SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
// need to be distinct
AlignedCodonFrame acf1 = new AlignedCodonFrame();
SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
// need to be distinct
AlignedCodonFrame acf1 = new AlignedCodonFrame();