isAligned assertion (bug 0008144)

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 1330cf6..1b2088e 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2288,7 +2288,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   public void PCAMenuItem_actionPerformed()
   {
     // are the sequences aligned?
-    if (!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned(false))
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();
@@ -2345,7 +2345,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
   void NewTreePanel(String type, String pwType, String title)
   {
     // are the sequences aligned?
-    if (!viewport.alignment.isAligned())
+    if (!viewport.alignment.isAligned(false))
     {
       SequenceI current;
       int Width = viewport.getAlignment().getWidth();