From 25b52338f677d211c04f6b60980188badf83db00 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 8 Mar 2005 16:44:11 +0000
Subject: [PATCH] fixed so that alignment percentage ID is used for distance
 calculation

---
 src/jalview/analysis/NJTree.java |    3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

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];
           }
         }
-- 
1.7.10.2