- System.err.println("Annotation Element Mismatch\nElement " + i
- + " in original: " + annot_or.annotations[i].toString()
- + "\nElement " + i + " in new: "
- + annot_new.annotations[i].toString());
- return false;
+ if (an_or.secondaryStructure != an_new.secondaryStructure
+ || an_or.value != an_new.value)
+ {
+ fail("Different RNA secondary structure at column " + i
+ + " expected: [" + annot_or.annotations[i].toString()
+ + "] but got: [" + annot_new.annotations[i].toString()
+ + "]");
+ }
+ }
+ else
+ {
+ // not RNA secondary structure, so expect all elements to match...
+ if (!an_or.displayCharacter.trim().equals(
+ an_new.displayCharacter.trim())
+ || !("" + an_or.secondaryStructure).trim().equals(
+ ("" + an_new.secondaryStructure).trim())
+ || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
+ .trim().length() == 0)
+ || (an_new.description == null && an_or.description
+ .trim().length() == 0) || an_or.description
+ .trim().equals(an_new.description.trim()))))
+ {
+ fail("Annotation Element Mismatch\nElement " + i
+ + " in original: " + annot_or.annotations[i].toString()
+ + "\nElement " + i + " in new: "
+ + annot_new.annotations[i].toString());
+ }