X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FPCAPanel.java;h=ee544784e258ee3616fdd557302453cf83cf9b78;hb=f683f4d6c8af43be0ffeb96513b52572619efed5;hp=a5268bff97b2cd22c9424d5464aab1840d9a3556;hpb=3d136290d42e4f4ae2deeed8ce3b9dae7c6e2eec;p=jalview.git

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index a5268bf..ee54478 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -219,8 +219,14 @@ public class PCAPanel
     // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
     // or create a selection box around columns in alignment view
     // test Alignment(SeqCigar[])
-    Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(av.
-        getGapCharacter());
+    char gc = '-';
+    try {
+      // we try to get the associated view's gap character
+      // but this may fail if the view was closed...
+      gc = av.
+      getGapCharacter();
+    } catch (Exception ex) {};
+    Object[] alAndColsel = seqstrings.getAlignmentAndColumnSelection(gc);
 
     if (alAndColsel != null && alAndColsel[0] != null)
     {