AlignmentI al = new Alignment(sqset);
al.setDataset(null);
AlignmentI ds = al.getDataset();
- SequenceFeature sf1 = new SequenceFeature("f1", "foo", "bleh", 2, 3,
- "far"), sf2 = new SequenceFeature("f2", "foo", "bleh", 2, 3,
- "far");
+ SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
+ SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
ds.getSequenceAt(0).addSequenceFeature(sf1);
Hashtable unq = SeqsetUtils.uniquify(sqset, true);
SequenceI[] sqset2 = new SequenceI[] {
new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
- Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sf1);
- Assert.assertEquals(sqset2[0].getSequenceFeatures(), null);
+ Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
+ Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
ds.getSequenceAt(0).addSequenceFeature(sf2);
- Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
+ Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
SeqsetUtils.deuniquify(unq, sqset2);
// explicitly test that original sequence features still exist because they
// are on the shared dataset sequence
- Assert.assertEquals(sqset[0].getSequenceFeatures().length, 2);
- Assert.assertEquals(sqset2[0].getSequenceFeatures().length, 2);
- Assert.assertTrue(sqset[0].getSequenceFeatures()[0] == sqset2[0]
- .getSequenceFeatures()[0]);
- Assert.assertTrue(sqset[0].getSequenceFeatures()[1] == sqset2[0]
- .getSequenceFeatures()[1]);
+ Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
+ Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
+ Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sqset2[0]
+ .getSequenceFeatures().get(0));
+ Assert.assertSame(sqset[0].getSequenceFeatures().get(1), sqset2[0]
+ .getSequenceFeatures().get(1));
}
}