struct_util.hpp
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- /*
- * ===========================================================================
- * PRODUCTION $Log: struct_util.hpp,v $
- * PRODUCTION Revision 1000.0 2004/06/01 18:12:13 gouriano
- * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.5
- * PRODUCTION
- * ===========================================================================
- */
- /* $Id: struct_util.hpp,v 1000.0 2004/06/01 18:12:13 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.
- *
- * ===========================================================================
- *
- * Authors: Paul Thiessen
- *
- * File Description:
- * alignment utility algorithms
- *
- * ===========================================================================
- */
- #ifndef STRUCT_UTIL__HPP
- #define STRUCT_UTIL__HPP
- #include <corelib/ncbistd.hpp>
- #include <objects/seqset/Seq_entry.hpp>
- #include <objects/seq/Seq_annot.hpp>
- BEGIN_SCOPE(struct_util)
- class SequenceSet;
- class AlignmentSet;
- class BlockMultipleAlignment;
- class AlignmentUtility
- {
- public:
- typedef std::list < ncbi::CRef < ncbi::objects::CSeq_entry > > SeqEntryList;
- typedef std::list< ncbi::CRef< ncbi::objects::CSeq_annot > > SeqAnnotList;
- AlignmentUtility(const ncbi::objects::CSeq_entry& seqEntry, const SeqAnnotList& seqAnnots);
- AlignmentUtility(const SeqEntryList& seqEntries, const SeqAnnotList& seqAnnots);
- ~AlignmentUtility();
- bool Okay(void) const { return m_okay; }
- // Get ASN data
- const SeqAnnotList& GetSeqAnnots(void);
- // do the intersect-by-master (IBM) algorithm
- bool DoIBM(void);
- // do the leave-one-out (LOO) algorithm (implies IBM) using the block aligner.
- // Numbering in these arguments starts from zero. Note that this currently requires
- // the file "data/BLOSUM62" to be present, used for PSSM calculation.
- bool DoLeaveOneOut(
- unsigned int row, const std::vector < unsigned int >& blocksToRealign, // what to realign
- double percentile, unsigned int extension, unsigned int cutoff); // to calculate max loop lengths
- private:
- // sequence data
- SeqEntryList m_seqEntries;
- SequenceSet *m_sequenceSet;
- // alignment data - the idea is that since these are redundant, we'll either have the
- // SeqAnnots+AlignmentSet or the BlockMultipleAlignment, not (usually) both. If one
- // changes, the other should be removed or recreated; if both are present, they must
- // contain the same data.
- SeqAnnotList m_seqAnnots;
- AlignmentSet *m_alignmentSet;
- BlockMultipleAlignment *m_currentMultiple;
- void Init(void);
- bool m_okay;
- // to delete parts of the data
- void RemoveMultiple(void);
- void RemoveAlignAnnot(void);
- };
- END_SCOPE(struct_util)
- #endif // STRUCT_UTIL__HPP
- /*
- * ---------------------------------------------------------------------------
- * $Log: struct_util.hpp,v $
- * Revision 1000.0 2004/06/01 18:12:13 gouriano
- * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.5
- *
- * Revision 1.5 2004/05/28 09:43:35 thiessen
- * add comment about data/BLOSUM62
- *
- * Revision 1.4 2004/05/26 14:30:53 thiessen
- * adjust handling of alingment data ; add row ordering
- *
- * Revision 1.3 2004/05/26 02:41:13 thiessen
- * progress towards LOO - all but PSSM and row ordering
- *
- * Revision 1.2 2004/05/25 15:50:46 thiessen
- * add BlockMultipleAlignment, IBM algorithm
- *
- * Revision 1.1 2004/05/24 23:05:10 thiessen
- * initial checkin
- *
- */