assertFalse(ann5.visible);
assertTrue(ann6.visible); // not sequence-related, not affected
}
+
+ /**
+ * Tests for the method that checks if one sequence cross-references another
+ */
+ @Test
+ public void testHasCrossRef()
+ {
+ assertFalse(AlignmentUtils.hasCrossRef(null, null));
+ SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
+ assertFalse(AlignmentUtils.hasCrossRef(seq1, null));
+ assertFalse(AlignmentUtils.hasCrossRef(null, seq1));
+ SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
+ assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
+
+ // different ref
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20193"));
+ assertFalse(AlignmentUtils.hasCrossRef(seq1, seq2));
+
+ // case-insensitive; version number is ignored
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "v20192"));
+ assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
+
+ // right case!
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(AlignmentUtils.hasCrossRef(seq1, seq2));
+ // test is one-way only
+ assertFalse(AlignmentUtils.hasCrossRef(seq2, seq1));
+ }
+
+ /**
+ * Tests for the method that checks if either sequence cross-references the
+ * other
+ */
+ @Test
+ public void testHaveCrossRef()
+ {
+ assertFalse(AlignmentUtils.hasCrossRef(null, null));
+ SequenceI seq1 = new Sequence("EMBL|A12345", "ABCDEF");
+ assertFalse(AlignmentUtils.haveCrossRef(seq1, null));
+ assertFalse(AlignmentUtils.haveCrossRef(null, seq1));
+ SequenceI seq2 = new Sequence("UNIPROT|V20192", "ABCDEF");
+ assertFalse(AlignmentUtils.haveCrossRef(seq1, seq2));
+
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
+ // next is true for haveCrossRef, false for hasCrossRef
+ assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
+
+ // now the other way round
+ seq1.setDBRef(null);
+ seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
+ assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
+ assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
+
+ // now both ways
+ seq1.addDBRef(new DBRefEntry("UNIPROT", "1", "V20192"));
+ assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
+ assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
+ }
}