/** @param args */ public static void main(String[] args) { if (args.length > 0 && (args[0].equals("-h") || args[0].equals("-help"))) { System.out.println( "\n \\**\n" + " * Pair Count \n" + " * True Positives : Correctly Predicted BP\n" + " * False Positives : Incorrectly Predicted BP \n" + " * False Negatives : Base pair exists in native structure\n" + " *\n" + " * Specificity = FN / (TP + FP)\n" + " * Sensitivity/Recall = TP / (TP + FN)\n" + " * Precision = TP / (TP + FP)\n" + " * True Negative Rate = TN / (TN + FP)\n" + " * Accuracy = (TP + TN) / (TP + TN + FP + FN)\n" + " * F-Measure = 2 * Precision * Recall / (Precision + Recall)\n" + " * Matthews Correlation\n" + " * Coefficient = (TP * TN - FP * FN) / ((TP + FP)(TP + FN)(FP + TN)(FP + FN))\n" + " */\n\n"); } if (args.length > 1) try { bf = new BufferedWriter(new FileWriter(args[1])); } catch (IOException e) { e.printStackTrace(); } if (args.length > 0) { processFile_RNA(new File(args[0])); } else display("Please enter a valid \".rna\" file."); if (bf != null) try { bf.close(); } catch (IOException e) { e.printStackTrace(); } }
public static void processDir(File base) { if (base == null || !base.exists()) return; display("Opening " + base.getAbsolutePath() + "\n\n"); File[] files = base.listFiles(); for (File f : files) { if (f.isDirectory()) processDir(f); else processFile_RNA(f); } }