- /*
- * ===========================================================================
- * PRODUCTION $Log: splign_simple.hpp,v $
- * PRODUCTION Revision 1000.0 2004/06/01 18:11:33 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
- * PRODUCTION
- * ===========================================================================
- */
- #ifndef ALGO_ALIGN_SPLIGN_SIMPLE__HPP
- #define ALGO_ALIGN_SPLIGN_SIMPLE__HPP
- /* $Id: splign_simple.hpp,v 1000.0 2004/06/01 18:11:33 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: Philip Johnson
- *
- * File Description:
- * CSplignSimple class definition -- simplified wrapper for calling splign
- *
- * ---------------------------------------------------------------------------
- */
- #include <corelib/ncbistd.hpp>
- #include <algo/align/splign/splign.hpp>
- #include <algo/blast/api/bl2seq.hpp>
- BEGIN_NCBI_SCOPE
- BEGIN_SCOPE(objects)
- class CSeq_loc;
- class CScope;
- class CSeq_align_set;
- END_SCOPE(objects)
- class NCBI_XALGOALIGN_EXPORT CSplignSimple {
- public:
- CSplignSimple(const objects::CSeq_loc &transcript,
- const objects::CSeq_loc &genomic,
- objects::CScope&);
- //Setters for customization; normally shouldn't need to adjust these
- CSplign& SetSplignObject(void) { return m_Splign; }
- blast::CBl2Seq& SetBlastObject(void) { return m_Blast; }
- const CSplign::TResults& Run(void);
- CRef<objects::CSeq_align_set> GetResultsAsAln(void) const;
- protected:
- CSplign m_Splign;
- blast::CBl2Seq m_Blast;
- CConstRef<objects::CSeq_id> m_TranscriptId;
- CConstRef<objects::CSeq_id> m_GenomicId;
- };
- END_NCBI_SCOPE
- /*
- * ===========================================================================
- *
- * $Log: splign_simple.hpp,v $
- * Revision 1000.0 2004/06/01 18:11:33 gouriano
- * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.3
- *
- * Revision 1.3 2004/05/04 20:49:03 johnson
- * return correct seq-ids in seq-align
- *
- * Revision 1.2 2004/05/04 15:23:44 ucko
- * Split splign code out of xalgoalign into new xalgosplign.
- *
- * Revision 1.1 2004/05/03 15:39:10 johnson
- * initial revision
- *
- *
- * ===========================================================================
- */
- #endif