remember: do not check in quick bug fixes that you didn't test.

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