import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceDummy;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
// transcript at (start+10000) length 501
SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
20500, 0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript (sub-type) at (start + 10500) length 101
sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// although strictly it is a sequence_variant in SO
sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
0f, null);
- sf.setValue("ID", "transcript:" + transcriptId);
+ sf.setValue("id", transcriptId);
sf.setStrand("+");
genomic.addSequenceFeature(sf);
// transcript with a different ID doesn't count
sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
- sf.setValue("ID", "transcript:anotherOne");
+ sf.setValue("id", "anotherOne");
genomic.addSequenceFeature(sf);
// parent of transcript feature doesn't count
20500, 0f, null);
assertFalse(testee.retainFeature(sf, accId));
- sf.setType("mature_transcript");
+ sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
+ null);
assertFalse(testee.retainFeature(sf, accId));
- sf.setType("NMD_transcript_variant");
+ sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
+ 0f, null);
assertFalse(testee.retainFeature(sf, accId));
// other feature with no parent is kept
- sf.setType("anything");
+ sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
assertTrue(testee.retainFeature(sf, accId));
// other feature with correct parent is kept
- sf.setValue("Parent", "transcript:" + accId);
+ sf.setValue("Parent", accId);
assertTrue(testee.retainFeature(sf, accId));
// other feature with wrong parent is not kept
- sf.setValue("Parent", "transcript:XYZ");
+ sf.setValue("Parent", "XYZ");
assertFalse(testee.retainFeature(sf, accId));
}
* accession id as ID
*/
@Test(groups = "Functional")
- public void testIdentifiesSequence()
+ public void testGetIdentifyingFeatures()
{
String accId = "ABC123";
- EnsemblGenome testee = new EnsemblGenome();
+ SequenceI seq = new Sequence(accId, "HEARTS");
// transcript with no ID not valid
- SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
+ SequenceFeature sf1 = new SequenceFeature("transcript", "", 1, 2, 0f,
null);
- assertFalse(testee.identifiesSequence(sf, accId));
+ seq.addSequenceFeature(sf1);
// transcript with wrong ID not valid
- sf.setValue("ID", "transcript");
- assertFalse(testee.identifiesSequence(sf, accId));
+ // NB change desc to avoid rejection of duplicate feature!
+ SequenceFeature sf2 = new SequenceFeature("transcript", "a", 1, 2, 0f,
+ null);
+ sf2.setValue("id", "transcript");
+ seq.addSequenceFeature(sf2);
// transcript with right ID is valid
- sf.setValue("ID", "transcript:" + accId);
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf3 = new SequenceFeature("transcript", "b", 1, 2, 0f,
+ null);
+ sf3.setValue("id", accId);
+ seq.addSequenceFeature(sf3);
// transcript sub-type with right ID is valid
- sf.setType("ncRNA");
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
+ sf4.setValue("id", accId);
+ seq.addSequenceFeature(sf4);
// Ensembl treats NMD_transcript_variant as if a transcript
- sf.setType("NMD_transcript_variant");
- assertTrue(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
+ 1, 2, 0f, null);
+ sf5.setValue("id", accId);
+ seq.addSequenceFeature(sf5);
// gene not valid:
- sf.setType("gene");
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
+ sf6.setValue("id", accId);
+ seq.addSequenceFeature(sf6);
// exon not valid:
- sf.setType("exon");
- assertFalse(testee.identifiesSequence(sf, accId));
+ SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
+ sf7.setValue("id", accId);
+ seq.addSequenceFeature(sf7);
+
+ List<SequenceFeature> sfs = new EnsemblGenome()
+ .getIdentifyingFeatures(seq, accId);
+ assertFalse(sfs.contains(sf1));
+ assertFalse(sfs.contains(sf2));
+ assertTrue(sfs.contains(sf3));
+ assertTrue(sfs.contains(sf4));
+ assertTrue(sfs.contains(sf5));
+ assertFalse(sfs.contains(sf6));
+ assertFalse(sfs.contains(sf7));
}
}