@Test(groups = { "Functional" })
public void testIndexEncode_nucleotide()
{
- AlignSeq as = new AlignSeq(new Sequence("s1", "TTAG"), new Sequence(
- "s2", "ACGT"), AlignSeq.DNA);
+ 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, -1, -1, 10, -1 };
String s = "aAcCgGtTuUiIxXrRyYnN .-?";
@Test(groups = { "Functional" })
public void testIndexEncode_peptide()
{
- AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
- "s2", "RQW"), AlignSeq.PEP);
+ 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, 23,
-1, -1, -1 };
String s = "aArRnNzZxX *.-?";