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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
/////////////////////////////////////////////////////////////////////////////
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "libGenome/gnFileSource.h"
#include <fstream>
#include "libGenome/gnFilter.h"
using namespace std;
namespace genome {
gnFileSource::gnFileSource() :
m_pFilter(gnFilter::fullDNASeqFilter())
{}
//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;
#pragma omp critical
{
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 )
{
boolean opened = true;
#pragma omp critical
{
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();
opened = false;
}
}
if(!opened)
Throw_gnEx(FileNotOpened());
}
void gnFileSource::Open( )
{
bool opened = true;
#pragma omp critical
{
m_ifstream.open( m_openString.c_str(), ios::in | ios::binary );
if( !m_ifstream.is_open() ){
opened = false;
m_ifstream.clear();
}
}
if(!opened)
Throw_gnEx(FileNotOpened());
}
void gnFileSource::Close()
{
#pragma omp critical
m_ifstream.close();
}
boolean gnFileSource::Read( const uint64 pos, char* buf, gnSeqI& bufLen)
{
bool failure = false;
#pragma omp critical
{
m_ifstream.seekg(pos, ios::beg);
m_ifstream.read(buf, bufLen);
failure = m_ifstream.fail();
}
if(failure){
#pragma omp critical
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;
}
}
}
} // end namespace genome
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