sequence_item.cpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: sequence_item.cpp,v $
- * PRODUCTION Revision 1000.1 2004/06/01 19:45:28 gouriano
- * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: sequence_item.cpp,v 1000.1 2004/06/01 19:45:28 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: Mati Shomrat, NCBI
- *
- * File Description:
- * flat-file generator -- origin item implementation
- *
- */
- #include <ncbi_pch.hpp>
- #include <corelib/ncbistd.hpp>
- #include <objects/seq/Bioseq.hpp>
- #include <objects/seqloc/Seq_loc.hpp>
- #include <objects/seqloc/Seq_interval.hpp>
- #include <objmgr/util/sequence.hpp>
- #include <objtools/format/formatter.hpp>
- #include <objtools/format/text_ostream.hpp>
- #include <objtools/format/items/sequence_item.hpp>
- #include <objtools/format/context.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- CSequenceItem::CSequenceItem
- (TSeqPos from,
- TSeqPos to,
- bool first,
- CBioseqContext& ctx) :
- CFlatItem(&ctx),
- m_From(from), m_To(to - 1), m_First(first)
- {
- x_GatherInfo(ctx);
- }
- void CSequenceItem::Format
- (IFormatter& formatter,
- IFlatTextOStream& text_os) const
- {
- formatter.FormatSequence(*this, text_os);
- }
- const CSeqVector& CSequenceItem::GetSequence(void) const
- {
- return m_Sequence;
- }
- TSeqPos CSequenceItem::GetFrom(void) const
- {
- return m_From + 1;
- }
- TSeqPos CSequenceItem::GetTo(void) const
- {
- return m_To + 1;
- }
- bool CSequenceItem::IsFirst(void) const
- {
- return m_First;
- }
- /***************************************************************************/
- /* PRIVATE */
- /***************************************************************************/
- void CSequenceItem::x_GatherInfo(CBioseqContext& ctx)
- {
- x_SetObject(*ctx.GetHandle().GetCompleteBioseq());
- const CSeq_loc& loc = ctx.GetLocation();
- TSeqPos offset = loc.GetStart(kInvalidSeqPos);
- TSeqPos start = m_From + offset;
- TSeqPos end = min(m_To + offset, ctx.GetHandle().GetInst_Length() - 1);
-
- CSeq_loc region;
- CSeq_loc::TInt& ival = region.SetInt();
- region.SetId(*ctx.GetPrimaryId());
- ival.SetFrom(start);
- ival.SetTo(end);
-
- m_Sequence =
- ctx.GetHandle().GetSequenceView(region, CBioseq_Handle::eViewConstructed);
- CSeqVector::TCoding code = CSeq_data::e_Iupacna;
- if ( ctx.IsProt() ) {
- code = ctx.Config().IsModeRelease() ?
- CSeq_data::e_Iupacaa : CSeq_data::e_Ncbieaa;
- }
- m_Sequence.SetCoding(code);
- }
- END_SCOPE(objects)
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- *
- * $Log: sequence_item.cpp,v $
- * Revision 1000.1 2004/06/01 19:45:28 gouriano
- * PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.7
- *
- * Revision 1.7 2004/05/21 21:42:54 gorelenk
- * Added PCH ncbi_pch.hpp
- *
- * Revision 1.6 2004/05/07 15:23:51 shomrat
- * Removed unreferenced varaible
- *
- * Revision 1.5 2004/04/27 15:14:36 shomrat
- * Bug fix
- *
- * Revision 1.4 2004/04/22 15:56:17 shomrat
- * Support partial region
- *
- * Revision 1.3 2004/02/11 22:56:37 shomrat
- * use IsModeRelease method
- *
- * Revision 1.2 2003/12/18 17:43:36 shomrat
- * context.hpp moved
- *
- * Revision 1.1 2003/12/17 20:24:39 shomrat
- * Initial Revision (adapted from flat lib)
- *
- *
- * ===========================================================================
- */