test-o-matic.cpp Source File

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# test-o-matic.cpp

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    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 }*/