TestgpSeqConverter.cpp Source File

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# TestgpSeqConverter.cpp

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    00001 #include "gn/gnSequence.h"
    00002 #include "gn/gnFASSource.h"
    00003 #include "gn/gnGBKSource.h"
    00004 #include <iostream>
    00005 #include <string>
    00006 #include "gn/gnTranslator.h"
    00007 #include "gn/gnDebug.h"
    00008 #include "gn/gnDNASequence.h"
    00009 #include "gn/gnDebug.h"
    00010
    00011 void runTests(gnSequence& seq);
    00012 void runTests(gnSequence& seq){
    00013         cout << "Testing with sequence:\n";
    00014         cout << seq << endl;
    00015
    00016         seq.setReverseComplement(true);
    00017         cout << "Reverse Complement:\n";
    00018         cout << seq << endl;
    00019
    00020         seq.setReverseComplement(false);
    00021         cout << "Forward sequence:\n";
    00022         cout << seq << endl;
    00023
    00024         seq.setFilter(gnTranslator::DNAProteinTranslator);
    00025         cout << "Translated to protein sequence:\n";
    00026         cout << seq << endl;
    00027
    00028         seq.setReverseComplement(true);
    00029         cout << "Reverse complement translated to protein sequence:\n";
    00030         cout << seq << endl;
    00031
    00032         list<const gnBaseFilter*> filter_list;
    00033         filter_list.push_back(gnTranslator::DNAProteinTranslator);
    00034         filter_list.push_back(gnTranslator::ProteinDNATranslator);
    00035         seq.setFilterList(filter_list);
    00036         cout << "Reverse Comp translated to protein sequence and back to dna:\n";
    00037         cout << seq << endl;
    00038 };
    00039
    00040 int main(int argc, char* argv[]){
    00041
    00042         gnDNASequence seq = "ACGTTAGCGTAT";
    00043         gnDNASequence seq2 = "A";
    00044         seq2 += "CG";
    00045         seq2 += "TTA";
    00046         seq2 += "GCGT";
    00047         seq2 += "AT";
    00048         string blah;
    00049         DebugMsg("Hello World.\n");
    00050         runTests(seq);
    00051         cout << "And now for the same thing with the same sequence.\n";
    00052         cin >> blah;
    00053         runTests(seq2);
    00054         cin >> blah;
    00055
    00056         do{
    00057                 cout << "Finally, enter a sequence file to play with: ";
    00058                 cin >> blah;
    00059         }while(!seq.LoadSource(blah));
    00060         seq.setFilter(NULL);
    00061         gnFASSource::Write(seq, "test_rc.fas");
    00062         gnGBKSource::Write(seq, "test_rc.gbk");
    00063
    00064         return 0;
    00065 }