JAL-1067 report any warning messages to user

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

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 198c3bd..e19581f 100755 (executable)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3958,7 +3958,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                  AlignmentI aln; 
                  if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
                      // TODO: raise a dialog box here rather than bomb out.
-                   throw new RuntimeException("The scores matrix does not match the alignment dimensions");
+               JOptionPane.showMessageDialog(Desktop.desktop, "The scores matrix does not match the alignment dimensions",
+                        "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE);
                  }
                  if (result.annotateAlignment(alignPanel.getAlignment(), true))
                  {
@@ -3970,12 +3971,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
                    tcoffeeColour.setEnabled(false);
                    tcoffeeColour.setSelected(false);
                  }
+                 if (result.getWarningMessage()!=null)
+                 {
+                   JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(),"Problem reading T-COFEEE score file", JOptionPane.WARNING_MESSAGE);
+                 }
              } 
              catch (Exception ex) {
                JOptionPane.showMessageDialog(
                                        Desktop.desktop, 
                                        ex.getMessage(), 
-                                       "Problem reading tree file", 
+                                       "unexpected problem reading T-COFFEE score file", 
                                        JOptionPane.WARNING_MESSAGE);
 
                ex.printStackTrace();