X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=4a93eef2dedb82a35b69a6ca40d596a9464a279d;hb=597b36936d89f172923e3321c8c5ea322cc5e5e5;hp=db572ac8f8f6c1aefdefcf91c1ff48d50d1a08a1;hpb=a49fdebf932bc4dbb55d3aaa9cc35ec2cfb181ff;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index db572ac..4a93eef 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -64,7 +64,7 @@ public class Conservation {
         if (sequences.elementAt(j) instanceof Sequence) {
           Sequence s = (Sequence)sequences.elementAt(j);
 
-          if (s.getSequence().length() > i) {
+          if (s.getLength() > i) {
             String res = s.getSequence().substring(i,i+1);
 
             if (residueHash.containsKey(res)) {
@@ -125,6 +125,9 @@ public class Conservation {
     int count = 0;
 
     for (int i = 0; i < sequences.size();i++) {
+      if( j+1 > ((Sequence)sequences.elementAt(i)).getSequence().length())
+      {  count++; continue;}
+
       String tmp = ((Sequence)sequences.elementAt(i)).getSequence().substring(j,j+1);
       if (tmp.equals(" ") || tmp.equals(".") || tmp.equals("-")) {
         count++;
@@ -140,42 +143,46 @@ public class Conservation {
       int totGaps = countGaps(i);
       float pgaps = (float)totGaps*100/(float)sequences.size();
 
-      if (percentageGaps > pgaps) {
+      if (percentageGaps > pgaps)
+      {
         Hashtable resultHash = (Hashtable)total.elementAt(i);
 
         //Now find the verdict
         int         count = 0;
         Enumeration e3    = resultHash.keys();
 
-        while (e3.hasMoreElements()) {
+        while (e3.hasMoreElements())
+        {
           String type    = (String)e3.nextElement();
           Integer result = (Integer)resultHash.get(type);
 
           //Do we want to count +ve conservation or +ve and -ve cons.?
 
-          if (consflag) {
-            if (result.intValue() == 1) {
+          if (consflag)
+          {
+            if (result.intValue() == 1)
               count++;
-            }
-          } else {
-            if (result.intValue() != -1) {
+          }
+          else
+          {
+            if (result.intValue() != -1)
               count++;
-            }
           }
         }
 
-        if (count < 10) {
+        if (count < 10)
           consString = consString + String.valueOf(count);
-        } else {
+        else
           consString = consString + "*";
-        }
-      } else {
+
+      }
+      else
+      {
         consString = consString + "-";
       }
     }
 
     consSequence = new DrawableSequence(name,consString,start,end);
-
   }
 
   public jalview.gui.DrawableSequence getConsSequence() {