+ matchesSequenceString("ACACAOACACAC"),
+ matchesSequenceString("ABAVAVAVABAV")
+ ));
+ }
+
+ @Test(groups = { "Functional"} )
+ public void testCreate_ContainsNonStandardAndFilterNonStandard_NonStandardToGap()
+ {
+ var alignment = new Alignment(new Sequence[] {
+ new Sequence("test1", "ACACAOACACAC"),
+ new Sequence("test2", "ABAVAVAVABAV")
+ });
+ var annotJob = AnnotationJob.create(alignment, true, true, true, true, 0);
+ assertThat(annotJob.getInputSequences(), contains(