Ejemplo n.º 1
0
 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 + "%");
 }
Ejemplo n.º 2
0
 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 + "%");
 }