seq_id_handle.hpp

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#ifndef OBJECTS_OBJMGR___SEQ_ID_HANDLE__HPP
#define OBJECTS_OBJMGR___SEQ_ID_HANDLE__HPP
 
/*  $Id: seq_id_handle.hpp 99793 2023-05-10 18:04:05Z 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, Eugene Vasilchenko
*
* File Description:
*   Seq-id handle for Object Manager
*
*/
 
 
#include <objects/seqloc/Seq_id.hpp>
 
#include <set>
#include <vector>
 
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(objects)
 
/** @addtogroup OBJECTS_Seqid
 *
 * @{
 */
 
 
/////////////////////////////////////////////////////////////////////
///
///  CSeq_id_Handle::
///
///    Handle to be used instead of CSeq_id to optimize indexing and sorting.
///    Comparing seq-id handles is not guaranteed to produce the same results
///    as comparing seq-ids, to be stable or to remain the same between application
///    runs. For stable sorting use CSeq_id_Handle::PLessOrdered functor.
///
 
// forward declaration
class CSeq_id;
class CSeq_id_Handle;
class CSeq_id_Mapper;
class CSeq_id_Which_Tree;
 
 
class CSeq_id_Info : public CObject
{
public:
    typedef TIntId TPacked;
    typedef Uint8 TVariant;
 
    NCBI_SEQ_EXPORT CSeq_id_Info(CSeq_id::E_Choice type,
                                 CSeq_id_Mapper* mapper);
    NCBI_SEQ_EXPORT CSeq_id_Info(const CConstRef<CSeq_id>& seq_id,
                                 CSeq_id_Mapper* mapper);
    NCBI_SEQ_EXPORT ~CSeq_id_Info(void);
 
    CConstRef<CSeq_id> GetSeqId(void) const
        {
            return m_Seq_id;
        }
    NCBI_SEQ_EXPORT virtual CConstRef<CSeq_id> GetPackedSeqId(TPacked packed, TVariant variant) const;
 
    // locking
    void AddLock(void) const
        {
            ++m_LockCounter;
        }
    void RemoveLock(void) const
        {
            if ( --m_LockCounter <= 0 ) {
                x_RemoveLastLock();
            }
        }
    bool IsLocked(void) const
        {
            return m_LockCounter != 0;
        }
 
    CSeq_id::E_Choice GetType(void) const
        {
            return m_Seq_id_Type.load(memory_order_relaxed);
        }
    CSeq_id_Mapper& GetMapper(void) const
        {
            return *m_Mapper;
        }
    NCBI_SEQ_EXPORT CSeq_id_Which_Tree& GetTree(void) const;
 
    virtual int CompareOrdered(const CSeq_id_Info& other, const CSeq_id_Handle& h_this, const CSeq_id_Handle& h_other) const;
 
protected:
    friend class CSeq_id_Which_Tree;
 
    NCBI_SEQ_EXPORT void x_RemoveLastLock(void) const;
 
    mutable atomic<Uint8>        m_LockCounter{0};
    atomic<CSeq_id::E_Choice>    m_Seq_id_Type;
    CConstRef<CSeq_id>           m_Seq_id;
    mutable CRef<CSeq_id_Mapper> m_Mapper;
 
private:
    // to prevent copying
    CSeq_id_Info(const CSeq_id_Info&);
    const CSeq_id_Info& operator=(const CSeq_id_Info&);
};
 
 
class CSeq_id_InfoLocker : public CObjectCounterLocker
{
public:
    void Lock(const CSeq_id_Info* info) const
        {
            CObjectCounterLocker::Lock(info);
            info->AddLock();
        }
    void Relock(const CSeq_id_Info* info) const
        {
            Lock(info);
        }
    void Unlock(const CSeq_id_Info* info) const
        {
            info->RemoveLock();
            CObjectCounterLocker::Unlock(info);
        }
};
 
 
enum EAllowWeakMatch {
    eNoWeakMatch,
    eAllowWeakMatch
};
 
 
class CSeq_id_Handle
{
public:
    typedef CSeq_id_Info::TPacked TPacked;
    typedef CSeq_id_Info::TVariant TVariant;
 
    // 'ctors
    CSeq_id_Handle(void)
        : m_Info(null), m_Packed(0), m_Variant(0)
        {
        }
    explicit CSeq_id_Handle(const CSeq_id_Info* info, TPacked packed = 0, TVariant variant = 0)
        : m_Info(info), m_Packed(packed), m_Variant(variant)
        {
            _ASSERT(info || (!packed && !variant));
        }
    CSeq_id_Handle(ENull /*null*/)
        : m_Info(null), m_Packed(0), m_Variant(0)
        {
        }
 
    /// Normal way of getting a handle, works for any seq-id.
    static NCBI_SEQ_EXPORT CSeq_id_Handle GetHandle(const CSeq_id& id);
 
    /// Construct CSeq_id from string representation and return handle for it.
    static NCBI_SEQ_EXPORT CSeq_id_Handle GetHandle(const string& str_id);
 
    /// Faster way to create a handle for a gi.
    static NCBI_SEQ_EXPORT CSeq_id_Handle GetHandle(TGi gi);
 
    /// Faster way to create a handle for a gi.
    static CSeq_id_Handle GetGiHandle(TGi gi)
        {
            return GetHandle(gi);
        }
    
    bool operator== (const CSeq_id_Handle& handle) const
        {
            return m_Packed == handle.m_Packed && m_Info == handle.m_Info;
        }
    bool operator!= (const CSeq_id_Handle& handle) const
        {
            return m_Packed != handle.m_Packed || m_Info != handle.m_Info;
        }
    bool operator<  (const CSeq_id_Handle& handle) const
        {
            // Packed (m_Packed != 0) first:
            // zeroes are converted to a highest unsigned value by decrement.
            TUintId p1 = INT_ID_TO(TUintId, m_Packed-1);
            TUintId p2 = INT_ID_TO(TUintId, handle.m_Packed-1);
            return p1 < p2 || (p1 == p2 && m_Info < handle.m_Info);
        }
    bool NCBI_SEQ_EXPORT operator== (const CSeq_id& id) const;
 
    /// Compare ids in a defined order (see CSeq_id::CompareOrdered())
    int NCBI_SEQ_EXPORT CompareOrdered(const CSeq_id_Handle& id) const;
    /// Predicate for sorting CSeq_id_Handles in a defined order.
    struct PLessOrdered
    {
        bool operator()(const CSeq_id_Handle& id1,
                        const CSeq_id_Handle& id2) const
            {
                return id1.CompareOrdered(id2) < 0;
            }
    };
 
    /// Check if the handle is a valid or an empty one
    DECLARE_OPERATOR_BOOL_REF(m_Info);
 
    /// Reset the handle (remove seq-id reference)
    void Reset(void)
        {
            m_Info.Reset();
            m_Packed = 0;
            m_Variant = 0;
        }
 
    //
    bool NCBI_SEQ_EXPORT HaveMatchingHandles(void) const;
    bool NCBI_SEQ_EXPORT HaveReverseMatch(void) const;
    bool NCBI_SEQ_EXPORT HaveMatchingHandles(EAllowWeakMatch allow_weak_match) const;
    bool NCBI_SEQ_EXPORT HaveReverseMatch(EAllowWeakMatch allow_weak_match) const;
 
    //
    typedef set<CSeq_id_Handle> TMatches;
    void NCBI_SEQ_EXPORT GetMatchingHandles(TMatches& matches) const;
    void NCBI_SEQ_EXPORT GetReverseMatchingHandles(TMatches& matches) const;
    void NCBI_SEQ_EXPORT GetMatchingHandles(TMatches& matches,
                                            EAllowWeakMatch allow_weak_match) const;
    void NCBI_SEQ_EXPORT GetReverseMatchingHandles(TMatches& matches,
                                                   EAllowWeakMatch allow_weak_match) const;
 
    /// True if *this matches to h.
    /// This mean that *this is either the same as h,
    /// or more generic version of h.
    bool NCBI_SEQ_EXPORT MatchesTo(const CSeq_id_Handle& h) const;
 
    /// True if "this" is a better bioseq than "h".
    bool NCBI_SEQ_EXPORT IsBetter(const CSeq_id_Handle& h) const;
 
    string NCBI_SEQ_EXPORT AsString(void) const;
 
    CSeq_id::E_Choice Which(void) const
        {
            return m_Info->GetType();
        }
    bool IsPacked(void) const
        {
            return m_Packed != 0;
        }
    TPacked GetPacked(void) const
        {
            return m_Packed;
        }
    bool IsSetVariant(void) const
        {
            return m_Variant != 0;
        }
    TVariant GetVariant(void) const
        {
            return m_Variant;
        }
    bool IsGi(void) const
        {
            return m_Packed && m_Info->GetType() == CSeq_id::e_Gi;
        }
    TGi GetGi(void) const
        {
            return IsGi()? TGi(m_Packed) : ZERO_GI;
        }
    bool IsAccVer(void) const
    {
        if (IsGi()) return false;
        auto seq_id = GetSeqId();
        if (!seq_id) return false;
        auto text_id = seq_id->GetTextseq_Id();
        return text_id &&
            text_id->IsSetAccession() &&
            text_id->IsSetVersion();
    }
    unsigned NCBI_SEQ_EXPORT GetHash(void) const;
 
    CSeq_id::EAccessionInfo IdentifyAccession(void) const
        {
            return GetSeqId()->IdentifyAccession();
        }
 
    CConstRef<CSeq_id> GetSeqId(void) const
        {
            CConstRef<CSeq_id> ret;
            if ( m_Packed || m_Variant ) {
                ret = m_Info->GetPackedSeqId(m_Packed, m_Variant);
            }
            else {
                ret = m_Info->GetSeqId();
            }
            return ret;
        }
    CConstRef<CSeq_id> GetSeqIdOrNull(void) const
        {
            if ( !m_Info ) {
                return null;
            }
            return GetSeqId();
        }
 
    CSeq_id_Mapper& GetMapper(void) const
        {
            return m_Info->GetMapper();
        }
 
    void Swap(CSeq_id_Handle& idh)
        {
            m_Info.Swap(idh.m_Info);
            swap(m_Packed, idh.m_Packed);
            swap(m_Variant, idh.m_Variant);
        }
 
    bool NCBI_SEQ_EXPORT IsAllowedSNPScaleLimit(CSeq_id::ESNPScaleLimit scale_limit) const;
 
public:
    const CSeq_id_Info* x_GetInfo(void) const {
        return m_Info;
    }
 
private:
    friend class CSeq_id_Mapper;
    friend class CSeq_id_Which_Tree;
 
    // Seq-id info
    CConstRef<CSeq_id_Info, CSeq_id_InfoLocker> m_Info;
    TPacked m_Packed;
    TVariant m_Variant;
};
 
/// Get CConstRef<CSeq_id> from a seq-id handle (for container
/// searching template functions)
template<>
inline
CConstRef<CSeq_id> Get_ConstRef_Seq_id(const CSeq_id_Handle& idh)
{
    return idh.GetSeqId();
}
 
 
/////////////////////////////////////////////////////////////////////
//
//  Inline methods
//
/////////////////////////////////////////////////////////////////////
 
/* @} */
 
 
/// Return best label for a sequence from single Seq-id, or set of Seq-ids.
/// Return empty string if the label cannot be determined.
/// GetDirectLabel() will return non-empty string only if the Seq-id is
/// very likely enough to get good label without loading full set of
/// sequence Seq-ids.
NCBI_SEQ_EXPORT string GetDirectLabel(const CSeq_id& id);
NCBI_SEQ_EXPORT string GetDirectLabel(const CSeq_id_Handle& id);
NCBI_SEQ_EXPORT string GetLabel(const CSeq_id& id);
NCBI_SEQ_EXPORT string GetLabel(const CSeq_id_Handle& id);
NCBI_SEQ_EXPORT string GetLabel(const vector<CSeq_id_Handle>& ids);
NCBI_SEQ_EXPORT string GetLabel(const vector<CRef<CSeq_id> >& ids);
 
 
NCBI_SEQ_EXPORT
CNcbiOstream& operator<<(CNcbiOstream& out, const CSeq_id_Handle& idh);
 
 
END_SCOPE(objects)
END_NCBI_SCOPE
 
BEGIN_STD_SCOPE
inline 
void swap(NCBI_NS_NCBI::objects::CSeq_id_Handle& idh1,
          NCBI_NS_NCBI::objects::CSeq_id_Handle& idh2)
{
    idh1.Swap(idh2);
}
 
END_STD_SCOPE
 
#endif  /* OBJECTS_OBJMGR___SEQ_ID_HANDLE__HPP */