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NCBI C++ ToolKit: src/sample/app/serial/seqannot_splicer_util.hpp File Reference

#include <list>
#include <corelib/ncbiobj.hpp>

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enum   EContextType { eNotSet , eBioseq_set , eBioseq }   enum   ESeqAnnotChoiceMaskFlags {
  fSAMF_NotSet = 0 , fSAMF_Ftable = (1 << 0) , fSAMF_Align = (1 << 1) , fSAMF_Graph = (1 << 2) ,
  fSAMF_Ids = (1 << 3) , fSAMF_Locs = (1 << 4) , fSAMF_Seq_table = (1 << 5) , fSAMF_All = (1 << 6) - 1 ,
  fSAMF_AllButSeq_table = fSAMF_All & ~fSAMF_Seq_table , fSAMF_Default = fSAMF_AllButSeq_table
}   enum   ESeqIdChoiceMaskFlags {
  fSIMF_NotSet = 0 , fSIMF_Local = (1 << 0) , fSIMF_Gibbsq = (1 << 1) , fSIMF_Gibbmt = (1 << 2) ,
  fSIMF_Giim = (1 << 3) , fSIMF_Genbank = (1 << 4) , fSIMF_Embl = (1 << 5) , fSIMF_Pir = (1 << 6) ,
  fSIMF_Swissprot = (1 << 7) , fSIMF_Patent = (1 << 8) , fSIMF_Other = (1 << 9) , fSIMF_General = (1 << 10) ,
  fSIMF_Gi = (1 << 11) , fSIMF_Ddbj = (1 << 12) , fSIMF_Prf = (1 << 13) , fSIMF_Pdb = (1 << 14) ,
  fSIMF_Tpg = (1 << 15) , fSIMF_Tpe = (1 << 16) , fSIMF_Tpd = (1 << 17) , fSIMF_Gpipe = (1 << 18) ,
  fSIMF_Named_annot_track = (1 << 19) , fSIMF_All = (1 << 20) - 1 , fSIMF_AllButLocal = fSIMF_All & ~fSIMF_Local , fSIMF_Default = fSIMF_All
}   ◆ TSeqAnnotChoiceMaskFlags ◆ TSeqIdChoiceMaskFlags ◆ TSeqRef ◆ EContextType ◆ ESeqAnnotChoiceMaskFlags Enumerator fSAMF_NotSet 

No variant selected.

fSAMF_Ftable  fSAMF_Align  fSAMF_Graph  fSAMF_Ids 

used for communication between tools

fSAMF_Locs 

used for communication between tools

fSAMF_Seq_table  fSAMF_All  fSAMF_AllButSeq_table  fSAMF_Default 

Definition at line 65 of file seqannot_splicer_util.hpp.

◆ ESeqIdChoiceMaskFlags Enumerator fSIMF_NotSet 

No variant selected.

fSIMF_Local 

local use

fSIMF_Gibbsq 

Geninfo backbone seqid.

fSIMF_Gibbmt 

Geninfo backbone moltype.

fSIMF_Giim 

Geninfo import id.

fSIMF_Genbank  fSIMF_Embl  fSIMF_Pir  fSIMF_Swissprot  fSIMF_Patent  fSIMF_Other 

for historical reasons, 'other' = 'refseq'

fSIMF_General 

for other databases

fSIMF_Gi 

GenInfo Integrated Database.

fSIMF_Ddbj  fSIMF_Prf 

PRF SEQDB.

fSIMF_Pdb 

PDB sequence.

fSIMF_Tpg 

Third Party Annot/Seq Genbank.

fSIMF_Tpe 

Third Party Annot/Seq EMBL.

fSIMF_Tpd 

Third Party Annot/Seq DDBJ.

fSIMF_Gpipe 

Internal NCBI genome pipeline processing ID.

fSIMF_Named_annot_track 

Internal named annotation tracking ID.

fSIMF_All  fSIMF_AllButLocal  fSIMF_Default 

Definition at line 89 of file seqannot_splicer_util.hpp.

◆ AddSeqIdToCurrentContext() void AddSeqIdToCurrentContext ( ncbi::CRef< ncbi::objects::CSeq_id >  id ) ◆ ContextEnd() ◆ ContextEnter() void ContextEnter ( void  ) ◆ ContextInit() void ContextInit ( void  ) ◆ ContextLeave() void ContextLeave ( void  ) ◆ ContextStart() void ContextStart ( ncbi::CObjectIStream &  in, EContextType  type  ) ◆ CurrentContextContainsSeqAnnots() void CurrentContextContainsSeqAnnots ( void  ) ◆ GetFormat() ◆ IsSeqAnnotChoiceSelected() [1/2] bool IsSeqAnnotChoiceSelected ( const ncbi::objects::CSeq_annot *  annot ) ◆ IsSeqAnnotChoiceSelected() [2/2] ◆ IsSeqIdChoiceSelected() [1/2] bool IsSeqIdChoiceSelected ( const ncbi::objects::CSeq_id *  seqid ) ◆ IsSeqIdChoiceSelected() [2/2] ◆ ProcessSeqEntryAnnot() void ProcessSeqEntryAnnot ( std::unique_ptr< ncbi::CObjectIStream > &  sai, ncbi::COStreamContainer &  osc  ) ◆ ResetSeqEntryProcessing() void ResetSeqEntryProcessing ( void  ) ◆ SeqAnnotMapSeqId() void SeqAnnotMapSeqId ( TSeqRef  seqid ) ◆ SeqAnnotSet_Pre() void SeqAnnotSet_Pre ( ncbi::CObjectIStream &  in ) ◆ SetSeqAnnotChoiceMask() [1/2] ◆ SetSeqAnnotChoiceMask() [2/2] ◆ SetSeqIdChoiceMask() [1/2] ◆ SetSeqIdChoiceMask() [2/2]

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