/* import java.util.Set;
   import java.util.Arrays;
   import java.util.TreeSet;
   static Set<String> start_codon_set = new TreeSet<String>();
   String p = params.toString().substring(1, 4)
          if (ORF_start_codons.trim().equals("")) {
           start_codon_set.add("atg");
           start_codon_set.add("gtg");
           start_codon_set.add("ttg");
           start_codon_set.add("ctg");
           start_codon_set.add("att");
           ORF_start_codons = "" + start_codon_set.toArray()[0];
           for (int i=1; i < start_codon_set.size(); i++) {
            ORF_start_codons += "," + start_codon_set.toArray()[i];
           }
        } else {
           String[] codons = ORF_start_codons.split(",");
           if (!start_codon_set.addAll(Arrays.asList(codons))) {
              System.out.println("Adding Array to Set fails.");
           }
        }
       //if (InputFile.OpenOkay("/home/u11/rli/NetBeansProjects/OliGo3", parameters_file)) { 
  ORF_start_codons.split(",").length*3==ORF_start_codons.replace(",","").length()
  for (String file : files) {
    System.out.println(file);
  }
      boolean b = m.matches();
      System.out.println(b);
      String s, line = null;
      s = System.getProperty("line.separator");
      System.out.println(s);
      s = System.setProperty("line.separator", ">");
      s = System.getProperty("line.separator");
      System.out.println(s);
      System.out.println(InputFile.br.readLine());
      System.out.println(InputFile.br.readLine());     
      System.out.println(s);     
      InputFile.br.close();
         Params.input_genes_file = Params.workdir + File.separator + Params.input_genes_file;
         Params.output_genes_file = Params.workdir + File.separator + Params.output_genes_file;
         Params.out_overlaps_file = Params.workdir + File.separator + Params.out_overlaps_file;
         Params.ORF_stats_file = Params.workdir + File.separator + Params.ORF_stats_file;
         Params.ORF_tags_file = Params.workdir + File.separator + Params.ORF_tags_file;
 */
package oligo3;
import java.io.IOException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
 *
 * @author rli
 */
public class Test {
    
    static boolean retVal = false;
    static Pattern p = Pattern.compile("^(\\s*\\w+)");
    static Pattern p1 = Pattern.compile("[\\.\\s_-]([^\\.\\s_-]+)\\.\\w{2,5}$");
    static Pattern p2 = Pattern.compile("[\\.\\s_-]([^\\.\\s_-]+)$");
    static Pattern p3 = Pattern.compile("(.{4})$");
    static Pattern h = Pattern.compile("^\\s*>\\s*\\S+.*");
    static Matcher m;
    
    public static void TestInput() throws IOException {
      //InputFile infile = new InputFile();
      //retVal = InputFile.OpenOkay("/home/u11/rli/dic.pl");
      //System.out.println(retVal);
      if (InputFile.OpenOkay(System.getProperty("user.home"),"dic.pl")) {
        try {
          System.out.println(InputFile.br.readLine());
        } catch (IOException e) {
          System.err.println("I/O error: " + e.getMessage());
        } finally {
          if (InputFile.br != null) InputFile.br.close();
        }
      } else {
        System.exit(1);
      }
    }
/*
    // Check if ORF oligos exist across all genes and eliminate oligo-free ORFs
    public static void purgeOligoFreeORF() {
      int len = 0, k = 0, e = seq.size()-1;
      seq_count = orf_count = 0;
      String oligo = "";
      for (i = e; i >= 0; i--) {
        System.out.println("Checking if ORF# " + i+1 + " has an oligo...");
        len = seq.get(i).length()-Params.oligo_probe_length;
        for (j = 0; j <= len; j++) {
          oligo = seq.get(i).substring(j, j+Params.oligo_probe_length);
          for (k = e; k >= 0; k--) {
           if (k != i) {
              if (seq.get(k).contains(oligo)) break;
           }
          }
          if (k < 0) {
             System.out.println("ORF "+gid.get(i)+" has oligo.");
             orf_count++;
             break;
          }
        }
        if (j > len) {
           System.out.println("ORF "+gid.get(i)+" has no oligo.");
           BioSeq.deleteSeq(i);
           e--;
           seq_count++;
        }
      }
      OutputFile.stats.println("Number of genes w/o oligos available = "+seq_count);
      OutputFile.stats.println("Number of genes w/ oligos available = "+orf_count+"\n");
    }
    public static void OutputQualityORF() {
      int len = 0, k = 0, e = seq.size()-1;
      orf_count = 0;
      for (i = 0; i <= e; i++) {
        OutputFile.genes.println(">"+gid.get(i)+" "+acn.get(i)
        +" "+gsb.get(i)+" "+loc.get(i)+" "+prd.get(i));
        len = seq.get(i).length();
        // Print sequence in lines of 60 bp
        for (j = 0; j < len; j += 60) {
          k = ((k=j+60)>len)?len:k;
          OutputFile.genes.println(seq.get(i).substring(j, k));
        }
        orf_count++;
      }
      OutputFile.stats.println("Number of output unique genes = "+orf_count);
      System.out.println("\nNumber of output unique genes = "+orf_count+"\n");
    }
     */
}