+ // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
+ seq1 = "a--b-cdefh";
+ seq2 = "a---bcdefg";
+ int length = seq1.length();
+
+ // match gap-residue, match gap-gap: 9/10 identical
+ assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false),
+ 0.001f);
+ // overloaded version of the method signature above:
+ assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f);
+
+ // don't match gap-residue, match gap-gap: 7/10 identical
+ assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
+ 0.001f);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsNucleotide()
+ {
+ assertTrue(Comparison.isNucleotide('a'));
+ assertTrue(Comparison.isNucleotide('A'));
+ assertTrue(Comparison.isNucleotide('c'));
+ assertTrue(Comparison.isNucleotide('C'));
+ assertTrue(Comparison.isNucleotide('g'));
+ assertTrue(Comparison.isNucleotide('G'));
+ assertTrue(Comparison.isNucleotide('t'));
+ assertTrue(Comparison.isNucleotide('T'));
+ assertTrue(Comparison.isNucleotide('u'));
+ assertTrue(Comparison.isNucleotide('U'));
+ assertFalse(Comparison.isNucleotide('-'));
+ assertFalse(Comparison.isNucleotide('P'));
+ }
+
+ /**
+ * Test the percentage identity calculation for two sequences
+ */
+ @Test(groups = { "Functional" })
+ public void testPID_ungappedOnly()
+ {
+ // 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
+ String seq1 = "a--b-cdefh";
+ String seq2 = "a---bcdefg";
+ int length = seq1.length();
+
+ /*
+ * As currently coded, 'ungappedOnly' ignores gap-residue but counts
+ * gap-gap. Is this a bug - should gap-gap also be ignored, giving a PID of
+ * 5/6?
+ *
+ * Note also there is no variant of the calculation that penalises
+ * gap-residue i.e. counts it as a mismatch. This would give a score of 5/8
+ * (if we ignore gap-gap) or 5/10 (if we count gap-gap as a match).
+ */
+ // match gap-residue, match gap-gap: 7/8 identical
+ assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, true, true),
+ 0.001f);
+
+ // don't match gap-residue with 'ungapped only' - same as above
+ assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true),
+ 0.001f);
+ }
+
+ @Test(groups = { "Functional" })
+ public void testIsNucleotideSequence()
+ {
+ assertFalse(Comparison.isNucleotideSequence(null, true));
+ assertTrue(Comparison.isNucleotideSequence("", true));
+ assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", true));
+ assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", false));
+ assertFalse(Comparison.isNucleotideSequence("xAgGcCtTuU", false));
+ assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false));
+ assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
+ assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));