+ 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");
+ }