- // working map of sequence index in alignment
- private final Map<SequenceI, Integer> sequenceIndices = new HashMap<SequenceI, Integer>();
+ /*
+ * working map of sequence index in alignment
+ */
+ private final Map<SequenceI, Integer> sequenceIndices = new HashMap<>();
+
+ /*
+ * if true, sort only repositions auto-calculated annotation (to top or bottom)
+ */
+ private boolean autocalcOnly;