gnSeqStringTest.cpp Source File

00001 #include "gnSequence.h"
00002 #include "gnFASSource.h"
00003 #include <string>
00004 #include <iostream>
00005 
00006 const uint32 SURROUND_BASES = 100;
00007 
00008 int main(int argc, char* argv[]){
00009 
00010         gnSequence sequence("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
00011         sequence.append("GGGGGGGGGGG");
00012         
00013         cout << sequence;
00014         char* dumbo;
00015         cin >> dumbo;
00016 
00017 
00018 /*      gnSequence sequence, output_seq;
00019         string seq_filename;
00020         string restriction_filename;
00021         string output_filename;
00022         fstream restriction_file;
00023         fstream output_file;
00024         
00025         do{
00026                 cout << "Enter the name of the restriction site list:\n";
00027                 cin >> restriction_filename;
00028                 restriction_file.open(restriction_filename.c_str(), ios::in);
00029                 if(!restriction_file.is_open())
00030                         cout << "Error opening file!  Try again.\n";
00031         }while(!restriction_file.is_open());
00032 
00033         do{
00034                 cout << "Enter the name of the sequence data FastA file:\n";
00035                 cin >> seq_filename;
00036         }while(!sequence.LoadSource(seq_filename));
00037         
00038         do{
00039                 cout << "Enter the name of an output file:\n";
00040                 cin >> output_filename;
00041                 output_file.open(output_filename.c_str(), ios::out);
00042                 if(!output_file.is_open())
00043                         cout << "Error creating file!  Try again.\n";
00044         }while(!output_file.is_open());
00045         output_file.close();
00046         
00047         
00048         while(restriction_file.good()){
00049                 string bubba;
00050                 restriction_file >> bubba;      //first four are junk
00051                 restriction_file >> bubba;
00052                 restriction_file >> bubba;
00053                 restriction_file >> bubba;
00054                 restriction_file >> bubba;      //this contains contig name
00055                 
00056                 gnSequence contig_seq = sequence.contigByName(bubba);
00057 
00058                 gnSeqI siteI = 0;
00059                 restriction_file >> siteI;
00060 
00061                 char dummy[1000];
00062                 restriction_file.getline(dummy, 999);
00063                 
00064                 //if the restriction site is too close to the beginning, set the start to 0
00065                 gnSeqI start_loc = siteI < SURROUND_BASES ? 0 : siteI - SURROUND_BASES;
00066                 output_seq += contig_seq.subseq(start_loc, SURROUND_BASES*2);
00067         }
00068 
00069         if(gnFASSource::Write(output_seq, output_filename))
00070                 cout << "All done, results are in " << output_filename << "\n";
00071         else
00072                 cout << "An error occurred while writing " << output_filename << "\n";
00073         */
00074 }