reference_item.hpp

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#ifndef OBJTOOLS_FORMAT_ITEMS___REFERENCE_ITEM__HPP
#define OBJTOOLS_FORMAT_ITEMS___REFERENCE_ITEM__HPP
 
/*  $Id: reference_item.hpp 99549 2023-04-17 14:20:00Z gotvyans $
* ===========================================================================
*
*                            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:  Aaron Ucko, NCBI
*          Mati Shomrat
*
* File Description:
*   Reference item for flat-file generator
*
*/
#include <corelib/ncbistd.hpp>
#include <objects/biblio/Cit_book.hpp>
#include <objects/seq/Pubdesc.hpp>
 
#include <objtools/format/items/item_base.hpp>
 
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
class CSubmit_block;
class CSeq_loc;
class CSeq_feat;
class CAuth_list;
class CCit_art;
class CCit_gen;
class CCit_jour;
class CCit_let;
class CCit_pat;
class CCit_proc;
class CCit_sub;
class CMedline_entry;
class CPub;
class CPub_set;
class CDate;
class CAffil;
class CBioseqContext;
class IFormatter;
 
 
class NCBI_FORMAT_EXPORT CCacheItem : public CFlatItem
{
public:
    // types
    typedef vector<string>* TCache;
 
    CCacheItem(CBioseqContext& ctx, TCache csh, int length, bool is_prot);
    void Format(IFormatter& formatter, IFlatTextOStream& text_os) const override;
 
    const TCache& GetCache(void) const { return m_Cache; }
    int GetLength(void) const { return m_Length; }
    bool IsProt(void) const { return m_IsProt; }
 
    EItem GetItemType() const override;
private:
 
    // data
    TCache m_Cache;
    int m_Length;
    bool m_IsProt;
};
 
 
class NCBI_FORMAT_EXPORT CReferenceItem : public CFlatItem
{
public:
    enum ECategory {
        eUnknown,     // none of the below
        ePublished,   // published paper
        eUnpublished, // unpublished paper
        eSubmission   // direct submission
    };
 
    enum EPubType
    {
        ePub_not_set,
        ePub_sub,
        ePub_gen,
        ePub_jour,
        ePub_book,
        ePub_book_art,
        ePub_thesis,
        ePub_pat
    };
 
    typedef ECategory                       TCategory;
    typedef EPubType                        TPubType;
    typedef vector< CRef<CReferenceItem> >  TReferences;
    typedef list<string>                    TStrList;
    typedef int                             TSeqid;
    typedef CPubdesc::TReftype              TReftype;
 
    /// constructors
    CReferenceItem(const CSeqdesc&  desc, CBioseqContext& ctx);
    CReferenceItem(const CSeq_feat& feat, CBioseqContext& ctx,
        const CSeq_loc* loc = nullptr);
    CReferenceItem(const CSubmit_block&  sub, CBioseqContext& ctx);
 
    /// destructor
    ~CReferenceItem();
 
    /// format
    void Format(IFormatter& formatter, IFlatTextOStream& text_os) const override;
 
    TPubType          GetPubType   (void) const { return m_PubType;    }
    TCategory         GetCategory  (void) const { return m_Category;   }
    const CPubdesc&   GetPubdesc   (void) const { return *m_Pubdesc;   }
    TReftype          GetReftype   (void) const;
    const CSeq_loc&   GetLoc       (void) const { return *m_Loc;       }
    int               GetSerial    (void) const { return m_Serial;     }
 
    // Date
    bool              IsSetDate    (void) const { return m_Date.NotEmpty();    }
    const CDate&      GetDate      (void) const { return *m_Date;              }
    //Authors
    bool              IsSetAuthors (void) const { return m_Authors.NotEmpty(); }
    const CAuth_list& GetAuthors   (void) const { return *m_Authors;           }
 
    bool              IsSetBook    (void) const { return m_Book.NotEmpty();    }
    const CCit_book&  GetBook      (void) const { return *m_Book;              }
 
    bool              IsSetPatent  (void) const { return m_Patent.NotEmpty();  }
    const CCit_pat&   GetPatent    (void) const { return *m_Patent;            }
    TSeqid            GetPatSeqid  (void) const { return m_PatentId;           }
 
    bool              IsSetGen     (void) const { return m_Gen.NotEmpty();     }
    const CCit_gen&   GetGen       (void) const { return *m_Gen;               }
 
    bool              IsSetSub     (void) const { return m_Sub.NotEmpty();     }
    const CCit_sub&   GetSub       (void) const { return *m_Sub;               }
 
    bool              IsSetJournal (void) const { return m_Journal.NotEmpty(); }
    const CCit_jour&  GetJournal   (void) const { return *m_Journal;           }
 
    TEntrezId         GetPMID      (void) const { return m_PMID;               }
    TEntrezId         GetMUID      (void) const { return m_MUID;               }
    const string&     GetDOI       (void) const { return m_DOI;                }
    const string&     GetPII       (void) const { return m_ELocationPII;       }
    const string&     GetOldPII    (void) const { return m_OldPII;             }
 
    const string&     GetTitle     (void) const { return m_Title;              }
 
    const string&     GetUniqueStr (void) const;
 
    bool              IsJustUids   (void) const { return m_JustUids;   }
    bool              IsElectronic (void) const { return m_Elect;      }
    const string&     GetConsortium(void) const { return m_Consortium; }
    const string&     GetRemark    (void) const { return m_Remark;     }
 
    void SetLoc(const CConstRef<CSeq_loc>& loc);
    void SetRemark( const CPubdesc::TFig* new_fig,
        const CPubdesc::TMaploc *new_maploc,
        const CPubdesc::TPoly_a *new_poly_a );
 
    // test if matches publication(s)
    bool Matches(const CPub_set& ps) const;
    bool Matches(const CPub& pub) const;
 
    // sort, merge duplicates and cleans up remaining items
    static void Rearrange(TReferences& refs, CBioseqContext& ctx);
    // get names from authors list
    static void GetAuthNames(const CAuth_list& alp, TStrList& authors);
    // format author list
    static void FormatAuthors(const CAuth_list& alp, string& auth);
    // format affiliation
    static void FormatAffil(const CAffil& affil, string& result, bool gen_sub = false);
 
    static void ChangeMedlineAuthorsToISO(CRef<CPub> pub);
 
    EItem GetItemType() const override;
private:
 
    CReferenceItem(const CReferenceItem& value);
    CReferenceItem& operator=(const CReferenceItem& value);
 
    void x_GatherInfo(CBioseqContext& ctx) override;
    void x_Init(const CPub&           pub,  CBioseqContext& ctx);
    void x_Init(const CCit_gen&       gen,  CBioseqContext& ctx);
    void x_Init(const CCit_sub&       sub,  CBioseqContext& ctx);
    void x_Init(const CMedline_entry& mle,  CBioseqContext& ctx);
    void x_Init(const CCit_art&       art,  CBioseqContext& ctx);
    void x_Init(const CCit_jour&      jour, CBioseqContext& ctx);
    void x_Init(const CCit_book&      book, CBioseqContext& ctx);
    void x_Init(const CCit_pat&       pat,  CBioseqContext& ctx);
    void x_Init(const CCit_let&       man,  CBioseqContext& ctx);
    void x_Init(const CCit_proc&      proc, CBioseqContext& ctx);
    void x_InitProc(const CCit_book&      book, CBioseqContext& ctx);
 
    void x_AddAuthors(const CAuth_list& auth);
    void x_AddImprint(const CImprint& imp, CBioseqContext& ctx);
 
    // Genbank format specific
    void x_GatherRemark(CBioseqContext& ctx);
 
    void x_CreateUniqueStr(void) const;
    void x_CleanData(void);
    void x_CapitalizeTitleIfNecessary(void);
 
    // data
    TPubType              m_PubType;
    TCategory             m_Category;
    CConstRef<CPubdesc>   m_Pubdesc;
    CConstRef<CAuth_list> m_Authors;
    CConstRef<CCit_book>  m_Book;
    CConstRef<CCit_pat>   m_Patent;
    TSeqid                m_PatentId;
    CConstRef<CCit_gen>   m_Gen;
    CConstRef<CCit_sub>   m_Sub;
    CConstRef<CCit_jour>  m_Journal;
    CConstRef<CSeq_loc>   m_Loc;
    CConstRef<CDate>      m_Date;
    TEntrezId             m_PMID;
    TEntrezId             m_MUID;
    string                m_DOI;
    string                m_ELocationPII;
    string                m_OldPII;
    int                   m_Serial;
    mutable string        m_UniqueStr;
    bool                  m_JustUids;
    string                m_Title;
    bool                  m_Elect;
    string                m_Consortium;
    string                m_Remark;      // genbank specific
};
 
 
///////////////////////////////////////////////////////////////////////////
//
// INLINE METHODS
 
inline
const string& CReferenceItem::GetUniqueStr(void) const
{
    // supress creation if other identifiers exist.
    if (m_MUID == ZERO_ENTREZ_ID  &&  m_PMID == ZERO_ENTREZ_ID) {
        x_CreateUniqueStr();
    }
    return m_UniqueStr;
}
 
 
inline
CReferenceItem::TReftype CReferenceItem::GetReftype(void) const
{
    return (m_Pubdesc.NotEmpty()) ? m_Pubdesc->GetReftype() : CPubdesc::eReftype_seq;
}
 
/*
inline string CReferenceItem::x_GetURL(int id)
{
    return "http://www.ncbi.nlm.nih.gov/entrez/utils/qmap.cgi?uid="
        + NStr::IntToString(id) + "&form=6&db=m&Dopt=r";
}
*/
END_SCOPE(objects)
END_NCBI_SCOPE
 
#endif  /* OBJTOOLS_FORMAT_ITEMS___REFERENCE_ITEM__HPP */