annot_types_ci.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: annot_types_ci.hpp,v $
 * PRODUCTION Revision 1000.3  2004/04/12 17:27:00  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.70
 * PRODUCTION
 * ===========================================================================
 */

#ifndef ANNOT_TYPES_CI__HPP
#define ANNOT_TYPES_CI__HPP

/*  $Id: annot_types_ci.hpp,v 1000.3 2004/04/12 17:27:00 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, Michael Kimelman, Eugene Vasilchenko
*
* File Description:
*   Object manager iterators
*
*/

#include <objmgr/impl/annot_collector.hpp>

BEGIN_NCBI_SCOPE

BEGIN_SCOPE(objects)

// Base class for specific annotation iterators
class NCBI_XOBJMGR_EXPORT CAnnotTypes_CI
{
public:
    typedef SAnnotSelector::TAnnotType TAnnotType;

    CAnnotTypes_CI(void);

    // short methods
    CAnnotTypes_CI(TAnnotType type,
                   CScope& scope,
                   const CSeq_loc& loc,
                   const SAnnotSelector& params);
    CAnnotTypes_CI(TAnnotType type,
                   const CBioseq_Handle& bioseq,
                   TSeqPos start, TSeqPos stop,
                   const SAnnotSelector& params);
    // Iterate everything from the seq-annot
    CAnnotTypes_CI(TAnnotType type,
                   const CSeq_annot_Handle& annot);
    // Iterate everything from the seq-annot
    CAnnotTypes_CI(TAnnotType type,
                   const CSeq_annot_Handle& annot,
                   const SAnnotSelector& params);
    // Iterate everything from the seq-entry
    CAnnotTypes_CI(TAnnotType type,
                   const CSeq_entry_Handle& entry);
    // Iterate everything from the seq-entry
    CAnnotTypes_CI(TAnnotType type,
                   const CSeq_entry_Handle& entry,
                   const SAnnotSelector& params);

    // Search all TSEs in all datasources, by default get annotations defined
    // on segments in the same TSE (eResolve_TSE method).
    CAnnotTypes_CI(TAnnotType type,
                   CScope& scope,
                   const CSeq_loc& loc,
                   //const SAnnotSelector& selector,
                   SAnnotSelector::EOverlapType overlap_type,
                   SAnnotSelector::EResolveMethod resolve);
    // Search only in TSE, containing the bioseq, by default get annotations
    // defined on segments in the same TSE (eResolve_TSE method).
    // If "entry" is set, search only annotations from the seq-entry specified
    // (but no its sub-entries or parent entry).
    CAnnotTypes_CI(TAnnotType type,
                   const CBioseq_Handle& bioseq,
                   TSeqPos start, TSeqPos stop,
                   //const SAnnotSelector& selector,
                   SAnnotSelector::EOverlapType overlap_type,
                   SAnnotSelector::EResolveMethod resolve);
    virtual ~CAnnotTypes_CI(void);

    // Rewind annot iterator to point to the very first annot object,
    // the same as immediately after construction.
    void Rewind(void);

    CSeq_annot_Handle GetAnnot(void) const;
    const CSeq_annot& GetSeq_annot(void) const;

    // Get number of annotations
    size_t GetSize(void) const;

protected:
    typedef CAnnot_Collector::TAnnotSet TAnnotSet;
    typedef TAnnotSet::const_iterator   TIterator;

    // Check if a datasource and an annotation are selected.
    bool IsValid(void) const;
    // Move to the next valid position
    void Next(void);
    void Prev(void);
    // Return current annotation
    const CAnnotObject_Ref& Get(void) const;
    CScope& GetScope(void) const;

    CAnnot_Collector& GetCollector(void);
    const TIterator& GetIterator(void) const;

private:
    const TAnnotSet& x_GetAnnotSet(void) const;

    CRef<CAnnot_Collector> m_DataCollector;
    // Current annotation
    TIterator              m_CurrAnnot;
};


/////////////////////////////////////////////////////////////////////////////
// CAnnotTypes_CI
/////////////////////////////////////////////////////////////////////////////


inline
const CAnnotTypes_CI::TAnnotSet& CAnnotTypes_CI::x_GetAnnotSet(void) const
{
    _ASSERT(m_DataCollector);
    return m_DataCollector->GetAnnotSet();
}


inline
bool CAnnotTypes_CI::IsValid(void) const
{
    return bool(m_DataCollector)
        &&  m_CurrAnnot != x_GetAnnotSet().end();
}


inline
void CAnnotTypes_CI::Rewind(void)
{
    m_CurrAnnot = x_GetAnnotSet().begin();
}


inline
void CAnnotTypes_CI::Next(void)
{
    ++m_CurrAnnot;
}


inline
void CAnnotTypes_CI::Prev(void)
{
    --m_CurrAnnot;
}


inline
const CAnnotObject_Ref& CAnnotTypes_CI::Get(void) const
{
    _ASSERT( IsValid() );
    return *m_CurrAnnot;
}


inline
CAnnot_Collector& CAnnotTypes_CI::GetCollector(void)
{
    _ASSERT(m_DataCollector);
    return *m_DataCollector;
}


inline
const CAnnotTypes_CI::TIterator& CAnnotTypes_CI::GetIterator(void) const
{
    _ASSERT( IsValid() );
    return m_CurrAnnot;
}


inline
size_t CAnnotTypes_CI::GetSize(void) const
{
    return x_GetAnnotSet().size();
}

inline
CScope& CAnnotTypes_CI::GetScope(void) const
{
    _ASSERT(m_DataCollector);
    return m_DataCollector->GetScope();
}


END_SCOPE(objects)
END_NCBI_SCOPE

/*
* ---------------------------------------------------------------------------
* $Log: annot_types_ci.hpp,v $
* Revision 1000.3  2004/04/12 17:27:00  gouriano
* PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.70
*
* Revision 1.70  2004/04/07 13:20:16  grichenk
* Moved more data from iterators to CAnnot_Collector
*
* Revision 1.69  2004/04/05 15:56:13  grichenk
* Redesigned CAnnotTypes_CI: moved all data and data collecting
* functions to CAnnotDataCollector. CAnnotTypes_CI is no more
* inherited from SAnnotSelector.
*
* Revision 1.68  2004/03/16 18:09:29  vasilche
* Include <memory> for auto_ptr
*
* Revision 1.67  2004/03/16 15:47:25  vasilche
* Added CBioseq_set_Handle and set of EditHandles
*
* Revision 1.66  2004/02/19 19:25:08  vasilche
* Hidded implementation of CAnnotObject_Ref.
* Added necessary access methods.
*
* Revision 1.65  2004/02/19 17:14:36  vasilche
* Removed unused include.
*
* Revision 1.64  2004/02/06 18:31:53  vasilche
* Fixed annot sorting class - deal with different annot types (graph align feat).
*
* Revision 1.63  2004/02/05 19:53:39  grichenk
* Fixed type matching in SAnnotSelector. Added IncludeAnnotType().
*