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/* $Id: fast_seqio.hpp,v 1.3 2004/04/06 04:53:17 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_FAST_SEQIO__HPP
#define EPCR_FAST_SEQIO__HPP
#include <epcr/build_cfg.h>
#include <epcr/faread.hpp>
#include <epcr/mmap.hpp>
#include <string>
#include <vector>
BEGIN_NCBI_SCOPE
BEGIN_SCOPE(EPCR_SCOPE)
class CFastaMapData;
class CFastaMapPrepare;
class CFastaMap;
class CMmSequence;
class CFastaMapData
{
public:
typedef off64_t TOffset;
typedef off64_t TSize;
protected:
vector<string> m_Ident;
vector<string> m_Defline;
vector<TOffset> m_Offset;
vector<TSize> m_Size;
};
class CFastaMapPrepare:public IFastaReaderCallback,protected CFastaMapData
{
public:
virtual void CbkDefline(const char * defline, unsigned length);
virtual void CbkIdent(const char * ident, unsigned length);
virtual void CbkSeqline(const char * data, unsigned length);
virtual void CbkEntryBegin();
virtual void CbkEntryEnd();
virtual void CbkFileBegin();
virtual void CbkFileEnd();
void Open(const string& fname);
void Close();
bool IsOpen() const { return m_Fptr!=0; }
void AddFile(const string& fname, const char * cvtTable=0);
virtual ~CFastaMapPrepare() throw () { Close(); }
CFastaMapPrepare():m_Fptr(0) {}
explicit CFastaMapPrepare(const string& fname):m_Fptr(0) { Open(fname); }
protected:
void WritePrologue();
void WriteEpilogue();
protected:
void * m_Fptr;
};
class CFastaMap:public CFastaMapData
{
public:
friend class CMmSequence;
~CFastaMap() throw ();
CFastaMap();
CFastaMap(const string& file);
bool IsOpen() const { return m_Fd!=-1; }
void Open(const string& file);
void Close();
unsigned SequenceCount() const { return m_Size.size(); }
const string& GetDefline(unsigned i) const
{ return m_Defline[i]; }
const string& GetIdent(unsigned i) const
{ return m_Ident[i]; }
unsigned GetSize(unsigned i) const
{ return m_Size[i]; }
unsigned GetCount() const
{ return m_Size.size(); }
protected:
void ReadPrologue();
void ReadEpilogue();
protected:
int m_Fd;
bool m_SwapBytes;
};
class CIndexAssert
{
public:
CIndexAssert(unsigned index, unsigned size, const string& msg="") {
if(index >= size) throw range_error(msg);
}
};
class CMmSequence:public CIndexAssert, public CMMap
{
public:
explicit CMmSequence(CFastaMap&, unsigned);
~CMmSequence() throw ();
operator const char * () const { return GetData(); }
// const char * Data() const { return GetData(); }
unsigned Length() const { return GetSize(); }
protected:
// const char * m_Data;
// unsigned m_Size;
};
END_SCOPE(EPCR_SCOPE)
END_NCBI_SCOPE
#endif
/*
* $Log: fast_seqio.hpp,v $
* Revision 1.3 2004/04/06 04:53:17 rotmistr
* All is compileable with BCC5.5 and runnable on WIndows
*
* Revision 1.2 2003/12/30 15:27:22 rotmistr
* Fixed bug with sequence end
*
* 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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