{
SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
- assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
- { seq } }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq } }));
seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("DNA", "ACTugGCCAG");
SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
/*
- * 90% DNA:
+ * 90% DNA but one protein sequence - expect false
*/
- assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
- seq, seq, seq, seq, seq, seq, seq2 }));
- assertTrue(Comparison.isNucleotide(new SequenceI[][] {
- new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
- new SequenceI[] { seq, seq, seq, seq, seq, seq2 } }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq, seq2 }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+ new SequenceI[]
+ { seq, seq, seq, seq, seq, seq2 } }));
/*
- * 80% DNA:
+ * 80% DNA but one protein sequence - Expect false
*/
- assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq,
- seq, seq, seq, seq, seq, seq2, seq2 }));
- assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
- { seq }, new SequenceI[] { seq, seq, seq },
- new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[]
+ { seq, seq, seq, seq, seq, seq, seq, seq, seq2, seq2 }));
+ assertFalse(
+ Comparison.isNucleotide(new SequenceI[][]
+ { new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq },
+ new SequenceI[]
+ { seq, seq, seq, seq, seq2, seq2, null } }));
seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt");
// 12/14 = 85.7%
@Test(groups = { "Functional" })
public void testPID_includingGaps()
{
- String seq1 = "ABCDEF";
+ String seq1 = "ABCDEFG"; // extra length here is ignored
String seq2 = "abcdef";
assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f);
public void testPID_ungappedOnly()
{
// 5 identical, 2 gap-gap, 2 gap-residue, 1 mismatch
- String seq1 = "a--b-cdefh";
+ // the extra length of seq1 is ignored
+ String seq1 = "a--b-cdefhr";
String seq2 = "a---bcdefg";
int length = seq1.length();