import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
-import org.testng.annotations.Test;
+
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import org.testng.annotations.Test;
+
public class ComparisonTest
{
- @Test
+ @Test(groups = { "Functional" })
public void testIsGap()
{
assertTrue(Comparison.isGap('-'));
* Test for isNucleotide is that sequences in a dataset are more than 85%
* AGCTU. Test is not case-sensitive and ignores gaps.
*/
- @Test
- public void testIsNucleotide() {
+ @Test(groups = { "Functional" })
+ public void testIsNucleotide()
+ {
SequenceI seq = new Sequence("eightypercent", "agctuAGCPV");
- assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq }));
- assertFalse(Comparison.isNucleotide(new SequenceI[][]
- { new SequenceI[]
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
+ assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[]
{ seq } }));
seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV");
- assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV");
- assertTrue(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("eightyfivepercentgapped",
"--agc--tuA--GCPV-a---gct-uA-GC---UV");
- assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("nineypercentgapped",
"ag--ct-u-A---GC---g----Vag--c---tuAGCUV");
- assertTrue(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("allgap", "---------");
- assertFalse(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ assertFalse(Comparison.isNucleotide(new SequenceI[] { seq }));
seq = new Sequence("DNA", "ACTugGCCAG");
SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW");
/*
* 90% DNA:
*/
- 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 } }));
+ 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 } }));
/*
* 80% DNA:
*/
- 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%
- assertTrue(Comparison.isNucleotide(new SequenceI[]
- { seq }));
+ assertTrue(Comparison.isNucleotide(new SequenceI[] { seq }));
assertFalse(Comparison.isNucleotide((SequenceI[]) null));
assertFalse(Comparison.isNucleotide((SequenceI[][]) null));
/**
* Test percentage identity calculation for two sequences.
*/
- @Test
+ @Test(groups = { "Functional" })
public void testPID_matchGaps()
{
String seq1 = "ABCDEF";