bioseq_base_info.hpp

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#ifndef OBJECTS_OBJMGR_IMPL___BIOSEQ_BASE_INFO__HPP
#define OBJECTS_OBJMGR_IMPL___BIOSEQ_BASE_INFO__HPP
 
/*  $Id: bioseq_base_info.hpp 100100 2023-06-15 14:04:06Z vasilche $
 * ===========================================================================
 *
 *                            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: Aleksey Grichenko, Eugene Vasilchenko
 *
 * File Description:
 *   Bioseq info for data source
 *
 */
 
#include <corelib/ncbiobj.hpp>
#include <corelib/ncbimtx.hpp>
#include <objmgr/impl/tse_info_object.hpp>
 
#include <objects/seq/seq_id_handle.hpp>
#include <objects/seq/Seq_descr.hpp>
 
#include <vector>
#include <list>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
class CDataSource;
class CTSE_Info;
class CSeq_entry;
class CSeq_entry_Info;
class CSeq_annot;
class CSeq_annot_Info;
class CSeq_descr;
class CSeqdesc;
 
// ID-5570 : Set of user object names
typedef set<string> TUserObjectTypesSet;
 
////////////////////////////////////////////////////////////////////
//
//  CBioseq_Info::
//
//    Structure to keep bioseq's parent seq-entry along with the list
//    of seq-id synonyms for the bioseq.
//
 
 
class NCBI_XOBJMGR_EXPORT CBioseq_Base_Info : public CTSE_Info_Object
{
    typedef CTSE_Info_Object TParent;
public:
    // 'ctors
    CBioseq_Base_Info(void);
    CBioseq_Base_Info(const CBioseq_Base_Info& src, TObjectCopyMap* copy_map);
    virtual ~CBioseq_Base_Info(void);
 
    // info tree
    const CSeq_entry_Info& GetParentSeq_entry_Info(void) const;
    CSeq_entry_Info& GetParentSeq_entry_Info(void);
 
    // member modification
    // descr
    typedef CSeq_descr TDescr;
    bool IsSetDescr(void) const;
    bool CanGetDescr(void) const;
    const TDescr& GetDescr(void) const;
    TDescr& SetDescr(void);
    void SetDescr(TDescr& v);
    void ResetDescr(void);
    bool AddSeqdesc(CSeqdesc& d);
    CRef<CSeqdesc> RemoveSeqdesc(const CSeqdesc& d);
    CRef<CSeqdesc> ReplaceSeqdesc(const CSeqdesc& old_desc, CSeqdesc& new_desc);
    void AddSeq_descr(const TDescr& v);
 
    virtual bool x_IsSetDescr(void) const = 0;
    virtual bool x_CanGetDescr(void) const = 0;
    virtual const TDescr& x_GetDescr(void) const = 0;
    virtual TDescr& x_SetDescr(void) = 0;
    virtual void x_SetDescr(TDescr& v) = 0;
    virtual void x_ResetDescr(void) = 0;
 
    // low level access for CSeqdesc_CI in case sequence is split
    typedef TDescr::Tdata TDescList;
    typedef TDescList::const_iterator TDesc_CI;
    typedef unsigned TDescTypeMask;
    
    const TDescList& x_GetDescList(void) const;
    TDesc_CI x_GetFirstDesc(TDescTypeMask types) const;
    TDesc_CI x_GetNextDesc(TDesc_CI iter, TDescTypeMask types) const;
    bool x_IsEndDesc(TDesc_CI iter) const;
 
    const CSeqdesc* x_SearchFirstDesc(TDescTypeMask type) const;
 
    TDescTypeMask x_GetExistingDescrMask(void) const;
 
    void x_AddExistingUserObjectTypes(TUserObjectTypesSet& uo_types) const;
 
    // annot
    typedef vector< CRef<CSeq_annot_Info> > TAnnot;
    typedef list< CRef<CSeq_annot> > TObjAnnot;
    bool IsSetAnnot(void) const;
    bool HasAnnots(void) const;
    const TAnnot& GetAnnot(void) const;
    const TAnnot& GetLoadedAnnot(void) const;
 
    void ResetAnnot(void);
    CRef<CSeq_annot_Info> AddAnnot(CSeq_annot& annot, int chunk_id = 0);
    void AddAnnot(CRef<CSeq_annot_Info> annot);
    void RemoveAnnot(CRef<CSeq_annot_Info> annot);
 
    // object initialization
    void x_AttachAnnot(CRef<CSeq_annot_Info> info);
    void x_DetachAnnot(CRef<CSeq_annot_Info> info);
 
    // info tree initialization
    virtual void x_DSAttachContents(CDataSource& ds);
    virtual void x_DSDetachContents(CDataSource& ds);
 
    virtual void x_TSEAttachContents(CTSE_Info& tse);
    virtual void x_TSEDetachContents(CTSE_Info& tse);
 
    virtual void x_ParentAttach(CSeq_entry_Info& parent);
    virtual void x_ParentDetach(CSeq_entry_Info& parent);
 
    // index support
    void x_UpdateAnnotIndexContents(CTSE_Info& tse);
 
    void x_SetAnnot(void);
    void x_SetAnnot(const CBioseq_Base_Info& info, TObjectCopyMap* copy_map);
 
    void x_AddDescrChunkId(const TDescTypeMask& types, TChunkId chunk_id);
    void x_AddAnnotChunkId(TChunkId chunk_id);
    const TChunkIds& x_GetDescrChunkIds() const;
 
    virtual TObjAnnot& x_SetObjAnnot(void) = 0;
    virtual void x_ResetObjAnnot(void) = 0;
 
    void x_DoUpdate(TNeedUpdateFlags flags);
    void x_SetNeedUpdateParent(TNeedUpdateFlags flags);
 
    void x_RealLoadDescr(const TDescr& v);
    
protected:
    typedef CFastMutex TDescrMutex;
    typedef CFastMutexGuard TDescrMutexGuard;
    bool x_IsEndNextDesc(TDesc_CI iter) const; // internal inlined method
    TDesc_CI x_FindDesc(TDescrMutexGuard& guard, TDesc_CI iter, TDescTypeMask types) const;
    void x_PrefetchDesc(TDescrMutexGuard& guard, TDesc_CI last, TDescTypeMask types) const;
 
    friend class CAnnotTypes_CI;
    friend class CSeq_annot_CI;
 
    // members
    TAnnot              m_Annot;
    TObjAnnot*          m_ObjAnnot;
 
    TChunkIds           m_DescrChunks;
    typedef vector<TDescTypeMask> TDescTypeMasks;
    TDescTypeMasks      m_DescrTypeMasks;
    TChunkIds           m_AnnotChunks;
    mutable TDescrMutex m_DescrMutex;
};
 
 
 
/////////////////////////////////////////////////////////////////////
//
//  Inline methods
//
/////////////////////////////////////////////////////////////////////
 
 
inline
bool CBioseq_Base_Info::IsSetDescr(void) const
{
    return x_NeedUpdate(fNeedUpdate_descr) || x_IsSetDescr();
}
 
 
inline
bool CBioseq_Base_Info::CanGetDescr(void) const
{
    return x_NeedUpdate(fNeedUpdate_descr) || x_CanGetDescr();
}
 
 
inline
bool CBioseq_Base_Info::IsSetAnnot(void) const
{
    return m_ObjAnnot != 0 || x_NeedUpdate(fNeedUpdate_annot);
}
 
 
inline
bool CBioseq_Base_Info::HasAnnots(void) const
{
    return !m_Annot.empty() || x_NeedUpdate(fNeedUpdate_annot);
}
 
 
inline
const CBioseq_Base_Info::TAnnot& CBioseq_Base_Info::GetAnnot(void) const
{
    x_Update(fNeedUpdate_annot);
    return m_Annot;
}
 
inline
const CBioseq_Base_Info::TAnnot& CBioseq_Base_Info::GetLoadedAnnot(void) const
{
    return m_Annot;
}
 
 
END_SCOPE(objects)
END_NCBI_SCOPE
 
#endif//OBJECTS_OBJMGR_IMPL___BIOSEQ_BASE_INFO__HPP