alnmix.hpp

ncbi源码

    int                   m_DS_Count;
    const CBioseq_Handle* m_BioseqHandle;
    CRef<CSeq_id>         m_SeqId;
    int                   m_Score;
    bool                  m_IsAA;
    int                   m_Width;
    int                   m_Frame;
    bool                  m_PositiveStrand;
    TStarts               m_Starts;
    CAlnMixSeq *          m_RefBy;
    CAlnMixSeq *          m_ExtraRow;
    int                   m_RowIndex;
    int                   m_SeqIndex;
    int                   m_DSIndex;
    TStarts::iterator     m_StartIt;
    TMatchList            m_MatchList;

    CSeqVector& GetSeqVector(void) {
        if ( !m_SeqVector ) {
            m_SeqVector = new CSeqVector
                (m_BioseqHandle->GetSeqVector(CBioseq_Handle::eCoding_Iupac));
        }
        return *m_SeqVector;
    }
private:
    CRef<CSeqVector> m_SeqVector;
};


class CAlnMixMatch : public CObject
{
public:
    CAlnMixMatch(void)
        : m_Score(0), m_Start1(0), m_Start2(0),
          m_Len(0), m_StrandsDiffer(false), m_DSIndex(0)
    {};
        
    int                              m_Score;
    CAlnMixSeq                       * m_AlnSeq1, * m_AlnSeq2;
    TSeqPos                          m_Start1, m_Start2, m_Len;
    bool                             m_StrandsDiffer;
    int                              m_DSIndex;
    CAlnMixSeq::TMatchList::iterator m_MatchIter1, m_MatchIter2;
};


///////////////////////////////////////////////////////////
///////////////////// inline methods //////////////////////
///////////////////////////////////////////////////////////

inline
CScope& CAlnMix::GetScope() const
{
    return const_cast<CScope&>(*m_Scope);
}


inline
const CAlnMix::TConstDSs& CAlnMix::GetInputDensegs() const
{
    return m_InputDSs;
}


inline
const CAlnMix::TConstAlns& CAlnMix::GetInputSeqAligns() const
{
    return m_InputAlns;
}


inline
const CDense_seg& CAlnMix::GetDenseg() const
{
    if (!m_DS) {
        NCBI_THROW(CAlnException, eMergeFailure,
                   "CAlnMix::GetDenseg(): "
                   "Dense_seg is not available until after Merge()");
    }
    return *m_DS;
}


inline
const CSeq_align& CAlnMix::GetSeqAlign() const
{
    if (!m_Aln) {
        NCBI_THROW(CAlnException, eMergeFailure,
                   "CAlnMix::GetSeqAlign(): "
                   "Seq_align is not available until after Merge()");
    }
    return *m_Aln;
}



///////////////////////////////////////////////////////////
////////////////// end of inline methods //////////////////
///////////////////////////////////////////////////////////

END_objects_SCOPE // namespace ncbi::objects::

END_NCBI_SCOPE

/*
* ===========================================================================
*
* $Log: alnmix.hpp,v $
* Revision 1000.3  2004/06/01 19:38:16  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.38
*
* Revision 1.38  2004/05/25 16:00:20  todorov
* remade truncation of overlaps
*
* Revision 1.37  2004/03/30 23:27:32  todorov
* Switch from CAlnMix::x_RankSeqId() to CSeq_id::BestRank()
*
* Revision 1.36  2004/03/15 17:46:03  todorov
* Avoid multiple inheritance since Workshop has problems placing the vtables.
* Now CAlnMix inherits from SSeqIdChooser which inherits from CObject
*
* Revision 1.35  2004/03/09 17:15:46  todorov
* + SSeqIdChooser implementation
*
* Revision 1.34  2003/12/22 18:30:38  todorov
* ObjMgr is no longer created internally. Scope should be passed as a reference in the ctor
*
* Revision 1.33  2003/12/08 21:28:04  todorov
* Forced Translation of Nucleotide Sequences
*
* Revision 1.32  2003/11/03 14:43:52  todorov
* Use CDense_seg::Validate()
*
* Revision 1.31  2003/08/20 19:35:41  todorov
* Added x_ValidateDenseg
*
* Revision 1.30  2003/08/20 15:06:25  todorov
* include path fixed
*
* Revision 1.29  2003/08/20 14:35:14  todorov
* Support for NA2AA Densegs
*
* Revision 1.28  2003/06/26 21:35:53  todorov
* + fFillUnalignedRegions
*
* Revision 1.27  2003/06/25 15:17:26  todorov
* truncation consistent for the whole segment now
*
* Revision 1.26  2003/06/24 15:24:28  todorov
* added optional truncation of overlaps
*
* Revision 1.25  2003/06/09 20:54:12  todorov
* Use of ObjMgr is now optional
*
* Revision 1.24  2003/06/02 16:01:38  dicuccio
* Rearranged include/objects/ subtree.  This includes the following shifts:
*     - include/objects/alnmgr --> include/objtools/alnmgr
*     - include/objects/cddalignview --> include/objtools/cddalignview
*     - include/objects/flat --> include/objtools/flat
*     - include/objects/objmgr/ --> include/objmgr/
*     - include/objects/util/ --> include/objmgr/util/
*     - include/objects/validator --> include/objtools/validator
*
* Revision 1.23  2003/05/30 17:42:45  todorov
* x_CreateSegmentsVector now uses a stack to order the segs
*
* Revision 1.22  2003/05/09 16:41:46  todorov
* Optional mixing of the query sequence only
*
* Revision 1.21  2003/03/28 16:47:22  todorov
* Introduced TAddFlags (fCalcScore for now)
*
* Revision 1.20  2003/03/26 16:38:31  todorov
* mix independent densegs
*
* Revision 1.19  2003/03/10 22:12:10  todorov
* fixed x_CompareAlnMatchScores callback
*
* Revision 1.18  2003/03/05 17:42:28  todorov
* Allowing multiple mixes + general case speed optimization
*
* Revision 1.17  2003/02/11 21:32:37  todorov
* fMinGap optional merging algorithm
*
* Revision 1.16  2003/01/23 16:30:36  todorov
* Moved calc score to alnvec
*
* Revision 1.15  2003/01/22 20:13:02  vasilche
* Changed use of CBioseqHandle::GetSeqVector() method.
*
* Revision 1.14  2003/01/10 00:42:42  todorov
* Optional sorting of seqs by score
*
* Revision 1.13  2003/01/02 16:39:57  todorov
* Added accessors to the input data
*
* Revision 1.12  2002/12/26 12:38:08  dicuccio
* Added Win32 export specifiers
*
* Revision 1.11  2002/12/24 16:20:57  todorov
* Fixed initializing of a CTypeConstIterator
*
* Revision 1.10  2002/12/23 18:03:41  todorov
* Support for putting in and getting out Seq-aligns
*
* Revision 1.9  2002/12/19 15:09:07  ucko
* Reorder some definitions to make Compaq's C++ compiler happy.
*
* Revision 1.8  2002/12/19 00:06:55  todorov
* Added optional consolidation of segments that are gapped on the query.
*
* Revision 1.7  2002/12/18 03:47:05  todorov
* created an algorithm for mixing alignments that share a single sequence.
*
* Revision 1.6  2002/11/08 19:43:33  grichenk
* CConstRef<> constructor made explicit
*
* Revision 1.5  2002/11/04 21:28:57  grichenk
* Fixed usage of const CRef<> and CRef<> constructor
*
* Revision 1.4  2002/10/25 20:02:20  todorov
* new fTryOtherMethodOnFail flag
*
* Revision 1.3  2002/10/24 21:31:33  todorov
* adding Dense-segs instead of Seq-aligns
*
* Revision 1.2  2002/10/08 18:02:09  todorov
* changed the aln lst input param
*
* Revision 1.1  2002/08/23 14:43:50  ucko
* Add the new C++ alignment manager to the public tree (thanks, Kamen!)
*
*
* ===========================================================================
*/

#endif // OBJECTS_ALNMGR___ALNMIX__HPP