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 writeCM124Answer(
String refFileName, String outFileName, HashMap<String, LinkedList<ShortTandemRepeat>> ref) {
BufferedReader br = null;
String genomeName = null;
try {
br =
new BufferedReader(
new InputStreamReader(Utilities.class.getResourceAsStream(refFileName), "UTF-8"));
genomeName = br.readLine();
System.out.println("Formatting for genome: " + genomeName);
} catch (Exception e) {
e.printStackTrace();
} finally {
if (br != null) {
try {
br.close();
} catch (IOException e) {
e.printStackTrace();
}
}
}
if (genomeName == null) {
throw new Error(refFileName + " does not have a genome name.");
}
List<ShortTandemRepeat> strs = refToSortedList(ref);
BufferedWriter bw = null;
File outFile = new File(outFileName);
try {
if (outFile.exists()) {
outFile.delete();
}
if (!outFile.createNewFile()) {
throw new RuntimeException(outFileName + " already exists.");
}
bw = new BufferedWriter(new FileWriter(outFile));
bw.write(genomeName);
bw.newLine();
bw.write(">STR");
for (ShortTandemRepeat str : strs) {
bw.newLine();
bw.write(str.toString());
}
} 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());
}
}
}