std_seg.cpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: Std_seg.cpp,v $
 * PRODUCTION Revision 1000.1  2004/06/01 19:33:42  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
 * PRODUCTION
 * ===========================================================================
 */

/* $Id: Std_seg.cpp,v 1000.1 2004/06/01 19:33:42 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

// generated includes
#include <ncbi_pch.hpp>
#include <objects/seqalign/Std_seg.hpp>

// generated classes

BEGIN_NCBI_SCOPE

BEGIN_objects_SCOPE // namespace ncbi::objects::

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


CStd_seg::TDim CStd_seg::CheckNumRows() const
{
    const size_t& dim = GetDim();
    if (dim != GetLoc().size()) {
        NCBI_THROW(CSeqalignException, eInvalidAlignment,
                   "CStd_seg::CheckNumRows():"
                   " loc.size is inconsistent with dim");
    }
    if (IsSetIds()  &&  dim != GetIds().size()) {
        NCBI_THROW(CSeqalignException, eInvalidAlignment,
                   "CStd_seg::CheckNumRows():"
                   " ids.size is inconsistent with dim");
    }
    return dim;
}


TSignedSeqPos CStd_seg::GetSeqStart(TDim row) const
{
    TDim row_i = 0;
    ITERATE (CStd_seg::TLoc, i, GetLoc()) {
        if (row_i++ == row) {
            if ((*i)->IsInt()) {
                return (*i)->GetInt().GetFrom();
            } else {
                return -1;
            }
        }
    }
    if (row < 0  ||  row >= GetDim()) {
        NCBI_THROW(CSeqalignException, eInvalidRowNumber,
                   "CStd_seg::GetSeqStart():"
                   " Invalid row number");
    }
    NCBI_THROW(CSeqalignException, eInvalidAlignment,
               "CStd_seg::GetSeqStart():"
               " loc.size is inconsistent with dim");
}


TSignedSeqPos CStd_seg::GetSeqStop(TDim row) const
{
    TDim dim = 0;
    ITERATE (CStd_seg::TLoc, i, GetLoc()) {
        if (dim++ == row) {
            if ((*i)->IsInt()) {
                return (*i)->GetInt().GetTo();
            } else {
                return -1;
            }
        }
    }
    if (row < 0  ||  row >= GetDim()) {
        NCBI_THROW(CSeqalignException, eInvalidRowNumber,
                   "CStd_seg::GetSeqStop():"
                   " Invalid row number");
    }
    NCBI_THROW(CSeqalignException, eInvalidAlignment,
               "CStd_seg::GetSeqStop():"
               " loc.size is inconsistent with dim");
}


void CStd_seg::Validate(bool full_test) const
{
    CheckNumRows();
}


CRange<TSignedSeqPos> CStd_seg::GetSeqRange(TDim row) const
{
    TDim dim = 0;
    ITERATE (CStd_seg::TLoc, i, GetLoc()) {
        if (dim++ == row) {
            if ((*i)->IsInt()) {
                const CSeq_interval& interval = (*i)->GetInt();
                return CRange<TSignedSeqPos>
                    (interval.GetFrom(), interval.GetTo());
            } else {
                return CRange<TSignedSeqPos>(-1, -1);
            }
        }
    }
    if (row < 0  ||  row >= GetDim()) {
        NCBI_THROW(CSeqalignException, eInvalidRowNumber,
                   "CStd_seg::GetSeqRange():"
                   " Invalid row number");
    }
    NCBI_THROW(CSeqalignException, eInvalidAlignment,
               "CStd_seg::GetSeqRange():"
               " loc.size is inconsistent with dim");
}


END_objects_SCOPE // namespace ncbi::objects::

END_NCBI_SCOPE


/*
* ===========================================================================
*
* $Log: Std_seg.cpp,v $
* Revision 1000.1  2004/06/01 19:33:42  gouriano
* PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.2
*
* Revision 1.2  2004/05/19 17:25:43  gorelenk
* Added include of PCH - ncbi_pch.hpp
*
* Revision 1.1  2003/09/16 16:17:12  todorov
* Added validation methods. Added seq range methods
*
*
* ===========================================================================
*/
/* Original file checksum: lines: 64, chars: 1879, CRC32: d01e569e */