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/////////////////////////////////////////////////////////////////////////////
// File: gnFastTranslator.h
// Purpose: Fast translator for all Sequences
// Description: Caches translations of each possible sequence in a tree
// 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 _gnFastTranslator_h_
#define _gnFastTranslator_h_
#include "libGenome/gnDefs.h"
#include <string>
#include <vector>
#include <map>
#include "libGenome/gnClone.h"
#include "libGenome/gnBaseFilter.h"
#include "libGenome/gnTranslator.h"
namespace genome {
class GNDLLEXPORT gnFastTranslator : public gnBaseFilter
{
public:
static const gnFastTranslator *ProteinDNATranslator();
static const gnFastTranslator *DNAProteinTranslator();
enum gnTranslatorType{
ProteinDNATranslatorType,
DNAProteinTranslatorType,
};
gnFastTranslator();
gnFastTranslator( gnTranslatorType t_type );
gnFastTranslator( const gnFastTranslator& sf );
gnFastTranslator& operator= (const gnFastTranslator& sf);
gnFastTranslator* Clone() const;
/**
* Queries the specified gnTranslator for every possible combination translation
* of the characters specified in the inputs std::string. An input_width may be specified
* so that every possible combination of "input_width" characters in "inputs" will be
* cached. This is useful for DNA to protein translations, for example.
* @param tranny The gnTranslator to cache.
* @param inputs The characters to cache from tranny.
* @param input_width The number of characters in each query to make to tranny.
*/
virtual void CacheTranslator(const gnTranslator* tranny, std::string inputs, const gnSeqI input_width);
// 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
void SetDefaultChar( const gnSeqC ch1 );
gnSeqC GetDefaultChar() const;
void UseDefaultChar( const boolean use = true);
// fill map
void SetPair( const std::string& ch1, const std::string& ch2 );
void RemovePair( const std::string& ch );
private:
void CreateProteinDNATranslator();
void CreateDNAProteinTranslator();
//map an input std::string to an output std::string
std::map<std::string, std::string> m_transCache;
const gnTranslator * m_translator;
boolean use_default;
gnSeqC m_defaultChar;
};//class gnFastTranslator
inline
gnFastTranslator* gnFastTranslator::Clone() const
{
return new gnFastTranslator(*this);
}
inline
void gnFastTranslator::SetDefaultChar( const gnSeqC ch1 )
{
m_defaultChar = ch1;
use_default = true;
}
inline
gnSeqC gnFastTranslator::GetDefaultChar() const
{
return m_defaultChar;
}
inline
void gnFastTranslator::UseDefaultChar(const boolean use)
{
use_default = use;
}
} // end namespace genome
#endif // _gnFastTranslator_h_
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