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package jalview.datamodel; |
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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.assertNull; |
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import static org.testng.AssertJUnit.assertSame; |
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import static org.testng.AssertJUnit.assertTrue; |
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import java.util.ArrayList; |
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import java.util.List; |
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import org.testng.annotations.BeforeClass; |
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import org.testng.annotations.Test; |
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import jalview.gui.JvOptionPane; |
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import jalview.util.MapList; |
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| 99.4% |
Uncovered Elements: 1 (173) |
Complexity: 9 |
Complexity Density: 0.06 |
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public class SequenceFeatureTest |
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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 (33) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testCopyConstructors() |
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{ |
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SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, |
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12.5f, "group"); |
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sf1.setValue("STRAND", "+"); |
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sf1.setValue("Note", "Testing"); |
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Integer count = Integer.valueOf(7); |
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sf1.setValue("Count", count); |
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SequenceFeature sf2 = new SequenceFeature(sf1); |
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assertEquals("type", sf2.getType()); |
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assertEquals("desc", sf2.getDescription()); |
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assertEquals(22, sf2.getBegin()); |
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assertEquals(33, sf2.getEnd()); |
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assertEquals(12.5f, sf2.getScore()); |
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assertEquals("+", sf2.getValue("STRAND")); |
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assertEquals("Testing", sf2.getValue("Note")); |
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assertSame(count, sf2.getValue("Count")); |
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SequenceFeature sf3 = new SequenceFeature(sf1, 11, 14, "group2", 17.4f); |
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assertEquals("type", sf3.getType()); |
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assertEquals("desc", sf3.getDescription()); |
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assertEquals(11, sf3.getBegin()); |
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assertEquals(14, sf3.getEnd()); |
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assertEquals(17.4f, sf3.getScore()); |
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assertEquals("+", sf3.getValue("STRAND")); |
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assertEquals("Testing", sf3.getValue("Note")); |
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assertSame(count, sf3.getValue("Count")); |
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SequenceFeature sf4 = new SequenceFeature(sf1, "Disulfide bond", 12, |
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15, "group3", -9.1f); |
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assertEquals("Disulfide bond", sf4.getType()); |
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assertTrue(sf4.isContactFeature()); |
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assertEquals("desc", sf4.getDescription()); |
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assertEquals(12, sf4.getBegin()); |
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assertEquals(15, sf4.getEnd()); |
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assertEquals(-9.1f, sf4.getScore()); |
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assertEquals("+", sf4.getValue("STRAND")); |
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assertEquals("Testing", sf4.getValue("Note")); |
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assertSame(count, sf4.getValue("Count")); |
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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 testGetValue() |
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{ |
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SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, |
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12.5f, "group"); |
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sf1.setValue("STRAND", "+"); |
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assertEquals("+", sf1.getValue("STRAND")); |
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assertNull(sf1.getValue("strand")); |
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assertEquals(".", sf1.getValue("unknown", ".")); |
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Integer i = Integer.valueOf(27); |
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assertSame(i, sf1.getValue("Unknown", i)); |
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} |
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| 100% |
Uncovered Elements: 0 (8) |
Complexity: 1 |
Complexity Density: 0.12 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testGetStrand() |
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{ |
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SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f, |
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"group"); |
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assertEquals(0, sf.getStrand()); |
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sf.setValue("STRAND", "+"); |
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assertEquals(1, sf.getStrand()); |
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sf.setValue("STRAND", "-"); |
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assertEquals(-1, sf.getStrand()); |
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sf.setValue("STRAND", "."); |
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assertEquals(0, sf.getStrand()); |
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} |
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| 98.6% |
Uncovered Elements: 1 (73) |
Complexity: 2 |
Complexity Density: 0.03 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testEqualsAndHashCode() |
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{ |
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SequenceFeature sf1 = new SequenceFeature("type", "desc", 22, 33, |
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12.5f, "group"); |
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sf1.setValue("ID", "id"); |
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sf1.setValue("Name", "name"); |
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sf1.setValue("Parent", "parent"); |
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sf1.setStrand("+"); |
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sf1.setPhase("1"); |
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SequenceFeature sf2 = new SequenceFeature("type", "desc", 22, 33, |
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12.5f, "group"); |
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sf2.setValue("ID", "id"); |
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sf2.setValue("Name", "name"); |
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sf2.setValue("Parent", "parent"); |
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sf2.setStrand("+"); |
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sf2.setPhase("1"); |
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assertFalse(sf1.equals(null)); |
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assertTrue(sf1.equals(sf2)); |
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assertTrue(sf2.equals(sf1)); |
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assertEquals(sf1.hashCode(), sf2.hashCode()); |
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SequenceFeature sf3 = new SequenceFeature("type", "desc", 22, 33, |
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12.5f, "group"); |
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SequenceFeature sf4 = new SequenceFeature("Type", "desc", 22, 33, |
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12.5f, "group"); |
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assertFalse(sf3.equals(sf4)); |
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String restores = sf2.getDescription(); |
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sf2.setDescription("Desc"); |
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assertFalse(sf1.equals(sf2)); |
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sf2.setDescription(restores); |
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float restoref = sf2.getScore(); |
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sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), |
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sf2.getFeatureGroup(), 10f); |
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assertFalse(sf1.equals(sf2)); |
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sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), |
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sf2.getFeatureGroup(), restoref); |
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restoref = sf2.getScore(); |
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sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), |
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sf2.getFeatureGroup(), Float.NaN); |
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assertFalse(sf1.equals(sf2)); |
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sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(), |
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sf1.getFeatureGroup(), Float.NaN); |
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assertTrue(sf1.equals(sf2)); |
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sf1 = new SequenceFeature(sf1, sf1.getBegin(), sf1.getEnd(), |
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sf1.getFeatureGroup(), restoref); |
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sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), |
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sf2.getFeatureGroup(), restoref); |
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int restorei = sf2.getBegin(); |
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sf2 = new SequenceFeature(sf2, 21, sf2.getEnd(), sf2.getFeatureGroup(), sf2.getScore()); |
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assertFalse(sf1.equals(sf2)); |
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sf2 = new SequenceFeature(sf2, restorei, sf2.getEnd(), |
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sf2.getFeatureGroup(), sf2.getScore()); |
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restorei = sf2.getEnd(); |
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sf2 = new SequenceFeature(sf2, sf2.getBegin(), 32, |
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sf2.getFeatureGroup(), sf2.getScore()); |
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assertFalse(sf1.equals(sf2)); |
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sf2 = new SequenceFeature(sf2, sf2.getBegin(), restorei, |
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sf2.getFeatureGroup(), sf2.getScore()); |
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restores = sf2.getFeatureGroup(); |
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sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), "Group", sf2.getScore()); |
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assertFalse(sf1.equals(sf2)); |
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sf2 = new SequenceFeature(sf2, sf2.getBegin(), sf2.getEnd(), restores, sf2.getScore()); |
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restores = (String) sf2.getValue("ID"); |
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sf2.setValue("ID", "id2"); |
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assertFalse(sf1.equals(sf2)); |
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sf2.setValue("ID", restores); |
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restores = (String) sf2.getValue("Name"); |
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sf2.setValue("Name", "Name"); |
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assertFalse(sf1.equals(sf2)); |
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sf2.setValue("Name", restores); |
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restores = (String) sf1.getValue("Parent"); |
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sf1.setValue("Parent", "Parent"); |
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assertFalse(sf1.equals(sf2)); |
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sf1.setValue("Parent", restores); |
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restorei = sf2.getStrand(); |
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sf2.setStrand("-"); |
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assertFalse(sf1.equals(sf2)); |
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sf2.setStrand(restorei == 1 ? "+" : "-"); |
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restores = sf1.getPhase(); |
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sf1.setPhase("2"); |
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assertFalse(sf1.equals(sf2)); |
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sf1.setPhase(restores); |
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assertTrue(sf1.equals(sf2)); |
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assertTrue(sf2.equals(sf1)); |
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assertEquals(sf1.hashCode(), sf2.hashCode()); |
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sf1.setStatus("new"); |
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assertTrue(sf1.equals(sf2)); |
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} |
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| 100% |
Uncovered Elements: 0 (14) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testIsContactFeature() |
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{ |
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SequenceFeature sf = new SequenceFeature("type", "desc", 22, 33, 12.5f, |
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"group"); |
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assertFalse(sf.isContactFeature()); |
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sf = new SequenceFeature("", "desc", 22, 33, 12.5f, "group"); |
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assertFalse(sf.isContactFeature()); |
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sf = new SequenceFeature(null, "desc", 22, 33, 12.5f, "group"); |
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assertFalse(sf.isContactFeature()); |
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sf = new SequenceFeature("Disulfide Bond", "desc", 22, 33, 12.5f, |
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"group"); |
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assertTrue(sf.isContactFeature()); |
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sf = new SequenceFeature("disulfide bond", "desc", 22, 33, 12.5f, |
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"group"); |
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assertTrue(sf.isContactFeature()); |
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sf = new SequenceFeature("Disulphide Bond", "desc", 22, 33, 12.5f, |
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"group"); |
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assertTrue(sf.isContactFeature()); |
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sf = new SequenceFeature("disulphide bond", "desc", 22, 33, 12.5f, |
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"group"); |
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assertTrue(sf.isContactFeature()); |
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} |
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| 100% |
Uncovered Elements: 0 (17) |
Complexity: 1 |
Complexity Density: 0.06 |
1PASS
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@Test(groups = { "Functional" })... |
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public void testGetDetailsReport() |
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{ |
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SequenceI seq = new Sequence("TestSeq", "PLRFQMD"); |
285 |
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String seqName = seq.getName(); |
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SequenceFeature sf = new SequenceFeature("variant", "G,C", 22, 22, null); |
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String expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22</td></tr>" |
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+ "<tr><td>Type</td><td>variant</td><td></td></tr>" |
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+ "<tr><td>Description</td><td>G,C</td><td></td></tr></table>"; |
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assertEquals(expected, sf.getDetailsReport(seqName, null)); |
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sf = new SequenceFeature("Disulphide Bond", "a description", 28, 31, |
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null); |
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expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>28:31</td></tr>" |
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+ "<tr><td>Type</td><td>Disulphide Bond</td><td></td></tr>" |
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+ "<tr><td>Description</td><td>a description</td><td></td></tr></table>"; |
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assertEquals(expected, sf.getDetailsReport(seqName, null)); |
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sf = new SequenceFeature("variant", "G,C", 22, 33, |
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12.5f, "group"); |
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sf.setValue("Parent", "ENSG001"); |
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sf.setValue("Child", "ENSP002"); |
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expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>22-33</td></tr>" |
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+ "<tr><td>Type</td><td>variant</td><td></td></tr>" |
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+ "<tr><td>Description</td><td>G,C</td><td></td></tr>" |
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+ "<tr><td>Score</td><td>12.5</td><td></td></tr>" |
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+ "<tr><td>Group</td><td>group</td><td></td></tr>" |
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+ "<tr><td>Child</td><td></td><td>ENSP002</td></tr>" |
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+ "<tr><td>Parent</td><td></td><td>ENSG001</td></tr></table>"; |
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assertEquals(expected, sf.getDetailsReport(seqName, null)); |
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String desc = "<html>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></html>"; |
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sf = new SequenceFeature("Pfam", desc, 8, 83, "Uniprot"); |
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expected = "<br><table><tr><td>Location</td><td>TestSeq</td><td>8-83</td></tr>" |
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+ "<tr><td>Type</td><td>Pfam</td><td></td></tr>" |
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+ "<tr><td>Description</td><td>Fer2 Status: True Positive <a href=\"http://pfam.xfam.org/family/PF00111\">Pfam 8_8</a></td><td></td></tr>" |
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+ "<tr><td>Group</td><td>Uniprot</td><td></td></tr></table>"; |
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assertEquals(expected, sf.getDetailsReport(seqName, null)); |
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} |
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|
327 |
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328 |
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329 |
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330 |
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| 100% |
Uncovered Elements: 0 (11) |
Complexity: 1 |
Complexity Density: 0.09 |
1PASS
|
|
332 |
1 |
@Test(groups = { "Functional" })... |
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public void testGetDetailsReport_virtualFeature() |
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{ |
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1 |
SequenceI cds = new Sequence("Cds/101-121", "CCTttgAGAtttCAAatgGAT"); |
336 |
1 |
SequenceI seq = new Sequence("TestSeq/8-14", "PLRFQMD"); |
337 |
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MapList map = new MapList(new int[] { 101, 118 }, new int[] { 8, 13 }, |
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3, 1); |
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Mapping mapping = new Mapping(seq, map); |
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List<SequenceFeature> features = new ArrayList<>(); |
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|
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SequenceFeature sf = new SequenceFeature("variant", "G,C", 106, 106, |
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null); |
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sf.setValue("alleles", "G,C"); |
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features.add(sf); |
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|
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1 |
MappedFeatures mf = new MappedFeatures(mapping, cds, 9, 'L', features); |
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|
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1 |
String expected = "<br><table><tr><td>Location</td><td>Cds</td><td>106</td></tr>" |
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+ "<tr><td>Peptide Location</td><td>TestSeq</td><td>9</td></tr>" |
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+ "<tr><td>Type</td><td>variant</td><td></td></tr>" |
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+ "<tr><td>Description</td><td>G,C</td><td></td></tr>" |
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+ "<tr><td>Consequence</td><td><i>Translated by Jalview</i></td><td>p.Leu9Phe</td></tr>" |
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+ "<tr><td>alleles</td><td></td><td>G,C</td></tr>" |
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+ "</table>"; |
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|
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assertEquals(expected, sf.getDetailsReport(seq.getName(), mf)); |
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} |
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} |