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gnFileSource.h

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/////////////////////////////////////////////////////////////////////////////
// File:            gnFileSource.h
// Purpose:         Implements gnBaseSource for .File files
// Description:     
// Changes:        
// Version:         libGenome 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnFileSource_h_
#define _gnFileSource_h_

#include "gn/gnDefs.h"

#include <string>
#include <fstream>
#include "gn/gnBaseSource.h"
#include "gn/gnFileContig.h"
#include "gn/gnException.h"

/**
 * gnFileSource is a standard interface to all file based sources of genetic information.
 * All file source classes are derived from this class.
 */
class GNDLLEXPORT gnFileSource : public gnBaseSource
{
public:
        gnFileSource(){}
        gnFileSource(const gnFileSource& gnfs);
        virtual ~gnFileSource(){}
        virtual gnFileSource* Clone() const = 0;
        // Open, Close  
        virtual void Open( string openString );
        virtual void Open();
        virtual void Close();
        virtual string GetOpenString() const ;
          // Filter
        virtual const gnFilter* GetFilter() const ;
        virtual void SetFilter( gnFilter* filter );

        virtual boolean Read( const uint64 pos, char* buf, uint32& bufLen );
        /**
         * Returns a pointer to the file contig corresponding to contigI or
         * null if none exists.
         */
        virtual gnFileContig* GetFileContig( const uint32 contigI ) const = 0;
protected:
        void DetermineNewlineType();

        string m_openString;
        ifstream m_ifstream;
        const gnFilter* m_pFilter;
        gnNewlineType m_newlineType;
        uint32 m_newlineSize;
private:
        virtual boolean ParseStream( istream& fin ) = 0;
};// class gnFileSource

inline
string gnFileSource::GetOpenString( ) const
{
        return m_openString;
}
// Filter
inline
const gnFilter* gnFileSource::GetFilter() const
{
        return m_pFilter;
}

inline
void gnFileSource::SetFilter( gnFilter* filter )
{
        if(filter == NULL){
                Throw_gnEx(NullPointer());
        }
        m_pFilter = filter;
}

#endif
        // _gnFileSource_h_

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