NCBI C++ ToolKit
Classes | Macros | Functions
gff3_writer.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/seqset/Seq_entry.hpp>
#include <objects/seq/Seq_annot.hpp>
#include <objects/seq/Annot_descr.hpp>
#include <objects/seq/so_map.hpp>
#include <objects/seqfeat/Seq_feat.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/general/User_object.hpp>
#include <objects/general/User_field.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/seqfeat/Feat_id.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/seqfeat/RNA_ref.hpp>
#include <objects/seqfeat/RNA_gen.hpp>
#include <objects/seqfeat/Trna_ext.hpp>
#include <objects/seqfeat/Cdregion.hpp>
#include <objects/seqfeat/Imp_feat.hpp>
#include <objects/seqfeat/Genetic_code.hpp>
#include <objects/seqfeat/Code_break.hpp>
#include <objects/seqfeat/SeqFeatXref.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgName.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objects/seqalign/Spliced_seg.hpp>
#include <objects/seqalign/Spliced_exon.hpp>
#include <objects/seqalign/Spliced_exon_chunk.hpp>
#include <objects/seqalign/Product_pos.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/annot_ci.hpp>
#include <objmgr/align_ci.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/mapped_feat.hpp>
#include <objmgr/util/feature.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/util/feature_edit.hpp>
#include <objmgr/util/weight.hpp>
#include <objtools/writers/writer_exception.hpp>
#include <objtools/writers/write_util.hpp>
#include <objects/seqalign/Score_set.hpp>
#include <objtools/writers/gff3_writer.hpp>
#include <objtools/writers/genbank_id_resolve.hpp>
#include <array>
#include <sstream>
+ Include dependency graph for gff3_writer.cpp:

Go to the source code of this file.

Go to the SVN repository for this file.

Classes

struct  SCompareAlignments
 

Macros

#define IS_INSERTION(sf, tf)    ( ((sf) & CAlnMap::fSeq) && !((tf) & CAlnMap::fSeq) )
 
#define IS_DELETION(sf, tf)    ( !((sf) & CAlnMap::fSeq) && ((tf) & CAlnMap::fSeq) )
 
#define IS_MATCH(sf, tf)    ( ((sf) & CAlnMap::fSeq) && ((tf) & CAlnMap::fSeq) )
 

Functions

 USING_SCOPE (objects)
 
void sGetWrapInfo (const list< CRef< CSeq_interval > > &subInts, CGffFeatureContext &fc, unsigned int &wrapSize, unsigned int &wrapPoint)
 
bool sInheritScores (const CSeq_align &alignFrom, CSeq_align &alignTo)
 
string sBestMatchType (const CSeq_id &source)
 
string s_GetAlignID (const CSeq_align &align)
 
bool s_RangeContains (const CRange< TSeqPos > &range, const TSeqPos pos)
 
bool sGetMethodFromModelEvidence (const CMappedFeat &mf, string &method)
 

Macro Definition Documentation

◆ IS_DELETION

#define IS_DELETION (   sf,
  tf 
)     ( !((sf) & CAlnMap::fSeq) && ((tf) & CAlnMap::fSeq) )

Definition at line 89 of file gff3_writer.cpp.

◆ IS_INSERTION

#define IS_INSERTION (   sf,
  tf 
)     ( ((sf) & CAlnMap::fSeq) && !((tf) & CAlnMap::fSeq) )

Definition at line 87 of file gff3_writer.cpp.

◆ IS_MATCH

#define IS_MATCH (   sf,
  tf 
)     ( ((sf) & CAlnMap::fSeq) && ((tf) & CAlnMap::fSeq) )

Definition at line 91 of file gff3_writer.cpp.

Function Documentation

◆ s_GetAlignID()

string s_GetAlignID ( const CSeq_align align)

◆ s_RangeContains()

bool s_RangeContains ( const CRange< TSeqPos > &  range,
const TSeqPos  pos 
)

Definition at line 1219 of file gff3_writer.cpp.

References compile_time_bits::range().

◆ sBestMatchType()

string sBestMatchType ( const CSeq_id source)

◆ sGetMethodFromModelEvidence()

bool sGetMethodFromModelEvidence ( const CMappedFeat mf,
string method 
)

◆ sGetWrapInfo()

void sGetWrapInfo ( const list< CRef< CSeq_interval > > &  subInts,
CGffFeatureContext fc,
unsigned int wrapSize,
unsigned int wrapPoint 
)

◆ sInheritScores()

bool sInheritScores ( const CSeq_align alignFrom,
CSeq_align alignTo 
)

◆ USING_SCOPE()

USING_SCOPE ( objects  )
Modified on Wed May 22 11:29:58 2024 by modify_doxy.py rev. 669887