X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;fp=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=15904df0f04b25272fc55d74a55a560bd49f7b01;hb=1379350f04bc63ca05bd428afb86717c4764755d;hp=c1dbf303c2923abee49fb2e73252531e9e5264a7;hpb=34d8b4dc08dcd27c3b5ac3bf7811f709b4db5938;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index c1dbf30..15904df 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -2335,7 +2335,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
         {
           try
           {
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+            sg.cs = cs.getClass().newInstance();
           } catch (Exception ex)
           {
             ex.printStackTrace();
@@ -3685,6 +3685,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,  ItemLis
 		  throw new RuntimeException("The file provided does not match the T-Coffee scores file format");
 	  }
 	  
+	  /*
+	   * check that the score matrix matches the alignment dimensions
+	   */
+	  AlignmentI aln; 
+	  if( (aln=viewport.alignment) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {
+		  throw new RuntimeException("The scores matrix does not match the alignment dimensions");
+	  }
+	  
 	  tcoffeeColour.setEnabled(true);
 	  tcoffeeScoreFile = file;