gnSeqStringTest.cpp Source File

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# gnSeqStringTest.cpp

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    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 }