graph_ci.hpp

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#ifndef GRAPH_CI__HPP
#define GRAPH_CI__HPP
 
/*  $Id: graph_ci.hpp 90176 2020-05-19 14:39:05Z 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, Michael Kimelman, Eugene Vasilchenko
*
* File Description:
*   Object manager iterators
*
*/
 
#include <objmgr/annot_types_ci.hpp>
#include <objmgr/seq_annot_handle.hpp>
#include <objmgr/seq_entry_handle.hpp>
#include <objects/seqres/Seq_graph.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <corelib/ncbistd.hpp>
#include <objmgr/seq_graph_handle.hpp>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
class CAnnot_Collector;
class CAnnotObject_Ref;
 
/** @addtogroup ObjectManagerIterators
 *
 * @{
 */
 
/////////////////////////////////////////////////////////////////////////////
///
///  CMappedGraph --
///
 
class NCBI_XOBJMGR_EXPORT CMappedGraph
{
public:
    /// empty CMappedGraph
    CMappedGraph()
        : m_GraphRef(0)
        {
        }
 
    /// Get original graph with unmapped location/product
    const CSeq_graph& GetOriginalGraph(void) const
        {
            return m_GraphRef->GetGraph();
        }
 
    /// Get containing annot handle
    CSeq_annot_Handle GetAnnot(void) const;
 
    /// Get original graph handle
    CSeq_graph_Handle GetSeq_graph_Handle(void) const;
 
    /// Check if it's the same graph
    bool operator==(const CMappedGraph& graph) const
    {
        return GetAnnot() == graph.GetAnnot() &&
            m_GraphRef->GetAnnotIndex() == graph.m_GraphRef->GetAnnotIndex();
    }
    bool operator!=(const CMappedGraph& graph) const
    {
        return !(*this == graph);
    }
    bool operator<(const CMappedGraph& graph) const
    {
        return (GetAnnot() < graph.GetAnnot()) ||
            (GetAnnot() == graph.GetAnnot() &&
             m_GraphRef->GetAnnotIndex() < graph.m_GraphRef->GetAnnotIndex());
    }
 
    /// Graph mapped to the master sequence.
    /// WARNING! The function is rather slow and should be used with care.
    const CSeq_graph& GetMappedGraph(void) const
        {
            if ( !m_MappedGraph ) {
                MakeMappedGraph();
            }
            return *m_MappedGraph;
        }
 
    bool IsSetTitle(void) const
        {
            return GetOriginalGraph().IsSetTitle();
        }
    const string& GetTitle(void) const
        {
            return GetOriginalGraph().GetTitle();
        }
 
    bool IsSetComment(void) const
        {
            return GetOriginalGraph().IsSetComment();
        }
    const string& GetComment(void) const
        {
            return GetOriginalGraph().GetComment();
        }
 
    const CSeq_loc& GetLoc(void) const
        {
            if ( !m_MappedLoc ) {
                MakeMappedLoc();
            }
            return *m_MappedLoc;
        }
 
    bool IsSetTitle_x(void) const
        {
            return GetOriginalGraph().IsSetTitle_x();
        }
    const string& GetTitle_x(void) const
        {
            return GetOriginalGraph().GetTitle_x();
        }
 
    bool IsSetTitle_y(void) const
        {
            return GetOriginalGraph().IsSetTitle_y();
        }
    const string& GetTitle_y(void) const
        {
            return GetOriginalGraph().GetTitle_y();
        }
 
    bool IsSetComp(void) const
        {
            return GetOriginalGraph().IsSetComp();
        }
    TSeqPos GetComp(void) const
        {
            return GetOriginalGraph().GetComp();
        }
 
    bool IsSetA(void) const
        {
            return GetOriginalGraph().IsSetA();
        }
    double GetA(void) const
        {
            return GetOriginalGraph().GetA();
        }
 
    bool IsSetB(void) const
        {
            return GetOriginalGraph().IsSetB();
        }
    double GetB(void) const
        {
            return GetOriginalGraph().GetB();
        }
 
    TSeqPos GetNumval(void) const
        {
            if ( m_MappedGraph ) {
                return m_MappedGraph->GetNumval();
            }
            if ( !m_GraphRef->GetMappingInfo().IsMapped() ) {
                return GetOriginalGraph().GetNumval();
            }
            TSeqPos numval = 0;
            ITERATE(TGraphRanges, it, GetMappedGraphRanges()) {
                numval += it->GetLength();
            }
            return numval;
        }
 
    const CSeq_graph::C_Graph& GetGraph(void) const;
 
    typedef CGraphRanges::TRange TRange;
    typedef CGraphRanges::TGraphRanges TGraphRanges;
 
    /// Get the range of graph data used in the mapped graph. The range is
    /// provided in the sequence coordinates, to get array index divide
    /// each value by 'comp'.
    const TRange& GetMappedGraphTotalRange(void) const;
    /// Get all mapped graph ranges. The ranges are provided in the sequence
    /// coordinates, to get array index divide each value by 'comp'.
    const TGraphRanges& GetMappedGraphRanges(void) const;
 
private:
    friend class CGraph_CI;
    friend class CAnnot_CI;
    friend class CAnnot_Collector;
 
    void Set(CAnnot_Collector& collector,
             const CAnnotObject_Ref& annot_ref);
    void Reset(void);
 
    void MakeMappedGraph(void) const;
    void MakeMappedLoc(void) const;
    void MakeMappedGraphData(CSeq_graph& dst) const;
 
    mutable CRef<CAnnot_Collector>  m_Collector;
    const CAnnotObject_Ref*         m_GraphRef;
 
    mutable CConstRef<CSeq_graph>   m_MappedGraph;
    mutable CConstRef<CSeq_loc>     m_MappedLoc;
};
 
 
/////////////////////////////////////////////////////////////////////////////
///
///  CGraph_CI --
///
 
class NCBI_XOBJMGR_EXPORT CGraph_CI : public CAnnotTypes_CI
{
public:
    /// Create an empty iterator
    CGraph_CI(void);
 
    /// Create an iterator that enumerates CSeq_graph objects 
    /// related to the given bioseq
    explicit
    CGraph_CI(const CBioseq_Handle& bioseq);
 
    /// Create an iterator that enumerates CSeq_graph objects 
    /// related to the given bioseq
    ///
    /// @sa
    ///   SAnnotSelector
    CGraph_CI(const CBioseq_Handle& bioseq,
              const SAnnotSelector& sel);
 
    /// Create an iterator that enumerates CSeq_graph objects 
    /// related to the given bioseq
    CGraph_CI(const CBioseq_Handle& bioseq,
              const CRange<TSeqPos>& range,
              ENa_strand strand = eNa_strand_unknown);
 
    /// Create an iterator that enumerates CSeq_graph objects 
    /// related to the given bioseq
    ///
    /// @sa
    ///   SAnnotSelector
    CGraph_CI(const CBioseq_Handle& bioseq,
              const CRange<TSeqPos>& range,
              const SAnnotSelector& sel);
 
    /// Create an iterator that enumerates CSeq_graph objects 
    /// related to the given bioseq
    ///
    /// @sa
    ///   SAnnotSelector
    CGraph_CI(const CBioseq_Handle& bioseq,
              const CRange<TSeqPos>& range,
              ENa_strand strand,
              const SAnnotSelector& sel);
 
    /// Create an iterator that enumerates CSeq_graph objects 
    /// related to the given seq-loc
    CGraph_CI(CScope& scope,
              const CSeq_loc& loc);
 
    /// Create an iterator that enumerates CSeq_graph objects 
    /// related to the given seq-loc
    ///
    /// @sa
    ///   SAnnotSelector
    CGraph_CI(CScope& scope,
              const CSeq_loc& loc,
              const SAnnotSelector& sel);
 
    /// Iterate all graphs from the seq-annot regardless of their location
    explicit
    CGraph_CI(const CSeq_annot_Handle& annot);
 
    /// Iterate all graphs from the seq-annot regardless of their location
    ///
    /// @sa
    ///   SAnnotSelector
    CGraph_CI(const CSeq_annot_Handle& annot,
              const SAnnotSelector& sel);
 
    /// Iterate all graphs from the seq-annot that annotate the location
    CGraph_CI(const CSeq_loc& loc,
              const CSeq_annot_Handle& annot);
 
    /// Iterate all graphs from the seq-annot that annotate the location
    ///
    /// @sa
    ///   SAnnotSelector
    CGraph_CI(const CSeq_loc& loc,
              const CSeq_annot_Handle& annot,
              const SAnnotSelector& sel);
 
    /// Iterate all graphs from the seq-entry regardless of their location
    explicit
    CGraph_CI(const CSeq_entry_Handle& entry);
 
    /// Iterate all graphs from the seq-entry regardless of their location
    ///
    /// @sa
    ///   SAnnotSelector
    CGraph_CI(const CSeq_entry_Handle& entry,
              const SAnnotSelector& sel);
 
    CGraph_CI(const CGraph_CI& iter);
    CGraph_CI& operator= (const CGraph_CI& iter);
    
    virtual ~CGraph_CI(void);
 
    CGraph_CI& operator++ (void);
    CGraph_CI& operator-- (void);
 
    void Rewind(void);
 
    DECLARE_OPERATOR_BOOL(IsValid());
 
    const CGraph_CI& begin() const
    {
        return *this;
    }
    CGraph_CI end() const
    {
        return CGraph_CI(*this, at_end);
    }
    bool operator!=(const CGraph_CI& it) const
    {
        return CAnnotTypes_CI::operator!=(it);
    }
 
    const CMappedGraph& operator* (void) const;
    const CMappedGraph* operator-> (void) const;
private:
    void x_Update(void);
 
    CGraph_CI operator++ (int);
    CGraph_CI operator-- (int);
 
    CGraph_CI(const CGraph_CI& it, EAtEnd)
        : CAnnotTypes_CI(it, at_end)
    {
    }
 
    CMappedGraph m_Graph; // current graph object returned by operator->()
};
 
 
inline
CGraph_CI::CGraph_CI(void)
{
}
 
 
inline
CGraph_CI::CGraph_CI(const CGraph_CI& iter)
    : CAnnotTypes_CI(iter)
{
    x_Update();
}
 
 
inline
CGraph_CI& CGraph_CI::operator++ (void)
{
    Next();
    x_Update();
    return *this;
}
 
inline
CGraph_CI& CGraph_CI::operator-- (void)
{
    Prev();
    x_Update();
    return *this;
}
 
 
inline
void CGraph_CI::Rewind(void)
{
    CAnnotTypes_CI::Rewind();
    x_Update();
}
 
 
inline
const CMappedGraph& CGraph_CI::operator* (void) const
{
    return m_Graph;
}
 
 
inline
const CMappedGraph* CGraph_CI::operator-> (void) const
{
    return &m_Graph;
}
 
 
/* @} */
 
 
END_SCOPE(objects)
END_NCBI_SCOPE
 
#endif  // GRAPH_CI__HPP