+ \r
+ /*\r
+ * check that the score matrix matches the alignment dimensions\r
+ */\r
+ AlignmentI aln; \r
+ if( (aln=viewport.alignment) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {\r
+ // TODO: raise a dialog box here rather than bomb out.\r
+ throw new RuntimeException("The scores matrix does not match the alignment dimensions");\r
+ \r
+ }\r
+ \r
+ // TODO add parameter to indicate if matching should be done\r