X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=3ba73192be43525bca54f8dce58871939b09e35b;hb=1379350f04bc63ca05bd428afb86717c4764755d;hp=b3e34fb7f6d00cb08d5e712edea2d9399caeaf52;hpb=34d8b4dc08dcd27c3b5ac3bf7811f709b4db5938;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b3e34fb..3ba7319 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1016,7 +1016,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       FormatAdapter f = new FormatAdapter();
       String output = f.formatSequences(format,
-              (Alignment) viewport.alignment, // class cast exceptions will
+              viewport.alignment, // class cast exceptions will
               // occur in the distant future
               omitHidden, f.getCacheSuffixDefault(format), viewport.colSel);
 
@@ -3067,7 +3067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
         {
           try
           {
-            sg.cs = (ColourSchemeI) cs.getClass().newInstance();
+            sg.cs = cs.getClass().newInstance();
           } catch (Exception ex)
           {
           }
@@ -3883,9 +3883,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 	      try 
 	      {
 	    	  TCoffeeScoreFile result = TCoffeeScoreFile.load(new File(sFilePath));
-	    	  if( result == null ) { throw new RuntimeException("The file provided does not match the T-Coffee scores file format"); }
+	    	  if( result == null ) { 
+	    		  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() != result.getHeight() || aln.getWidth() != result.getWidth()) ) {
+	    		  throw new RuntimeException("The scores matrix does not match the alignment dimensions");
+	    	  }
 
-	    	  // TODO check that the loaded scores matches the current MSA 'dimension'
 	    	  changeColour( new TCoffeeColourScheme(result) );
 	    	  tcoffeeScoreFile = result;
 	    	  tcoffeeColour.setEnabled(true);