import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
public class ComparisonTest
{
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
@Test(groups = { "Functional" })
public void testIsGap()
{
int length = seq1.length();
// match gap-residue, match gap-gap: 9/10 identical
+ // TODO should gap-gap be included in a PID score? JAL-791
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
+ // TODO should gap-gap be included in a PID score?
assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false),
0.001f);
}
assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true));
assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false));
}
+
+ @Test(groups = { "Functional" })
+ public void testIsSameResidue()
+ {
+ assertTrue(Comparison.isSameResidue('a', 'a', false));
+ assertTrue(Comparison.isSameResidue('a', 'a', true));
+ assertTrue(Comparison.isSameResidue('A', 'a', false));
+ assertTrue(Comparison.isSameResidue('a', 'A', false));
+
+ assertFalse(Comparison.isSameResidue('a', 'A', true));
+ assertFalse(Comparison.isSameResidue('A', 'a', true));
+ }
}