Package versusSNP.genome

Examples of versusSNP.genome.Genome

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      } else if (dialog.getPath2().equals("")) {
        JOptionPane.showMessageDialog(null, UICaption.dialog_error_orfloader_no_orf_sequence, UICaption.dialog_caption_error, JOptionPane.ERROR_MESSAGE);
        loopORFLoader(dialog);
      }
      Parameter.path_previous_dir = dialog.getPath1().substring(0, dialog.getPath1().lastIndexOf(File.separator));
      Genome genome = new Genome(dialog.getName());
      new Thread(new ORFFile(dialog.getPath1(), dialog.getPath2(), genome, document, (dialog.getPath1().endsWith("csv") ? ORFFile.COMMA : ORFFile.TAB))).start();
    }
  }
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    new UICaption(Locale.ENGLISH);
    new Size();
//    args = new String[]{"NC_000962", "NC_002755"};
    new CodonTable();
    if (args.length > 0) {
      Genome genome1 = new Genome(args[0]);
      new ORFFile().readFile(args[0] + ".txt", genome1);
      genome1.sortOrfList();
      FastaFile fastaFile1 = new FastaFile();
      fastaFile1.readFile(args[0] + ".fasta", genome1);
      genome1.attachSequences(fastaFile1.getSequences());
      Genome genome2 = new Genome(args[1]);
      new ORFFile().readFile(args[1] + ".txt", genome2);
      genome2.sortOrfList();
      FastaFile fastaFile2 = new FastaFile();
      fastaFile2.readFile(args[1] + ".fasta", genome2);
      genome2.attachSequences(fastaFile2.getSequences());
      BlastParser parser = new BlastParser();
      parser.parse(args[0] + "-" + args[1]);
      genome1.attachBlastSets(parser.getBlastList(), genome2, true);
      genome1.printSNPSummary(genome2);
    } else {
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  @Override
  public void actionPerformed(ActionEvent ae) {
    Object obj = ae.getSource();
    if (obj.equals(selector1)) {
      Genome referenceGenome = (Genome) selector1.getSelectedItem();
      if (selector2.getReferenceGenome() == null ||
        selector2.getReferenceGenome() != referenceGenome) {
        selector2.setReferenceGenomeAndAddORF(referenceGenome);
      }
    } else if (obj.equals(selector2)) {
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Related Classes of versusSNP.genome.Genome

  • versusSNP.blast.BlastSet
  • versusSNP.blast.util.SNPList
  • versusSNP.gui.dialogs.TrimSequenceDialog
  • versusSNP.Main
  • versusSNP.VersusSNP
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