Package versusSNP.io

Examples of versusSNP.io.ORFFile

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        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 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();
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Related Classes of versusSNP.io.ORFFile

  • versusSNP.genome.ORF
  • versusSNP.gui.widgets.ProgressBar
  • versusSNP.Main
  • versusSNP.VersusSNP
  • java.io.File
  • java.io.InputStreamReader
  • java.io.FileInputStream
  • java.io.BufferedReader
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