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gnPosSpecificTranslator.cpp

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/////////////////////////////////////////////////////////////////////////////
// File:            gnPosSpecificTranslator.cpp
// 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
/////////////////////////////////////////////////////////////////////////////

#include "gn/gnPosSpecificTranslator.h"

//      static data access, avoids static initialization order fiasco
const gnPosSpecificTranslator *gnPosSpecificTranslator::ProteinDNATranslator(){
        const static gnPosSpecificTranslator* t_trans = new gnPosSpecificTranslator(ProteinDNATranslatorType);
        return t_trans;
}
const gnPosSpecificTranslator *gnPosSpecificTranslator::DNAProteinTranslator(){
        const static gnPosSpecificTranslator* t_trans = new gnPosSpecificTranslator(DNAProteinTranslatorType);
        return t_trans;
}

//      public:
gnPosSpecificTranslator::gnPosSpecificTranslator()
{
}

gnPosSpecificTranslator::gnPosSpecificTranslator( const gnPosSpecificTranslator &sf )
{
        m_name = sf.m_name;
}
gnPosSpecificTranslator::gnPosSpecificTranslator( gnTranslatorType t_type )
{
        m_type = t_type;
        switch(t_type){
                case ProteinDNATranslatorType:
                        // not special done for this case
                        filter = gnFastTranslator::ProteinDNATranslator();
                        break;
                case DNAProteinTranslatorType:
                        filter = gnFastTranslator::DNAProteinTranslator();
                        break;
        }
}

// gnSeqC
gnSeqC gnPosSpecificTranslator::Filter( const gnSeqC ch ) const{
        return filter->Filter(ch);
}

void gnPosSpecificTranslator::Filter( gnSeqC** seq, uint32& len ) const{
        return filter->Filter(seq, len);
}
        // string
void gnPosSpecificTranslator::Filter( string &seq ) const{
        switch(m_type){
                case ProteinDNATranslatorType:
                        filter->Filter( seq );
                        break;
                case DNAProteinTranslatorType:
                        string first_codon = seq.substr(0,3);
                        filter->Filter( seq );
                        for(int charI = 0; charI < first_codon.length(); charI++ )
                                first_codon[charI] = tolower(first_codon[charI]);
                        if( first_codon == "ttg" || first_codon == "gtg" )
                                seq[0] = 'M';
                        break;
        }
}

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