TestgpSeqConverter.cpp Source File

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 }