dont adjust aligments if they're the same size

diff --git a/src/jalview/appletgui/PaintRefresher.java b/src/jalview/appletgui/PaintRefresher.java
index 322466b..1195210 100755 (executable)
--- a/src/jalview/appletgui/PaintRefresher.java
+++ b/src/jalview/appletgui/PaintRefresher.java
@@ -147,6 +147,10 @@ public class PaintRefresher
         a2 = comp.getSequencesArray();\r
 \r
       int i, iSize=a1.length, j, jSize=a2.length;\r
+\r
+      if(iSize == jSize)\r
+        return;\r
+\r
       boolean exists = false;\r
       for(i=0; i<iSize; i++)\r
       {\r

diff --git a/src/jalview/gui/PaintRefresher.java b/src/jalview/gui/PaintRefresher.java
index 1def794..de1d5d8 100755 (executable)
--- a/src/jalview/gui/PaintRefresher.java
+++ b/src/jalview/gui/PaintRefresher.java
@@ -147,6 +147,10 @@ public class PaintRefresher
         a2 = comp.getSequencesArray();\r
 \r
       int i, iSize=a1.length, j, jSize=a2.length;\r
+\r
+      if(iSize == jSize)\r
+        return;\r
+\r
       boolean exists = false;\r
       for(i=0; i<iSize; i++)\r
       {\r