ) static

Definition at line 253 of file prefetch_manager_impl.cpp.

References CThreadPool_Thread::GetCurrentTask(), CThread::GetCurrentThread(), and CThreadPool_Task::IsCancelRequested().

Referenced by CScope_Impl::GetAccVer(), CScope_Impl::GetAccVers(), CScope_Impl::GetBulkIds(), CScope_Impl::GetCDDAnnots(), CScope_Impl::GetGi(), CScope_Impl::GetGis(), CScope_Impl::GetIds(), CScope_Impl::GetLabels(), CScope_Impl::GetSequenceHash(), CScope_Impl::GetSequenceHashes(), CScope_Impl::GetSequenceLength(), CScope_Impl::GetSequenceLengths(), CScope_Impl::GetSequenceState(), CScope_Impl::GetSequenceStates(), CScope_Impl::GetSequenceType(), CScope_Impl::GetSequenceTypes(), CScope_Impl::GetTaxIds(), CScope_Impl::x_FindBioseqInfo(), CScope_Impl::x_GetTSESetWithBioseqAnnots(), CScope_Impl::x_GetTSESetWithOrphanAnnots(), CTSE_Split_Info::x_LoadChunk(), and CTSE_Split_Info::x_LoadChunks().

◆ IsCreated() ◆ IsDataLoaderMatches() virtual bool CObjectManager::IDataLoaderFilter::IsDataLoaderMatches ( CDataLoader &  loader ) const pure virtual ◆ IsDone() bool CPrefetchRequest::IsDone ( void  ) const inline ◆ IsProcessedNA() ◆ IsRequestedAnyNA() ◆ IsRequestedNA() ◆ IsSameBioseq() ◆ KeepNonmappingRanges() ◆ LastIsPartial() bool CSeq_loc_Mapper_Base::LastIsPartial ( void  ) inline ◆ LessByTypeId() ◆ Map() [1/5] ◆ Map() [2/5] ◆ Map() [3/5]

Map seq-graph.

This will map both location and data. The data may be truncated to match the new location.

Definition at line 4173 of file seq_loc_mapper_base.cpp.

References CSerialObject::Assign(), CopyGraphData(), CSeq_graph_Base::C_Graph::e_Byte, CSeq_graph_Base::C_Graph::e_Int, CSeq_graph_Base::C_Graph::e_Real, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSeq_unknown, CByte_graph_Base::GetAxis(), CInt_graph_Base::GetAxis(), CReal_graph_Base::GetAxis(), CSeq_graph_Base::C_Graph::GetByte(), CSeq_graph_Base::GetComp(), CSeq_graph_Base::GetGraph(), CSeq_graph_Base::C_Graph::GetInt(), CSeq_graph_Base::GetLoc(), CByte_graph_Base::GetMax(), CInt_graph_Base::GetMax(), CReal_graph_Base::GetMax(), CByte_graph_Base::GetMin(), CInt_graph_Base::GetMin(), CReal_graph_Base::GetMin(), CGraphRanges::GetRanges(), CSeq_graph_Base::C_Graph::GetReal(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CByte_graph_Base::GetValues(), CInt_graph_Base::GetValues(), CReal_graph_Base::GetValues(), CSeq_graph_Base::IsSetComp(), ITERATE, CSeq_loc_Mapper_Base::m_GraphRanges, CSeq_loc_Mapper_Base::Map(), NCBI_THROW, CRef< C, Locker >::Reset(), CSeq_graph_Base::C_Graph::Reset(), CByte_graph_Base::SetAxis(), CInt_graph_Base::SetAxis(), CReal_graph_Base::SetAxis(), CSeq_graph_Base::C_Graph::SetByte(), CSeq_graph_Base::SetComp(), CSeq_graph_Base::SetGraph(), CSeq_graph_Base::C_Graph::SetInt(), CSeq_graph_Base::SetLoc(), CByte_graph_Base::SetMax(), CInt_graph_Base::SetMax(), CReal_graph_Base::SetMax(), CByte_graph_Base::SetMin(), CInt_graph_Base::SetMin(), CReal_graph_Base::SetMin(), CSeq_graph_Base::SetNumval(), CSeq_graph_Base::C_Graph::SetReal(), CByte_graph_Base::SetValues(), CInt_graph_Base::SetValues(), CReal_graph_Base::SetValues(), and CSeq_graph_Base::C_Graph::Which().

◆ Map() [4/5]

Map seq-loc.

Definition at line 3647 of file seq_loc_mapper_base.cpp.

References CSeq_loc_Mapper_Base::fFuzzOption_CStyle, CSeq_loc_Mapper_Base::m_Dst_loc, CSeq_loc_Mapper_Base::m_FuzzOption, CSeq_loc_Mapper_Base::m_LastTruncated, CSeq_loc_Mapper_Base::m_Partial, CSeq_loc_Mapper_Base::m_SrcLocs, CRef< C, Locker >::Reset(), CSeq_loc::SetEquiv(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CSeq_loc_Mapper_Base::x_PushRangesToDstMix(), and CSeq_loc_Mapper_Base::x_StripExtraneousFuzz().

Referenced by CFeatGapInfo::AdjustProteinSeq(), CEditSequence::AdjustProtFeatureLocations(), BadSeqLocSortOrder(), CConvertProtToImp::Convert(), variation::CreateUnknownProtConsequenceVariation(), variation::CVariationUtil::FindLocationProperties(), CInternalStopFinder::FindStartStopRanges(), CScore_StartStopCodon::Get(), variation::CVariationUtil::CCdregionIndex::GetCachedLiteralAtLoc(), CEditSequence::GetProteinFeatures(), CCleanup::GetProteinLocationFromNucleotideLocation(), CSeq_loc_Mapper_Base::Map(), CLocMapper_Default::Map(), CBioseq_Handle::MapLocation(), CSeq_loc_Mapper_Base::MapTotalRange(), variation_ref::CVariationUtil::PrecursorToProt(), ProjectAndCollapseCDS(), RemapAlignToLoc(), RemapOtherProtFeats(), CFeatureLoadingJob::Run(), CFeatCompareJob_Align::Run(), CDemoApp::Run(), CTestSingleAln_All::RunTest(), s_AdjustToAnnotatedCDS(), s_CodonVariation(), s_CombineDustMasksWithUserProvidedMasks(), s_GetRnaMappingLocs(), s_MapSingleAA(), CFeatureGenerator::s_ProjectRNA(), variation_ref::CVariationUtil::s_Remap(), CFeatureGenerator::SImplementation::StitchSmallHoles(), TestMappingSeq_align(), TestMappingSeq_align_Exception(), TestMappingSeq_graph(), TestMappingSeq_graph_Exception(), TestMappingSeq_loc(), TestMappingSeq_loc_Exception(), CMacroFunction_ReplaceStopWithSelenocysteine::TheFunction(), variation::CVariationUtil::TranslateNAtoAA(), CFeatureGenerator::SImplementation::x_CollectMrnaSequence(), CFlatGatherer::x_CollectSourceFeatures(), CPromote::x_CopyCdregionToRNA(), CFlatGatherer::x_CopyCDSFromCDNA(), CSGAlignmentJob::x_CreateFeatGlyph(), CBLASTSeqToolJob::x_CreateProjectItems(), CMSAToolJob::x_CreateProjectItems(), CCreateNeedlemanWunschJob::x_CreateProjectItems(), CFeatureGenerator::SImplementation::x_CreateProteinBioseq(), CFlatGatherer::x_GatherAlignments(), CFlatGatherer::x_GatherFeatures(), CFlatGatherer::x_GatherFeaturesIdx(), CFlatGatherer::x_GatherFeaturesOnRange(), CFlatGatherer::x_GatherFeaturesOnRangeIdx(), CSeq_align_Mapper_Base::x_GetDstSpliced(), CFlatGatherer::x_GetFeatsOnCdsProduct(), CFlatGatherer::x_GetFeatsOnCdsProductIdx(), CCompareSeqRegions::x_GetSelfLoc(), CFeatureGenerator::SImplementation::x_HandleCdsExceptions(), variation::CVariationUtil::x_InferNAfromAA(), CBioseqIndex::x_InitFeats(), CSGAlignmentJob::x_LoadAlignmentFeats(), CBatchFeatJob::x_LoadFeatProducts(), CFeatureGenerator::SImplementation::x_MapFeature(), CSeq_id_Resolver__ChrNamesFromGC::x_MapLoc(), CConvertFeatureBase::x_MoveFeatureToProtein(), CXcompareAnnotsApplication::x_ProcessMappingRanges(), CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile(), variation_ref::CVariationUtil::x_ProtToPrecursor(), CIdMapperTestApp::x_RecurseMapSeqAligns(), variation::CVariationUtil::x_Remap(), CReportTrim::x_RetranslateCDS(), CSGAlnQualityScore::x_RetrieveQualityMap(), CBlastFormat::x_ReverseQuery(), COligoSpecificityCheck::x_SequencesMappedToSameTarget(), CFeatureGenerator::SImplementation::x_SetComment(), CBioseqContext::x_SetLocation(), CCdregionValidator::x_ValidateCDSPeptides(), and CGff3Writer::xWriteFeatureProtein().

◆ Map() [5/5]

Map each object from the Seq-annot and replace the original with the mapped one.

Definition at line 4317 of file seq_loc_mapper_base.cpp.

References CSeq_annot_Base::C_Data::e_Align, CSeq_annot_Base::C_Data::e_Ftable, CSeq_annot_Base::C_Data::e_Graph, eDiag_Error, CSeq_loc_Mapper_Base::eMapped_All, CSeq_loc_Mapper_Base::eMapped_None, CSeq_loc_Mapper_Base::eMapped_Some, ERASE_ITERATE, ERR_POST_X, CSeq_loc_Mapper_Base::fAnnotMap_Location, CSeq_loc_Mapper_Base::fAnnotMap_Product, CSeq_loc_Mapper_Base::fAnnotMap_RemoveNonMapping, CSeq_loc_Mapper_Base::fAnnotMap_ThrowOnFailure, flags, ftable, CSeq_annot_Base::GetData(), CSeq_feat_Base::GetLocation(), CException::GetMsg(), CSeq_feat_Base::GetProduct(), IMessageListener::HaveListeners(), CSeq_loc_Base::IsNull(), CSeq_feat_Base::IsSetProduct(), CSeq_loc_Mapper_Base::Map(), msg(), NCBI_THROW, IMessageListener::Post(), CSeq_annot_Base::SetData(), CSeq_feat_Base::SetLocation(), CSeq_feat_Base::SetProduct(), Warning(), and CSeq_annot_Base::C_Data::Which().

◆ Map_Fuzz() ◆ Map_Pos() ◆ Map_Range()

Map an interval, set fuzz when the mapping truncates the original range.

Definition at line 243 of file seq_loc_mapper_base.cpp.

References CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, kInvalidSeqPos, CMappingRange::m_Dst_from, CMappingRange::m_Dst_len, CMappingRange::m_ExtTo, CMappingRange::m_Frame, CMappingRange::m_Reverse, CMappingRange::m_Src_bioseq_len, CMappingRange::m_Src_from, CMappingRange::m_Src_to, CMappingRange::Map_Pos(), max(), min(), CRange_Base::SetFrom(), and CRange_Base::SetTo().

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

◆ Map_Strand() ◆ MapTotalRange() ◆ MixedAlignsAsSpliced() ◆ NCBI_DECLARE_INTERFACE_VERSION() NCBI_DECLARE_INTERFACE_VERSION ( objects::CDataLoader  , "xloader"  , 9  , 0  , 0    ) ◆ NCBI_EXCEPTION_DEFAULT() [1/12] ◆ NCBI_EXCEPTION_DEFAULT() [2/12] ◆ NCBI_EXCEPTION_DEFAULT() [3/12] ◆ NCBI_EXCEPTION_DEFAULT() [4/12] ◆ NCBI_EXCEPTION_DEFAULT() [5/12] ◆ NCBI_EXCEPTION_DEFAULT() [6/12] ◆ NCBI_EXCEPTION_DEFAULT() [7/12] ◆ NCBI_EXCEPTION_DEFAULT() [8/12] ◆ NCBI_EXCEPTION_DEFAULT() [9/12] ◆ NCBI_EXCEPTION_DEFAULT() [10/12] ◆ NCBI_EXCEPTION_DEFAULT() [11/12] ◆ NCBI_EXCEPTION_DEFAULT() [12/12] ◆ New() ◆ NextBioseqHandle() ◆ OnStatusChange() void CPrefetchRequest::OnStatusChange ( EStatus  old ) virtual ◆ operator!=() ◆ operator()() [1/7] ◆ operator()() [2/7] ◆ operator()() [3/7] ◆ operator()() [4/7] ◆ operator()() [5/7] ◆ operator()() [6/7] ◆ operator()() [7/7] ◆ operator*() ◆ operator->() ◆ operator<() [1/4]

Implemented in CBlobIdFor< Value, Converter >, CPsgBlobId, CVDBGraphBlobId, CSRABlobId, CWGSBlobId, CSNPBlobId, CCSRABlobId, CBAMBlobId, CBlob_id, and CCDDBlobId.

◆ operator<() [2/4]

template<typename Value , class Converter = PConvertToString<Value>>

◆ operator<() [3/4] ◆ operator<() [4/4] ◆ operator<<() [1/2] ◆ operator<<() [2/2] ◆ operator=() [1/7] ◆ operator=() [2/7] ◆ operator=() [3/7] ◆ operator=() [4/7] ◆ operator=() [5/7] ◆ operator=() [6/7] ◆ operator=() [7/7] ◆ operator==() [1/3]

Reimplemented in CBlobIdFor< Value, Converter >, CPsgBlobId, CVDBGraphBlobId, CSRABlobId, CWGSBlobId, CSNPBlobId, CCSRABlobId, CBAMBlobId, CBlob_id, and CCDDBlobId.

Definition at line 1007 of file data_loader.cpp.

◆ operator==() [2/3]

template<typename Value , class Converter = PConvertToString<Value>>

◆ operator==() [3/3] ◆ PrefetchNotify() ◆ RegisterDataLoader() [1/2] ◆ RegisterDataLoader() [2/2] ◆ RegisterInObjectManager()

Register the loader only if the name is not yet registered in the object manager.

Definition at line 53 of file data_loader.cpp.

References om.

Referenced by CCDDDataLoader::RegisterInObjectManager(), CLDS2_DataLoader::RegisterInObjectManager(), CSRADataLoader::RegisterInObjectManager(), CVDBGraphDataLoader::RegisterInObjectManager(), CGBDataLoader_Native::RegisterInObjectManager(), CPSGDataLoader::RegisterInObjectManager(), CBAMDataLoader::RegisterInObjectManager(), CCSRADataLoader::RegisterInObjectManager(), CSNPDataLoader::RegisterInObjectManager(), CWGSDataLoader::RegisterInObjectManager(), CSplitDataLoader::RegisterInObjectManager(), CAsnCache_DataLoader::RegisterInObjectManager(), CBlastDbDataLoader::RegisterInObjectManager(), CRemoteBlastDbDataLoader::RegisterInObjectManager(), CHugeAsnDataLoader::RegisterInObjectManager(), CDataLoaderPatcher::RegisterInObjectManager(), and CBuffer_DataLoader::RegisterInObjectManager().

◆ RegisterScope() void CObjectManager::RegisterScope ( CScope_Impl &  scope ) protected ◆ ReleaseDataSource()

Definition at line 526 of file object_manager.cpp.

References _ASSERT, map_checker< Container >::end(), map_checker< Container >::erase(), ERR_POST_X, map_checker< Container >::find(), CDataSource::GetDataLoader(), CDataSource::GetSharedObject(), ncbi::grid::netcache::search::fields::key, CObjectManager::m_mapToSource, CObjectManager::m_OM_Lock, CObject::Referenced(), CObject::ReferencedOnlyOnce(), CGuard< Resource, Lock, Unlock, ReportExceptions >::Release(), and CRef< C, Locker >::Reset().

Referenced by CDataSource_ScopeInfo::DetachScope().

◆ RemoveAnnot() ◆ RemoveBioseq() ◆ RemoveDataLoader() ◆ RemoveEntry() ◆ RemoveFromHistory() [1/4] ◆ RemoveFromHistory() [2/4] ◆ RemoveFromHistory() [3/4] ◆ RemoveFromHistory() [4/4] ◆ RemoveSeq_annot() ◆ RemoveTopLevelSeqEntry() [1/2] ◆ RemoveTopLevelSeqEntry() [2/2]

Revoke TSE previously added using AddTopLevelSeqEntry() or AddBioseq().

Throw exception if the TSE is still in use or not found in the scope.

Definition at line 376 of file scope.cpp.

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

Referenced by BOOST_AUTO_TEST_CASE(), CCleanupApp::HandleSeqEntry(), CAsn2FastaApp::HandleSeqEntry(), MakeRegulatoryFeatureTest(), CBiosampleChkApp::ProcessSeqEntry(), CTLSHandler::ProcessSeqEntry(), CAsnvalThreadState::ReadClassMember(), CScope::RemoveTopLevelSeqEntry(), s_DetachEntryFromScope(), TestOneGapSeq(), TestTrimForFrame(), TryOneCDSCase(), CLocalFileRestorer::x_DetachOrigObject(), CAsn2FastaApp::x_ProcessIStream(), CCDSTranslationPanel::x_SetLocationForProtein(), CFeatureTableReader::xAddProteinToSeqEntry(), and CFeatureTableReader::xParseCdregions().

◆ ReplaceAnnot() ◆ ReportExtra() void CLoaderException::ReportExtra ( ostream &  out ) const overrideprotectedvirtual ◆ ResetDataAndHistory() [1/2] ◆ ResetDataAndHistory() [2/2] void CScope::ResetDataAndHistory ( void  )

Clear all information in the scope except added data loaders.

Definition at line 331 of file scope.cpp.

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

Referenced by CdBlaster::blast(), BLASTer::CreateNewPairwiseAlignmentsByBlast(), CId1FetchApp::LookUpGI(), SBlobCopier::operator()(), OutputEmblAsn(), CBlastFormat::ResetScopeHistory(), CGBProjectTool::Run(), CSeqDescrRetrievalJob::Run(), CAlnVecMultiDataSource::s_CleanScope(), sParseFlatfile(), CGapStatsApplication::x_ReadFileOrAccn(), CEmbl2Asn::xGetEntry(), CGenbank2Asn::xGetEntry(), CSwissProt2Asn::xGetEntry(), and CXml2Asn::xGetEntry().

◆ ResetHistory()

Clean all unused TSEs from the scope's cache and release the memory.

TSEs referenced by any handles are not removed. Explicitly added entries are not removed. Edited entries retrieved from a data loader are removed, so that their unmodified version will be visible.

Definition at line 325 of file scope.cpp.

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

Referenced by AddSentinelRNASeq(), CGBDocument::AttachDataLoader(), CGBDocument::DetachDataLoader(), CHugeFileProcess::ForEachEntry(), CAsn2FastaApp::HandleSeqEntry(), CSelectFeatureDlg::OnButtonLoadFile(), CSplitCacheApp::ProcessSeqId(), CAsnvalThreadState::ReadClassMember(), IEditingActionFeat::ResetScope(), CBlastInputDemoApplication::Run(), CXcompareAnnotsApplication::Run(), CDemoApp::Run(), CScopedProcess::SeqEntryFinalize(), sParseFlatfile(), CAsn2FastaApp::x_ProcessIStream(), and CXcompareAnnotsApplication::x_ProcessSeqAlignSetFromFile().

◆ ResetObject() void CSeq_loc_Mapper_Message::ResetObject ( void  ) ◆ ResolveConflict() ◆ RevokeAllDataLoaders() void CObjectManager::RevokeAllDataLoaders ( void  )

Revoke all registered data loaders, even if they were still used.

This method should be called at application's end to release data loader plugins for unloading of their shared library.

Definition at line 235 of file object_manager.cpp.

References map_checker< Container >::clear(), set< Key, Compare >::clear(), CObjectManager::m_mapNameToLoader, CObjectManager::m_mapToSource, CObjectManager::m_OM_Lock, CObjectManager::m_setDefaultSource, and NON_CONST_ITERATE.

Referenced by BOOST_AUTO_TEST_CASE(), CShowBlastDeflineTest::GetDeflineInfo(), CAlnPrinterFixture::PrintAlignment(), and s_ReadAndTestQueryFromString().

◆ RevokeDataLoader() [1/2]

Revoke previously registered data loader.

Return FALSE if the loader is still in use (by some scope). Throw an exception if the loader is not registered with this ObjMgr.

Definition at line 203 of file object_manager.cpp.

References CDataLoader::GetName(), CObjectManager::m_OM_Lock, NCBI_THROW, CRef< C, Locker >::NotEmpty(), CGuard< Resource, Lock, Unlock, ReportExceptions >::Release(), CObjectManager::x_GetLoaderByName(), and CObjectManager::x_RevokeDataLoader().

Referenced by CBlastScopeSource::RevokeBlastDbDataLoader(), TestUtil::CBlastOM::RevokeBlastDbDataLoader(), CHugeFileDemoApp::Run(), CSplitCacheApp::TestSplit(), and CGenBankFixture::~CGenBankFixture().

◆ RevokeDataLoader() [2/2] ◆ RevokeDataLoaders()

Revoke data loaders by filter, even if they were still used.

This method should be called from data loader's plugin unloadin code.

Definition at line 252 of file object_manager.cpp.

References map_checker< Container >::erase(), set< Key, Compare >::erase(), ERASE_ITERATE, CDataLoader::GetName(), CObjectManager::IDataLoaderFilter::IsDataLoaderMatches(), CObjectManager::m_mapNameToLoader, CObjectManager::m_mapToSource, CObjectManager::m_OM_Lock, CObjectManager::m_setDefaultSource, and rapidjson::source.

Referenced by CRevoker::~CRevoker().

◆ RevokeScope() void CObjectManager::RevokeScope ( CScope_Impl &  scope ) protected ◆ SAccVerFound() CDataLoader::SAccVerFound::SAccVerFound ( ) inline

Definition at line 304 of file data_loader.hpp.

◆ SequenceExists() ◆ Set() ◆ SetAlign() ◆ SetAlign_Dense_seg_TotalRange() ◆ SetAlign_Sparse_ToFirst() ◆ SetAlign_Sparse_ToSecond() ◆ SetCheckStrand() ◆ SetDefaultKeepExternalAnnotsForEdit() void CScope::SetDefaultKeepExternalAnnotsForEdit ( bool  keep = true ) static ◆ SetErrorOnPartial() ◆ SetFailedCall() void CLoaderException::SetFailedCall ( const string &  call )

Definition at line 121 of file objmgr_exception.cpp.

References CLoaderException::m_FailedCall.

Referenced by CDataSource::GetAccVer(), CDataSource::GetAccVers(), CDataSource::GetBulkIds(), CDataSource::GetCDDAnnots(), CDataSource::GetGi(), CDataSource::GetGis(), CDataSource::GetIds(), CDataSource::GetLabel(), CDataSource::GetLabels(), CDataSource::GetSeq_entry_Lock(), CDataSource::GetSequenceHash(), CDataSource::GetSequenceHashes(), CDataSource::GetSequenceLength(), CDataSource::GetSequenceLengths(), CDataSource::GetSequenceState(), CDataSource::GetSequenceStates(), CDataSource::GetSequenceType(), CDataSource::GetSequenceTypes(), CDataSource::GetTaxId(), CDataSource::GetTaxIds(), CDataSource::GetTSESetWithBioseqAnnots(), CDataSource::GetTSESetWithOrphanAnnots(), s_GetBlobs(), and CDataSource::x_GetRecords().

◆ SetFeat() ◆ SetFuzzOption() void CSeq_loc_Mapper_Base::SetFuzzOption ( TFuzzOption  newOption ) ◆ SetGapPreserve() ◆ SetGapRemove() ◆ SetGraph() ◆ SetGroup() void CMappingRange::SetGroup ( int  grp ) inline ◆ SetKeepExternalAnnotsForEdit() void CScope::SetKeepExternalAnnotsForEdit ( bool  keep = true ) ◆ SetListener() ◆ SetLoaderOptions()

Update loader's default-ness and priority.

Definition at line 311 of file object_manager.cpp.

References _ASSERT, CObjectManager::eDefault, map_checker< Container >::end(), set< Key, Compare >::end(), CObjectManager::eNonDefault, set< Key, Compare >::erase(), map_checker< Container >::find(), set< Key, Compare >::find(), set< Key, Compare >::insert(), CObjectManager::kPriority_Default, CObjectManager::m_mapToSource, CObjectManager::m_OM_Lock, CObjectManager::m_setDefaultSource, NCBI_THROW, and CObjectManager::x_GetLoaderByName().

Referenced by CGenBankUIDataSource::Open().

◆ SetLoc() ◆ SetMapperSequenceInfo() ◆ SetMapSingleLevel() ◆ SetMergeAbutting()

Merge only abutting intervals, keep overlapping.

Definition at line 1168 of file seq_loc_mapper_base.hpp.

References CSeq_loc_Mapper_Base::eMergeAbutting, and CSeq_loc_Mapper_Base::m_MergeFlag.

Referenced by CEditSequence::AdjustProtFeatureLocations(), CConvertProtToImp::Convert(), CCdsToMatPeptide::ConvertInner(), CEditSequence::GetProteinFeatures(), CCdsToMatPeptide::MergeConvert(), RemapOtherProtFeats(), CFeatCompareJob_Align::Run(), TestMapping_Merging(), CPromote::x_CopyCdregionToRNA(), CConvertFeatureBase::x_MoveFeatureToProtein(), CReportTrim::x_RetranslateCDS(), and CBioseqContext::x_SetMapper().

◆ SetMergeAll() ◆ SetMergeBySeg() ◆ SetMergeContained() ◆ SetMergeNone() ◆ SetName() void CDataLoader::SetName ( const string &  loader_name ) protected ◆ SetOffset() void CGraphRanges::SetOffset ( TSeqPos  offset ) inline ◆ SetProcessedNA() ◆ SetProgress() ◆ SetReverseDst() void CMappingRanges::SetReverseDst ( bool  value = true ) inline ◆ SetReverseSrc() void CMappingRanges::SetReverseSrc ( bool  value = true ) inline ◆ SetSeqTypeById() [1/2] ◆ SetSeqTypeById() [2/2]

Methods for setting sequence types.

May be used to populate the cache before mapping huge alignments if the types are already known. Throw exception if the sequence type is already set to a different value. NOTE: setting sequence type does not adjust mapping ranges for this id. All mapping ranges must use genomic coordinates.

Definition at line 2296 of file seq_loc_mapper_base.cpp.

References CSeq_loc_Mapper_Base::CollectSynonyms(), map_checker< Container >::end(), CSeq_loc_Mapper_Base::eSeq_unknown, map_checker< Container >::find(), CSeq_loc_Mapper_Base::m_SeqTypes, and NCBI_THROW.

Referenced by CSeq_loc_Mapper_Base::GetSeqType(), CSeq_loc_Mapper_Base::SetSeqTypeById(), CSeq_loc_Mapper_Base::x_AdjustSeqTypesToProt(), CBLASTSeqToolJob::x_CreateProjectItems(), CMSAToolJob::x_CreateProjectItems(), CSeq_align_Mapper_Base::x_Init(), CSeq_loc_Mapper_Base::x_InitializeFeat(), CSeq_loc_Mapper_Base::x_InitializeLocs(), and CSeq_loc_Mapper_Base::x_InitSpliced().

◆ SetTargetDataSource() void CDataLoader::SetTargetDataSource ( CDataSource &  data_source ) ◆ SetTrimMappedLocation() ◆ SetTrimSplicedSeg() ◆ SGiFound() CDataLoader::SGiFound::SGiFound ( ) inline

Definition at line 319 of file data_loader.hpp.

◆ SHashFound() CDataLoader::SHashFound::SHashFound ( ) inline

Definition at line 369 of file data_loader.hpp.

◆ Shutdown() void CPrefetchManager::Shutdown ( void  ) ◆ SMappedRange() [1/2] ◆ SMappedRange() [2/2] ◆ SRegisterLoaderInfo() ◆ SRequestDetails() SRequestDetails::SRequestDetails ( void  ) inline

Definition at line 88 of file data_loader.hpp.

◆ STypeFound() CDataLoader::STypeFound::STypeFound ( ) inline

Definition at line 348 of file data_loader.hpp.

◆ sx_GetExonPartLength()

Definition at line 1913 of file seq_loc_mapper_base.cpp.

References CSpliced_exon_chunk_Base::e_Diag, CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, ERR_POST_X, CSpliced_exon_chunk_Base::GetDiag(), CSpliced_exon_chunk_Base::GetGenomic_ins(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), CSpliced_exon_chunk_Base::GetProduct_ins(), CSpliced_exon_chunk_Base::SelectionName(), Warning(), and CSpliced_exon_chunk_Base::Which().

Referenced by CSeq_align_Mapper_Base::InitExon(), and CSeq_loc_Mapper_Base::x_IterateExonParts().

◆ ToString() [1/3]

template<typename Value , class Converter = PConvertToString<Value>>

◆ ToString() [2/3] string CBlobIdKey::ToString ( void  ) const inline

Definition at line 176 of file blob_id.hpp.

References CBlobIdKey::m_Id, and CBlobId::ToString().

Referenced by CTSE_Info::GetDescription(), CCSRARefSeqInfo::LoadAnnotAlignChunk(), CCSRARefSeqInfo::LoadAnnotMainChunk(), CCSRARefSeqInfo::LoadAnnotPileupChunk(), CCSRARefSeqInfo::LoadRefSeqChunk(), CPSGL_GetChunk_Processor::PrintChunk(), CDemoApp::Run(), CDataLoaderPatcher::x_ApplyPatches(), x_CreateEmptyLocalCDDEntry(), CDataLoaderPatcher::x_IsPatchNeeded(), and CPSGDataLoader_Impl::x_ReadCDDChunk().

◆ ToString() [3/3] virtual string CBlobId::ToString ( void  ) const pure virtual

Get string representation of blob id.

Should be unique for all blob ids from the same data loader.

Implemented in CPsgBlobId, CVDBGraphBlobId, CSRABlobId, CSNPBlobId, CWGSBlobId, CSNPBlobId, CCSRABlobId, CBAMBlobId, CBlob_id, CCDDBlobId, and CBlobIdFor< Value, Converter >.

Referenced by CPsgBlobId::GetPsgBlobId(), CPSGDataLoader_Impl::LoadChunksOnce(), and CBlobIdKey::ToString().

◆ TruncateNonmappingRanges() ◆ UpdateAnnotIndex() void CScope::UpdateAnnotIndex ( void  ) ◆ Wait() ◆ Which() EObjectType CSeq_loc_Mapper_Message::Which ( void  ) const inline ◆ Write() void CSeq_loc_Mapper_Message::Write ( CNcbiOstream &  out ) const virtual

Print the message and any additional information to the stream.

Reimplemented from CMessage_Basic.

Definition at line 518 of file seq_loc_mapper_base.cpp.

References CSeq_loc_Mapper_Message::eNot_set, CSeq_loc_Mapper_Message::eSeq_align, CSeq_loc_Mapper_Message::eSeq_feat, CSeq_loc_Mapper_Message::eSeq_graph, CSeq_loc_Mapper_Message::eSeq_loc, CSeq_loc_Mapper_Message::GetAlign(), CSeq_loc_Mapper_Message::GetFeat(), CSeq_loc_Mapper_Message::GetGraph(), CSeq_loc_Mapper_Message::GetLoc(), MSerial_AsnText, out(), CSeq_loc_Mapper_Message::Which(), and CMessage_Basic::Write().

◆ x_AddBioseq()

Definition at line 328 of file gc_assembly_parser.cpp.

References CSeq_id::Assign(), CGC_Sequence::CanGetLength(), CSeq_inst_Base::eMol_na, CSeq_inst_Base::eRepr_delta, CSeq_inst_Base::eRepr_virtual, CGC_Assembly_Parser::fSkipDuplicates, CGC_Sequence::GetLength(), CGC_Sequence_Base::GetStructure(), set< Key, Compare >::insert(), CGC_Sequence_Base::IsSetStructure(), ITERATE, CGC_Assembly_Parser::m_AllSeqs, CGC_Assembly_Parser::m_Flags, CBioseq_Base::SetId(), CBioseq_Base::SetInst(), CSeq_entry_Base::SetSeq(), CBioseq_set_Base::SetSeq_set(), and CSeq_entry_Base::SetSet().

Referenced by CGC_Assembly_Parser::x_ParseGCSequence().

◆ x_AddConversion() 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  ) protected

Definition at line 2594 of file seq_loc_mapper_base.cpp.

References CMappingRanges::AddConversion(), CSeq_loc_Mapper_Base::CollectSynonyms(), CSeq_loc_Mapper_Base::eSeq_prot, CSeq_id_Handle::GetHandle(), CSeq_loc_Mapper_Base::GetSeqType(), CSeq_loc_Mapper_Base::GetSequenceLength(), CSeq_loc_Mapper_Options::GetTrimMappedLocation(), kInvalidSeqPos, CSeq_loc_Mapper_Base::m_CurrentGroup, CSeq_loc_Mapper_Base::m_DstRanges, CSeq_loc_Mapper_Base::m_MapOptions, CSeq_loc_Mapper_Base::m_Mappings, and SameOrientation().

Referenced by CSeq_loc_Mapper::x_InitGCSequence(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

◆ x_AddExonPartsMapping() ◆ x_AddVirtualBioseq()

Definition at line 740 of file seq_loc_mapper.cpp.

References CScope::AddBioseq(), CSeq_id::Assign(), CGC_Sequence::CanGetLength(), CSeq_inst_Base::eMol_na, CSeq_inst_Base::eRepr_virtual, CScope::GetBioseqHandle(), CGC_Sequence::GetLength(), CHeapScope::GetScope(), ITERATE, CSeq_loc_Mapper::m_Scope, CBioseq_Base::SetId(), and CBioseq_Base::SetInst().

Referenced by CSeq_loc_Mapper::x_InitGCSequence().

◆ x_AdjustSeqTypesToProt()

Definition at line 2399 of file seq_loc_mapper_base.cpp.

References CMappingRanges::AddConversion(), CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSeq_unknown, CMappingRange::GetGroup(), CMappingRanges::GetIdMap(), CSeq_loc_Mapper_Base::GetSeqTypeById(), ITERATE, kInvalidSeqPos, len, CMappingRange::m_Dst_from, CMappingRange::m_Dst_id_Handle, CMappingRange::m_Dst_strand, CSeq_loc_Mapper_Base::m_DstRanges, CMappingRange::m_ExtTo, CSeq_loc_Mapper_Base::m_Mappings, CMappingRange::m_Src_from, CMappingRange::m_Src_id_Handle, CMappingRange::m_Src_strand, CMappingRange::m_Src_to, NCBI_THROW, NON_CONST_ITERATE, CRef< C, Locker >::Reset(), CSeq_loc_Mapper_Base::SetSeqTypeById(), and CSeq_loc_Mapper_Base::x_GetPrimaryId().

Referenced by CSeq_align_Mapper_Base::x_Init().

◆ x_CheckSeqTypes() ◆ x_Clone() inlineoverrideprotectedvirtual ◆ x_CopyData()

Definition at line 95 of file gc_assembly_parser.cpp.

References CSerialObject::Assign(), desc_copy(), CGC_Assembly_Parser::fIgnoreAnnots, CGC_Assembly_Parser::fIgnoreDescr, CSeq_descr_Base::Get(), CGC_AssemblyDesc_Base::GetAnnot(), CGC_AssemblyDesc_Base::GetDescr(), CGC_AssemblyDesc_Base::IsSetAnnot(), CGC_AssemblyDesc_Base::IsSetDescr(), ITERATE, CGC_Assembly_Parser::m_Flags, CSeq_entry::SetAnnot(), and CSeq_entry::SetDescr().

Referenced by CGC_Assembly_Parser::x_ParseGCAssembly().

◆ x_FindDataSource() ◆ x_FixNonsenseFuzz()

Definition at line 2778 of file seq_loc_mapper_base.cpp.

References CSeq_loc::Assign(), CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Pnt, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CSeq_point_Base::GetFuzz(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_loc_Base::GetInt(), CInt_fuzz_Base::GetLim(), CSeq_loc_Base::GetPnt(), CInt_fuzz_Base::IsLim(), CInt_fuzz_Base::IsRange(), CSeq_point_Base::IsSetFuzz(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_loc::SetInt(), CSeq_loc::SetPnt(), and CSeq_loc_Base::Which().

Referenced by CSeq_loc_Mapper_Base::x_StripExtraneousFuzz().

◆ x_ForceSeqTypes() ◆ x_GetAccVer() ◆ x_GetGi() ◆ x_GetLoaderByName() ◆ x_GetMappedRanges() ◆ x_GetMappedSeq_loc() CRef< CSeq_loc > CSeq_loc_Mapper_Base::x_GetMappedSeq_loc ( void  ) private

Definition at line 4033 of file seq_loc_mapper_base.cpp.

References map_checker< Container >::clear(), CSeq_loc_Mapper_Base::eGapPreserve, CSeq_loc_Mapper_Base::eMergeAbutting, CSeq_loc_Mapper_Base::eMergeAll, CSeq_loc_Mapper_Base::eMergeBySeg, CSeq_loc_Mapper_Base::eMergeContained, int, kEmptyFuzz, kInvalidSeqPos, CSeq_loc_Mapper_Base::m_GapFlag, CSeq_loc_Mapper_Base::m_MappedLocs, CSeq_loc_Mapper_Base::m_MergeFlag, NON_CONST_ITERATE, CSeq_loc::SetEmpty(), CSeq_loc::SetMix(), CSeq_loc::SetNull(), str(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CSeq_loc_Mapper_Base::x_RangeToSeq_loc(), and CSeq_loc_Mapper_Base::x_ReverseRangeOrder().

Referenced by CSeq_loc_Mapper_Base::x_MapSeq_loc(), and CSeq_loc_Mapper_Base::x_PushRangesToDstMix().

◆ x_GetPluginManager() ◆ x_GetPrimaryId() ◆ x_GetRangeLength() ◆ x_InitAlign() [1/4] void CSeq_loc_Mapper_Base::x_InitAlign ( const CDense_diag &  diag, size_t  to_row, size_t  from_row  ) private

Definition at line 1584 of file seq_loc_mapper_base.cpp.

References _ASSERT, eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_prot, CDense_diag_Base::GetDim(), CDense_diag_Base::GetIds(), CDense_diag_Base::GetLen(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CDense_diag_Base::GetStarts(), CDense_diag_Base::GetStrands(), CDense_diag_Base::IsSetStrands(), kInvalidRow, min(), row, Warning(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

Referenced by CSeq_loc_Mapper_Base::x_InitializeAlign().

◆ x_InitAlign() [2/4] void CSeq_loc_Mapper_Base::x_InitAlign ( const CDense_seg &  denseg, size_t  to_row, size_t  from_row  ) private

Definition at line 1648 of file seq_loc_mapper_base.cpp.

References _ASSERT, eNa_strand_unknown, ERR_POST_X, Error(), CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Options::GetAlign_Dense_seg_TotalRange(), CDense_seg_Base::GetDim(), CRange_Base::GetFrom(), CDense_seg_Base::GetIds(), COpenRange< Position >::GetLength(), CDense_seg_Base::GetLens(), CDense_seg_Base::GetNumseg(), CDense_seg::GetSeqRange(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CDense_seg_Base::GetStarts(), CDense_seg_Base::GetStrands(), CDense_seg_Base::IsSetStrands(), kInvalidRow, CSeq_loc_Mapper_Base::m_MapOptions, min(), NCBI_THROW, row, Warning(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

◆ x_InitAlign() [3/4] void CSeq_loc_Mapper_Base::x_InitAlign ( const CPacked_seg &  pseg, size_t  to_row, size_t  from_row  ) private

Definition at line 1801 of file seq_loc_mapper_base.cpp.

References _ASSERT, eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_prot, CPacked_seg_Base::GetDim(), CPacked_seg_Base::GetIds(), CPacked_seg_Base::GetLens(), CPacked_seg_Base::GetNumseg(), CPacked_seg_Base::GetPresent(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CPacked_seg_Base::GetStarts(), CPacked_seg_Base::GetStrands(), CPacked_seg_Base::IsSetStrands(), kInvalidRow, min(), row, Warning(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

◆ x_InitAlign() [4/4] void CSeq_loc_Mapper_Base::x_InitAlign ( const CStd_seg &  sseg, size_t  to_row  ) private ◆ x_InitGCAssembly()

Definition at line 765 of file seq_loc_mapper.cpp.

References CGC_Assembly_Base::GetAssembly_set(), CGC_AssemblyUnit_Base::GetMols(), CGC_AssemblySet_Base::GetMore_assemblies(), CGC_AssemblyUnit_Base::GetOther_sequences(), CGC_AssemblySet_Base::GetPrimary_assembly(), CGC_Replicon_Base::C_Sequence::GetSet(), CGC_Replicon_Base::C_Sequence::GetSingle(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_AssemblyUnit_Base::IsSetMols(), CGC_AssemblySet_Base::IsSetMore_assemblies(), CGC_AssemblyUnit_Base::IsSetOther_sequences(), CGC_Replicon_Base::C_Sequence::IsSingle(), CGC_Assembly_Base::IsUnit(), ITERATE, and CSeq_loc_Mapper::x_InitGCSequence().

Referenced by CSeq_loc_Mapper::CSeq_loc_Mapper().

◆ x_InitGCSequence()

Definition at line 908 of file seq_loc_mapper.cpp.

References _ASSERT, CBioseq_Handle::CanGetInst_Length(), CGC_TypedSeqId_Base::e_External, CGC_TypedSeqId_Base::e_Genbank, CGC_TypedSeqId_Base::e_Private, CGC_TypedSeqId_Base::e_Refseq, CSeq_loc_Mapper::eGCA_Refseq, CSeq_loc_Mapper::eGCA_UCSC, eNa_strand_unknown, CDelta_ext_Base::Get(), CRange_Base::GetFrom(), CSeq_id_Handle::GetHandle(), GetId(), CBioseq_Handle::GetInst_Length(), COpenRange< Position >::GetLength(), CSeq_loc_CI::GetRange(), CGC_Sequence_Base::GetSeq_id(), CSeq_loc_CI::GetSeq_id(), CGC_Sequence_Base::GetSeq_id_synonyms(), CGC_Sequence_Base::GetSequences(), CSeq_loc_CI::GetStrand(), CGC_Sequence_Base::GetStructure(), COpenRange< TSeqPos >::GetWholeLength(), set< Key, Compare >::insert(), CSeq_loc_CI::IsEmpty(), CGC_Sequence_Base::IsSetSeq_id_synonyms(), CGC_Sequence_Base::IsSetSequences(), CSeq_loc_CI::IsSetStrand(), ITERATE, kInvalidSeqPos, NCBI_THROW, CConstRef< C, Locker >::Reset(), s_GetSeqIdAlias(), CSeq_loc_Mapper_Base::x_AddConversion(), CSeq_loc_Mapper::x_AddVirtualBioseq(), CSeq_loc_Mapper::x_IsUCSCRandomChr(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

Referenced by CSeq_loc_Mapper::x_InitGCAssembly().

◆ x_InitializeAlign() [1/3] ◆ x_InitializeAlign() [2/3]

Definition at line 1347 of file seq_loc_mapper_base.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), CDense_seg_Base::GetIds(), CPacked_seg_Base::GetIds(), CSeq_align_Base::C_Segs::GetPacked(), CSparse_seg_Base::GetRows(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::GetStd(), i, ITERATE, kInvalidRow, CSeq_loc_Mapper_Base::m_CurrentGroup, CSeq_loc_Mapper_Base::m_MapOptions, NCBI_THROW, row, CSeq_loc_Mapper_Options::SetAlign_Sparse_ToFirst(), CSeq_loc_Mapper_Options::SetAlign_Sparse_ToSecond(), ncbi::grid::netcache::search::fields::size, CSeq_align_Base::C_Segs::Which(), CSeq_loc_Mapper_Base::x_InitAlign(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CSeq_loc_Mapper_Base::x_InitSparse(), CSeq_loc_Mapper_Base::x_InitSpliced(), and CSeq_loc_Mapper_Base::x_IsSynonym().

◆ x_InitializeAlign() [3/3] void CSeq_loc_Mapper_Base::x_InitializeAlign ( const CSeq_align &  map_align, size_t  to_row, size_t  from_row = size_t(-1)  ) protected

Definition at line 1510 of file seq_loc_mapper_base.cpp.

References CSeq_align_Base::C_Segs::e_Dendiag, CSeq_align_Base::C_Segs::e_Denseg, CSeq_align_Base::C_Segs::e_Disc, CSeq_align_Base::C_Segs::e_Packed, CSeq_align_Base::C_Segs::e_Sparse, CSeq_align_Base::C_Segs::e_Spliced, CSeq_align_Base::C_Segs::e_Std, CSeq_align_set_Base::Get(), CSeq_align_Base::C_Segs::GetDendiag(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), CSeq_align_Base::C_Segs::GetPacked(), CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSparse(), CSeq_align_Base::C_Segs::GetSpliced(), CSeq_align_Base::C_Segs::GetStd(), ITERATE, CSeq_loc_Mapper_Base::m_CurrentGroup, NCBI_THROW, CSeq_align_Base::C_Segs::Which(), CSeq_loc_Mapper_Base::x_InitAlign(), CSeq_loc_Mapper_Base::x_InitializeAlign(), CSeq_loc_Mapper_Base::x_InitSparse(), and CSeq_loc_Mapper_Base::x_InitSpliced().

◆ x_InitializeFeat()

Definition at line 835 of file seq_loc_mapper_base.cpp.

References _ASSERT, CSeqFeatData_Base::e_Cdregion, CSeqFeatData_Base::e_Gene, CSeqFeatData_Base::e_Prot, CSeqFeatData_Base::e_Rna, CSeq_loc_Mapper_Base::eLocationToProduct, CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSeq_unknown, CSeqFeatData_Base::GetCdregion(), CSeq_feat_Base::GetData(), CCdregion_Base::GetFrame(), CSeq_feat_Base::GetLocation(), CSeq_feat_Base::GetProduct(), CSeqFeatData_Base::IsCdregion(), CSeq_feat_Base::IsSetProduct(), CSeq_loc_Mapper_Base::SetSeqTypeById(), CSeqFeatData_Base::Which(), and CSeq_loc_Mapper_Base::x_InitializeLocs().

Referenced by CSeq_loc_Mapper::CSeq_loc_Mapper(), and CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base().

◆ x_InitializeLocs()

Definition at line 913 of file seq_loc_mapper_base.cpp.

References CSeq_loc_CI::eEmpty_Skip, COpenRange< Position >::Empty(), CSeq_loc_CI::eOrder_Biological, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSeq_unknown, CRange_Base::GetFrom(), CSeq_loc_CI::GetFuzzFrom(), CSeq_loc_CI::GetFuzzTo(), CSeq_loc::GetId(), CSeq_loc_CI::GetRange(), CSeq_loc_CI::GetSeq_id(), CSeq_loc_CI::GetSeq_id_Handle(), CSeq_loc_Mapper_Base::GetSequenceLength(), CSeq_loc_CI::GetStrand(), CSeq_loc_Mapper_Options::GetTrimMappedLocation(), Info(), CSeq_loc_Base::IsEmpty(), IsReverse(), CSeq_loc::IsReverseStrand(), COpenRange< Position >::IsWhole(), kInvalidSeqPos, CSeq_loc_Mapper_Base::m_CurrentGroup, CSeq_loc_Mapper_Base::m_MapOptions, CSeq_loc_Mapper_Base::m_Mappings, NCBI_THROW, r(), CMappingRanges::SetReverseDst(), CMappingRanges::SetReverseSrc(), CSeq_loc_Mapper_Base::SetSeqTypeById(), rapidjson::source, Warning(), CSeq_loc_Mapper_Base::x_CheckSeqTypes(), CSeq_loc_Mapper_Base::x_ForceSeqTypes(), CSeq_loc_Mapper_Base::x_GetRangeLength(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

Referenced by CSeq_loc_Mapper::CSeq_loc_Mapper(), CSeq_loc_Mapper_Base::CSeq_loc_Mapper_Base(), CSeq_loc_Mapper_Base::x_InitAlign(), and CSeq_loc_Mapper_Base::x_InitializeFeat().

◆ x_InitializeSeqMap() [1/4] ◆ x_InitializeSeqMap() [2/4] ◆ x_InitializeSeqMap() [3/4] ◆ x_InitializeSeqMap() [4/4] ◆ x_InitializeSeqMapDown() ◆ x_InitializeSeqMapSingleLevel()

Definition at line 614 of file seq_loc_mapper.cpp.

References _ASSERT, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, CSeq_loc_Mapper::eSeqMap_Down, CSeq_loc_Mapper::eSeqMap_Up, CSeqMap_CI::GetDepth(), CSeq_id_Handle::GetHandle(), CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CSeqMap_CI::GetRefSeqid(), CSeq_id_Handle::GetSeqId(), COpenRange< TSeqPos >::GetWhole(), CSeq_loc_Mapper_Base::m_DstRanges, and CSeq_loc_Mapper_Base::x_NextMappingRange().

Referenced by CSeq_loc_Mapper::x_InitializeSeqMap().

◆ x_InitializeSeqMapUp()

Definition at line 502 of file seq_loc_mapper.cpp.

References _ASSERT, eNa_strand_minus, eNa_strand_plus, eNa_strand_unknown, CSeqMap_CI::GetDepth(), CSeqMap_CI::GetLength(), CSeqMap_CI::GetPosition(), CSeqMap_CI::GetRefMinusStrand(), CSeqMap_CI::GetRefPosition(), CSeqMap_CI::GetRefSeqid(), CSeq_id_Handle::GetSeqId(), CConstRef< C, Locker >::Reset(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

Referenced by CSeq_loc_Mapper::x_InitializeSeqMap().

◆ x_InitSeq_entry() ◆ x_InitSparse() void CSeq_loc_Mapper_Base::x_InitSparse ( const CSparse_seg &  sparse, size_t  to_row  ) private

Definition at line 2139 of file seq_loc_mapper_base.cpp.

References _ASSERT, eNa_strand_unknown, ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Options::GetAlign_Sparse_ToSecond(), CSparse_seg_Base::GetRows(), CSeq_loc_Mapper_Base::GetSeqTypeById(), i, CSeq_loc_Mapper_Base::m_MapOptions, min(), row, Warning(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

Referenced by CSeq_loc_Mapper_Base::x_InitializeAlign().

◆ x_InitSpliced() [1/2]

Definition at line 1881 of file seq_loc_mapper_base.cpp.

References CSeq_loc_Mapper_Base::eSplicedRow_Gen, CSeq_loc_Mapper_Base::eSplicedRow_Prod, CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_id(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetProduct_id(), CSpliced_seg_Base::GetProduct_id(), CSpliced_exon_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_exon_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_id(), ITERATE, and CSeq_loc_Mapper_Base::x_IsSynonym().

Referenced by CSeq_loc_Mapper_Base::x_InitializeAlign().

◆ x_InitSpliced() [2/2]

Definition at line 2039 of file seq_loc_mapper_base.cpp.

References CProduct_pos::AsSeqPos(), eNa_strand_unknown, CSpliced_seg_Base::eProduct_type_protein, CSpliced_seg_Base::eProduct_type_transcript, ERR_POST_X, Error(), CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSplicedRow_Prod, CSpliced_seg_Base::GetExons(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_exon_Base::GetGenomic_id(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_exon_Base::GetGenomic_strand(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::GetProduct_end(), CSpliced_exon_Base::GetProduct_id(), CSpliced_seg_Base::GetProduct_id(), CSpliced_exon_Base::GetProduct_start(), CSpliced_exon_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_strand(), CSpliced_seg_Base::GetProduct_type(), CProduct_pos_Base::IsProtpos(), CSpliced_exon_Base::IsSetGenomic_id(), CSpliced_seg_Base::IsSetGenomic_id(), CSpliced_exon_Base::IsSetGenomic_strand(), CSpliced_seg_Base::IsSetGenomic_strand(), CSpliced_exon_Base::IsSetParts(), CSpliced_exon_Base::IsSetProduct_id(), CSpliced_seg_Base::IsSetProduct_id(), CSpliced_exon_Base::IsSetProduct_strand(), CSpliced_seg_Base::IsSetProduct_strand(), ITERATE, CSeq_loc_Mapper_Base::m_CurrentGroup, CSeq_loc_Mapper_Base::SetSeqTypeById(), CSeq_loc_Mapper_Base::x_IterateExonParts(), and CSeq_loc_Mapper_Base::x_NextMappingRange().

◆ x_IsSetMiscFlag() ◆ x_IsSetOption() bool CSeq_loc_Mapper_Options::x_IsSetOption ( int  opt ) const inlineprivate ◆ x_IsSynonym() ◆ x_IsUCSCRandomChr()

Definition at line 810 of file seq_loc_mapper.cpp.

References set< Key, Compare >::clear(), CGC_TypedSeqId_Base::e_External, CGC_TypedSeqId_Base::e_Genbank, CGC_TypedSeqId_Base::e_Private, CGC_TypedSeqId_Base::e_Refseq, CGC_TypedSeqId_Base::GetExternal(), CGC_TypedSeqId_Base::GetGenbank(), CGC_SeqIdAlias_Base::GetGi(), CSeq_id_Handle::GetHandle(), CGC_External_Seqid_Base::GetId(), CSeq_id_Base::GetLocal(), CGC_TypedSeqId_Base::GetPrivate(), CGC_TypedSeqId_Base::GetRefseq(), CGC_Sequence_Base::GetSeq_id(), CGC_Sequence_Base::GetSeq_id_synonyms(), CObject_id_Base::GetStr(), set< Key, Compare >::insert(), CGC_SeqIdAlias_Base::IsSetGi(), CGC_Sequence_Base::IsSetStructure(), ITERATE, CConstRef< C, Locker >::Reset(), s_IsLocalRandomChrId(), CSeq_id_Base::SetLocal(), CObject_id_Base::SetStr(), NStr::StartsWith(), and CGC_TypedSeqId_Base::Which().

Referenced by CSeq_loc_Mapper::x_InitGCSequence().

◆ x_IterateExonParts() ◆ x_Map_Fuzz() void CMappingRange::x_Map_Fuzz ( TFuzz &  fuzz ) const private

Definition at line 358 of file seq_loc_mapper_base.cpp.

References CSerialObject::Assign(), CMappingRange::CanMap(), CInt_fuzz_Base::e_Alt, CInt_fuzz_Base::e_Lim, CInt_fuzz_Base::e_Range, COpenRange< Position >::Empty(), eNa_strand_unknown, CInt_fuzz_Base::GetAlt(), COpenRange< TSeqPos >::GetEmpty(), CRange_Base::GetFrom(), CInt_fuzz_Base::GetLim(), CInt_fuzz_Base::GetRange(), CRange_Base::GetTo(), ITERATE, CMappingRange::m_Reverse, CMappingRange::Map_Pos(), CMappingRange::Map_Range(), CRef< C, Locker >::Reset(), CInt_fuzz_Base::SetAlt(), CInt_fuzz_Base::SetLim(), CInt_fuzz_Base::SetRange(), CInt_fuzz_Base::Which(), and CMappingRange::x_ReverseFuzzLim().

Referenced by CMappingRange::Map_Fuzz().

◆ x_Map_PackedInt_Element()

Definition at line 3230 of file seq_loc_mapper_base.cpp.

References eNa_strand_unknown, CSeq_loc_Mapper_Base::fKeepNonmapping, CSeq_id_Handle::GetHandle(), kEmptyFuzz, CSeq_loc_Mapper_Base::m_Partial, si, STRAND_TO_INDEX, CSeq_loc_Mapper_Base::x_IsSetMiscFlag(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_PushMappedRange(), and CSeq_loc_Mapper_Base::x_PushRangesToDstMix().

Referenced by CSeq_loc_Mapper_Base::x_MapSeq_loc().

◆ x_Map_PackedPnt_Element()

Definition at line 3269 of file seq_loc_mapper_base.cpp.

References eNa_strand_unknown, CSeq_loc_Mapper_Base::fKeepNonmapping, CPacked_seqpnt_Base::GetFuzz(), CSeq_id_Handle::GetHandle(), CPacked_seqpnt_Base::GetId(), CPacked_seqpnt_Base::GetStrand(), CPacked_seqpnt_Base::IsSetFuzz(), CPacked_seqpnt_Base::IsSetStrand(), kEmptyFuzz, CSeq_loc_Mapper_Base::m_Partial, STRAND_TO_INDEX, CSeq_loc_Mapper_Base::x_IsSetMiscFlag(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_PushMappedRange(), and CSeq_loc_Mapper_Base::x_PushRangesToDstMix().

Referenced by CSeq_loc_Mapper_Base::x_MapSeq_loc().

◆ x_MapInterval()

Definition at line 3134 of file seq_loc_mapper_base.cpp.

References CMappingRanges::BeginMappingRanges(), COpenRange< Position >::Empty(), CRef< C, Locker >::Empty(), ERR_POST_X, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::eSeq_unknown, CRange_Base::GetFrom(), CSeq_id_Handle::GetHandle(), COpenRange< Position >::GetLength(), CGraphRanges::GetOffset(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CRange_Base::GetTo(), CGraphRanges::IncOffset(), IsReverse(), COpenRange< Position >::IsWhole(), kInvalidSeqPos, CMappingRange::m_Dst_from, CMappingRange::m_Dst_len, CMappingRange::m_Frame, CSeq_loc_Mapper_Base::m_GraphRanges, CSeq_loc_Mapper_Base::m_Mappings, CMappingRange::m_Reverse, CRange_Base::SetFrom(), CGraphRanges::SetOffset(), CRange_Base::SetTo(), ct::sort(), Warning(), CSeq_loc_Mapper_Base::x_GetPrimaryId(), CSeq_loc_Mapper_Base::x_MapNextRange(), and CSeq_loc_Mapper_Base::x_SetLastTruncated().

Referenced by CSeq_loc_Mapper_Base::x_Map_PackedInt_Element(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().

◆ x_MapNextRange()

Definition at line 2930 of file seq_loc_mapper_base.cpp.

References CGraphRanges::AddRange(), CSeq_id_Handle::AsString(), CMappingRange::CanMap(), CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, CInt_fuzz_Base::eLim_tl, CInt_fuzz_Base::eLim_tr, COpenRange< Position >::Empty(), CSeq_loc_Mapper_Base::fCheckStrand, CSeq_loc_Mapper_Base::fErrorOnPartial, CSeq_loc_Mapper_Base::fFuzzOption_CStyle, CSeq_loc_Mapper_Base::fFuzzOption_RemoveLimTlOrTr, CRange_Base::GetFrom(), COpenRange< Position >::GetLength(), CSeq_loc_Mapper_Base::GetNonMappingAsNull(), CRange_Base::GetTo(), CGraphRanges::IncOffset(), IsReverse(), COpenRange< Position >::IsWhole(), kInvalidSeqPos, CMappingRange::m_Dst_id_Handle, CSeq_loc_Mapper_Base::m_FuzzOption, CSeq_loc_Mapper_Base::m_GraphRanges, CMappingRange::m_Group, CSeq_loc_Mapper_Base::m_LastTruncated, CMappingRange::m_Reverse, CMappingRange::m_Src_from, CMappingRange::m_Src_id_Handle, CMappingRange::m_Src_to, CMappingRange::Map_Fuzz(), CMappingRange::Map_Range(), CMappingRange::Map_Strand(), NCBI_THROW, NStr::NumericToString(), COpenRange< Position >::Set(), CRange_Base::SetFrom(), COpenRange< Position >::SetLength(), COpenRange< Position >::SetOpen(), STRAND_TO_INDEX, CSeq_loc_Mapper_Base::x_IsSetMiscFlag(), CSeq_loc_Mapper_Base::x_PushMappedRange(), and CSeq_loc_Mapper_Base::x_PushSourceRange().

Referenced by CSeq_loc_Mapper_Base::x_MapInterval().

◆ x_MapSeq_align() ◆ x_MapSeq_loc() void CSeq_loc_Mapper_Base::x_MapSeq_loc ( const CSeq_loc &  src_loc ) protected

Definition at line 3308 of file seq_loc_mapper_base.cpp.

References _ASSERT, CSeq_loc::Assign(), CMappingRanges::BeginMappingRanges(), CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_Mapper_Base::eGapRemove, CInt_fuzz_Base::eLim_gt, eNa_strand_unknown, CSeq_loc_Mapper_Base::fFuzzOption_CStyle, CSeq_loc_Mapper_Base::fKeepNonmapping, CPacked_seqint_Base::Get(), CSeq_loc_equiv_Base::Get(), CSeq_loc_mix_Base::Get(), CSeq_bond_Base::GetA(), CSeq_bond_Base::GetB(), CSeq_loc_Base::GetBond(), CMappingRange::GetDstIdHandle(), COpenRange< TSeqPos >::GetEmpty(), CSeq_loc_Base::GetEmpty(), CSeq_loc_Base::GetEquiv(), CSeq_interval_Base::GetFrom(), COpenRange< Position >::GetFrom(), CSeq_point_Base::GetFuzz(), CSeq_interval_Base::GetFuzz_from(), CSeq_interval_Base::GetFuzz_to(), CSeq_id_Handle::GetHandle(), CSeq_interval_Base::GetId(), CSeq_point_Base::GetId(), CSeq_loc_Base::GetInt(), CSeq_loc_Base::GetMix(), CSeq_loc_Mapper_Base::GetNonMappingAsNull(), CSeq_loc_Base::GetPacked_int(), CSeq_loc_Base::GetPacked_pnt(), CSeq_loc_Base::GetPnt(), CSeq_point_Base::GetPoint(), CPacked_seqpnt_Base::GetPoints(), CSeq_loc_Mapper_Base::GetSequenceLength(), CSeq_interval_Base::GetStrand(), CSeq_point_Base::GetStrand(), CSeq_interval_Base::GetTo(), COpenRange< Position >::GetTo(), COpenRange< TSeqPos >::GetWhole(), CSeq_loc_Base::GetWhole(), CMappingRange::GoodSrcId(), i, CSeq_loc_Base::IsPnt(), CSeq_bond_Base::IsSetB(), CSeq_point_Base::IsSetFuzz(), CSeq_interval_Base::IsSetFuzz_from(), CSeq_interval_Base::IsSetFuzz_to(), CSeq_interval_Base::IsSetStrand(), CSeq_point_Base::IsSetStrand(), ITERATE, kEmptyFuzz, kInvalidSeqPos, CSeq_loc_Mapper_Base::m_Dst_loc, CSeq_loc_Mapper_Base::m_FuzzOption, CSeq_loc_Mapper_Base::m_GapFlag, CSeq_loc_Mapper_Base::m_LastTruncated, CSeq_loc_Mapper_Base::m_Mappings, CSeq_loc_Mapper_Base::m_Partial, NCBI_THROW, prev(), CRef< C, Locker >::Reset(), CSeq_loc_mix_Base::Set(), CSeq_bond_Base::SetA(), CSeq_bond_Base::SetB(), CSeq_loc::SetBond(), CSeq_loc::SetEquiv(), CSeq_loc::SetMix(), CSeq_loc::SetNull(), COpenRange< Position >::SetOpen(), CSeq_loc::SetPnt(), STRAND_TO_INDEX, CSeq_loc_Base::Which(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), CSeq_loc_Mapper_Base::x_GetPrimaryId(), CSeq_loc_Mapper_Base::x_IsSetMiscFlag(), CSeq_loc_Mapper_Base::x_Map_PackedInt_Element(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), CSeq_loc_Mapper_Base::x_MapInterval(), CSeq_loc_Mapper_Base::x_OptimizeSeq_loc(), CSeq_loc_Mapper_Base::x_PushLocToDstMix(), CSeq_loc_Mapper_Base::x_PushMappedRange(), CSeq_loc_Mapper_Base::x_PushNullLoc(), and CSeq_loc_Mapper_Base::x_PushRangesToDstMix().

Referenced by CSeq_loc_Mapper_Base::Map().

◆ x_NextMappingRange() 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  ) protected

Definition at line 2488 of file seq_loc_mapper_base.cpp.

References _ASSERT, CInt_fuzz_Base::eLim_gt, CInt_fuzz_Base::eLim_lt, eNa_strand_unknown, CSeq_loc_Mapper_Base::eSeq_nuc, CSeq_loc_Mapper_Base::eSeq_prot, CInt_fuzz_Base::GetLim(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CSeq_loc_Mapper_Base::GetSequenceLength(), CInt_fuzz_Base::IsLim(), IsReverse(), kInvalidSeqPos, and CSeq_loc_Mapper_Base::x_AddConversion().

Referenced by CSeq_loc_Mapper_Base::x_AddExonPartsMapping(), CSeq_loc_Mapper_Base::x_InitAlign(), CSeq_loc_Mapper::x_InitGCSequence(), CSeq_loc_Mapper_Base::x_InitializeLocs(), CSeq_loc_Mapper::x_InitializeSeqMapDown(), CSeq_loc_Mapper::x_InitializeSeqMapSingleLevel(), CSeq_loc_Mapper::x_InitializeSeqMapUp(), CSeq_loc_Mapper_Base::x_InitSparse(), and CSeq_loc_Mapper_Base::x_InitSpliced().

◆ x_OptimizeSeq_loc() void CSeq_loc_Mapper_Base::x_OptimizeSeq_loc ( CRef< CSeq_loc > &  loc ) const private

Definition at line 2839 of file seq_loc_mapper_base.cpp.

References CSeq_loc_Base::e_Bond, CSeq_loc_Base::e_Empty, CSeq_loc_Base::e_Equiv, CSeq_loc_Base::e_Feat, CSeq_loc_Base::e_Int, CSeq_loc_Base::e_Mix, CSeq_loc_Base::e_not_set, CSeq_loc_Base::e_Null, CSeq_loc_Base::e_Packed_int, CSeq_loc_Base::e_Packed_pnt, CSeq_loc_Base::e_Pnt, CSeq_loc_Base::e_Whole, CSeq_loc_mix_Base::Get(), CSeq_loc_Base::GetMix(), CSeq_loc_Mapper_Base::GetNonMappingAsNull(), NCBI_THROW, NON_CONST_ITERATE, Ref(), CRef< C, Locker >::Reset(), CSeq_loc::SetMix(), CSeq_loc::SetNull(), CSeq_loc::SetPacked_int(), and CSeq_loc_Base::Which().

Referenced by CSeq_loc_Mapper_Base::Map(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().

◆ x_ParseGCAssembly()

Definition at line 116 of file gc_assembly_parser.cpp.

References CGC_Assembly_Base::GetAssembly_set(), CGC_AssemblySet_Base::GetDesc(), CGC_AssemblyUnit_Base::GetDesc(), CGC_AssemblyUnit_Base::GetMols(), CGC_AssemblySet_Base::GetMore_assemblies(), CGC_AssemblyUnit_Base::GetOther_sequences(), CGC_AssemblySet_Base::GetPrimary_assembly(), CGC_Replicon_Base::C_Sequence::GetSet(), CGC_Replicon_Base::C_Sequence::GetSingle(), CGC_Assembly_Base::GetUnit(), CGC_Assembly_Base::IsAssembly_set(), CGC_AssemblySet_Base::IsSetDesc(), CGC_AssemblyUnit_Base::IsSetDesc(), CGC_AssemblyUnit_Base::IsSetMols(), CGC_AssemblySet_Base::IsSetMore_assemblies(), CGC_AssemblyUnit_Base::IsSetOther_sequences(), CGC_Replicon_Base::C_Sequence::IsSingle(), CGC_Assembly_Base::IsUnit(), ITERATE, NULL, CGC_Assembly_Parser::x_CopyData(), CGC_Assembly_Parser::x_InitSeq_entry(), and CGC_Assembly_Parser::x_ParseGCSequence().

Referenced by CGC_Assembly_Parser::CGC_Assembly_Parser().

◆ x_ParseGCSequence()

Definition at line 169 of file gc_assembly_parser.cpp.

References CSerialObject::Assign(), delta(), desc_copy(), CGC_TypedSeqId_Base::e_External, CGC_TypedSeqId_Base::e_Genbank, CSeq_loc_Base::e_Int, CGC_TypedSeqId_Base::e_Private, CGC_TypedSeqId_Base::e_Refseq, CSeq_loc_Base::e_Whole, set< Key, Compare >::end(), CGC_TaggedSequences_Base::eState_placed, CGC_Assembly_Parser::fIgnoreAnnots, CGC_Assembly_Parser::fIgnoreDescr, CGC_Assembly_Parser::fIgnoreExternalIds, CGC_Assembly_Parser::fIgnoreLocalIds, set< Key, Compare >::find(), CDelta_ext_Base::Get(), CSeq_descr_Base::Get(), CGC_Sequence_Base::GetAnnot(), CGC_Sequence_Base::GetDescr(), CGC_TypedSeqId_Base::GetExternal(), CSeq_interval_Base::GetFrom(), CGC_TypedSeqId_Base::GetGenbank(), CGC_SeqIdAlias_Base::GetGi(), CGC_SeqIdAlias_Base::GetGpipe(), CSeq_id_Handle::GetHandle(), CGC_External_Seqid_Base::GetId(), CSeq_interval_Base::GetId(), CSeq_loc_Base::GetInt(), CGC_TypedSeqId_Base::GetPrivate(), CGC_SeqIdAlias_Base::GetPublic(), CGC_TypedSeqId_Base::GetRefseq(), CGC_Sequence_Base::GetSeq_id(), CGC_Sequence_Base::GetSeq_id_synonyms(), CGC_TaggedSequences_Base::GetSeqs(), CGC_Sequence_Base::GetSequences(), CGC_Sequence_Base::GetStructure(), CSeq_loc_Base::GetWhole(), set< Key, Compare >::insert(), CSeq_id_Base::IsLocal(), CGC_Sequence_Base::IsSetAnnot(), CGC_Sequence_Base::IsSetDescr(), CGC_SeqIdAlias_Base::IsSetGi(), CGC_SeqIdAlias_Base::IsSetGpipe(), CGC_Sequence_Base::IsSetSeq_id_synonyms(), CGC_Sequence_Base::IsSetSequences(), CGC_Sequence_Base::IsSetStructure(), ITERATE, CGC_Assembly_Parser::m_Flags, CGC_Assembly_Parser::m_TopSeqs, NCBI_THROW, CRef< C, Locker >::Reset(), CSeq_entry::SetAnnot(), CSeq_entry::SetDescr(), CGC_TypedSeqId_Base::Which(), CSeq_loc_Base::Which(), CGC_Assembly_Parser::x_AddBioseq(), and CGC_Assembly_Parser::x_InitSeq_entry().

Referenced by CGC_Assembly_Parser::x_ParseGCAssembly().

◆ x_PreserveDestinationLocs() void CSeq_loc_Mapper_Base::x_PreserveDestinationLocs ( void  ) protected ◆ x_PushLocToDstMix() void CSeq_loc_Mapper_Base::x_PushLocToDstMix ( CRef< CSeq_loc >  loc ) private

Definition at line 3984 of file seq_loc_mapper_base.cpp.

References _ASSERT, CSeq_loc_Mapper_Base::eGapRemove, CSeq_loc_Base::IsMix(), CSeq_loc_Base::IsNull(), CSeq_loc_Mapper_Base::m_Dst_loc, CSeq_loc_Mapper_Base::m_GapFlag, CRef< C, Locker >::Reset(), CSeq_loc::SetMix(), and tmp.

Referenced by CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_PushNullLoc(), and CSeq_loc_Mapper_Base::x_PushRangesToDstMix().

◆ x_PushMappedRange()

Definition at line 3803 of file seq_loc_mapper_base.cpp.

References map_checker< Container >::begin(), CSeq_loc_Mapper_Base::eMergeAbutting, CSeq_loc_Mapper_Base::eMergeAll, CSeq_loc_Mapper_Base::eMergeBySeg, CSeq_loc_Mapper_Base::eMergeContained, CSeq_loc_Mapper_Base::eMergeNone, map_checker< Container >::end(), CSeq_loc_Mapper_Base::fIncludeSrcLocs, CSeq_loc_Mapper_Base::SMappedRange::fuzz, CRange_Base::GetFrom(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), CSeq_loc_Mapper_Base::SMappedRange::group, INDEX_TO_STRAND, IsReverse(), CSeq_loc_Mapper_Base::m_MappedLocs, CSeq_loc_Mapper_Base::m_MergeFlag, NCBI_THROW, CSeq_loc_Mapper_Base::SMappedRange::range, CRange_Base::SetFrom(), CRange_Base::SetTo(), CSeq_loc_Mapper_Base::x_GetMappedRanges(), CSeq_loc_Mapper_Base::x_IsSetMiscFlag(), and CSeq_loc_Mapper_Base::x_PushRangesToDstMix().

Referenced by CSeq_loc_Mapper_Base::x_Map_PackedInt_Element(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), CSeq_loc_Mapper_Base::x_MapNextRange(), and CSeq_loc_Mapper_Base::x_MapSeq_loc().

◆ x_PushNullLoc() void CSeq_loc_Mapper_Base::x_PushNullLoc ( void  ) private ◆ x_PushRangesToDstMix() void CSeq_loc_Mapper_Base::x_PushRangesToDstMix ( void  ) protected

Definition at line 3962 of file seq_loc_mapper_base.cpp.

References CSeq_loc_Base::IsNull(), CSeq_loc_Mapper_Base::m_Dst_loc, CSeq_loc_Mapper_Base::m_MappedLocs, map_checker< Container >::size(), CSeq_loc_Mapper_Base::x_GetMappedSeq_loc(), and CSeq_loc_Mapper_Base::x_PushLocToDstMix().

Referenced by CSeq_loc_Mapper_Base::Map(), CSeq_loc_Mapper_Base::x_Map_PackedInt_Element(), CSeq_loc_Mapper_Base::x_Map_PackedPnt_Element(), CSeq_loc_Mapper_Base::x_MapSeq_loc(), CSeq_loc_Mapper_Base::x_PushMappedRange(), CSeq_loc_Mapper_Base::x_PushNullLoc(), and CSeq_loc_Mapper_Base::x_SetLastTruncated().

◆ x_PushSourceRange()

Definition at line 3917 of file seq_loc_mapper_base.cpp.

References COpenRange< Position >::Empty(), eNa_strand_unknown, CSeq_loc_Mapper_Base::eSeq_prot, CSeq_loc_Mapper_Base::fIncludeSrcLocs, CRange_Base::GetFrom(), CSeq_id_Handle::GetSeqId(), CSeq_loc_Mapper_Base::GetSeqTypeById(), CRange_Base::GetTo(), INDEX_TO_STRAND, COpenRange< Position >::IsWhole(), CSeq_loc_Mapper_Base::m_SrcLocs, CRef< C, Locker >::Reset(), SameOrientation(), CSeq_loc::SetEmpty(), CSeq_loc::SetInt(), CSeq_loc::SetMix(), CSeq_loc::SetStrand(), CSeq_loc::SetWhole(), and CSeq_loc_Mapper_Base::x_IsSetMiscFlag().

Referenced by CSeq_loc_Mapper_Base::x_MapNextRange().

◆ x_RangeToSeq_loc() ◆ x_RegisterLoader()

Definition at line 476 of file object_manager.cpp.

References _ASSERT, _VERIFY, CObjectManager::CDataSource, CObjectManager::eDefault, map_checker< Container >::end(), ERR_POST_X, map_checker< Container >::find(), CDataLoader::GetName(), map_checker< Container >::insert(), set< Key, Compare >::insert(), CObjectManager::kPriority_Default, CObjectManager::m_mapNameToLoader, CObjectManager::m_mapToSource, CObjectManager::m_setDefaultSource, NCBI_THROW, rapidjson::source, and Warning().

Referenced by CObjectManager::AcquireDataLoader(), and CObjectManager::RegisterDataLoader().

◆ x_ReverseFuzzLim() ◆ x_ReverseRangeOrder() bool CSeq_loc_Mapper_Base::x_ReverseRangeOrder ( int  str ) const private ◆ x_RevokeDataLoader()

Definition at line 269 of file object_manager.cpp.

References _ASSERT, _VERIFY, map_checker< Container >::end(), map_checker< Container >::erase(), set< Key, Compare >::erase(), ERR_POST_X, map_checker< Container >::find(), CDataLoader::GetName(), set< Key, Compare >::insert(), CObjectManager::m_mapNameToLoader, CObjectManager::m_mapToSource, and CObjectManager::m_setDefaultSource.

Referenced by CObjectManager::RevokeDataLoader().

◆ x_SetLastTruncated() void CSeq_loc_Mapper_Base::x_SetLastTruncated ( void  ) private

Definition at line 3102 of file seq_loc_mapper_base.cpp.

References eExtreme_Biological, CSeq_loc_Mapper_Base::fFuzzOption_RemoveLimTlOrTr, CSeq_loc_Mapper_Base::fKeepNonmapping, CSeq_loc_Mapper_Base::GetNonMappingAsNull(), CSeq_loc::IsPartialStop(), CSeq_loc_Mapper_Base::m_Dst_loc, CSeq_loc_Mapper_Base::m_FuzzOption, CSeq_loc_Mapper_Base::m_LastTruncated, CSeq_loc::SetPartialStop(), CSeq_loc::SetTruncatedStop(), CSeq_loc_Mapper_Base::x_IsSetMiscFlag(), CSeq_loc_Mapper_Base::x_PushNullLoc(), and CSeq_loc_Mapper_Base::x_PushRangesToDstMix().

Referenced by CSeq_loc_Mapper_Base::x_MapInterval().

◆ x_SetMiscFlag() void CSeq_loc_Mapper_Base::x_SetMiscFlag ( EMiscFlags  flag, bool  value  ) private ◆ x_SetOption() void CSeq_loc_Mapper_Options::x_SetOption ( int  opt, bool  enable  ) inlineprivate ◆ x_StripExtraneousFuzz() void CSeq_loc_Mapper_Base::x_StripExtraneousFuzz ( CRef< CSeq_loc > &  loc ) const private

Definition at line 2738 of file seq_loc_mapper_base.cpp.

References CSeq_loc::Add(), CSeq_loc::Assign(), CSeq_loc_CI::eEmpty_Allow, eExtreme_Biological, CSeq_loc::end(), CSeq_loc_CI::GetRangeAsSeq_loc(), CSeq_loc::IsPartialStart(), CSeq_loc::IsPartialStop(), CSeq_loc::SetPartialStart(), CSeq_loc::SetPartialStop(), and CSeq_loc_Mapper_Base::x_FixNonsenseFuzz().

Referenced by CSeq_loc_Mapper_Base::Map().

◆ ~CBlobId() ◆ ~CBlobStateException() virtual CBlobStateException::~CBlobStateException ( void  ) inlinevirtualnoexcept

Definition at line 184 of file objmgr_exception.hpp.

◆ ~CDataLoader() CDataLoader::~CDataLoader ( void  ) virtual

Definition at line 80 of file data_loader.cpp.

◆ ~CGC_Assembly_Parser() ◆ ~CLoaderMaker_Base() virtual CLoaderMaker_Base::~CLoaderMaker_Base ( void  ) inlinevirtual

Definition at line 110 of file data_loader.hpp.

◆ ~CObjectManager() CObjectManager::~CObjectManager ( void  ) virtual

Definition at line 117 of file object_manager.cpp.

References _ASSERT, map_checker< Container >::begin(), set< Key, Compare >::begin(), set< Key, Compare >::clear(), map_checker< Container >::empty(), set< Key, Compare >::empty(), map_checker< Container >::erase(), ERR_POST_X, CObjectManager::m_mapToSource, CObjectManager::m_OM_Lock, CObjectManager::m_setDefaultSource, CObjectManager::m_setScope, and CObject::ReferencedOnlyOnce().

◆ ~CParamLoaderMaker()

template<class TDataLoader , class TParam >

Definition at line 162 of file data_loader.hpp.

◆ ~CPrefetchManager() ◆ ~CPrefetchManager_Impl() ◆ ~CPrefetchRequest() ◆ ~CPrefetchSequence() CPrefetchSequence::~CPrefetchSequence ( void  ) ◆ ~CPrefetchTokenOld() CPrefetchTokenOld::~CPrefetchTokenOld ( void  ) inline ◆ ~CScope() ◆ ~CSeq_loc_Mapper() ◆ ~CSeq_loc_Mapper_Base() ◆ ~CSeq_loc_Mapper_Message() ◆ ~CSimpleLoaderMaker() ◆ ~IDataLoaderFilter() CObjectManager::IDataLoaderFilter::~IDataLoaderFilter ( ) virtual

Definition at line 247 of file object_manager.cpp.

◆ ~IPrefetchAction() ◆ ~IPrefetchActionSource() IPrefetchActionSource::~IPrefetchActionSource ( void  ) virtual

Definition at line 50 of file prefetch_manager.cpp.

◆ ~IPrefetchListener() ◆ ~ISeq_idSource() ◆ acc_ver ◆ fuzz TRangeFuzz CSeq_loc_Mapper_Base::SMappedRange::fuzz ◆ gi TGi CDataLoader::SGiFound::gi ◆ group int CSeq_loc_Mapper_Base::SMappedRange::group ◆ hash int CDataLoader::SHashFound::hash ◆ hash_known bool CDataLoader::SHashFound::hash_known ◆ m_Action ◆ m_ActiveTokens ◆ m_AllSeqs TSeqIds CGC_Assembly_Parser::m_AllSeqs private ◆ m_AnnotBlobType ◆ m_BaseScope ◆ m_BlobState ◆ m_Container

template<class Container >

◆ m_Created ◆ m_CurrentGroup int CSeq_loc_Mapper_Base::m_CurrentGroup protected ◆ m_DataSource ◆ m_Dst_from ◆ m_Dst_id_Handle ◆ m_Dst_len ◆ m_Dst_loc ◆ m_Dst_strand ◆ m_DstRanges ◆ m_ExtTo bool CMappingRange::m_ExtTo private ◆ m_FailedCall string CLoaderException::m_FailedCall private ◆ m_Flags ◆ m_Frame int CMappingRange::m_Frame private ◆ m_FuzzOption ◆ m_GapFlag ◆ m_GraphRanges ◆ m_Group int CMappingRange::m_Group private ◆ m_Handle ◆ m_HeapScope ◆ m_Id ◆ m_IdMap TIdMap CMappingRanges::m_IdMap private ◆ m_Ids [1/2] ◆ m_Ids [2/2] ◆ m_Impl [1/3] ◆ m_Impl [2/3] ◆ m_Impl [3/3]

Definition at line 717 of file scope.hpp.

Referenced by CScope::AddBioseq(), CScope::AddDataLoader(), CScope::AddDefaults(), CScope::AddScope(), CScope::AddSeq_annot(), CScope::AddSeq_submit(), CScope::AddTopLevelSeqEntry(), CScope::Exists(), CScope::GetAccVer(), CScope::GetAllTSEs(), CScope::GetBioseq_setEditHandle(), CScope::GetBioseq_setHandle(), CScope::GetBioseqEditHandle(), CScope::GetBioseqHandle(), CScope::GetBioseqHandleFromTSE(), CScope::GetBioseqHandles(), CScope::GetBioseqHandlesFromTSE(), CScope::GetCDDAnnots(), CScope::GetEditHandle(), CScope::GetGi(), CScope::GetIds(), CScope::GetImpl(), CHeapScope::GetImpl(), CScope::GetKeepExternalAnnotsForEdit(), CScope::GetLabel(), CScope::GetObjectManager(), CScope::GetSeq_annotEditHandle(), CScope::GetSeq_annotHandle(), CScope::GetSeq_entryEditHandle(), CScope::GetSeq_entryHandle(), CScope::GetSeq_featHandle(), CScope::GetSequenceHash(), CScope::GetSequenceLength(), CScope::GetSequenceState(), CScope::GetSequenceType(), CScope::GetSynonyms(), CScope::GetTaxId(), CScope::IsSameBioseq(), CScope::RemoveBioseq(), CScope::RemoveDataLoader(), CScope::RemoveFromHistory(), CScope::RemoveSeq_annot(), CScope::RemoveTopLevelSeqEntry(), CScope::ResetDataAndHistory(), CScope::ResetHistory(), CScope::SetKeepExternalAnnotsForEdit(), CScope::UpdateAnnotIndex(), and CScope::~CScope().

◆ m_Iterator

template<class Container >

◆ m_LastTruncated bool CSeq_loc_Mapper_Base::m_LastTruncated protected ◆ m_LengthMap ◆ m_Listener ◆ m_Loader ◆ m_Loc ◆ m_Manager ◆ m_mapNameToLoader ◆ m_MapOptions ◆ m_MappedLocs ◆ m_Mappings ◆ m_mapToSource

Definition at line 264 of file object_manager.hpp.

Referenced by CObjectManager::AcquireSharedBioseq(), CObjectManager::AcquireSharedSeq_annot(), CObjectManager::AcquireSharedSeq_entry(), CObjectManager::ReleaseDataSource(), CObjectManager::RevokeAllDataLoaders(), CObjectManager::RevokeDataLoaders(), CObjectManager::SetLoaderOptions(), CObjectManager::x_FindDataSource(), CObjectManager::x_RegisterLoader(), CObjectManager::x_RevokeDataLoader(), and CObjectManager::~CObjectManager().

◆ m_MergeFlag ◆ m_MiscFlags ◆ m_Mutex CMutex CPrefetchSequence::m_Mutex private ◆ m_Name [1/2] string CLoaderMaker_Base::m_Name protected ◆ m_Name [2/2] ◆ m_NeedAnnots ◆ m_NeedSeqData TRange SRequestDetails::m_NeedSeqData ◆ m_NeedSeqMap TRange SRequestDetails::m_NeedSeqMap ◆ m_Obj ◆ m_ObjType ◆ m_Offset ◆ m_OM_Lock

Definition at line 271 of file object_manager.hpp.

Referenced by CObjectManager::AcquireDataLoader(), CObjectManager::AcquireDefaultDataSources(), CObjectManager::AcquireSharedBioseq(), CObjectManager::AcquireSharedSeq_annot(), CObjectManager::AcquireSharedSeq_entry(), CObjectManager::FindDataLoader(), CObjectManager::GetRegisteredNames(), CObjectManager::RegisterDataLoader(), CObjectManager::ReleaseDataSource(), CObjectManager::RevokeAllDataLoaders(), CObjectManager::RevokeDataLoader(), CObjectManager::RevokeDataLoaders(), CObjectManager::SetLoaderOptions(), CObjectManager::x_GetPluginManager(), and CObjectManager::~CObjectManager().

◆ m_OM_ScopeLock TRWLock CObjectManager::m_OM_ScopeLock mutableprivate ◆ m_Options ◆ m_Param

template<class TDataLoader , class TParam >

◆ m_Partial bool CSeq_loc_Mapper_Base::m_Partial protected ◆ m_PluginManager ◆ m_Progress ◆ m_Range ◆ m_Ranges ◆ m_RegisterInfo ◆ m_Result [1/4] ◆ m_Result [2/4] ◆ m_Result [3/4] ◆ m_Result [4/4] ◆ m_Reverse bool CMappingRange::m_Reverse private ◆ m_ReverseDst bool CMappingRanges::m_ReverseDst private ◆ m_ReverseSrc bool CMappingRanges::m_ReverseSrc private ◆ m_Scope [1/4] ◆ m_Scope [2/4] ◆ m_Scope [3/4] ◆ m_Scope [4/4] ◆ m_Selector [1/2] ◆ m_Selector [2/2] ◆ m_Seq_id ◆ m_Seq_id_Mapper ◆ m_SeqInfo ◆ m_SeqTypes ◆ m_setDefaultSource ◆ m_setScope ◆ m_Source ◆ m_Src_bioseq_len TSeqPos CMappingRange::m_Src_bioseq_len private ◆ m_Src_from ◆ m_Src_id_Handle ◆ m_Src_strand ◆ m_Src_to ◆ m_SrcLocs ◆ m_StateMutex [1/2] ◆ m_StateMutex [2/2] ◆ m_Strand ◆ m_SynonymMap ◆ m_ThreadPool ◆ m_TopSeqs TSeqIds CGC_Assembly_Parser::m_TopSeqs private ◆ m_TotalRange TRange CGraphRanges::m_TotalRange private ◆ m_TSE ◆ m_Value

template<typename Value , class Converter = PConvertToString<Value>>

◆ range TRange CSeq_loc_Mapper_Base::SMappedRange::range ◆ sequence_found [1/4] bool CDataLoader::SAccVerFound::sequence_found ◆ sequence_found [2/4] bool CDataLoader::SGiFound::sequence_found ◆ sequence_found [3/4] bool CDataLoader::STypeFound::sequence_found ◆ sequence_found [4/4] bool CDataLoader::SHashFound::sequence_found ◆ type ◆ CAnnot_Collector ◆ CBioseq_CI ◆ CDataLoader ◆ CDataSource ◆ CGBReaderRequestResult ◆ CHeapScope ◆ CMappingRangeRef_Less ◆ CMappingRangeRef_LessRev ◆ CMappingRanges ◆ CObjectManager [1/2] ◆ CObjectManager [2/2] ◆ CPrefetchManager [1/2] ◆ CPrefetchManager [2/2] ◆ CPrefetchManager_Impl ◆ CPrefetchRequest ◆ CPrefetchTokenOld_Impl ◆ CSafeStatic_Allocator< CObjectManager > ◆ CScope_Impl [1/2] ◆ CScope_Impl [2/2] ◆ CScopeTransaction ◆ CSeq_align_Mapper_Base [1/2] ◆ CSeq_align_Mapper_Base [2/2] ◆ CSeq_annot_CI ◆ CSeq_loc_Mapper_Base [1/2] ◆ CSeq_loc_Mapper_Base [2/2] ◆ CSeqMap_CI ◆ CTotalRangeSynonymMapper

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