isAligned assertion (bug 0008144)

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 3e57430..f9b6413 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3365,8 +3365,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      // are the sequences aligned?
-      if (!viewport.alignment.isAligned())
+      // are the visible sequences aligned?
+      if (!viewport.alignment.isAligned(false))
       {
         JOptionPane
                 .showMessageDialog(
@@ -3635,7 +3635,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     // jobs
     // TODO: viewport.alignment.isAligned is a global state - the local
     // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
-    if (!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned(false))
     {
       seqs.setSequences(new SeqCigar[]
       { seqs.getSequences()[0] });