X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPaintRefresher.java;h=c6d3b588755f5a457a51045aebead9e1ba3ae3d2;hb=27f51f19a31e2d2cb3543ae858b248c91c1e9428;hp=1b253859e3a4e60ca35979da416c7dedbd0ee1fd;hpb=04fe5ab63df768c865eb40c9300b52239fbe8746;p=jalview.git

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 1b25385..c6d3b58 100755
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -178,7 +178,7 @@ public class PaintRefresher
 
       if (!exists)
       {
-        if (i < jSize)
+        if (i < comp.getHeight())
         {
           comp.getSequences().insertElementAt(a1[i], i);
         }
@@ -187,8 +187,6 @@ public class PaintRefresher
           comp.addSequence(a1[i]);
         }
 
-        jSize++;
-
         if (comp.getHiddenSequences().getSize() > 0)
         {
           a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
@@ -197,6 +195,8 @@ public class PaintRefresher
         {
           a2 = comp.getSequencesArray();
         }
+
+        jSize = a2.length;
       }
     }