/* * =========================================================================== * PRODUCTION $Log: seq_entry_handle.hpp,v $ * PRODUCTION Revision 1000.2  2004/06/01 19:21:38  gouriano * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.11 * PRODUCTION * =========================================================================== */#ifndef SEQ_ENTRY_HANDLE__HPP#define SEQ_ENTRY_HANDLE__HPP/*  $Id: seq_entry_handle.hpp,v 1000.2 2004/06/01 19:21:38 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: Aleksey Grichenko, Eugene Vasilchenko** File Description:*    Handle to Seq-entry object**/#include <corelib/ncbiobj.hpp>#include <objects/seqset/Seq_entry.hpp>#include <objects/seqset/Bioseq_set.hpp>#include <objmgr/impl/heap_scope.hpp>BEGIN_NCBI_SCOPEBEGIN_SCOPE(objects)/////////////////////////////////////////////////////////////////////////////// CSeq_entry_Handle/////////////////////////////////////////////////////////////////////////////class CScope;class CSeq_entry_Handle;class CBioseq_set_Handle;class CBioseq_Handle;class CSeq_annot_Handle;class CSeq_entry_EditHandle;class CBioseq_set_EditHandle;class CBioseq_EditHandle;class CSeq_annot_EditHandle;class CSeq_entry_Info;class CTSE_Info;class CSeqdesc;class NCBI_XOBJMGR_EXPORT CSeq_entry_Handle{public:    // default constructor    CSeq_entry_Handle(void);    // Get scope this handle belongs to    CScope& GetScope(void) const;    // Navigate object tree    bool HasParentEntry(void) const;    CBioseq_set_Handle GetParentBioseq_set(void) const;    CSeq_entry_Handle GetParentEntry(void) const;    CSeq_entry_Handle GetSingleSubEntry(void) const;    CSeq_entry_Handle GetTopLevelEntry(void) const;    // Get 'edit' version of handle    CSeq_entry_EditHandle GetEditHandle(void) const;    // Get controlled object    CConstRef<CSeq_entry> GetCompleteSeq_entry(void) const;    CConstRef<CSeq_entry> GetSeq_entryCore(void) const;    // Seq-entry accessors    typedef CSeq_entry::E_Choice E_Choice;    E_Choice Which(void) const;    // Bioseq access    bool IsSeq(void) const;    typedef CBioseq_Handle TSeq;    TSeq GetSeq(void) const;    // Bioseq_set access    bool IsSet(void) const;    typedef CBioseq_set_Handle TSet;    TSet GetSet(void) const;    // descr field is in both Bioseq and Bioseq-set    bool IsSetDescr(void) const;    typedef CSeq_descr TDescr;    const TDescr& GetDescr(void) const;    typedef CBioseq_set::TClass TClass;    CConstRef<CObject> GetBlobId(void) const;    // Utility methods/operators    operator bool(void) const;    bool operator!(void) const;    void Reset(void);    bool operator ==(const CSeq_entry_Handle& handle) const;    bool operator !=(const CSeq_entry_Handle& handle) const;    bool operator <(const CSeq_entry_Handle& handle) const;protected:    friend class CScope_Impl;    friend class CBioseq_Handle;    friend class CBioseq_set_Handle;    friend class CSeq_annot_Handle;    friend class CSeqMap_CI;    friend class CSeq_entry_CI;    CSeq_entry_Handle(CScope& scope, const CSeq_entry_Info& info);    CHeapScope          m_Scope;    CConstRef<CObject>  m_Info;public: // non-public section    CConstRef<CTSE_Info> GetTSE_Info(void) const;    const CSeq_entry_Info& x_GetInfo(void) const;};class NCBI_XOBJMGR_EXPORT CSeq_entry_EditHandle : public CSeq_entry_Handle{public:    // Default constructor    CSeq_entry_EditHandle(void);    // Navigate object tree    CBioseq_set_EditHandle GetParentBioseq_set(void) const;    CSeq_entry_EditHandle GetParentEntry(void) const;    CSeq_entry_EditHandle GetSingleSubEntry(void) const;    // Change descriptions    void SetDescr(TDescr& v) const;    void ResetDescr(void) const;    bool AddSeqdesc(CSeqdesc& v) const;    bool RemoveSeqdesc(const CSeqdesc& v) const;    void AddDescr(const CSeq_entry_EditHandle& src_entry) const;    typedef CBioseq_EditHandle TSeq;    typedef CBioseq_set_EditHandle TSet;    TSet SetSet(void) const;    TSeq SetSeq(void) const;    // Make this Seq-entry to be empty.    // Old contents of the entry will be deleted.    void SelectNone(void) const;    // Convert the empty Seq-entry to Bioseq-set.    // Returns new Bioseq-set handle.    TSet SelectSet(TClass set_class = CBioseq_set::eClass_not_set) const;    // Make the empty Seq-entry be in set state with given Bioseq-set object.    // Returns new Bioseq-set handle.    TSet SelectSet(CBioseq_set& seqset) const;    // Make the empty Seq-entry be in set state with given Bioseq-set object.    // Returns new Bioseq-set handle.    TSet CopySet(const CBioseq_set_Handle& seqset) const;    // Make the empty Seq-entry be in set state with moving Bioseq-set object    // from the argument seqset.    // Returns new Bioseq-set handle which could be different from the argument    // is the argument is from another scope.    TSet TakeSet(const TSet& seqset) const;    // Make the empty Seq-entry be in seq state with specified Bioseq object.    // Returns new Bioseq handle.    TSeq SelectSeq(CBioseq& seq) const;    // Make the empty Seq-entry be in seq state with specified Bioseq object.    // Returns new Bioseq handle.    TSeq CopySeq(const CBioseq_Handle& seq) const;    // Make the empty Seq-entry be in seq state with moving bioseq object    // from the argument seq.    // Returns new Bioseq handle which could be different from the argument    // is the argument is from another scope.    TSeq TakeSeq(const TSeq& seq) const;    // Convert the entry from Bioseq to Bioseq-set.    // Old Bioseq will become the only entry of new Bioseq-set.    // New Bioseq-set will have the specified class.    // If the set_class argument is omitted,    // or equals to CBioseq_set::eClass_not_set,    // the class field of new Bioseq-set object will not be initialized.    // Returns new Bioseq-set handle.    TSet ConvertSeqToSet(TClass set_class = CBioseq_set::eClass_not_set) const;    // Collapse one level of Bioseq-set.    // The Bioseq-set should originally contain only one sub-entry.    // Current Seq-entry will become the same type as sub-entry.    // All Seq-annot and Seq-descr objects from old Bioseq-set    // will be moved to new contents (sub-entry).    void CollapseSet(void) const;    // Do the same as CollapseSet() when sub-entry is of type bioseq.    // Throws an exception in other cases.    // Returns resulting Bioseq handle.    TSeq ConvertSetToSeq(void) const;    // Attach new Seq-annot to Bioseq or Bioseq-set    CSeq_annot_EditHandle AttachAnnot(const CSeq_annot& annot) const;    CSeq_annot_EditHandle CopyAnnot(const CSeq_annot_Handle&annot) const;    CSeq_annot_EditHandle TakeAnnot(const CSeq_annot_EditHandle& annot) const;    void TakeAllAnnots(const CSeq_entry_EditHandle& src_entry) const;    // Attach new sub objects to Bioseq-set    // index < 0 or index >= current number of entries means to add at the end.    CBioseq_EditHandle AttachBioseq(CBioseq& seq,                                    int index = -1) const;    CBioseq_EditHandle CopyBioseq(const CBioseq_Handle& seq,                                  int index = -1) const;    CBioseq_EditHandle TakeBioseq(const CBioseq_EditHandle& seq,                                  int index = -1) const;    CSeq_entry_EditHandle AttachEntry(CSeq_entry& entry,                                      int index = -1) const;    CSeq_entry_EditHandle CopyEntry(const CSeq_entry_Handle& entry,                                    int index = -1) const;    CSeq_entry_EditHandle TakeEntry(const CSeq_entry_EditHandle& entry,                                    int index = -1) const;    // Remove this Seq-entry from parent,    // or scope if it's top level Seq-entry.    void Remove(void) const;protected:    friend class CScope_Impl;    friend class CBioseq_EditHandle;    friend class CBioseq_set_EditHandle;    friend class CSeq_annot_EditHandle;    friend class CSeq_entry_I;    CSeq_entry_EditHandle(const CSeq_entry_Handle& h);    CSeq_entry_EditHandle(CScope& scope, CSeq_entry_Info& info);public: // non-public section    CSeq_entry_Info& x_GetInfo(void) const;};/////////////////////////////////////////////////////////////////////////////// CSeq_entry_Handle inline methods/////////////////////////////////////////////////////////////////////////////inlineCSeq_entry_Handle::CSeq_entry_Handle(void){}inlineCScope& CSeq_entry_Handle::GetScope(void) const{    return m_Scope;}inlineCSeq_entry_Handle::operator bool(void) const{    return m_Info;}inlinebool CSeq_entry_Handle::operator!(void) const{    return !m_Info;}inlineconst CSeq_entry_Info& CSeq_entry_Handle::x_GetInfo(void) const{    return reinterpret_cast<const CSeq_entry_Info&>(*m_Info);}inlinebool CSeq_entry_Handle::operator ==(const CSeq_entry_Handle& handle) const{    return m_Scope == handle.m_Scope  &&  m_Info == handle.m_Info;}inlinebool CSeq_entry_Handle::operator !=(const CSeq_entry_Handle& handle) const{    return m_Scope != handle.m_Scope  ||  m_Info != handle.m_Info;}inlinebool CSeq_entry_Handle::operator <(const CSeq_entry_Handle& handle) const{    if ( m_Scope != handle.m_Scope ) {        return m_Scope < handle.m_Scope;    }    return m_Info < handle.m_Info;}inlinebool CSeq_entry_Handle::IsSeq(void) const{    return Which() == CSeq_entry::e_Seq;}inlinebool CSeq_entry_Handle::IsSet(void) const{    return Which() == CSeq_entry::e_Set;}/////////////////////////////////////////////////////////////////////////////// CSeq_entry_EditHandle/////////////////////////////////////////////////////////////////////////////inlineCSeq_entry_EditHandle::CSeq_entry_EditHandle(void){}inlineCSeq_entry_EditHandle::CSeq_entry_EditHandle(const CSeq_entry_Handle& h)    : CSeq_entry_Handle(h){}inlineCSeq_entry_EditHandle::CSeq_entry_EditHandle(CScope& scope,                                             CSeq_entry_Info& info)    : CSeq_entry_Handle(scope, info){}END_SCOPE(objects)END_NCBI_SCOPE/** ---------------------------------------------------------------------------* $Log: seq_entry_handle.hpp,v $* Revision 1000.2  2004/06/01 19:21:38  gouriano* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.11** Revision 1.11  2004/04/29 15:44:30  grichenk* Added GetTopLevelEntry()** Revision 1.10  2004/03/31 19:54:08  vasilche* Fixed removal of bioseqs and bioseq-sets.** Revision 1.9  2004/03/31 17:08:06  vasilche* Implemented ConvertSeqToSet and ConvertSetToSeq.** Revision 1.8  2004/03/29 20:13:05  vasilche* Implemented whole set of methods to modify Seq-entry object tree.* Added CBioseq_Handle::GetExactComplexityLevel().** Revision 1.7  2004/03/25 20:06:41  vasilche* Fixed typo TSet -> TSeq.** Revision 1.6  2004/03/24 18:30:28  vasilche* Fixed edit API.* Every *_Info object has its own shallow copy of original object.** Revision 1.5  2004/03/16 21:01:32  vasilche* Added methods to move Bioseq withing Seq-entry** Revision 1.4  2004/03/16 15:47:26  vasilche* Added CBioseq_set_Handle and set of EditHandles** Revision 1.3  2004/02/09 19:18:50  grichenk* Renamed CDesc_CI to CSeq_descr_CI. Redesigned CSeq_descr_CI* and CSeqdesc_CI to avoid using data directly.** Revision 1.2  2003/12/03 16:40:03  grichenk* Added GetParentEntry()** Revision 1.1  2003/11/28 15:12:30  grichenk* Initial revision*** ===========================================================================*/#endif //SEQ_ENTRY_HANDLE__HPP