/usr/include/libGenome-1.3/libGenome/gnPosSpecificTranslator.h is in libgenome-1.3-dev 1.3.1-9.
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: gnPosSpecificTranslator.h
// Purpose: Special case ORF translation
// Description: Used to translate sequences differently based on the position of
// input characters. Useful for tranlating genes because the first
// codon is translated differently
// 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 _gnPosSpecificTranslator_h_
#define _gnPosSpecificTranslator_h_
#include "libGenome/gnDefs.h"
#include <string>
#include <vector>
#include <map>
#include "libGenome/gnClone.h"
#include "libGenome/gnBaseFilter.h"
#include "libGenome/gnFastTranslator.h"
namespace genome {
/**
* Used to translate sequences differently based on the position of
* input characters. Useful for tranlating genes because the first
* codon is translated differently.
*/
class GNDLLEXPORT gnPosSpecificTranslator : public gnBaseFilter
{
public:
static const gnPosSpecificTranslator *ProteinDNATranslator();
static const gnPosSpecificTranslator *DNAProteinTranslator();
enum gnTranslatorType{
ProteinDNATranslatorType,
DNAProteinTranslatorType,
};
gnPosSpecificTranslator();
gnPosSpecificTranslator( gnTranslatorType t_type );
gnPosSpecificTranslator( const gnPosSpecificTranslator& sf );
gnPosSpecificTranslator& operator= (const gnPosSpecificTranslator& sf);
gnPosSpecificTranslator* Clone() const;
// gnSeqC
virtual gnSeqC Filter( const gnSeqC ch ) const;
virtual void Filter( gnSeqC** seq, gnSeqI& len ) const;
// std::string
virtual void Filter( std::string &seq ) const;
private:
gnTranslatorType m_type; // defines the type of translator this is
const gnBaseFilter* filter; // this is the filter used to do the translation
void CreateProteinDNATranslator();
void CreateDNAProteinTranslator();
};//class gnPosSpecificTranslator
inline
gnPosSpecificTranslator* gnPosSpecificTranslator::Clone() const
{
return new gnPosSpecificTranslator(*this);
}
} // end namespace genome
#endif // _gnPosSpecificTranslator_h_
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