+
+ /**
+ * Calculate the visible start and end index of an alignment. The result is
+ * returned an int array where: int[0] = startIndex, and int[1] = endIndex.
+ *
+ * @param hiddenCols
+ * @return
+ */
+ public int[] getVisibleStartAndEndIndex(List<int[]> hiddenCols);
+
+ public void setHiddenColumns(HiddenColumns cols);
+
+ public List<SequenceI> getHMMConsensusSequences(boolean remove);
+
+ void insertSequenceAt(int i, SequenceI snew);
+
+
+