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gnTranslator.h

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// File:            gnTranslator.h
// Purpose:         Translator for all Sequences
// Description:     Translates DNA and protein sequences
// Changes:        
// Version:         libGenome 0.1.0 
// Author:          Aaron Darling 
// Last Edited:     April 15, 2001, 10:34:50pm 
// Modified by:     
// Copyright:       (c) Aaron Darling 
// Licenses:        Proprietary 
#ifndef _gnTranslator_h_
#define _gnTranslator_h_


#include "gn/gnDefs.h"

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


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

        // Default gnSeqC
        void SetDefaultChar( const gnSeqC ch1 );
        gnSeqC GetDefaultChar() const;
        void UseDefaultChar( const boolean use = true);
        void SetDefaultInputWidth( const uint32 defaultInputWidth);
        uint32 GetDefaultInputWidth() const;

        // fill map
        void SetPair( const string& input, const string& output );
        void RemovePair( const string& input );
        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.
        vector<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;
}

#endif // _gnTranslator_h_

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