public static void printIdentified(
HashMap<String, LinkedList<ShortTandemRepeat>> ref,
HashMap<ShortTandemRepeat, ShortTandemRepeat> priv) {
int total;
int found = 0;
int lost = 0;
int zero = 0;
List<ShortTandemRepeat> refs = refToSortedList(ref);
total = refs.size();
Iterator<ShortTandemRepeat> refIter = refs.iterator();
while (refIter.hasNext()) {
ShortTandemRepeat r = refIter.next();
if (priv.containsKey(r)) {
ShortTandemRepeat p = priv.get(r);
if (p.getRepeats() == 0) {
zero++;
lost++;
} else {
found++;
}
} else {
lost++;
}
}
double accuracy = 0;
if (total != 0) {
accuracy = (double) found / total * 100;
}
System.out.println("\n####Identification####");
System.out.println("Reference total STRs: " + total);
System.out.println("Private identified STRs: " + found);
System.out.println("Private identified STRs with 0 count: " + zero);
System.out.println("Private unidentified STRs (including 0 counts): " + lost);
System.out.println("Identification accuracy: " + accuracy + "%");
}
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 printCounts(HashMap<ShortTandemRepeat, ShortTandemRepeat> res) {
int total = 0;
int found = 0;
int lost = 0;
int mismatches = 0;
double accuracy = 0;
int repeatCount = 0;
Set<ShortTandemRepeat> ref = res.keySet();
Iterator<ShortTandemRepeat> refIter = ref.iterator();
while (refIter.hasNext()) {
ShortTandemRepeat refStr = refIter.next();
ShortTandemRepeat readStr = res.get(refStr);
if (refStr.isLost()) {
lost += readStr.getRepeats();
} else {
total += refStr.getRepeats();
found += readStr.getRepeats();
mismatches += Math.abs(refStr.getRepeats() - readStr.getRepeats());
accuracy += (double) (total - mismatches) / total;
repeatCount++;
}
}
if (repeatCount != 0) {
accuracy = accuracy / repeatCount * 100;
}
System.out.println("\n####Aggregate Counts####");
System.out.println("Reference count: " + total);
System.out.println("Private identified count: " + found);
System.out.println("Private unidentified count: " + lost);
System.out.println("Private mismatch count: " + mismatches);
System.out.println("Average STR accuracy: " + accuracy + "%");
}
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());
}
}
}