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gnFileSource.cpp

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// File:            gnFileSource.h
// Purpose:         Implements generic gnBaseSource methods
// Description:     Provides a general implementation for accessing DNA
//                  sequence contig data files.
// Changes:        
// Version:         libGenome 0.1.0 
// Author:          Aaron Darling 
// Last Edited:     April 15, 2001, 11:13:00pm 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        Proprietary 
#include "gn/gnFileSource.h"
#include <fstream>
#include "gn/gnFilter.h"

//copy constructor
gnFileSource::gnFileSource(const gnFileSource& gnfs){
        m_openString = gnfs.m_openString;
        m_pFilter = gnfs.m_pFilter;
        m_newlineType = gnfs.m_newlineType;
        m_newlineSize = gnfs.m_newlineSize;
        m_ifstream.open( m_openString.c_str(), ios::in | ios::binary );
        if( !m_ifstream.is_open() )
                m_ifstream.clear();
}

// Open, Close  
void gnFileSource::Open( string openString )
{
        m_ifstream.open(openString.c_str(), ios::in | ios::binary );
        if( m_ifstream.is_open() )
        {
                m_openString = openString;
                if( ParseStream(m_ifstream) )
                {
                        ;
                }
                else{
                        m_ifstream.clear();
                        m_ifstream.close();
                }
        }else{
                m_ifstream.clear();
                Throw_gnEx(FileNotOpened());
        }
}
void gnFileSource::Open( )
{
        m_ifstream.open( m_openString.c_str(), ios::in | ios::binary );
        if( !m_ifstream.is_open() ){
                m_ifstream.clear();
                Throw_gnEx(FileNotOpened());
        }
}
void gnFileSource::Close()
{
        m_ifstream.close();
        if( m_ifstream.is_open() )
                Throw_gnEx(IOStreamFailed());
}

boolean gnFileSource::Read( const uint64 pos, char* buf, uint32& bufLen) 
{
        m_ifstream.seekg(pos, ios::beg);
        m_ifstream.read(buf, bufLen);
        if(m_ifstream.fail()){
                m_ifstream.clear();
                return false;
        }
        return true;
}

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