/** @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 processFile_RNA(File f) {
if (f == null || !f.exists()) return;
if (f.isDirectory()) {
processDir(f);
return;
}
display("[Processing: " + f.getAbsolutePath() + "\n\n");
try {
Scanner scan = new Scanner(f);
String[] arr = new String[4];
int count = 0;
while (scan.hasNextLine() && count < 4) {
arr[count++] = scan.nextLine();
}
scan.close();
if (arr[1] != null && arr[2] != null) {
Map<String, StringBuilder> ht = parseNative(arr[1]);
double[] vals = parsePredicted(arr[2], ht);
String header =
"Native Structure vs. MFE Predicted Structure\n"
+ "--------------------------------------------\n";
printCalculations(vals, header);
if (arr[3] != null) {
vals = parsePredicted(arr[3], ht);
header =
"Native Structure vs. Custom Predicted Structure\n"
+ "-----------------------------------------------\n";
printCalculations(vals, header);
}
}
} catch (Exception 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);
}
}
public static void printCalculations(double[] arr, String header) {
StringBuilder sb = new StringBuilder(header);
sb.append("-Specificity\t= ").append(specificity(arr)).append("\n");
sb.append("-Sensitivity\t= ").append(sensitivity(arr)).append("\n");
sb.append("-Precision\t= ").append(precision(arr)).append("\n");
sb.append("-F-Measure\t= ").append(fMeasure(arr)).append("\n\n");
sb.append("See \"-help\" for equations.\n\n");
display(sb.toString());
}
