NCBI C++ Toolkit Cross Reference

  C++/include/objtools/readers/gff_reader.hpp


#ifndef OBJTOOLS_READERS___GFF_READER__HPP #define OBJTOOLS_READERS___GFF_READER__HPP /* $Id: gff_reader.hpp 67312 2015-05-07 14:26:38Z foleyjp $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Authors: Aaron Ucko, Wratko Hlavina * */ /// @file gff_reader.hpp /// Reader for GFF (including GTF) files. /// /// These formats are somewhat loosely defined, so the reader allows /// heavy use-specific tuning, both via flags and via virtual methods. /// /// URLs to relevant specifications: /// www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml (GFF 2) /// genes.cs.wustl.edu/GTF2.html /// song.sourceforge.net/gff3-jan04.shtml (support incomplete) #include <corelib/ncbiutil.hpp> #include <util/range_coll.hpp> #include <objects/seq/Bioseq.hpp> #include <objects/seqalign/Seq_align.hpp> #include <objects/seqfeat/Seq_feat.hpp> #include <objects/seqloc/Seq_id.hpp> #include <objects/seqloc/Seq_loc.hpp> #include <objects/seqset/Seq_entry.hpp> #include <objtools/readers/reader_exception.hpp> #include <set> BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) /** @addtogroup Miscellaneous * * @{ */ class NCBI_XOBJREAD_EXPORT CGFFReader { public: enum EFlags { ///< don't honor/recognize GTF conventions fNoGTF = 0x01, ///< attribute tags are GenBank qualifiers fGBQuals = 0x02, ///< merge exons with the same transcript_id fMergeExons = 0x04, ///< restrict merging to just CDS and mRNA features fMergeOnyCdsMrna = 0x08, ///< move protein_id and transcript_id to products for mRNA and CDS ///< features fSetProducts = 0x10, ///< create gene features for mRNAs and CDSs if none exist already fCreateGeneFeats = 0x20, ///< numeric identifiers are local IDs fNumericIdsAsLocal = 0x40, ///< all identifiers are local IDs fAllIdsAsLocal = 0x80, ///< all identifiers are local IDs fSetVersion3 = 0x100, fDefaults = 0 }; typedef int TFlags; CGFFReader() { m_Flags = 0; }; virtual ~CGFFReader() { } CRef<CSeq_entry> Read(CNcbiIstream& in, TFlags flags = fDefaults); CRef<CSeq_entry> Read(ILineReader& in, TFlags flags = fDefaults); struct NCBI_XOBJREAD_EXPORT SRecord : public CObject { struct SSubLoc { string accession; ENa_strand strand; /// the set of ranges that make up this location /// this allows us to separately assign frame even if the ranges in /// question do not appear in the correct order set<TSeqRange> ranges; /// a subsidiary set of ranges that is merged into ranges after /// parsing. this is used to account for things like start/stop /// codons, that are CDS intervals and should be merged into CDS /// intervals set<TSeqRange> merge_ranges; }; typedef set<vector<string> > TAttrs; typedef vector<SSubLoc> TLoc; enum EType { eFeat, eAlign }; TLoc loc; ///< from accession, start, stop, strand string source; string key; string score; TAttrs attrs; int frame; unsigned int line_no; EType type; // gff3 specific properties string id; string parent; string name; TAttrs::const_iterator FindAttribute(const string& att_name, size_t min_values = 1) const; }; protected: typedef map<string, CRef<CSeq_id>, PNocase> TSeqNameCache; typedef map<CConstRef<CSeq_id>, CRef<CBioseq>, PPtrLess<CConstRef<CSeq_id> > > TSeqCache; typedef map<string, CRef<SRecord>, PNocase> TDelayedRecords; typedef map<string, CRef<CGene_ref> > TGeneRefs; typedef CTempString TStr; typedef vector<TStr> TStrVec; virtual void x_Info(const string& message, unsigned int line = 0); virtual void x_Warn(const string& message, unsigned int line = 0); virtual void x_Error(const string& message, unsigned int line = 0); /// Reset all state, since we're between streams. virtual void x_Reset(void); TFlags x_GetFlags(void) const { return m_Flags; } unsigned int x_GetLineNumber(void) { return m_LineNumber; } virtual bool x_ParseStructuredComment(const TStr& line); virtual void x_ParseDateComment(const TStr& date); virtual void x_ParseTypeComment(const TStr& moltype, const TStr& seqname); virtual void x_ReadFastaSequences(ILineReader& in); virtual CRef<SRecord> x_ParseFeatureInterval(const TStr& line); virtual CRef<SRecord> x_NewRecord(void) { return CRef<SRecord>(new SRecord); } virtual CRef<CSeq_feat> x_ParseFeatRecord(const SRecord& record); virtual CRef<CSeq_align> x_ParseAlignRecord(const SRecord& record); virtual CRef<CSeq_loc> x_ResolveLoc(const SRecord::TLoc& loc); virtual void x_ParseV2Attributes(SRecord& record, const TStrVec& v, SIZE_TYPE& i); virtual void x_ParseV3Attributes(SRecord& record, const TStrVec& v, SIZE_TYPE& i); virtual void x_AddAttribute(SRecord& record, vector<string>& attr); /// Returning the empty string indicates that record constitutes /// an entire feature. Returning anything else requests merging /// with other records that yield the same ID. virtual string x_FeatureID(const SRecord& record); virtual void x_MergeRecords(SRecord& dest, const SRecord& src); virtual void x_MergeAttributes(SRecord& dest, const SRecord& src); virtual void x_PlaceFeature(CSeq_feat& feat, const SRecord& record); virtual void x_PlaceAlignment(CSeq_align& align, const SRecord& record); virtual void x_ParseAndPlace(const SRecord& record); /// Falls back to x_ResolveNewSeqName on cache misses. virtual CRef<CSeq_id> x_ResolveSeqName(const string& name); virtual CRef<CSeq_id> x_ResolveNewSeqName(const string& name); /// Falls back to x_ResolveNewID on cache misses. virtual CRef<CBioseq> x_ResolveID(const CSeq_id& id, const TStr& mol); /// The base version just constructs a shell so as not to depend /// on the object manager, but derived versions may consult it. virtual CRef<CBioseq> x_ResolveNewID(const CSeq_id& id, const string& mol); virtual void x_PlaceSeq(CBioseq& seq); virtual bool x_IsLineUcscMetaInformation(const TStr&); virtual bool x_SplitKeyValuePair( const string&, string&, string& ); virtual void x_SetProducts( CRef<CSeq_entry>& ); virtual void x_CreateGeneFeatures( CRef<CSeq_entry>& ); virtual void x_RemapGeneRefs( CRef<CSeq_entry>&, TGeneRefs& ); protected: CRef<CSeq_entry> m_TSE; TSeqNameCache m_SeqNameCache; TSeqCache m_SeqCache; TDelayedRecords m_DelayedRecords; TGeneRefs m_GeneRefs; string m_DefMol; unsigned int m_LineNumber; TFlags m_Flags; ILineReader* m_LineReader; int m_Version; }; END_SCOPE(objects) END_NCBI_SCOPE /* @} */ #endif /* OBJTOOLS_READERS___GFF_READER__HPP */

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