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/////////////////////////////////////////////////////////////////////////////
// File: gnRAWSource.h
// Purpose: Implements gnBaseSource for raw data files
// Description:
// 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/gnFilter.h"
#include "libGenome/gnRAWSource.h"
#include "libGenome/gnGenomeSpec.h"
#include "libGenome/gnFragmentSpec.h"
#include "libGenome/gnSourceSpec.h"
#include "libGenome/gnStringTools.h"
#include "libGenome/gnDebug.h"
using namespace std;
namespace genome {
gnRAWSource::gnRAWSource()
{
m_openString = "";
m_contig = NULL;
m_pFilter = NULL;
}
gnRAWSource::gnRAWSource( const gnRAWSource& s ) : gnFileSource(s)
{
m_contig = NULL;
if(s.m_contig != NULL)
m_contig = s.m_contig->Clone();
}
gnRAWSource::~gnRAWSource()
{
m_ifstream.close();
delete m_contig;
}
boolean gnRAWSource::HasContig( const string& name ) const
{
if( name.length() == 0 )
return true;
return false;
}
uint32 gnRAWSource::GetContigID( const string& name ) const
{
return ALL_CONTIGS;
}
string gnRAWSource::GetContigName( const uint32 i ) const
{
return "";
}
gnSeqI gnRAWSource::GetContigSeqLength( const uint32 i ) const
{
if( m_contig && (i == 0 || i == ALL_CONTIGS))
return m_contig->GetSeqLength();
return GNSEQI_ERROR;
}
boolean gnRAWSource::SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI ){
return Read( start, buf, bufLen );
}
gnGenomeSpec *gnRAWSource::GetSpec() const{
return m_spec->Clone();
}
boolean gnRAWSource::Write(gnSequence& seq, const string& filename){
ofstream m_ofstream(filename.c_str(), ios::out | ios::binary);
if(!m_ofstream.is_open())
return false;
gnSeqC buf[BUFFER_SIZE + 1];
buf[BUFFER_SIZE] = 0;
gnSeqI readOffset = 0;
gnSeqI readLength = seq.length();
while(readLength > 0){ //buffer the read/writes
gnSeqI writeLen = readLength < BUFFER_SIZE ? readLength : BUFFER_SIZE;
if(!seq.ToArray(buf, writeLen, readOffset + 1))
return false;
m_ofstream.write( buf, writeLen );
readLength -= writeLen;
readOffset += writeLen;
}
m_ofstream.flush();
m_ofstream.close();
return true;
}
gnFileContig* gnRAWSource::GetFileContig( const uint32 contigI ) const{
if(contigI > 0)
return NULL;
return m_contig;
}
//File parsing access routine
boolean gnRAWSource::ParseStream( istream& fin )
{
// init variables
uint64 streamPos = 0;
uint64 bufReadLen = 0;
Array<char> array_buf( BUFFER_SIZE );
char* buf = array_buf.data;
gnSeqI seqLength = 0;
if( m_contig == NULL )
m_contig = new gnFileContig();
m_contig->SetName( "Raw Data" );
m_contig->SetRepeatSeqGap(true);
m_contig->SetSectStart(gnContigSequence, 0);
uint64 offset = 0;
if( !CheckRawData() ){
fin.seekg( 0, ios::end );
offset = fin.tellg();
}
else
{
while( !fin.eof() )
{
// read chars
fin.read( buf , BUFFER_SIZE );
bufReadLen = fin.gcount();
for( uint32 i=0 ; i < bufReadLen ; i++ )
{
if(m_pFilter == NULL || m_pFilter->IsValid(buf[i]))
seqLength++;
else{
m_contig->SetRepeatSeqGap(false);
}
}
streamPos += bufReadLen;
}
}
m_contig->SetSectEnd(gnContigSequence, streamPos + offset);
m_contig->SetSeqLength(seqLength + offset );
m_spec = new gnGenomeSpec();
gnFragmentSpec* fragspec = new gnFragmentSpec();
gnSourceSpec* sspec = new gnSourceSpec(this);
sspec->SetSourceName(m_openString);
m_spec->AddSpec(fragspec);
fragspec->AddSpec(sspec);
m_ifstream.clear();
return true;
}
} // end namespace genome
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