import static org.testng.AssertJUnit.assertTrue;
import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
@BeforeClass(alwaysRun = true)
public void setUp()
{
+ Cache.loadProperties("test/jalview/io/testProps.jvprops");
SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
}
// NMD_transcript_variant treated like transcript in Ensembl
SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
22000, 22500, 0f, null);
- sf3.setValue("Parent", "gene:" + geneId);
+ // id matching should not be case-sensitive
+ sf3.setValue("Parent", "gene:" + geneId.toLowerCase());
sf3.setValue("transcript_id", "transcript3");
genomic.addSequenceFeature(sf3);
sf.setValue("ID", "gene:" + accId);
assertTrue(testee.identifiesSequence(sf, accId));
+ // test is not case-sensitive
+ assertTrue(testee.identifiesSequence(sf, accId.toLowerCase()));
+
// transcript not valid:
sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
sf.setValue("ID", "gene:" + accId);