genomic.addSequenceFeature(sf1);
// transcript sub-type feature
- SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500,
- 0f, null);
+ SequenceFeature sf2 = new SequenceFeature("snRNA", "", 21000, 21500, 0f,
+ null);
sf2.setValue("Parent", geneId);
sf2.setValue("id", "transcript2");
genomic.addSequenceFeature(sf2);
genomic.addSequenceFeature(sf3);
// transcript for a different gene - ignored
- SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500,
- 0f, null);
+ SequenceFeature sf4 = new SequenceFeature("snRNA", "", 23000, 23500, 0f,
+ null);
sf4.setValue("Parent", "XYZ");
sf4.setValue("id", "transcript4");
genomic.addSequenceFeature(sf4);
sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
- sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
- 0f, null);
+ sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500, 0f,
+ null);
sf.setValue("Parent", geneId);
assertTrue(testee.retainFeature(sf, geneId));
seq.addSequenceFeature(sf3);
// gene sub-type with right ID is valid
- SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f, null);
+ SequenceFeature sf4 = new SequenceFeature("snRNA_gene", "", 1, 2, 0f,
+ null);
sf4.setValue("id", accId);
seq.addSequenceFeature(sf4);
// transcript not valid:
- SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f, null);
+ SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
+ null);
sf5.setValue("id", accId);
seq.addSequenceFeature(sf5);
SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
sf6.setValue("id", accId);
seq.addSequenceFeature(sf6);
-
+
List<SequenceFeature> sfs = new EnsemblGene()
.getIdentifyingFeatures(seq, accId);
assertFalse(sfs.contains(sf1));
assertTrue(fc.isFeatureHidden("transcript"));
assertTrue(fc.isFeatureHidden("CDS"));
- assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
- .getColour());
- assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
- .getColour());
+ 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"));
assertTrue(geneIds.contains("ENSDARG00000017661")); // zebrafish
assertTrue(geneIds.contains("ENSGALG00000012865")); // chicken
assertEquals(8, geneIds.size());
-
+
}
}