alnvec.hpp

ncbi源码

{
    return GetSeqString(buffer, row,
                        GetStart(row, seg, offset),
                        GetStop (row, seg, offset));
}


inline
string& CAlnVec::GetSeqString(string& buffer,
                              TNumrow row,
                              const CAlnMap::TRange& seq_rng) const
{
    return GetSeqString(buffer, row,
                        seq_rng.GetFrom(),
                        seq_rng.GetTo());
}


inline
void CAlnVec::SetGapChar(TResidue gap_char)
{
    m_GapChar = gap_char;
    m_set_GapChar = true;
}

inline
void CAlnVec::UnsetGapChar()
{
    m_set_GapChar = false;
}

inline
bool CAlnVec::IsSetGapChar() const
{
    return m_set_GapChar;
}

inline
CSeqVector::TResidue CAlnVec::GetGapChar(TNumrow row) const
{
    if (IsSetGapChar()) {
        return m_GapChar;
    } else {
        return x_GetSeqVector(row).GetGapChar();
    }
}

inline
void CAlnVec::SetEndChar(TResidue end_char)
{
    m_EndChar = end_char;
    m_set_EndChar = true;
}

inline
bool CAlnVec::IsSetEndChar() const
{
    return m_set_EndChar;
}

inline
CSeqVector::TResidue CAlnVec::GetEndChar() const
{
    if (IsSetEndChar()) {
        return m_EndChar;
    } else {
        return ' ';
    }
}


//
// these are a temporary work-around
// CSeqportUtil contains routines for converting sequence data from one
// format to another, but it places a requirement on the data: it must in
// a CSeq_data class.  I can get this for my data, but it is a bit of work
// (much more work than calling CSeqVector::GetSeqdata(), which, if I use the
// internal sequence vector, is guaranteed to be in IUPAC notation)
//
inline
unsigned char CAlnVec::FromIupac(unsigned char c)
{
    switch (c)
    {
    case 'A': return 0x01;
    case 'C': return 0x02;
    case 'M': return 0x03;
    case 'G': return 0x04;
    case 'R': return 0x05;
    case 'S': return 0x06;
    case 'V': return 0x07;
    case 'T': return 0x08;
    case 'W': return 0x09;
    case 'Y': return 0x0a;
    case 'H': return 0x0b;
    case 'K': return 0x0c;
    case 'D': return 0x0d;
    case 'B': return 0x0e;
    case 'N': return 0x0f;
    }

    return 0x00;
}

inline unsigned char CAlnVec::ToIupac(unsigned char c)
{
    const char *data = "-ACMGRSVTWYHKDBN";
    return ((c < 16) ? data[c] : 0);
}


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

END_objects_SCOPE // namespace ncbi::objects::
END_NCBI_SCOPE


/*
 * ===========================================================================
 *
 * $Log: alnvec.hpp,v $
 * Revision 1000.1  2004/04/12 17:34:45  gouriano
 * PRODUCTION: UPGRADED [CATCHUP_003] Dev-tree R1.33
 *
 * Revision 1.33  2004/03/30 16:37:43  todorov
 * +GetColumnVector comments
 *
 * Revision 1.32  2003/12/22 19:14:13  todorov
 * Only left constructors that accept CScope&
 *
 * Revision 1.31  2003/12/22 18:30:38  todorov
 * ObjMgr is no longer created internally. Scope should be passed as a reference in the ctor
 *
 * Revision 1.30  2003/12/18 19:48:28  todorov
 * + GetColumnVector & CalculatePercentIdentity
 *
 * Revision 1.29  2003/12/17 17:01:07  todorov
 * Added translated GetResidue
 *
 * Revision 1.28  2003/12/10 17:17:40  todorov
 * CalcScore now const
 *
 * Revision 1.27  2003/10/15 21:18:57  yazhuk
 * Made TResidue declaration public
 *
 * Revision 1.26  2003/09/10 15:28:11  todorov
 * improved the Get{,Seg,Aln}SeqString comments
 *
 * Revision 1.25  2003/08/29 18:17:50  dicuccio
 * Changed API for creating consensus - CreateConsensus() now returns the new
 * dense-seg, rather than altering the existing alignment manager
 *
 * Revision 1.24  2003/08/25 16:35:06  todorov
 * exposed GetWidth
 *
 * Revision 1.23  2003/08/20 14:35:14  todorov
 * Support for NA2AA Densegs
 *
 * Revision 1.22  2003/07/23 20:40:54  todorov
 * +aln_starts for the inserts in GetWhole...
 *
 * Revision 1.21  2003/07/17 22:46:09  todorov
 * +GetWholeAlnSeqString
 *
 * Revision 1.20  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 1.19  2003/02/11 21:32:37  todorov
 * fMinGap optional merging algorithm
 *
 * Revision 1.18  2003/01/27 22:30:24  todorov
 * Attune to seq_vector interface change
 *
 * Revision 1.17  2003/01/23 21:30:50  todorov
 * Removing the original, inefficient GetXXXString methods
 *
 * Revision 1.16  2003/01/23 16:31:56  todorov
 * Added calc score methods
 *
 * Revision 1.15  2003/01/22 22:54:04  todorov
 * Removed an obsolete function
 *
 * Revision 1.14  2003/01/17 18:17:29  todorov
 * Added a better-performing set of GetXXXString methods
 *
 * Revision 1.13  2003/01/16 20:46:30  todorov
 * Added Gap/EndChar set flags
 *
 * Revision 1.12  2002/12/26 12:38:08  dicuccio
 * Added Win32 export specifiers
 *
 * Revision 1.11  2002/10/21 19:15:12  todorov
 * added GetAlnSeqString
 *
 * Revision 1.10  2002/10/04 17:31:36  todorov
 * Added gap char and end char
 *
 * Revision 1.9  2002/09/27 17:01:16  todorov
 * changed order of params for GetSeqPosFrom{Seq,Aln}Pos
 *
 * Revision 1.8  2002/09/25 19:34:15  todorov
 * "un-inlined" x_GetSeqVector
 *
 * Revision 1.7  2002/09/25 18:16:26  dicuccio
 * Reworked computation of consensus sequence - this is now stored directly
 * in the underlying CDense_seg
 * Added exception class; currently used only on access of non-existent
 * consensus.
 *
 * Revision 1.6  2002/09/23 18:22:45  vakatov
 * Workaround an older MSVC++ compiler bug.
 * Get rid of "signed/unsigned" comp.warning, and some code prettification.
 *
 * Revision 1.5  2002/09/19 18:22:28  todorov
 * New function name for GetSegSeqString to avoid confusion
 *
 * Revision 1.4  2002/09/19 18:19:18  todorov
 * fixed unsigned to signed return type for GetConsensusSeq{Start,Stop}
 *
 * Revision 1.3  2002/09/05 19:31:18  dicuccio
 * - added ability to reference a consensus sequence for a given alignment
 * - added caching of CSeqVector (big performance win)
 * - many small bugs fixed
 *
 * Revision 1.2  2002/08/29 18:40:53  dicuccio
 * added caching mechanism for CSeqVector - this greatly improves speed in
 * accessing sequence data.
 *
 * 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___ALNVEC__HPP */