update

Author: neukamm

src/IO/writer/Writer.java

@@ -184,7 +184,7 @@ private void addValToString(int linecounter, int i){
      * @param distancematrix_d
      */
     public void addDistanceMatrixToResult(double[][] distancematrix_d){
-        printmatrix(distancematrix_d, "DistanceMethods matrix (gamma corrected)" +
+        printmatrix(distancematrix_d, "DistanceMethods matrix" +
                 "-----------------------------------------\n");
     }
 

src/Main/FstCalculator.java

@@ -20,6 +20,7 @@ public class FstCalculator {
     private final HashMap<String, List<String>> data;
     private String distance_method = "Pairwise Difference";
     private Writer writer;
+    private String[] groupnames;
 
 
     public FstCalculator(HashMap<String, List<String>> data,
@@ -62,7 +63,11 @@ private double[][] runAmova() throws IOException {
         standardAMOVA.setData(data);
 
         double[][] fsts_amova = standardAMOVA.calculateFst();
-        double[][] pvalues = standardAMOVA.calculatePermutatedFst();
+        double[][] pvalues = null;
+        if(number_of_permutations > 0){
+            pvalues = standardAMOVA.calculatePermutatedFst();
+        }
+
 
 
         writer = new Writer(number_of_permutations);
@@ -90,6 +95,8 @@ private double[][] runAmova() throws IOException {
 
         writer.writeResultsToFile("resultsFstStatisticsAMOVA.tsv");
 
+        groupnames = standardAMOVA.getGroupnames();
+
         return fsts_amova;
 
     }
@@ -99,5 +106,7 @@ public String getResultString(){
         return writer.getResult_as_string();
     }
 
-
+    public String[] getGroupnames() {
+        return groupnames;
+    }
 }

src/fst/FstAMOVA.java

@@ -5,6 +5,7 @@
 import methods.UsefulFunctions;
 
 import java.io.IOException;
+import java.math.BigInteger;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
@@ -47,6 +48,8 @@ public double[][] calculateFst() throws IOException {
         fsts = new double[populations.size()][populations.size()];
 
         // iterate over list, calculateWP distance between each pair of individuals
+        BigInteger totalNumberOfComparisons = choose(populations.size(), 2);
+        int pairsDone = 0;
         for(int i = 0; i < populations.size(); i++){
             for(int j = i+1; j < populations.size(); j++){
                 List<String> pop1 = data.get(populations.get(j));
@@ -56,6 +59,8 @@ public double[][] calculateFst() throws IOException {
                         pop2.toArray(new String[pop2.size()])
                 );
                 fsts[i][j] = fst;
+                pairsDone++;
+                System.out.println("("+ pairsDone+"/"+totalNumberOfComparisons+") pairs compared");
             }
         }
         return fsts;
@@ -269,6 +274,21 @@ private double calculatePvalue(double[] fsts_permuted, double fst_original) {
     }
 
 
+    public static BigInteger choose(int x, int y) {
+        if (y < 0 || y > x)
+            return BigInteger.ZERO;
+        if (y == 0 || y == x)
+            return BigInteger.ONE;
+
+        BigInteger answer = BigInteger.ONE;
+        for (int i = x - y + 1; i <= x; i++) {
+            answer = answer.multiply(BigInteger.valueOf(i));
+        }
+        for (int j = 1; j <= y; j++) {
+            answer = answer.divide(BigInteger.valueOf(j));
+        }
+        return answer;
+    }
 
     /*
             Setter and Getter