From 748203f18005f8e513644c88909a5a14fde50b2d Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 8 Apr 2005 14:07:18 +0000
Subject: [PATCH] remember: do not check in quick bug fixes that you didn't
 test.

---
 src/jalview/analysis/Conservation.java |    7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 38047f8..9786362 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -255,6 +255,9 @@ public class Conservation {
         for (int i = 1; i < sqnum.length; i++) {
           cons2[i-1][sqnum[i]]++;
         }
+        for (int i=sqnum.length-1; i<maxLength; i++) {
+          cons2[i][23]++; // gap count
+        }
         j++;
       }
 
@@ -292,7 +295,7 @@ public void findQuality(int start, int end) {
     int[] lengths = new int[size];
 
     for (int l = 0; l < size; l++)
-      lengths[l] = ((int[]) seqNums.get(l)).length;
+      lengths[l] = ((int[]) seqNums.get(l)).length-1;
 
     for (int j=start; j <= end; j++) {
       double bigtot = 0;
@@ -318,7 +321,7 @@ public void findQuality(int start, int end) {
 	double tot = 0;
 	double[] xx = new double[24];
         int seqNum =
-            ((j+1)<lengths[size])
+            (j<lengths[k])
             ? ((int[]) seqNums.get(k))[j+1]
             : 23; // Sequence, or gap at the end
 
-- 
1.7.10.2