dense_seg.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: Dense_seg.cpp,v $
 * PRODUCTION Revision 1000.4  2004/06/01 19:33:35  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.13
 * PRODUCTION
 * ===========================================================================
 */

/* $Id: Dense_seg.cpp,v 1000.4 2004/06/01 19:33:35 gouriano Exp $
 * ===========================================================================
 *
 *                            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:  .......
 *
 * File Description:
 *   .......
 *
 * Remark:
 *   This code was originally generated by application DATATOOL
 *   using specifications from the data definition file
 *   'seqalign.asn'.
 */

// standard includes
#include <ncbi_pch.hpp>
#include <algorithm>
#include <objects/seqalign/seqalign_exception.hpp>

// generated includes
#include <objects/seqalign/Dense_seg.hpp>

#include <objects/seqloc/Seq_id.hpp>
#include <objects/seqloc/Seq_loc.hpp>

// generated classes

BEGIN_NCBI_SCOPE

BEGIN_objects_SCOPE // namespace ncbi::objects::

// destructor
CDense_seg::~CDense_seg(void)
{
}


CDense_seg::TNumseg CDense_seg::CheckNumSegs() const
{
    const CDense_seg::TStarts&  starts  = GetStarts();
    const CDense_seg::TStrands& strands = GetStrands();
    const CDense_seg::TLens&    lens    = GetLens();
    const CDense_seg::TWidths&  widths  = GetWidths();

    const size_t& numrows = GetDim();
    const size_t& numsegs = GetNumseg();
    const size_t  num     = numrows * numsegs;

    if (starts.size() != num) {
        string errstr = string("CDense_seg::CheckNumSegs():")
            + " starts.size is inconsistent with dim * numseg";
        NCBI_THROW(CSeqalignException, eInvalidAlignment, errstr);
    }
    if (lens.size() != numsegs) {
        string errstr = string("CDense_seg::CheckNumSegs():")
            + " lens.size is inconsistent with numseg";
        NCBI_THROW(CSeqalignException, eInvalidAlignment, errstr);
    }
    if (strands.size()  &&  strands.size() != num) {
        string errstr = string("CDense_seg::CheckNumSegs():")
            + " strands.size is inconsistent with dim * numseg";
        NCBI_THROW(CSeqalignException, eInvalidAlignment, errstr);
    }
    if (widths.size()  &&  widths.size() != numrows) {
        string errstr = string("CDense_seg::CheckNumSegs():")
            + " widths.size is inconsistent with dim";
        NCBI_THROW(CSeqalignException, eInvalidAlignment, errstr);
    }
    return numsegs;
}


TSeqPos CDense_seg::GetSeqStart(TDim row) const
{
    const TDim&    dim    = GetDim();
    const TNumseg& numseg = CheckNumSegs();
    const TStarts& starts = GetStarts();

    if (row < 0  ||  row >= dim) {
        NCBI_THROW(CSeqalignException, eInvalidRowNumber,
                   "CDense_seg::GetSeqStop():"
                   " Invalid row number");
    }

    TSignedSeqPos start;
    if (CanGetStrands()  &&  GetStrands().size()  &&  GetStrands()[row] == eNa_strand_minus) {
        TNumseg seg = numseg;
        int pos = (seg - 1) * dim + row;
        while (seg--) {
            if ((start = starts[pos]) >= 0) {
                return start;
            }
            pos -= dim;
        }
    } else {
        TNumseg seg = -1;
        int pos = row;
        while (++seg < numseg) {
            if ((start = starts[pos]) >= 0) {
                return start;
            }
            pos += dim;
        }
    }
    NCBI_THROW(CSeqalignException, eInvalidAlignment,
               "CDense_seg::GetSeqStart(): Row is empty");
}


TSeqPos CDense_seg::GetSeqStop(TDim row) const
{
    const TDim& dim       = GetDim();
    const TNumseg& numseg = CheckNumSegs();
    const TStarts& starts = GetStarts();

    if (row < 0  ||  row >= dim) {
        NCBI_THROW(CSeqalignException, eInvalidRowNumber,
                   "CDense_seg::GetSeqStop():"
                   " Invalid row number");
    }

    TSignedSeqPos start;
    if (CanGetStrands()  &&  GetStrands().size()  &&  GetStrands()[row] == eNa_strand_minus) {
        TNumseg seg = -1;
        int pos = row;
        while (++seg < numseg) {
            if ((start = starts[pos]) >= 0) {
                return start + GetLens()[seg] - 1;
            }
            pos += dim;
        }
    } else {
        TNumseg seg = numseg;
        int pos = (seg - 1) * dim + row;
        while (seg--) {
            if ((start = starts[pos]) >= 0) {
                return start + GetLens()[seg] - 1;
            }
            pos -= dim;
        }        
    }
    NCBI_THROW(CSeqalignException, eInvalidAlignment,
               "CDense_seg::GetSeqStop(): Row is empty");
}


void CDense_seg::Validate(bool full_test) const
{
    const CDense_seg::TStarts&  starts  = GetStarts();
    const CDense_seg::TStrands& strands = GetStrands();
    const CDense_seg::TLens&    lens    = GetLens();
    const CDense_seg::TWidths&  widths  = GetWidths();

    const size_t& numrows = CheckNumRows();
    const size_t& numsegs = CheckNumSegs();

    if (full_test) {
        const size_t  max     = numrows * (numsegs -1);

        bool strands_exist = !strands.empty();

        size_t numseg = 0, numrow = 0, offset = 0;
        for (numrow = 0;  numrow < numrows;  numrow++) {
            TSignedSeqPos min_start = -1, start;
            bool plus = strands_exist ? 
                strands[numrow] != eNa_strand_minus:
                true;
            
            if (plus) {
                offset = 0;
            } else {
                offset = max;
            }
            
            for (numseg = 0;  numseg < numsegs;  numseg++) {
                start = starts[offset + numrow];
                if (start >= 0) {
                    if (start < min_start) {
                        string errstr = string("CDense_seg::Validate():")
                            + " Starts are not consistent!"
                            + " Row=" + NStr::IntToString(numrow) +
                            " Seg=" + NStr::IntToString(plus ? numseg :
                                                        numsegs - 1 - numseg) +
                            " MinStart=" + NStr::IntToString(min_start) +
                            " Start=" + NStr::IntToString(start);
                        
                        NCBI_THROW(CSeqalignException, eInvalidAlignment,
                                   errstr);
                    }
                    min_start = start + 
                        lens[plus ? numseg : numsegs - 1 - numseg] *
                        (widths.size() == numrows ?
                         widths[numrow] : 1);
                }
                if (plus) {
                    offset += numrows;
                } else {
                    offset -= numrows;
                }
            }
        }
    }
}


//-----------------------------------------------------------------------------
// PRE : none
// POST: same alignment, opposite orientation
void CDense_seg::Reverse(void)
{
    //flip strands
    NON_CONST_ITERATE (CDense_seg::TStrands, i, SetStrands()) {
        switch (*i) {
        case eNa_strand_plus:  *i = eNa_strand_minus; break;
        case eNa_strand_minus: *i = eNa_strand_plus;  break;
        default:                    break;//do nothing if not + or -
        }
    }

    //reverse list o' lengths
    {
        CDense_seg::TLens::iterator f = SetLens().begin();
        CDense_seg::TLens::iterator r = SetLens().end();
        while (f < r) {
            swap(*(f++), *(--r));
        }
    }

    //reverse list o' starts
    CDense_seg::TStarts &starts = SetStarts();
    int f = 0;
    int r = (GetNumseg() - 1) * GetDim();
    while (f < r) {
        for (int i = 0;  i < GetDim();  ++i) {
            swap(starts[f+i], starts[r+i]);
        }
        f += GetDim();
        r -= GetDim();
    }
}