/usr/include/libGenome-1.3/libGenome/gnTranslator.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: gnTranslator.h
// Purpose: Translator for all Sequences
// Description: Translates DNA and protein sequences
// 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 _gnTranslator_h_
#define _gnTranslator_h_
#include "libGenome/gnDefs.h"
#include <string>
#include <vector>
#include "libGenome/gnClone.h"
#include "libGenome/gnBaseFilter.h"
#include "libGenome/gnCompare.h"
namespace genome {
/**
* The gnTranslator class facilitates the translation of ambiguous DNA and RNA
* sequences to protein sequence. It can also perform reverse translation from
* Protein to RNA or DNA though the utility of this functionality is somewhat
* questionable since it does not assign nucleotides probabilistically.
* Do not attempt to instantiate this class unless you are defining a new
* translation type. Instead use the static member access functions ProteinDNATranslator(),
* ProteinRNATranslator(), DNAProteinTranslator(), and RNAProteinTranslator()
* In general, the gnFastTranslator class should be used instead of this one.
* @see gnFastTranslator
*/
class GNDLLEXPORT gnTranslator : public gnBaseFilter
{
public:
static const gnTranslator *ProteinDNATranslator();
static const gnTranslator *ProteinRNATranslator();
static const gnTranslator *DNAProteinTranslator();
static const gnTranslator *RNAProteinTranslator();
enum gnTranslatorType{
ProteinDNATranslatorType,
ProteinRNATranslatorType,
DNAProteinTranslatorType,
RNAProteinTranslatorType,
};
gnTranslator();
gnTranslator( gnTranslatorType t_type );
gnTranslator( const gnTranslator& sf );
gnTranslator* 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;
// Default gnSeqC
/**
* Sets the default character to insert when no valid translation exists.
* @param ch1 The default character
*/
void SetDefaultChar( const gnSeqC ch1 );
/**
* Gets the default character which is inserted into the destination
* sequence when no valid translation exists.
* @return The default character
*/
gnSeqC GetDefaultChar() const;
/**
* Set whether the default character is inserted upon translation failure.
* @param use True if the default character should be used.
*/
void UseDefaultChar( const boolean use = true);
/**
* Set the expected number of characters in each unit of translation. For DNA to
* Protein, for instance, this is 3 because each codon is 3 characters of input.
* @param defaultInputWidth The expected input width
*/
void SetDefaultInputWidth( const uint32 defaultInputWidth);
/**
* Get the expected number of characters in each unit of translation. For DNA to
* Protein, for instance, this is 3 because each codon is 3 characters of input.
* @return The expected input width
*/
uint32 GetDefaultInputWidth() const;
// fill map
/**
* Set a translation mapping. The first value is the input, the second value is the
* output. During translation, any occurrences of the first std::string will be transformed
* to the second std::string. A gnCompare object is used to facilitate ambiguity matching.
* @param input The input std::string
* @param output The std::string to output every time the input std::string is encountered
*/
void SetPair( const std::string& input, const std::string& output );
/**
* Removes a translation mapping. RemovePair removes the translation mapping
* corresponding to the given input std::string.
* @param input The input std::string to delete
*/
void RemovePair( const std::string& input );
/**
* Set the comparator to use. Ambiguous base matching is facilitated using a gnCompare
* object. This must be set to allow sequences to be compared.
* @param comp A pointer to the gnCompare object to use.
*/
void SetCompare( const gnCompare* comp );
private:
void CreateProteinDNATranslator();
void CreateProteinRNATranslator();
void CreateDNAProteinTranslator();
void CreateRNAProteinTranslator();
//for each entry in the input table there is a corresponding
//entry in the output table.
std::vector<std::string> m_inputTable, m_outputTable;
const gnCompare* compare;
boolean use_default;
gnSeqC m_defaultChar;
uint32 m_defaultInputWidth;
};//class gnTranslator
inline
gnTranslator* gnTranslator::Clone() const
{
return new gnTranslator(*this);
}
inline
void gnTranslator::SetDefaultChar( const gnSeqC ch1 )
{
m_defaultChar = ch1;
use_default = true;
}
inline
gnSeqC gnTranslator::GetDefaultChar() const
{
return m_defaultChar;
}
inline
void gnTranslator::UseDefaultChar(const boolean use)
{
use_default = use;
}
inline
void gnTranslator::SetDefaultInputWidth( const uint32 defaultInputWidth){
m_defaultInputWidth = defaultInputWidth;
}
inline
uint32 gnTranslator::GetDefaultInputWidth() const{
return m_defaultInputWidth;
}
inline
void gnTranslator::SetCompare( const gnCompare* comp ){
compare = comp;
}
} // end namespace genome
#endif // _gnTranslator_h_
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