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package jalview.ext.ensembl; |
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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.assertTrue; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceDummy; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.gui.JvOptionPane; |
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import jalview.io.gff.SequenceOntologyFactory; |
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import jalview.io.gff.SequenceOntologyLite; |
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import jalview.util.MapList; |
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import java.util.List; |
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import org.testng.Assert; |
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import org.testng.annotations.AfterClass; |
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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 (135) |
Complexity: 9 |
Complexity Density: 0.07 |
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public class EnsemblCdnaTest |
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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 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@BeforeClass(alwaysRun = true)... |
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public void setUp() |
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{ |
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SequenceOntologyFactory.setInstance(new SequenceOntologyLite()); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
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@AfterClass(alwaysRun = true)... |
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public void tearDown() |
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{ |
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SequenceOntologyFactory.setInstance(null); |
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} |
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| 100% |
Uncovered Elements: 0 (29) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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@Test(groups = "Functional")... |
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public void testGetGenomicRangesFromFeatures_reverseStrand() |
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{ |
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EnsemblCdna testee = new EnsemblCdna(); |
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SequenceI genomic = new SequenceDummy("chr7"); |
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genomic.setStart(10000); |
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genomic.setEnd(50000); |
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String transcriptId = "ABC123"; |
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SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f, |
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null); |
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sf.setValue("Parent", transcriptId); |
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sf.setStrand("-"); |
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genomic.addSequenceFeature(sf); |
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sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null); |
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sf.setValue("Parent", transcriptId); |
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sf.setStrand("-"); |
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genomic.addSequenceFeature(sf); |
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sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null); |
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sf.setValue("Parent", "anotherOne"); |
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genomic.addSequenceFeature(sf); |
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sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null); |
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genomic.addSequenceFeature(sf); |
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MapList ranges = testee.getGenomicRangesFromFeatures(genomic, |
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transcriptId, 23); |
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List<int[]> fromRanges = ranges.getFromRanges(); |
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assertEquals(2, fromRanges.size()); |
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assertEquals(20500, fromRanges.get(0)[0]); |
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assertEquals(20000, fromRanges.get(0)[1]); |
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assertEquals(10600, fromRanges.get(1)[0]); |
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assertEquals(10500, fromRanges.get(1)[1]); |
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List<int[]> toRanges = ranges.getToRanges(); |
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assertEquals(1, toRanges.size()); |
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assertEquals(23, toRanges.get(0)[0]); |
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assertEquals(624, toRanges.get(0)[1]); |
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} |
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| 100% |
Uncovered Elements: 0 (30) |
Complexity: 1 |
Complexity Density: 0.03 |
1PASS
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@Test(groups = "Functional")... |
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public void testGetGenomicRangesFromFeatures() |
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{ |
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EnsemblCdna testee = new EnsemblCdna(); |
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SequenceI genomic = new SequenceDummy("chr7"); |
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genomic.setStart(10000); |
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genomic.setEnd(50000); |
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String transcriptId = "ABC123"; |
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SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f, |
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null); |
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sf.setValue("Parent", transcriptId); |
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sf.setStrand("+"); |
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genomic.addSequenceFeature(sf); |
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sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null); |
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sf.setValue("Parent", transcriptId); |
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sf.setStrand("+"); |
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genomic.addSequenceFeature(sf); |
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sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null); |
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sf.setValue("Parent", "anotherOne"); |
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genomic.addSequenceFeature(sf); |
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sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null); |
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sf.setStrand("-"); |
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genomic.addSequenceFeature(sf); |
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MapList ranges = testee.getGenomicRangesFromFeatures(genomic, |
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transcriptId, 23); |
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List<int[]> fromRanges = ranges.getFromRanges(); |
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assertEquals(2, fromRanges.size()); |
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assertEquals(10500, fromRanges.get(0)[0]); |
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assertEquals(10600, fromRanges.get(0)[1]); |
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assertEquals(20000, fromRanges.get(1)[0]); |
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assertEquals(20500, fromRanges.get(1)[1]); |
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List<int[]> toRanges = ranges.getToRanges(); |
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assertEquals(1, toRanges.size()); |
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assertEquals(23, toRanges.get(0)[0]); |
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assertEquals(624, toRanges.get(0)[1]); |
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} |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = "Functional")... |
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public void testGetGenomicRangesFromFeatures_mixedStrand() |
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{ |
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EnsemblCdna testee = new EnsemblCdna(); |
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SequenceI genomic = new SequenceDummy("chr7"); |
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genomic.setStart(10000); |
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genomic.setEnd(50000); |
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String transcriptId = "ABC123"; |
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SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f, |
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null); |
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sf.setValue("Parent", "transcript:" + transcriptId); |
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sf.setStrand("-"); |
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genomic.addSequenceFeature(sf); |
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sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null); |
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sf.setValue("Parent", "transcript:" + transcriptId); |
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sf.setStrand("+"); |
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genomic.addSequenceFeature(sf); |
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MapList ranges = testee.getGenomicRangesFromFeatures(genomic, |
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transcriptId, 23); |
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assertNull(ranges); |
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} |
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| 100% |
Uncovered Elements: 0 (15) |
Complexity: 1 |
Complexity Density: 0.07 |
1PASS
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@Test(groups = "Functional")... |
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public void testRetainFeature() |
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{ |
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String accId = "ABC123"; |
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EnsemblCdna testee = new EnsemblCdna(); |
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SequenceFeature sf = new SequenceFeature("transcript", "", 20000, |
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20500, 0f, null); |
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assertFalse(testee.retainFeature(sf, accId)); |
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sf = new SequenceFeature("aberrant_processed_transcript", "", 20000, |
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20500, 0f, null); |
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assertFalse(testee.retainFeature(sf, accId)); |
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sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, |
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0f, null); |
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assertFalse(testee.retainFeature(sf, accId)); |
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sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null); |
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assertTrue(testee.retainFeature(sf, accId)); |
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sf.setValue("Parent", accId); |
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assertTrue(testee.retainFeature(sf, accId)); |
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assertTrue(testee.retainFeature(sf, accId.toLowerCase())); |
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sf.setValue("Parent", "XYZ"); |
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assertFalse(testee.retainFeature(sf, accId)); |
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} |
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| 100% |
Uncovered Elements: 0 (26) |
Complexity: 1 |
Complexity Density: 0.04 |
1PASS
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@Test(groups = "Functional")... |
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public void testGetIdentifyingFeatures() |
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{ |
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String accId = "ABC123"; |
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SequenceI seq = new Sequence(accId, "MKLNFRQIE"); |
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SequenceFeature sf1 = new SequenceFeature("exon", "", 1, 2, 0f, null); |
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seq.addSequenceFeature(sf1); |
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SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null); |
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sf2.setValue("Parent", "XYZ"); |
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seq.addSequenceFeature(sf2); |
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SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null); |
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sf3.setValue("Parent", accId); |
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seq.addSequenceFeature(sf3); |
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SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f, |
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null); |
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sf4.setValue("Parent", accId); |
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seq.addSequenceFeature(sf4); |
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SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, |
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null); |
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sf5.setValue("Parent", accId); |
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seq.addSequenceFeature(sf5); |
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SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f, |
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null); |
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sf6.setValue("Parent", accId); |
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seq.addSequenceFeature(sf6); |
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List<SequenceFeature> sfs = new EnsemblCdna() |
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.getIdentifyingFeatures(seq, accId); |
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assertFalse(sfs.contains(sf1)); |
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assertFalse(sfs.contains(sf2)); |
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assertTrue(sfs.contains(sf3)); |
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assertTrue(sfs.contains(sf4)); |
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assertFalse(sfs.contains(sf5)); |
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assertFalse(sfs.contains(sf6)); |
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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 testIsValidReference() throws Exception |
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{ |
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EnsemblSequenceFetcher esq = new EnsemblCdna(); |
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Assert.assertTrue(esq.isValidReference("CCDS5863.1")); |
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Assert.assertTrue(esq.isValidReference("ENST00000288602")); |
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Assert.assertTrue(esq.isValidReference("ENSG00000288602")); |
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Assert.assertFalse(esq.isValidReference("ENSP00000288602")); |
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Assert.assertFalse(esq.isValidReference("ENST0000288602")); |
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Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398")); |
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} |
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} |