*
* TODO: split into separate tests
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testSomething() throws Exception
{
String o_seq = "asdfktryasdtqwrtsaslldddptyipqqwaslchvhttt";
*/
assertEquals("Failed getWidth", sub_gapped_s.length(),
sub_gapped.getWidth());
-
+
sub_gapped.getFullWidth();
assertFalse("hasDeletedRegions is incorrect",
sub_gapped.hasDeletedRegions());
}
}
- SeqCigar[] set = new SeqCigar[]
- { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
- new SeqCigar(s_gapped) };
+ SeqCigar[] set = new SeqCigar[] { new SeqCigar(s),
+ new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
Alignment al = new Alignment(set);
for (int i = 0; i < al.getHeight(); i++)
{
}
System.out.println("Gapped.");
- set = new SeqCigar[]
- { new SeqCigar(s), new SeqCigar(s_subsequence_gapped, 8, 48),
- new SeqCigar(s_gapped) };
+ set = new SeqCigar[] { new SeqCigar(s),
+ new SeqCigar(s_subsequence_gapped, 8, 48), new SeqCigar(s_gapped) };
set[0].deleteRange(20, 25);
al = new Alignment(set);
for (int i = 0; i < al.getHeight(); i++)
* @return String
*/
-
protected void testCigar_string(Sequence seq, String ex_cs_gapped)
{
SeqCigar c_sgapped = new SeqCigar(seq);
String cs_gapped = c_sgapped.getCigarstring();
- assertEquals("Failed getCigarstring", ex_cs_gapped,
- cs_gapped);
+ assertEquals("Failed getCigarstring", ex_cs_gapped, cs_gapped);
}
-
- protected void testSeqRecovery(SeqCigar gen_sgapped,
- SequenceI s_gapped)
+ protected void testSeqRecovery(SeqCigar gen_sgapped, SequenceI s_gapped)
{
// this is non-rigorous - start and end recovery is not tested.
SequenceI gen_sgapped_s = gen_sgapped.getSeq('-');