/usr/include/libGenome-1.3/libGenome/gnFASSource.h is in libgenome-1.3-dev 1.3.1-7.
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: gnFASSource.h
// Purpose: Implements gnBaseSource for .FAS 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 _gnFASSource_h_
#define _gnFASSource_h_
#include "libGenome/gnDefs.h"
#include <string>
#include <fstream>
#include <vector>
#include "libGenome/gnFileSource.h"
#include "libGenome/gnSequence.h"
namespace genome {
#define FAS_LINE_WIDTH 80
/**
* gnFASSource reads and writes FastA files.
* gnFASSource is used by gnSourceFactory to read files.
* Files can be written in the FastA file format by calling
* gnFASSource::Write( mySpec, "C:\\myFasFile.fas");
*/
class GNDLLEXPORT gnFASSource : public gnFileSource
{
public:
/**
* Empty Constructor, does nothing.
*/
gnFASSource();
/**
* Clone Constructor copies the specified gnFASSource.
* @param s The gnFASSource to copy.
*/
gnFASSource( const gnFASSource& s );
/**
* Destructor, frees memory.
*/
~gnFASSource();
/**
* Returns an exact copy of this class.
*/
gnFASSource* Clone() const;
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;
gnFileContig* GetContig( const uint32 i ) const;
boolean SeqRead( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ) ;
/**
* Write the given gnSequence to a FastA file.
* @param sequence The gnSequence to write out.
* @param filename The name of the file to write.
* @param write_coords If true each entry's name will be followed by the coordinates of the entry
* in the context of the entrire file.
* @param enforce_unique_names If true each entry's name will be recorded as they are written. Each
* successive duplicate name that is found will have an underscore and a
* number appended to it, indicating the number of entries by the same
* name which have already been written.
* Turning this off will yield a slight performance improvement when writing
* files with a large number of entries. (More than 1000)
* @throws A FileNotOpened() exception may be thrown.
*/
static void Write(gnSequence& sequence, const std::string& filename, boolean write_coords = true, boolean enforce_unique_names = true);
/**
* Write the given gnSequence to an ostream.
* @param sequence The gnSequence to write out.
* @param m_ostream The output stream to write to.
* @param write_coords If true each entry's name will be followed by the coordinates of the entry
* in the context of the entrire file.
* @param enforce_unique_names If true each entry's name will be recorded as they are written. Each
* successive duplicate name that is found will have an underscore and a
* number appended to it, indicating the number of entries by the same
* name which have already been written.
* Turning this off will yield a slight performance improvement when writing
* files with a large number of entries. (More than 1000)
*/
static void Write(gnSequence& sequence, std::ostream& m_ostream, boolean write_coords = true, boolean enforce_unique_names = true);
/**
* Deprecated - do not use.
* Write the given source to a FastA file.
* @param source The spec to write out.
* @param filename The name of the file to write.
*/
static boolean Write(gnBaseSource *source, const std::string& filename);
gnGenomeSpec *GetSpec() const;
gnFileContig* GetFileContig( const uint32 contigI ) const;
private:
boolean SeqReadImpl( const gnSeqI start, char* buf, gnSeqI& bufLen, const uint32 contigI=ALL_CONTIGS ) ;
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 );
std::vector< gnFileContig* > m_contigList;
};// class gnFASSource
inline
gnFASSource* gnFASSource::Clone() const
{
return new gnFASSource( *this );
}
inline
uint32 gnFASSource::GetContigListLength() const
{
return m_contigList.size();
}
} // end namespace genome
#endif
// _gnFASSource_h_
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