X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPaintRefresher.java;h=7e0edf7191abf702507daa9b5d58b55031b14337;hb=94e19634c669879ab63bbb82d5489c200cdb18f8;hp=f7bec9884a9571c7416429d07340b40e25632f01;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index f7bec98..7e0edf7 100755
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -182,7 +182,7 @@ public class PaintRefresher
 
       if (!exists)
       {
-        if (i < jSize)
+        if (i < comp.getHeight())
         {
           comp.getSequences().insertElementAt(a1[i], i);
         }
@@ -191,8 +191,6 @@ public class PaintRefresher
           comp.addSequence(a1[i]);
         }
 
-        jSize++;
-
         if (comp.getHiddenSequences().getSize() > 0)
         {
           a2 = comp.getHiddenSequences().getFullAlignment().getSequencesArray();
@@ -201,6 +199,8 @@ public class PaintRefresher
         {
           a2 = comp.getSequencesArray();
         }
+
+        jSize = a2.length;
       }
     }