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", "TTAG"), new Sequence(
"s2", "ACGT"), AlignSeq.DNA);
int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 3, 3, 4, 4, 5, 5, 6, 6,
- 7, 7, 8, 8, 9, 9, 10, -1, 11, -1 };
+ 7, 7, 8, 8, 9, 9, -1, -1, 10, -1 };
String s = "aAcCgGtTuUiIxXrRyYnN .-?";
assertArrayEquals(expected, as.indexEncode(s));
}
{
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, 23, 24,
+ 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));