- EnsemblSeqProxy testee = new EnsemblGene();
- assertFalse(testee.isGeneIdentifier(null));
- assertFalse(testee.isGeneIdentifier(""));
- assertFalse(testee.isGeneIdentifier("ENST00000012345"));
- assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
- assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
- assertFalse(testee.isGeneIdentifier("ensg00000012345"));
- assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
- assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
+ SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
+ SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
+ SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
+ SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
+ List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
+ sf2, sf3, sf4 });
+
+ // sort by start position ascending (forward strand)
+ // sf2 and sf3 tie and should not be reordered by sorting
+ SequenceFeatures.sortFeatures(sfs, true);
+ assertSame(sfs.get(0), sf2);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf1);
+ assertSame(sfs.get(3), sf4);
+
+ // sort by end position descending (reverse strand)
+ SequenceFeatures.sortFeatures(sfs, false);
+ assertSame(sfs.get(0), sf1);
+ assertSame(sfs.get(1), sf3);
+ assertSame(sfs.get(2), sf2);
+ assertSame(sfs.get(3), sf4);