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gnPosSpecificTranslator.h

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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 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnPosSpecificTranslator_h_
#define _gnPosSpecificTranslator_h_


#include "gn/gnDefs.h"

#include <string>
#include <vector>
#include <map>
#include "gn/gnClone.h"
#include "gn/gnBaseFilter.h"
#include "gn/gnFastTranslator.h"

/** 
 * 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, uint32& len ) const;
        // string
        virtual void Filter( 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);
}

#endif // _gnPosSpecificTranslator_h_

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