X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=ad7113aad1015e73f240a560f6656b77feed78ac;hb=6c4bc68ae8b1c5005e79661bb2d8246515cb787d;hp=40d67b028c64d3a99648cd1f470f88a5c431e5ec;hpb=4d2e0d36506302cc00677527725bcccbdf27d766;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 40d67b0..ad7113a 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -296,7 +296,7 @@ public class AlignViewport
           cons.findQuality();
         }
 
-        String sequence = cons.getConsSequence().getSequence();
+        char [] sequence = cons.getConsSequence().getSequence();
         float minR;
         float minG;
         float minB;
@@ -331,7 +331,7 @@ public class AlignViewport
         {
           float value = 0;
 
-          c = sequence.charAt(i);
+          c = sequence[i];
 
           if (Character.isDigit(c))
             value = (int) (c - '0');
@@ -1201,7 +1201,7 @@ public class AlignViewport
       }
       else
       {
-        selection[i] = seqs[i].getSequence(start, end);
+        selection[i] = seqs[i].getSequenceAsString(start, end);
       }
     }