*/
package jalview.ext.ensembl;
+import java.util.Locale;
+
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNull;
@BeforeClass(alwaysRun = true)
public void setUp()
{
- SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
+ SequenceOntologyFactory.setSequenceOntology(new SequenceOntologyLite());
}
@AfterClass(alwaysRun = true)
public void tearDown()
{
- SequenceOntologyFactory.setInstance(null);
+ SequenceOntologyFactory.setSequenceOntology(null);
}
/**
String accId = "ABC123";
EnsemblCdna testee = new EnsemblCdna();
- SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
- 20500, 0f, null);
+ SequenceFeature sf = new SequenceFeature("transcript", "", 20000, 20500,
+ 0f, null);
assertFalse(testee.retainFeature(sf, accId));
sf = new SequenceFeature("aberrant_processed_transcript", "", 20000,
20500, 0f, null);
assertFalse(testee.retainFeature(sf, accId));
- sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
- 0f, null);
+ sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+ null);
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is retained
- sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f, null);
+ sf = new SequenceFeature("sequence_variant", "", 20000, 20500, 0f,
+ null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
assertTrue(testee.retainFeature(sf, accId));
// test is not case-sensitive
- assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
+ assertTrue(testee.retainFeature(sf, accId.toLowerCase(Locale.ROOT)));
// feature with wrong parent is not retained
sf.setValue("Parent", "XYZ");