NCBI C++ Toolkit Cross Reference

  C++/include/objtools/readers/gff2_data.hpp


/* $Id: gff2_data.hpp 74134 2016-08-15 17:45:20Z 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. * * =========================================================================== * * Author: Frank Ludwig * * File Description: * GFF3 transient data structures * */ #ifndef OBJTOOLS_READERS___GFF2DATA__HPP #define OBJTOOLS_READERS___GFF2DATA__HPP BEGIN_NCBI_SCOPE BEGIN_objects_SCOPE // namespace ncbi::objects:: // ---------------------------------------------------------------------------- class CGff2Record // ---------------------------------------------------------------------------- { public: typedef CCdregion::EFrame TFrame; typedef map<string, string> TAttributes; typedef TAttributes::iterator TAttrIt; typedef TAttributes::const_iterator TAttrCit; public: CGff2Record(); virtual ~CGff2Record(); static unsigned int NextId(); static void ResetId(); // // Input/output: // virtual bool AssignFromGff( const string& ); // // Accessors: // const string& Id() const { return m_strId; }; size_t SeqStart() const { return m_uSeqStart; }; size_t SeqStop() const { return m_uSeqStop; }; const string& Source() const { return m_strSource; }; const string& Type() const { return m_strType; }; double Score() const { return IsSetScore() ? *m_pdScore : 0.0; }; ENa_strand Strand() const { return IsSetStrand() ? *m_peStrand : eNa_strand_unknown; }; TFrame Phase() const { return IsSetPhase() ? *m_pePhase : CCdregion::eFrame_not_set; }; const string& AttributesLiteral() const { return m_strAttributes; }; bool IsSetScore() const { return m_pdScore != 0; }; bool IsSetStrand() const { return m_peStrand != 0; }; bool IsSetPhase() const { return m_pePhase != 0; }; bool IsAlignmentRecord() const { if (NStr::StartsWith(Type(), "match") || NStr::EndsWith(Type(), "_match")) { return true; } return false; }; CRef<CSeq_id> GetSeqId( int ) const; CRef<CSeq_loc> GetSeqLoc( int ) const; const TAttributes& Attributes() const { return m_Attributes; }; bool GetAttribute( const string&, string& ) const; bool GetAttribute( const string&, list<string>& ) const; virtual bool InitializeFeature( int, CRef<CSeq_feat> ) const; virtual bool UpdateFeature( int, CRef<CSeq_feat> ) const; static void TokenizeGFF(vector<CTempStringEx>& columns, const CTempStringEx& line); protected: virtual bool x_AssignAttributesFromGff( const string&, const string& ); bool x_SplitGffAttributes( const string&, vector< string >& ) const; virtual bool x_MigrateId( CRef<CSeq_feat> ) const; virtual bool x_MigrateStartStopStrand( CRef<CSeq_feat> ) const; virtual bool x_MigrateType( CRef<CSeq_feat> ) const; virtual bool x_MigrateScore( CRef<CSeq_feat> ) const; virtual bool x_MigratePhase( CRef<CSeq_feat> ) const; virtual bool x_MigrateAttributes( int, CRef<CSeq_feat> ) const; virtual bool x_InitFeatureLocation( int, CRef<CSeq_feat> ) const; virtual bool xInitFeatureData( int, CRef<CSeq_feat> ) const; virtual bool xInitFeatureDataBond( int, CRef<CSeq_feat> ) const; virtual bool xInitFeatureDataNcrna( int, CRef<CSeq_feat> ) const; virtual bool xInitFeatureDataSpecialImp( int, CRef<CSeq_feat> ) const; virtual bool xUpdateFeatureData( int, CRef<CSeq_feat>) const; virtual bool x_MigrateAttributesSubSource( int, CRef<CSeq_feat>, TAttributes& ) const; virtual bool x_MigrateAttributesOrgName( int, CRef<CSeq_feat>, TAttributes& ) const; //utility helpers: // static string xNormalizedAttributeKey( const CTempString&); static string xNormalizedAttributeValue( const CTempString&); static bool xMigrateAttributeDefault( TAttributes&, const string&, CRef<CSeq_feat>, const string&, int); static bool xMigrateAttributeSingle( TAttributes&, const string&, CRef<CSeq_feat>, const string&, int); // // Data: // string m_strId; size_t m_uSeqStart; size_t m_uSeqStop; string m_strSource; string m_strType; double* m_pdScore; ENa_strand* m_peStrand; TFrame* m_pePhase; string m_strAttributes; TAttributes m_Attributes; static unsigned int m_nextId; }; END_objects_SCOPE END_NCBI_SCOPE #endif // OBJTOOLS_READERS___GFF2DATA__HPP

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