1 #ifndef SEQANNOT_SPLICER_UTIL__HPP
2 #define SEQANNOT_SPLICER_UTIL__HPP
45 typedef ncbi::CRef<ncbi::objects::CSeq_id>
TSeqRef;
142 ncbi::COStreamContainer& osc);
ESerialDataFormat
Data file format.
Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.
std::istream & in(std::istream &in_, double &x_)
unsigned int TSeqAnnotChoiceMaskFlags
Binary OR of "ESeqAnnotChoiceMaskFlags".
@ fSIMF_Gpipe
Internal NCBI genome pipeline processing ID.
@ fSIMF_General
for other databases
@ fSIMF_Tpg
Third Party Annot/Seq Genbank.
@ fSIMF_Giim
Geninfo import id.
@ fSIMF_NotSet
No variant selected.
@ fSIMF_Gi
GenInfo Integrated Database.
@ fSIMF_Named_annot_track
Internal named annotation tracking ID.
@ fSIMF_Tpe
Third Party Annot/Seq EMBL.
@ fSIMF_Gibbsq
Geninfo backbone seqid.
@ fSIMF_Other
for historical reasons, 'other' = 'refseq'
@ fSIMF_Tpd
Third Party Annot/Seq DDBJ.
@ fSIMF_Gibbmt
Geninfo backbone moltype.
bool IsSeqIdChoiceSelected(TSeqIdChoiceMaskFlags flags)
void SetSeqIdChoiceMask(const std::string &mask)
ncbi::CRef< ncbi::objects::CSeq_id > TSeqRef
unsigned int TSeqIdChoiceMaskFlags
Binary OR of "ESeqIdChoiceMaskFlags".
void ProcessSeqEntryAnnot(std::unique_ptr< ncbi::CObjectIStream > &sai, ncbi::COStreamContainer &osc)
void CurrentContextContainsSeqAnnots(void)
void AddSeqIdToCurrentContext(ncbi::CRef< ncbi::objects::CSeq_id > id)
@ fSAMF_Ids
used for communication between tools
@ fSAMF_Locs
used for communication between tools
@ fSAMF_NotSet
No variant selected.
void SetSeqAnnotChoiceMask(const std::string &mask)
void ResetSeqEntryProcessing(void)
void SeqAnnotSet_Pre(ncbi::CObjectIStream &in)
void SeqAnnotMapSeqId(TSeqRef seqid)
void ContextStart(ncbi::CObjectIStream &in, EContextType type)
ncbi::ESerialDataFormat GetFormat(const std::string &name)
bool IsSeqAnnotChoiceSelected(TSeqAnnotChoiceMaskFlags flags)