+ assertEquals("acdeuv", sr.getCharacters());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testEquals()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResults sr1 = new SearchResults();
+ SearchResults sr2 = new SearchResults();
+
+ assertFalse(sr1.equals(null)); // null object
+ assertFalse(sr1.equals(seq1)); // wrong type
+ assertTrue(sr1.equals(sr1)); // self
+ assertTrue(sr1.equals(sr2)); // empty
+ assertTrue(sr2.equals(sr1)); // reflexive
+
+ /*
+ * only one result is not empty
+ */
+ sr1.addResult(seq1, 1, 1);
+ assertTrue(sr1.equals(sr1));
+ assertFalse(sr1.equals(sr2));
+ assertFalse(sr2.equals(sr1));
+
+ /*
+ * both the same
+ */
+ sr2.addResult(seq1, 1, 1);
+ assertTrue(sr1.equals(sr2));
+ assertTrue(sr2.equals(sr1));
+
+ /*
+ * both have three matches
+ */
+ sr1.addResult(seq1, 3, 4);
+ sr1.addResult(seq1, 6, 8);
+ sr2.addResult(seq1, 3, 4);
+ sr2.addResult(seq1, 6, 8);
+ assertTrue(sr1.equals(sr1));
+ assertTrue(sr2.equals(sr2));
+ assertTrue(sr1.equals(sr2));
+ assertTrue(sr2.equals(sr1));
+ }
+
+ /**
+ * Matches that are similar but for distinct sequences are not equal
+ */
+ @Test(groups = { "Functional" })
+ public void testEquals_distinctSequences()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SequenceI seq2 = new Sequence("", "abcdefghijklm");
+ SearchResults sr1 = new SearchResults();
+ SearchResults sr2 = new SearchResults();
+
+ sr1.addResult(seq1, 1, 1);
+ sr2.addResult(seq2, 1, 1);
+ assertFalse(sr1.equals(sr2));
+ assertFalse(sr2.equals(sr1));
+ }
+
+ /**
+ * Matches that are the same except for ordering are not equal
+ */
+ @Test(groups = { "Functional" })
+ public void testEquals_orderDiffers()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResults sr1 = new SearchResults();
+ SearchResults sr2 = new SearchResults();
+
+ sr1.addResult(seq1, 1, 1);
+ sr1.addResult(seq1, 2, 2);
+ sr2.addResult(seq1, 2, 2);
+ sr2.addResult(seq1, 1, 1);
+ assertFalse(sr1.equals(sr2));
+ assertFalse(sr2.equals(sr1));
+ }
+
+ /**
+ * Verify that hashCode matches for equal objects
+ */
+ @Test(groups = { "Functional" })
+ public void testHashcode()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ SearchResults sr1 = new SearchResults();
+ SearchResults sr2 = new SearchResults();
+
+ /*
+ * both empty
+ */
+ assertEquals(sr1.hashCode(), sr2.hashCode());
+
+ /*
+ * both one match
+ */
+ sr1.addResult(seq1, 1, 1);
+ sr2.addResult(seq1, 1, 1);
+ assertEquals(sr1.hashCode(), sr2.hashCode());
+
+ /*
+ * both three matches
+ */
+ sr1.addResult(seq1, 3, 4);
+ sr1.addResult(seq1, 6, 8);
+ sr2.addResult(seq1, 3, 4);
+ sr2.addResult(seq1, 6, 8);
+ assertEquals(sr1.hashCode(), sr2.hashCode());
+ }
+
+ /**
+ * Verify that SearchResults$Match constructor normalises start/end to the
+ * 'forwards' direction
+ */
+ @Test(groups = { "Functional" })
+ public void testMatchConstructor()
+ {
+ SequenceI seq1 = new Sequence("", "abcdefghijklm");
+ Match m = new SearchResults().new Match(seq1, 2, 5);
+ assertSame(seq1, m.getSequence());
+ assertEquals(2, m.getStart());
+ assertEquals(5, m.getEnd());
+
+ // now a reverse mapping:
+ m = new SearchResults().new Match(seq1, 5, 2);
+ assertSame(seq1, m.getSequence());
+ assertEquals(2, m.getStart());
+ assertEquals(5, m.getEnd());