/**
 * Package for designing oligonucleotide probes for microarrays.
 * @author Ruming Li, Dept. of Plant Science, University of Manitoba
 * @author Brian Fristensky, Dept. of Plant Science, University of Manitoba
 */
package oligo3;

public class OliGo {
    /**
     * @param args: the command line arguments
     */
    public static void main(String[] args) throws Exception {
      // Load parameters if parameter file name is typed on command line,
      // otherwise, all default parameters are used to run the program.
/**        
      if (ParseOptions.parseCmdLine(args)) Params.loadParams();
      Params.printParams();
      RunJob.getStdInput();
      RunJob.runSelectedJob();
      OutputFile.createOutFiles();
      //for (String file : RunJob.files) System.out.println(file);
      Fasta.readFiles();
      ORF.getValidORF();
      ORF.purgeDuplicateORF();
      ORF.purgeOverlapORF();
      if (Params.remove_similarity > 0) ORF.purgeSimilarORF();
      if (Params.eliminate_homology > 0) ORF.purgeHomologORF();
      ORF.purgeOligoFreeORF();
      ORF.OutputQualityORF();

      OutputFile.genes.close();
      OutputFile.overlaps.close();
      OutputFile.stats.close();
      OutputFile.tags.close();
      System.out.println("Done.\n");
      if (RunJob.s.equalsIgnoreCase("b")) {
      System.out.println("Please type fg to return to the foreground and exit.");
      }
 */
      NN.mapNNdimer();

    }
}