import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
@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);
}
/**
// exon at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("-");
genomic.addSequenceFeature(sf);
// exon (sub-type) at (start + exon_variant) length 101
sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("-");
genomic.addSequenceFeature(sf);
// exon belonging to a different transcript doesn't count
sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// transcript feature doesn't count
// exon at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// exon (sub-type) at (start + exon_variant) length 101
sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
- sf.setValue("Parent", "transcript:" + transcriptId);
+ sf.setValue("Parent", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// exon belonging to a different transcript doesn't count
sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
- sf.setValue("Parent", "transcript:anotherOne");
+ sf.setValue("Parent", "anotherOne");
genomic.addSequenceFeature(sf);
// transcript feature doesn't count
assertTrue(testee.retainFeature(sf, accId));
// other feature with desired parent is retained
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
+ // test is not case-sensitive
+ assertTrue(testee.retainFeature(sf, accId.toLowerCase()));
+
// feature with wrong parent is not retained
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
* accession id as parent
*/
@Test(groups = "Functional")
- public void testIdentifiesSequence()
+ public void testGetIdentifyingFeatures()
{
String accId = "ABC123";
- EnsemblCdna testee = new EnsemblCdna();
+ SequenceI seq = new Sequence(accId, "MKLNFRQIE");
- // exon with no parent not valid
- SequenceFeature sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
- assertFalse(testee.identifiesSequence(sf, accId));
+ // exon with no parent: not valid
+ SequenceFeature sf1 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ seq.addSequenceFeature(sf1);
- // exon with wrong parent not valid
- sf.setValue("Parent", "transcript:XYZ");
- assertFalse(testee.identifiesSequence(sf, accId));
+ // exon with wrong parent: not valid
+ SequenceFeature sf2 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf2.setValue("Parent", "XYZ");
+ seq.addSequenceFeature(sf2);
// exon with right parent is valid
- sf.setValue("Parent", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf3 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf3.setValue("Parent", accId);
+ seq.addSequenceFeature(sf3);
// exon sub-type with right parent is valid
- sf = new SequenceFeature("coding_exon", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf4 = new SequenceFeature("coding_exon", "", 1, 2, 0f,
+ null);
+ sf4.setValue("Parent", accId);
+ seq.addSequenceFeature(sf4);
// transcript not valid:
- sf = new SequenceFeature("transcript", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
+ sf5.setValue("Parent", accId);
+ seq.addSequenceFeature(sf5);
// CDS not valid:
- sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
- sf.setValue("Parent", "transcript:" + accId);
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf6 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
+ sf6.setValue("Parent", accId);
+ seq.addSequenceFeature(sf6);
+
+ List<SequenceFeature> sfs = new EnsemblCdna()
+ .getIdentifyingFeatures(seq, accId);
+ assertFalse(sfs.contains(sf1));
+ assertFalse(sfs.contains(sf2));
+ assertTrue(sfs.contains(sf3));
+ assertTrue(sfs.contains(sf4));
+ assertFalse(sfs.contains(sf5));
+ assertFalse(sfs.contains(sf6));
}
@Test(groups = "Functional")