* AGCTU. Test is not case-sensitive and ignores gaps.
*/
@Test(groups = { "Functional" })
- public void testIsNucleotide()
+ public void testIsNucleotide_sequences()
{
SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
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
*/
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));
+ }
}