From: jprocter <Jim Procter>
Date: Tue, 8 Mar 2005 16:44:11 +0000 (+0000)
Subject: fixed so that alignment percentage ID is used for distance calculation
X-Git-Tag: Release_2_0~617
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=25b52338f677d211c04f6b60980188badf83db00;p=jalview.git

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