private static void writeStrs(
String outFileName, List<ShortTandemRepeat> strs, boolean writeAll) {
BufferedWriter bw = null;
File outFile = new File(outFileName);
try {
if (outFile.exists()) {
outFile.delete();
}
bw = new BufferedWriter(new FileWriter(outFile));
if (writeAll) {
for (ShortTandemRepeat str : strs) {
bw.write(str.toString());
bw.newLine();
}
} else {
for (ShortTandemRepeat str : strs) {
bw.write(str.toSmallString());
bw.newLine();
}
}
} catch (IOException e) {
e.printStackTrace();
} finally {
if (bw != null) {
try {
bw.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
}
public static void printRef(
HashMap<String, LinkedList<ShortTandemRepeat>> ref, boolean printAll) {
List<ShortTandemRepeat> strs = refToSortedList(ref);
System.out.println("\n####Reference Results####");
if (printAll) {
for (ShortTandemRepeat str : strs) {
System.out.println(str.toString());
}
} else {
for (ShortTandemRepeat str : strs) {
System.out.println(str.toSmallString());
}
}
}
public static void printPriv(
HashMap<ShortTandemRepeat, ShortTandemRepeat> priv, boolean printAll) {
List<ShortTandemRepeat> strs = privToSortedList(priv);
System.out.println("\n####Private results####");
if (printAll) {
for (ShortTandemRepeat str : strs) {
System.out.println(str.toString());
}
} else {
for (ShortTandemRepeat str : strs) {
if (str.isLost()) {
break;
}
System.out.println(str.toSmallString());
}
}
}