- String before0 = al2.getSequenceAt(0).getSequenceAsString();
- String before1 = al2.getSequenceAt(1).getSequenceAsString();
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList ml = new MapList(new int[]
+ { 1, 12 }, new int[]
+ { 1, 4 }, 3, 1);
+ acf.addMap(al1.getSequenceAt(0), al2.getSequenceAt(0), ml);
+ acf.addMap(al1.getSequenceAt(1), al2.getSequenceAt(1), ml);
+ al2.addCodonFrame(acf);