// writes the passed string to the passed file
private void setContents(File file, String content) {
try {
BufferedWriter output = new BufferedWriter(new FileWriter(file));
output.write(content);
output.close();
} catch (Exception e) {
System.out.println("Encryption/Decryption File Error: " + e);
}
}
public void run() {
try {
BufferedReader br =
new BufferedReader(new InputStreamReader(new FileInputStream(file), charset));
if (outputFile != null) {
bw =
new BufferedWriter(new OutputStreamWriter(new FileOutputStream(outputFile), charset));
}
String line;
while ((line = br.readLine()) != null) {
filePosition += line.length() + 2;
line = line.trim();
if (!line.startsWith("#")) {
String[] sides = split(line);
if ((sides != null) && !sides[0].equals("key")) {
if (searchPHI) {
// Search the decrypted PHI for the searchText
sides[0] = decrypt(sides[0]);
if (sides[0].indexOf(searchText) != -1) {
output(sides[0] + " = " + sides[1] + "\n");
}
} else {
// Search the trial ID for the searchText
if (sides[1].indexOf(searchText) != -1) {
sides[0] = decrypt(sides[0]);
output(sides[0] + " = " + sides[1] + "\n");
}
}
}
}
}
br.close();
if (bw != null) {
bw.flush();
bw.close();
}
} catch (Exception e) {
append("\n\n" + e.getClass().getName() + ": " + e.getMessage() + "\n");
}
append("\nDone.\n");
setMessage("Ready...");
}
private void output(String string) throws Exception {
if (bw != null) bw.write(string);
else append(string);
// Set the fraction done.
long pct = (filePosition * 100) / fileLength;
if (pct != percentDone) {
percentDone = pct;
setMessage("Working... (" + pct + "%)");
}
}