/usr/include/libGenome-1.3/libGenome/gnRAWSource.h is in libgenome-1.3-0-dev 1.3.1-3build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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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
#ifndef _gnRAWSource_h_
#define _gnRAWSource_h_
#include "libGenome/gnDefs.h"
#include <string>
#include <fstream>
#include <vector>
#include "libGenome/gnFileSource.h"
#include "libGenome/gnFileContig.h"
#include "libGenome/gnSourceSpec.h"
#include "libGenome/gnSequence.h"
namespace genome {
/**
* gnRAWSource reads raw sequence data from a text file.
* This class reads and writes raw sequence to and from files.
* A raw sequence does not contain any newlines, fragment delimiters, or other
* type of annotation.
* gnRAWSource is used by gnSourceFactory to read files and should only be used
* directly.when writing out raw files by calling gnRAWSource::Write( mySpec, "C:\\myFile.txt");
*/
class GNDLLEXPORT gnRAWSource : public gnFileSource
{
public:
/**
* Empty Constructor, does nothing.
*/
gnRAWSource();
/**
* Clone Constructor copies the specified gnRAWSource.
* @param s The gnRAWSource to copy.
*/
gnRAWSource( const gnRAWSource& s );
/**
* Destructor, frees memory.
*/
~gnRAWSource();
/**
* Returns an exact copy of this class.
*/
gnRAWSource* Clone() const;
// Contig Access methods
uint32 GetContigListLength() const;
boolean HasContig( const std::string& name ) const;
uint32 GetContigID( const std::string& name ) const;
std::string GetContigName( const uint32 i ) const;
gnSeqI GetContigSeqLength( const uint32 i ) const;
boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS );
/**
* Writes the specified gnSequence to a raw file named "filename".
* @param sequence The gnSequence to write out.
* @param filename The name of the file to write.
* @return True if successful, false otherwise.
*/
static boolean Write(gnSequence& sequence, const std::string& filename);
/**
* Writes the specified source to a raw file named "filename".
* @param source The source to write out.
* @param filename The name of the file to write.
* @return True if successful, false otherwise.
*/
static boolean Write(gnBaseSource *source, const std::string& filename);
gnGenomeSpec *GetSpec() const;
gnFileContig* GetFileContig( const uint32 contigI ) const;
static boolean CheckRawData( boolean set = false, boolean check = false );
private:
boolean SeqSeek( const gnSeqI start, const uint32& contigI, uint64& startPos, uint64& readableBytes );
boolean SeqStartPos( const gnSeqI start, gnFileContig& contig, uint64& startPos, uint64& readableBytes );
boolean ParseStream( std::istream& fin );
gnFileContig* m_contig;
gnGenomeSpec* m_spec;
};// class gnRAWSource
// Clone
inline
gnRAWSource* gnRAWSource::Clone() const
{
return new gnRAWSource( *this );
}
// Contig Access methods
inline
uint32 gnRAWSource::GetContigListLength() const
{
return m_contig == NULL? 0 : 1;
}
inline
boolean gnRAWSource::Write(gnBaseSource *source, const std::string& filename){
gnSequence gns(*source->GetSpec());
return Write(gns, filename);
}
inline
boolean gnRAWSource::CheckRawData( boolean set, boolean check ){
static boolean check_raw_data = false;
if( set ){
check_raw_data = check;
}
return check_raw_data;
}
} // end namespace genome
#endif
// _gnRAWSource_h_
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