+ int nsecStr = 0, nsTemp = 0;
+ // test for presence of transferred annotation on sequence
+ for (AlignmentAnnotation alan : sq.getAnnotation())
+ {
+ if (alan.hasIcons)
+ {
+ nsecStr++;
+ }
+ if (alan.graph == alan.LINE_GRAPH)
+ {
+ nsTemp++;
+ }
+ }
+ assertEquals(
+ "Only one secondary structure should be transferred to associated sequence.",
+ 1, nsecStr);
+ assertEquals(
+ "Only two line graphs should be transferred to associated sequence.",
+ 2, nsTemp);
+ // Now test the transfer function and compare annotated positions