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TestgpSeqConverter.cpp

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#include "gn/gnSequence.h"
#include "gn/gnFASSource.h"
#include "gn/gnGBKSource.h"
#include <iostream>
#include <string>
#include "gn/gnTranslator.h"
#include "gn/gnDebug.h"
#include "gn/gnDNASequence.h"
#include "gn/gnDebug.h"

void runTests(gnSequence& seq);
void runTests(gnSequence& seq){
        cout << "Testing with sequence:\n";
        cout << seq << endl;

        seq.setReverseComplement(true);
        cout << "Reverse Complement:\n";
        cout << seq << endl;

        seq.setReverseComplement(false);
        cout << "Forward sequence:\n";
        cout << seq << endl;

        seq.setFilter(gnTranslator::DNAProteinTranslator);
        cout << "Translated to protein sequence:\n";
        cout << seq << endl;

        seq.setReverseComplement(true);
        cout << "Reverse complement translated to protein sequence:\n";
        cout << seq << endl;

        list<const gnBaseFilter*> filter_list;
        filter_list.push_back(gnTranslator::DNAProteinTranslator);
        filter_list.push_back(gnTranslator::ProteinDNATranslator);
        seq.setFilterList(filter_list);
        cout << "Reverse Comp translated to protein sequence and back to dna:\n";
        cout << seq << endl;
};

int main(int argc, char* argv[]){

        gnDNASequence seq = "ACGTTAGCGTAT";
        gnDNASequence seq2 = "A";
        seq2 += "CG";
        seq2 += "TTA";
        seq2 += "GCGT";
        seq2 += "AT";
        string blah;
        DebugMsg("Hello World.\n");
        runTests(seq);
        cout << "And now for the same thing with the same sequence.\n";
        cin >> blah;
        runTests(seq2);
        cin >> blah;
        
        do{
                cout << "Finally, enter a sequence file to play with: ";
                cin >> blah;
        }while(!seq.LoadSource(blah));
        seq.setFilter(NULL);
        gnFASSource::Write(seq, "test_rc.fas");
        gnGBKSource::Write(seq, "test_rc.gbk");
        
        return 0;
}

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