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package jalview.util; |
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import static org.testng.AssertJUnit.assertEquals; |
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import static org.testng.AssertJUnit.assertFalse; |
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import static org.testng.AssertJUnit.assertTrue; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.JvOptionPane; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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| 100% |
Uncovered Elements: 0 (82) |
Complexity: 8 |
Complexity Density: 0.11 |
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public class ComparisonTest |
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{ |
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| 100% |
Uncovered Elements: 0 (2) |
Complexity: 1 |
Complexity Density: 0.5 |
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@BeforeClass(alwaysRun = true)... |
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public void setUpJvOptionPane() |
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{ |
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JvOptionPane.setInteractiveMode(false); |
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JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); |
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} |
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| 100% |
Uncovered Elements: 0 (7) |
Complexity: 1 |
Complexity Density: 0.14 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testIsGap() |
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{ |
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assertTrue(Comparison.isGap('-')); |
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assertTrue(Comparison.isGap('.')); |
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assertTrue(Comparison.isGap(' ')); |
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assertFalse(Comparison.isGap('X')); |
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assertFalse(Comparison.isGap('x')); |
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assertFalse(Comparison.isGap('*')); |
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assertFalse(Comparison.isGap('G')); |
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} |
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| 100% |
Uncovered Elements: 0 (23) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testIsNucleotide_sequences() |
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{ |
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SequenceI seq = new Sequence("eightypercent", "agctuAGCPV"); |
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assertFalse(Comparison.isNucleotide(new SequenceI[] { seq })); |
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assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[] |
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{ seq } })); |
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seq = new Sequence("eightyfivepercent", "agctuAGCPVagctuAGCUV"); |
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assertFalse(Comparison.isNucleotide(new SequenceI[] { seq })); |
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seq = new Sequence("nineypercent", "agctuAGCgVagctuAGCUV"); |
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assertTrue(Comparison.isNucleotide(new SequenceI[] { seq })); |
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seq = new Sequence("eightyfivepercentgapped", |
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"--agc--tuA--GCPV-a---gct-uA-GC---UV"); |
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assertFalse(Comparison.isNucleotide(new SequenceI[] { seq })); |
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seq = new Sequence("nineypercentgapped", |
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"ag--ct-u-A---GC---g----Vag--c---tuAGCUV"); |
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assertTrue(Comparison.isNucleotide(new SequenceI[] { seq })); |
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seq = new Sequence("allgap", "---------"); |
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assertFalse(Comparison.isNucleotide(new SequenceI[] { seq })); |
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seq = new Sequence("DNA", "ACTugGCCAG"); |
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SequenceI seq2 = new Sequence("Protein", "FLIMVSPTYW"); |
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assertTrue(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq, |
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seq, seq, seq, seq, seq, seq, seq2 })); |
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assertTrue(Comparison.isNucleotide(new SequenceI[][] { |
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new SequenceI[] { seq }, new SequenceI[] { seq, seq, seq }, |
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new SequenceI[] { seq, seq, seq, seq, seq, seq2 } })); |
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assertFalse(Comparison.isNucleotide(new SequenceI[] { seq, seq, seq, |
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seq, seq, seq, seq, seq, seq2, seq2 })); |
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assertFalse(Comparison.isNucleotide(new SequenceI[][] { new SequenceI[] |
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{ seq }, new SequenceI[] { seq, seq, seq }, |
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new SequenceI[] { seq, seq, seq, seq, seq2, seq2, null } })); |
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seq = new Sequence("ProteinThatLooksLikeDNA", "WYATGCCTGAgtcgt"); |
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assertTrue(Comparison.isNucleotide(new SequenceI[] { seq })); |
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assertFalse(Comparison.isNucleotide((SequenceI[]) null)); |
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assertFalse(Comparison.isNucleotide((SequenceI[][]) null)); |
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} |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testPID_includingGaps() |
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{ |
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String seq1 = "ABCDEFG"; |
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String seq2 = "abcdef"; |
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assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f); |
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seq2 = "abcdefghijklmnopqrstuvwxyz"; |
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assertEquals("identical", 100f, Comparison.PID(seq1, seq2), 0.001f); |
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seq1 = "a--b-cdefh"; |
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seq2 = "a---bcdefg"; |
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int length = seq1.length(); |
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assertEquals(90f, Comparison.PID(seq1, seq2, 0, length, true, false), |
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0.001f); |
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assertEquals(90f, Comparison.PID(seq1, seq2), 0.001f); |
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assertEquals(70f, Comparison.PID(seq1, seq2, 0, length, false, false), |
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0.001f); |
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} |
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| 100% |
Uncovered Elements: 0 (12) |
Complexity: 1 |
Complexity Density: 0.08 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testIsNucleotide() |
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{ |
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assertTrue(Comparison.isNucleotide('a')); |
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assertTrue(Comparison.isNucleotide('A')); |
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assertTrue(Comparison.isNucleotide('c')); |
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assertTrue(Comparison.isNucleotide('C')); |
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assertTrue(Comparison.isNucleotide('g')); |
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assertTrue(Comparison.isNucleotide('G')); |
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assertTrue(Comparison.isNucleotide('t')); |
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assertTrue(Comparison.isNucleotide('T')); |
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assertTrue(Comparison.isNucleotide('u')); |
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assertTrue(Comparison.isNucleotide('U')); |
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assertFalse(Comparison.isNucleotide('-')); |
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assertFalse(Comparison.isNucleotide('P')); |
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} |
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| 100% |
Uncovered Elements: 0 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testPID_ungappedOnly() |
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{ |
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String seq1 = "a--b-cdefhr"; |
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String seq2 = "a---bcdefg"; |
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int length = seq1.length(); |
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assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, true, true), |
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0.001f); |
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assertEquals(87.5f, Comparison.PID(seq1, seq2, 0, length, false, true), |
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0.001f); |
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} |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
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1 |
@Test(groups = { "Functional" })... |
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public void testIsNucleotideSequence() |
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{ |
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assertFalse(Comparison.isNucleotideSequence(null, true)); |
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assertTrue(Comparison.isNucleotideSequence("", true)); |
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assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", true)); |
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assertTrue(Comparison.isNucleotideSequence("aAgGcCtTuU", false)); |
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assertFalse(Comparison.isNucleotideSequence("xAgGcCtTuU", false)); |
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assertFalse(Comparison.isNucleotideSequence("aAgGcCtTuUx", false)); |
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assertTrue(Comparison.isNucleotideSequence("a A-g.GcCtTuU", true)); |
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assertFalse(Comparison.isNucleotideSequence("a A-g.GcCtTuU", false)); |
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} |
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| 100% |
Uncovered Elements: 0 (6) |
Complexity: 1 |
Complexity Density: 0.17 |
1PASS
|
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@Test(groups = { "Functional" })... |
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public void testIsSameResidue() |
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{ |
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assertTrue(Comparison.isSameResidue('a', 'a', false)); |
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assertTrue(Comparison.isSameResidue('a', 'a', true)); |
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assertTrue(Comparison.isSameResidue('A', 'a', false)); |
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assertTrue(Comparison.isSameResidue('a', 'A', false)); |
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assertFalse(Comparison.isSameResidue('a', 'A', true)); |
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assertFalse(Comparison.isSameResidue('A', 'a', true)); |
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} |
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} |