test-o-matic.cpp Source File

00001 #include "gn/gnFASSource.h"
00002 #include "gn/gnSequence.h"
00003 #include "gn/gnTranslator.h"
00004 #include "gn/gnStringSpec.h"
00005 #include <fstream>
00006 int main()
00007 {
00008         ifstream gbk1("cpneuJ.gbk");
00009         ifstream gbk2("test_rc.gbk");
00010 
00011         uint32 badline = 0;
00012         char buf[30000];
00013         char buf2[30000];
00014         while(gbk1.good() && gbk2.good()){
00015                 gbk1.getline(buf, 30000);
00016                 gbk2.getline(buf2, 30000);
00017                 if(strcmp(buf, buf2)){
00018                         cout << "mismatched line: " << badline << "\n";
00019                         cout << buf << endl << buf2 << endl;
00020                         cout << "Length 1: " << strlen(buf) << "   Length 2: " << strlen(buf2) << endl;
00021                         cin >> buf;
00022                 }
00023                 badline++;
00024         }
00025 
00026 /*      gnStringSpec s("");
00027         cout <<s.GetLength()<<endl;
00028         
00029         gnSequence t = "ACTATATA";
00030         if(t == string("TATATA")){
00031                 cout << "ASDFASDFSADF";
00032         }*/
00033 }
00034 /*      // define a string to store the sequence file name
00035         
00036         string filename;
00037         string nseq,pseq;       
00038         // define a gnSequence to store the sequence
00039         gnSequence file_sequence;
00040         gnSequence prot_trans;
00041         
00042         //nseq = "BXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXXBXX";
00043         //nseq = "WSTYYYBBB";
00044     //nseq="ATGCUXGCNGGGTATGAATEQILPFP";
00045         //nseq="ATGGTXAGCGGNTAR";       
00046         cout<<nseq<<" (original)---->  \n";
00047         gnSequence aSeq(nseq);
00048         cout<<aSeq<<" (gnSequence)----> \n";
00049 
00050     gnTranslator::ProteinDNAConverter->ToProtein(nseq);
00051     
00052     cout << nseq << '\n';;
00053   
00054   
00055   
00056   
00057   //  prot_trans.append(nseq);
00058         // output the first ten bases of the sequence
00059 //      cout << prot_trans.subseq(1,10);
00060 
00061         return 0;
00062         
00063 }
00064 
00065 /*#include "gn/gnSequence.h"
00066 #include <iostream>
00067 #include <string>
00068 #include "gn/gnTranslator.h"
00069 #include "gn/gnFASSource.h"
00070 
00071 int main(int argc, char* argv[]){
00072         gnSequence gps;
00073         string seq_filename;
00074         string out_filename;
00075         
00076         /* Get the name of the dnx file to convert to FastA /
00077         cout << "Debug-o-matic!\n";
00078         cout << "Please give the name of the fof to test: ";
00079         cin >> seq_filename;
00080         
00081         gps.LoadSource(seq_filename);
00082 
00083         cout << "Output filename: ";
00084         cin >> out_filename;
00085         gnFASSource::Write(gps, out_filename);
00086         
00087         return 0;       
00088 
00089 }*/