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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 0.5.1 
// Author:          Aaron Darling 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        See COPYING file for details
/////////////////////////////////////////////////////////////////////////////
#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;
}

void gnFileSource::DetermineNewlineType()
{
        // set default values
        m_newlineType = gnNewlineUnix;
        m_newlineSize = 1;

        //decide what type of newlines we have
        char buf[ BUFFER_SIZE ];
        m_ifstream.getline( buf, BUFFER_SIZE);
        m_ifstream.seekg(-2, ios::cur);
        m_ifstream.read( buf, 2);
        m_ifstream.seekg(0);
        if(buf[1] == '\n'){
                if(buf[0] == '\r'){
                        m_newlineType = gnNewlineWindows;
                        m_newlineSize = 2;
                }else{ 
                        if(buf[1] == '\r')
                                m_newlineType = gnNewlineMac;
                        else
                                m_newlineType = gnNewlineUnix;
                }
        }
}

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