seqlocinfo.hpp

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/*  $Id: seqlocinfo.hpp 45453 2010-04-15 13:44:21Z satskyse $
* ===========================================================================
*
*                            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.
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*  and reliability of the software and data, the NLM and the U.S.
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*  may be obtained by using this software or data. The NLM and the U.S.
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* Author:  Christiam Camacho, Vahram Avagyan
*
*/
 
#ifndef OBJECTS_SEQ___SEQLOCINFO__HPP
#define OBJECTS_SEQ___SEQLOCINFO__HPP
 
#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_interval.hpp>
#include <util/range.hpp>       // For TSeqRange
 
BEGIN_NCBI_SCOPE
 
BEGIN_SCOPE(objects)
    class CSeq_loc;
    class CPacked_seqint;
END_SCOPE(objects)
 
//Note: The following types have been refactored
//      from algo/blast/api/blast_aux.hpp
 
///structure for seqloc info
class NCBI_SEQ_EXPORT CSeqLocInfo : public CObject {
public:
    enum ETranslationFrame {
        eFramePlus1  =  1,
        eFramePlus2  =  2,
        eFramePlus3  =  3,
        eFrameMinus1 = -1,
        eFrameMinus2 = -2,
        eFrameMinus3 = -3,
        eFrameNotSet = 0
    };
 
    CSeqLocInfo(objects::CSeq_interval* interval, int frame)
        : m_Interval(interval)
    { SetFrame(frame); }
 
    CSeqLocInfo(objects::CSeq_id& id, TSeqRange& range, int frame)
        : m_Interval(new objects::CSeq_interval(id, range.GetFrom(),
                                                range.GetToOpen()))
    { SetFrame(frame); }
 
    const objects::CSeq_interval& GetInterval() const { return *m_Interval; }
 
    const objects::CSeq_id& GetSeqId() const { return m_Interval->GetId(); }
 
    void SetInterval(objects::CSeq_interval* interval) 
    { m_Interval.Reset(interval); }
 
    /// Convert the frame to a strand
    objects::ENa_strand GetStrand() const;
 
    int GetFrame() const { return (int) m_Frame; }
 
    void SetFrame(int frame); // Throws exception on out-of-range input
 
    operator TSeqRange() const {
        return TSeqRange(m_Interval->GetFrom(), m_Interval->GetTo()-1);
    }
 
    operator pair<TSeqPos, TSeqPos>() const {
        return make_pair<TSeqPos, TSeqPos>(m_Interval->GetFrom(), 
                                           m_Interval->GetTo());
    }
 
    friend ostream& operator<<(ostream& out, const CSeqLocInfo& rhs) {
        out << "CSeqLocInfo = { " << MSerial_AsnText << *rhs.m_Interval 
            << "ETranslationFrame = " << rhs.m_Frame << "\n}";
        return out;
    }
 
    bool operator==(const CSeqLocInfo& rhs) const;
 
    bool operator!=(const CSeqLocInfo& rhs) const {
        return ! (*this == rhs);
    }
 
private:
    CRef<objects::CSeq_interval> m_Interval; 
    ETranslationFrame m_Frame;         // For translated nucleotide sequence
};
 
typedef list< CRef<CSeqLocInfo> >   TSeqLocInfoCRefList;
 
/// Collection of masked regions for a single query sequence
class NCBI_SEQ_EXPORT TMaskedQueryRegions : public TSeqLocInfoCRefList
{
public:
    /// Return a new instance of this object that is restricted to the location
    /// specified
    /// @param location location describing the range to restrict. Note that
    /// only the provided range is examined, the Seq-id and strand of the 
    /// location (if assigned and different from unknown) is copied verbatim 
    /// into the return value of this method [in]
    /// @return empty TMaskedQueryRegions if this object is empty, otherwise 
    /// the intersection of location and this object
    TMaskedQueryRegions 
    RestrictToSeqInt(const objects::CSeq_interval& location) const;
 
    /// Converts this object to a CPacked_seqint (this is the convention used
    /// to encode masking locations in the network BLAST 4 protocol)
    CRef<objects::CPacked_seqint> ConvertToCPacked_seqint() const;
 
    /// Returns true if there are masks on the negative strand
    bool HasNegativeStrandMasks() const;
};
 
/// TMaskedSubjRegions defined as synonym to TMaskedQueryRegions
typedef TMaskedQueryRegions TMaskedSubjRegions;
 
/// Collection of masked regions for all queries in a BLAST search
/// @note this supports tra
typedef vector< TMaskedQueryRegions > TSeqLocInfoVector;
 
END_NCBI_SCOPE
 
#endif  /* OBJECTS_SEQ___SEQLOCINFO__HPP */