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/* $Id: faread.hpp,v 1.5 2007/07/11 20:49:29 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_FAREAD__HPP
#define EPCR_FAREAD__HPP
#include <epcr/build_cfg.h>
#include <stdexcept>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(EPCR_SCOPE)
class CFastaReader;
class IFastaReaderCallback;
class CFastaReader
{
public:
virtual ~CFastaReader() throw () { Close(); }
CFastaReader() : m_Fptr(0), m_CvtTable(0) {}
explicit CFastaReader( const string& fname ):
m_Fptr( 0 ), m_CvtTable( 0 ) { Open( fname ); }
bool IsOpen() const { return m_Fptr; }
void Open( const string& fname );
void PipeIn( const string& cmd );
void Close();
virtual void ReadFile( IFastaReaderCallback* cbk );
// virtual bool ReadEntry(IFastaReaderCallback* cbk);
void SetCvtTable( const char * table = 0 ) { m_CvtTable = table; }
// These tables should have '\0' in all positions to be "eaten"
// (f.e. for space and tab), everything else will be xlated
static char sm_Nucleotides[];
static char sm_NucleotidesUc[];
static char sm_NucleotidesExt[];
static char sm_NucleotidesExtUc[];
protected:
void SeqlineCbk( IFastaReaderCallback * cbk, char * data, unsigned length );
protected:
void * m_Fptr;
const char * m_CvtTable;
};
class IFastaReaderCallback
{
public:
virtual ~IFastaReaderCallback() throw () {}
virtual void CbkDefline( const char * defline, unsigned length ) = 0;
virtual void CbkIdent( const char * ident, unsigned length ) = 0;
virtual void CbkSeqline( const char * data, unsigned length ) = 0;
virtual void CbkEntryBegin() {}
virtual void CbkEntryEnd() = 0;
virtual void CbkFileBegin() {}
virtual void CbkFileEnd() {}
};
END_SCOPE(EPCR_SCOPE)
END_NCBI_SCOPE
#endif
/*
* $Log: faread.hpp,v $
* Revision 1.5 2007/07/11 20:49:29 rotmistr
* Made 64bit-compatible
*
* Revision 1.4 2004/03/07 06:35:59 rotmistr
* Many bugfixes and optimisations -- cgi is to go to production
*
* Revision 1.3 2004/02/04 21:23:22 rotmistr
* - gcc-3.3.2 compatible
* - better postfiltering for reverse-e-PCR for discontiguos words
* - cgi added, that supports:
* -- contig to chromosome mapping
* -- simple mapviewer links
* -- unists links
* -- discontiguos words
*
* Revision 1.2 2004/01/08 23:22:41 rotmistr
* Fixed init error in faread,
* Adjusted output to standard,
* Added output format style and output file to parameters.
*
* Revision 1.1.1.1 2003/12/23 18:17:28 rotmistr
* Package that includes e-PCR, reverse e-PCR, and sequence data preparation
* program for reverse e-PCR looks ready
*
*/
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