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gnFastTranslator.h

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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 
/////////////////////////////////////////////////////////////////////////////
#ifndef _gnFastTranslator_h_
#define _gnFastTranslator_h_


#include "gn/gnDefs.h"

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

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 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, string inputs, const gnSeqI input_width);

        // 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);
        // fill map
        void SetPair( const string& ch1, const string& ch2 );
        void RemovePair( const string& ch );

private:

        void CreateProteinDNATranslator();
        void CreateDNAProteinTranslator();

        //map an input string to an output string
        map<string, 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;
}

#endif // _gnFastTranslator_h_

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