+ // make the verify pass by adding the outsider back in
+ al.getDataset().addSequence(sqout);
+ assertVerifyAlignment(al, true,
+ "verify should have passed after adding dbref->to sequence in to dataset");
+ // and now the same for a codon mapping...
+ SequenceI sqanotherout = new Sequence("sqanotherout",
+ "aggtutaggcagcagcag");
+
+ AlignedCodonFrame alc = new AlignedCodonFrame();
+ alc.addMap(sqanotherout, sqnew, new MapList(new int[] { 1, 6 },
+ new int[] { 1, 18 }, 3, 1));
+
+ al.addCodonFrame(alc);
+ Assert.assertEquals(al.getDataset().getCodonFrames().size(), 1);
+
+ assertVerifyAlignment(
+ al,
+ false,
+ "verify passed when alCodonFrame mapping to sequence outside of dataset was added");
+ // make the verify pass by adding the outsider back in
+ al.getDataset().addSequence(sqanotherout);
+ assertVerifyAlignment(
+ al,
+ true,
+ "verify should have passed once all sequences involved in alCodonFrame were added to dataset");
+