NCBI C++ Toolkit Cross Reference

  C++/include/objtools/edit/feattable_edit.hpp


/* $Id: feattable_edit.hpp 68564 2015-08-14 16:32:49Z 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. * * =========================================================================== * * Author: Frank Ludwig, NCBI * * File Description: * Convenience wrapper around some of the other feature processing finctions * in the xobjedit library. */ #ifndef _FEATTABLE_EDIT_H_ #define _FEATTABLE_EDIT_H_ #include <corelib/ncbistd.hpp> #include <objects/seq/Seq_annot.hpp> #include <objmgr/scope.hpp> #include <objmgr/util/feature.hpp> #include <objtools/readers/message_listener.hpp> BEGIN_NCBI_SCOPE BEGIN_SCOPE(objects) BEGIN_SCOPE(edit) class NCBI_XOBJEDIT_EXPORT CFeatTableEdit { typedef list<CRef<CSeq_feat> > FEATS; public: CFeatTableEdit( CSeq_annot&, const string& = "", unsigned int = 1, ILineErrorListener* =0); ~CFeatTableEdit(); void GenerateLocusTags(); void InferParentMrnas(); void InferParentGenes(); void InferPartials(); void EliminateBadQualifiers(); void GenerateProteinAndTranscriptIds(); void GenerateLocusIds(); void SubmitFixProducts(); unsigned int PendingLocusTagNumber() const { return mLocusTagNumber; } protected: void xGenerateLocusIdsUseExisting(); void xGenerateLocusIdsRegenerate(); string xNextFeatId(); string xNextLocusTag(); string xNextProteinId( const CMappedFeat&); string xNextTranscriptId( const CMappedFeat&); void xPutErrorMissingLocustag( CMappedFeat); void xPutErrorMissingTranscriptId( CMappedFeat); void xPutErrorMissingProteinId( CMappedFeat); void xFeatureAddQualifier( CMappedFeat, const std::string&, // qual key const std::string&); // qual value void xFeatureAddProteinId( CMappedFeat); void xFeatureAddTranscriptId( CMappedFeat); CRef<CSeq_feat> xMakeGeneForMrna( const CMappedFeat&); CSeq_annot& mAnnot; CRef<CScope> mpScope; CSeq_annot_Handle mHandle; feature::CFeatTree mTree; CSeq_annot_EditHandle mEditHandle; ILineErrorListener* mpMessageListener; unsigned int mNextFeatId; unsigned int mLocusTagNumber; string mLocusTagPrefix; map<string, int> mMapProtIdCounts; }; END_SCOPE(edit) END_SCOPE(objects) END_NCBI_SCOPE #endif

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