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/* $Id: align.hpp,v 1.5 2008/03/26 16:04:29 rotmistr 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: Kirill Rotmistrovsky
*
* ========================================================================= */
#ifndef EPCR_ALIGN__HPP
#define EPCR_ALIGN__HPP
#include <epcr/build_cfg.h>
#include <epcr/minilcs.hpp>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(EPCR_SCOPE)
class IAlign;
class CAlignExact;
class CAlignNoGaps;
class CAlignFast;
class CAlignLCS;
class CAlignCompromise;
char * FlipSequence(const char * seq, unsigned len= ~0U);
char * UCaseSequence(const char * seq, unsigned len= ~0U);
class IAlign
{
public:
virtual ~IAlign() throw () {};
virtual bool Forward(const char * seq_ptr,
const char * seq_end,
const char * primer,
int length) = 0;
virtual bool Reverse(const char * seq_start,
const char * seq_ptr,
const char * primer,
int length) = 0;
virtual int GetIdentities() const { return 0; }
virtual int GetMismatches() const { return 0; }
virtual int GetGaps() const { return 0; }
virtual int GetFloppy() const { return 0; }
};
class CAlignExact:public virtual IAlign
{
public:
CAlignExact():m_Identities(0) {}
virtual ~CAlignExact() throw () {};
bool Forward(const char * seq_ptr,
const char * seq_end,
const char * primer,
int length);
bool Reverse(const char * seq_start,
const char * seq_ptr,
const char * primer,
int length);
int GetIdentities() const { return m_Identities; }
protected:
int m_Identities;
};
class CAlignNoGaps:public CAlignExact
{
public:
virtual ~CAlignNoGaps() throw () {};
bool Forward(const char * seq_ptr,
const char * seq_end,
const char * primer,
int length);
bool Reverse(const char * seq_start,
const char * seq_ptr,
const char * primer,
int length);
CAlignNoGaps(int mm=1):m_MaxMismatch(mm),m_Mism(0) {}
int GetMismatches() const { return m_Mism; }
protected:
bool x_Compare(const char * a, const char * b, int l);
protected:
int m_MaxMismatch;
int m_Mism;
};
class CAlignFast:public CAlignNoGaps
{
public:
virtual ~CAlignFast() throw () {};
bool Forward(const char * seq_ptr,
const char * seq_end,
const char * primer,
int length);
bool Reverse(const char * seq_start,
const char * seq_ptr,
const char * primer,
int length);
CAlignFast(int mm=1, int gg=1):CAlignNoGaps(mm),m_MaxGaps(gg),m_Gaps(0) {}
int GetGaps() const { return m_Gaps; }
protected:
int m_MaxGaps;
int m_Gaps;
};
class CAlignLCS:public virtual IAlign
{
public:
virtual ~CAlignLCS() throw () {};
bool Forward(const char * seq_ptr,
const char * seq_end,
const char * primer,
int length);
bool Reverse(const char * seq_start,
const char * seq_ptr,
const char * primer,
int length);
CAlignLCS(int mm=1, int gg=1);
int GetIdentities() const { return m_Matrix.GetMatches(); }
int GetMismatches() const { return m_Matrix.GetMismatches(); }
int GetGaps() const { return m_Matrix.GetGaps(); }
protected:
int m_MaxMismatch;
int m_MaxGaps;
CLcsMatrix<char> m_Matrix;
};
class CAlignCompromise:public virtual CAlignLCS, public virtual CAlignNoGaps
{
public:
virtual ~CAlignCompromise() throw () {};
bool Forward(const char * seq_ptr,
const char * seq_end,
const char * primer,
int length);
bool Reverse(const char * seq_start,
const char * seq_ptr,
const char * primer,
int length);
CAlignCompromise(int mm=1, int gg=1);
int GetIdentities() const { return m_Identities; }
int GetMismatches() const { return m_Mismatches; }
int GetGaps() const { return m_Gaps; }
protected:
int m_Identities, m_Mismatches, m_Gaps;
};
//class CAlignFloppy : public virtual CAlignLCS
END_SCOPE(EPCR_SCOPE)
END_NCBI_SCOPE
#endif
/*
* $Log: align.hpp,v $
* Revision 1.5 2008/03/26 16:04:29 rotmistr
* Added support for blastdb files
*
* Revision 1.4 2004/10/26 17:16:33 rotmistr
* Added 5'-end masking for primers
*
* Revision 1.3 2004/06/08 20:32:50 rotmistr
* Fixup for gap+insert special case
*
* Revision 1.2 2004/06/08 16:14:55 rotmistr
* *** empty log message ***
*
* Revision 1.1 2004/06/03 23:37:19 rotmistr
* New aligner added.
*
*/
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