Seq_feat.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: Seq_feat.hpp,v $
- * PRODUCTION Revision 1000.1 2004/04/12 17:23:55 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.16
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: Seq_feat.hpp,v 1000.1 2004/04/12 17:23:55 gouriano Exp $
- * ===========================================================================
- *
- * 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: .......
- *
- * File Description:
- * .......
- *
- * Remark:
- * This code was originally generated by application DATATOOL
- * using specifications from the ASN data definition file
- * 'seqfeat.asn'.
- */
- #ifndef OBJECTS_SEQFEAT_SEQ_FEAT_HPP
- #define OBJECTS_SEQFEAT_SEQ_FEAT_HPP
- // generated includes
- #include <objects/seqfeat/Seq_feat_.hpp>
- #include <objects/seqfeat/Gene_ref.hpp>
- #include <objects/seqfeat/Prot_ref.hpp>
- #include <objects/seqfeat/SeqFeatData.hpp>
- #include <objects/seqloc/Seq_loc.hpp>
- // generated classes
- BEGIN_NCBI_SCOPE
- BEGIN_objects_SCOPE // namespace ncbi::objects::
- class NCBI_SEQFEAT_EXPORT CSeq_feat : public CSeq_feat_Base
- {
- typedef CSeq_feat_Base Tparent;
- public:
- // constructor
- CSeq_feat(void);
- // destructor
- ~CSeq_feat(void);
-
- //
- // See related function in util/feature.hpp
- //
- // void GetLabel (const CSeq_feat&, string*, ELabelType, CScope*)
- //
- // get gene (if present) from Seq-feat.xref list
- const CGene_ref* GetGeneXref(void) const;
- void SetGeneXref(CGene_ref& value);
- CGene_ref& SetGeneXref(void);
- // get protein (if present) from Seq-feat.xref list
- const CProt_ref* GetProtXref(void) const;
- void SetProtXref(CProt_ref& value);
- CProt_ref& SetProtXref(void);
- // Add a qualifier to this feature
- void AddQualifier(const string& qual_name, const string& qual_val);
- // add a DB xref to this feature
- void AddDbxref(const string& db_name, const string& db_key);
- void AddDbxref(const string& db_name, int db_key);
- // Optional locations are used for features with locations
- // re-mapped to a master sequence
- int CompareNonLocation(const CSeq_feat& f2,
- const CSeq_loc& loc1, const CSeq_loc& loc2) const;
- int GetTypeSortingOrder(void) const;
- static int GetTypeSortingOrder(CSeqFeatData::E_Choice type);
- int Compare(const CSeq_feat& f2) const;
- int Compare(const CSeq_feat& f2,
- const CSeq_loc& mapped1, const CSeq_loc& mapped2) const;
- private:
- // Prohibit copy constructor and assignment operator
- CSeq_feat(const CSeq_feat& value);
- CSeq_feat& operator=(const CSeq_feat& value);
- };
- /////////////////// CSeq_feat inline methods
- // constructor
- inline
- CSeq_feat::CSeq_feat(void)
- {
- }
- // Corresponds to SortFeatItemListByPos from the C toolkit
- inline
- int CSeq_feat::Compare(const CSeq_feat& f2,
- const CSeq_loc& loc1, const CSeq_loc& loc2) const
- {
- int diff = loc1.Compare(loc2);
- return diff != 0? diff: CompareNonLocation(f2, loc1, loc2);
- }
- // Corresponds to SortFeatItemListByPos from the C toolkit
- inline
- int CSeq_feat::Compare(const CSeq_feat& f2) const
- {
- return Compare(f2, GetLocation(), f2.GetLocation());
- }
- inline
- int CSeq_feat::GetTypeSortingOrder(void) const
- {
- return GetTypeSortingOrder(GetData().Which());
- }
- NCBI_SEQFEAT_EXPORT
- inline
- bool operator< (const CSeq_feat& f1, const CSeq_feat& f2)
- {
- return f1.Compare(f2) < 0;
- }
- /////////////////// end of CSeq_feat inline methods
- END_objects_SCOPE // namespace ncbi::objects::
- END_NCBI_SCOPE
- #endif // OBJECTS_SEQFEAT_SEQ_FEAT_HPP
- /* Original file checksum: lines: 90, chars: 2388, CRC32: c285198b */
- /*
- * ===========================================================================
- * $Log: Seq_feat.hpp,v $
- * Revision 1000.1 2004/04/12 17:23:55 gouriano
- * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.16
- *
- * Revision 1.16 2004/01/05 19:16:36 dicuccio
- * Added APIs to ease adding qualifiers and dbxrefs
- *
- * Revision 1.15 2003/12/31 15:36:07 grichenk
- * Moved CompareLocations() from CSeq_feat to CSeq_loc,
- * renamed it to Compare().
- *
- * Revision 1.14 2003/08/07 21:42:03 kans
- * added SetGeneXref and SetProtXref
- *
- * Revision 1.13 2003/04/24 16:15:31 vasilche
- * Fixed CSeq_feat::Compare().
- *
- * Revision 1.12 2003/02/26 17:53:06 vasilche
- * Added public version of feature comparison assuming that
- * total range check is done already.
- *
- * Revision 1.11 2003/02/24 18:52:57 vasilche
- * Added optional mapped locations arguments to feature comparison.
- *
- * Revision 1.10 2003/02/10 15:52:07 grichenk
- * CSeq_feat::Compare() takes optional seq-locs for remapped features
- *
- * Revision 1.9 2003/02/06 22:24:23 vasilche
- * Added int CSeq_feat::Compare().
- * Fixed slow comparison of CSeq_feat with mix seq locs.
- *
- * Revision 1.8 2003/01/29 17:43:22 vasilche
- * Added Compare(CSeq_feat, CSeq_feat) returning int for easier comparison.
- * operator<(CSeq_feat, CSeq_feat) uses Compare().
- *
- * Revision 1.7 2002/12/26 12:43:27 dicuccio
- * Added Win32 export specifiers
- *
- * Revision 1.6 2002/12/19 22:12:03 kans
- * include Gene_ref.hpp and Prot_ref.hpp, move log to bottom of file
- *
- * Revision 1.5 2002/12/19 21:31:09 kans
- * added GetGeneXref and GetProtXref
- *
- * Revision 1.4 2002/06/07 11:59:10 clausen
- * Added related function comment
- *
- * Revision 1.3 2002/06/06 20:56:30 clausen
- * Moved GetLabel to objects/util/feature.hpp
- *
- * Revision 1.2 2002/01/10 19:55:01 clausen
- * Added GetLabel
- *
- * Revision 1.1 2001/10/30 20:25:57 ucko
- * Implement feature labels/keys, subtypes, and sorting
- *
- *
- * ===========================================================================
- */