assertEquals(AlignSeq.extractGaps(" -", " AC-G.T"), "ACG.T");
assertEquals(AlignSeq.extractGaps(" -.", " AC-G.T ."), "ACGT");
assertEquals(AlignSeq.extractGaps("-", " AC-G.T"), " ACG.T");
+ assertEquals(AlignSeq.extractGaps("-. ", " -. .-"), "");
}
@Test(groups = { "Functional" })
{
AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
"s2", "RQW"), AlignSeq.PEP);
- int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 24,
- -1, 23, -1 };
+ int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 23,
+ -1, -1, -1 };
String s = "aArRnNzZxX *.-?";
assertArrayEquals(expected, as.indexEncode(s));
}