#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:

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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)