/usr/include/libGenome-1.3/libGenome/gnABISource.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: gnABISource.h
// Purpose: Implements gnBaseSource for ABI 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 _gnABISource_h_
#define _gnABISource_h_
#include "libGenome/gnDefs.h"
#include <string>
#include "libGenome/gnSequence.h"
#include "libGenome/gnFileSource.h"
#include "libGenome/gnFileContig.h"
#include "libGenome/gnSourceSpec.h"
#include "libGenome/gnGenomeSpec.h"
#include "libGenome/gnFilter.h"
namespace genome {
/**
* gnABISource is not implemented.
*/
class GNDLLEXPORT gnABISource : public gnFileSource
{
public:
gnABISource();
/**
* Clone Constructor copies the specified gnSEQSource.
* @param s The gnABISource to copy.
*/
gnABISource( const gnABISource& s );
~gnABISource();
gnABISource* 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 );
/**
* Writes the specified gnSequence to an ABI 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);
gnGenomeSpec *GetSpec() const;
gnFileContig* GetFileContig( const uint32 contigI ) const;
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 );
gnGenomeSpec *m_spec;
std::vector< gnFileContig* > m_contigList;
};// class gnABISource
inline
gnABISource* gnABISource::Clone() const
{
return new gnABISource( *this );
}
inline
uint32 gnABISource::GetContigListLength() const
{
return m_contigList.size();
}
inline
gnGenomeSpec *gnABISource::GetSpec() const
{
return m_spec->Clone();
}
} // end namespace genome
#endif
// _gnABISource_h_
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