assertEquals("Q", codon.product);
assertFalse(codons.hasNext());
}
+
+ /**
+ * Test for a case with sequence (and mappings) not starting at 1
+ */
+ @Test(groups = { "Functional" })
+ public void testNext_withOffset()
+ {
+ SequenceI from = new Sequence("Seq1", "-CgC-C-cCtAG-AtG-Gc", 7, 20);
+ from.createDatasetSequence();
+ SequenceI to = new Sequence("Seq1/10-12", "-PQ-R-");
+ to.createDatasetSequence();
+ MapList map = new MapList(new int[] { 7, 7, 9, 10, 12, 12, 14, 16, 18,
+ 19 }, new int[] { 10, 12 }, 3, 1);
+ Mapping m = new Mapping(to.getDatasetSequence(), map);
+
+ Iterator<AlignedCodon> codons = m.getCodonIterator(from, '-');
+ AlignedCodon codon = codons.next();
+ assertEquals("[1, 3, 5]", codon.toString());
+ assertEquals("P", codon.product);
+ codon = codons.next();
+ assertEquals("[8, 10, 11]", codon.toString());
+ assertEquals("Q", codon.product);
+ codon = codons.next();
+ assertEquals("[13, 15, 17]", codon.toString());
+ assertEquals("R", codon.product);
+ assertFalse(codons.hasNext());
+ }
}