NCBI C++ Toolkit Cross Reference

  C++/include/objtools/writers/feature_context.hpp


/* $Id: feature_context.hpp 67813 2015-06-15 15:32:56Z ludwigf $ * =========================================================================== * * 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: Frank Ludwig * * File Description: * */ #ifndef OBJTOOLS_WRITERS___FEATURE_CONTEXT__HPP #define OBJTOOLS_WRITERS___FEATURE_CONTEXT__HPP #include <corelib/ncbistd.hpp> #include <objmgr/bioseq_handle.hpp> #include <objmgr/seq_annot_handle.hpp> #include <objmgr/feat_ci.hpp> BEGIN_NCBI_SCOPE BEGIN_objects_SCOPE // ---------------------------------------------------------------------------- class NCBI_XOBJWRITE_EXPORT CGffFeatureContext // ---------------------------------------------------------------------------- { public: CGffFeatureContext() {}; CGffFeatureContext( const CFeat_CI& feat_iter, CBioseq_Handle bsh=CBioseq_Handle(), CSeq_annot_Handle sah=CSeq_annot_Handle()) : m_ft(feat_iter), m_bsh(bsh), m_sah(sah), m_bSequenceIsGenomicRecord(false) { xAssignSequenceIsGenomicRecord(); }; feature::CFeatTree& FeatTree() { return m_ft; }; CBioseq_Handle BioseqHandle() const { return m_bsh; }; CSeq_annot_Handle AnnotHandle() const { return m_sah; }; CMappedFeat FindBestGeneParent(const CMappedFeat& mf); bool IsSequenceGenomicRecord() const { return m_bSequenceIsGenomicRecord; }; protected: feature::CFeatTree m_ft; CMappedFeat m_mfLastIn, m_mfLastOut; CBioseq_Handle m_bsh; CSeq_annot_Handle m_sah; bool m_bSequenceIsGenomicRecord; void xAssignSequenceIsGenomicRecord(); private: CGffFeatureContext(const CGffFeatureContext&); CGffFeatureContext& operator=(const CGffFeatureContext&); }; END_objects_SCOPE END_NCBI_SCOPE #endif // OBJTOOLS_WRITERS___FEATURE_CONTEXT__HPP

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