fixed so that alignment percentage ID is used for distance calculation

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 4aeee3d..7324b6c 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -331,14 +331,13 @@ public class NJTree {
   public float[][] findDistances() {\r
 \r
     float[][] distance = new float[noseqs][noseqs];\r
-\r
     if (pwtype.equals("PID")) {\r
       for (int i = 0; i < noseqs-1; i++) {\r
         for (int j = i; j < noseqs; j++) {\r
           if (j==i) {\r
             distance[i][i] = 0;\r
           } else {\r
-            distance[i][j] = 100-Comparison.compare(sequence[i],sequence[j],start,end);\r
+            distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j]);\r
             distance[j][i] = distance[i][j];\r
           }\r
         }\r