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gnSeqStringTest.cpp

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#include "gnSequence.h"
#include "gnFASSource.h"
#include <string>
#include <iostream>

const uint32 SURROUND_BASES = 100;

int main(int argc, char* argv[]){

        gnSequence sequence("AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA");
        sequence.append("GGGGGGGGGGG");
        
        cout << sequence;
        char* dumbo;
        cin >> dumbo;


/*      gnSequence sequence, output_seq;
        string seq_filename;
        string restriction_filename;
        string output_filename;
        fstream restriction_file;
        fstream output_file;
        
        do{
                cout << "Enter the name of the restriction site list:\n";
                cin >> restriction_filename;
                restriction_file.open(restriction_filename.c_str(), ios::in);
                if(!restriction_file.is_open())
                        cout << "Error opening file!  Try again.\n";
        }while(!restriction_file.is_open());

        do{
                cout << "Enter the name of the sequence data FastA file:\n";
                cin >> seq_filename;
        }while(!sequence.LoadSource(seq_filename));
        
        do{
                cout << "Enter the name of an output file:\n";
                cin >> output_filename;
                output_file.open(output_filename.c_str(), ios::out);
                if(!output_file.is_open())
                        cout << "Error creating file!  Try again.\n";
        }while(!output_file.is_open());
        output_file.close();
        
        
        while(restriction_file.good()){
                string bubba;
                restriction_file >> bubba;      //first four are junk
                restriction_file >> bubba;
                restriction_file >> bubba;
                restriction_file >> bubba;
                restriction_file >> bubba;      //this contains contig name
                
                gnSequence contig_seq = sequence.contigByName(bubba);

                gnSeqI siteI = 0;
                restriction_file >> siteI;

                char dummy[1000];
                restriction_file.getline(dummy, 999);
                
                //if the restriction site is too close to the beginning, set the start to 0
                gnSeqI start_loc = siteI < SURROUND_BASES ? 0 : siteI - SURROUND_BASES;
                output_seq += contig_seq.subseq(start_loc, SURROUND_BASES*2);
        }

        if(gnFASSource::Write(output_seq, output_filename))
                cout << "All done, results are in " << output_filename << "\n";
        else
                cout << "An error occurred while writing " << output_filename << "\n";
        */
}

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