import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.api.FeatureSettingsModelI;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntologyLite;
import jalview.util.MapList;
+import java.awt.Color;
import java.util.List;
import org.testng.annotations.AfterClass;
public class EnsemblGeneTest
{
- @BeforeClass
+ @BeforeClass(alwaysRun = true)
public void setUp()
{
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
- @AfterClass
+ @AfterClass(alwaysRun = true)
public void tearDown()
{
SequenceOntologyFactory.setInstance(null);
SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
sf1.setValue("Parent", "gene:" + geneId);
+ sf1.setValue("transcript_id", "transcript1");
genomic.addSequenceFeature(sf1);
// transcript sub-type feature
SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000,
20500, 0f, null);
sf2.setValue("Parent", "gene:" + geneId);
+ sf2.setValue("transcript_id", "transcript2");
genomic.addSequenceFeature(sf2);
// NMD_transcript_variant treated like transcript in Ensembl
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
20000, 20500, 0f, null);
sf3.setValue("Parent", "gene:" + geneId);
+ sf3.setValue("transcript_id", "transcript3");
genomic.addSequenceFeature(sf3);
// transcript for a different gene - ignored
SequenceFeature sf4 = new SequenceFeature("snRNA", "", 20000, 20500,
0f, null);
sf4.setValue("Parent", "gene:XYZ");
+ sf4.setValue("transcript_id", "transcript4");
genomic.addSequenceFeature(sf4);
EnsemblGene testee = new EnsemblGene();
+
+ /*
+ * with no filter
+ */
List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
genomic);
assertEquals(3, features.size());
sf.setType("exon");
assertFalse(testee.identifiesSequence(sf, accId));
}
+
+ /**
+ * Check behaviour of feature colour scheme for EnsemblGene sequences.
+ * Currently coded to display exon and sequence_variant (or sub-types) only,
+ * with sequence_variant in red above exon coloured by label.
+ */
+ @Test(groups = "Functional")
+ public void testGetFeatureColourScheme()
+ {
+ FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
+ assertTrue(fc.isFeatureDisplayed("exon"));
+ assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
+ assertTrue(fc.isFeatureDisplayed("sequence_variant"));
+ assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
+ assertFalse(fc.isFeatureDisplayed("transcript"));
+ assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
+ .getColour());
+ assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
+ .getColour());
+ assertTrue(fc.getFeatureColour("exon").isColourByLabel());
+ assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
+ assertEquals(1, fc.compare("sequence_variant", "exon"));
+ assertEquals(-1, fc.compare("exon", "sequence_variant"));
+ assertEquals(1, fc.compare("feature_variant", "coding_exon"));
+ assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
+ assertEquals(1f, fc.getTransparency());
+ }
}