+ /**
+ * @param index
+ * The sequence index in the MSA
+ */
+ public void setIndex(int index);
+
+ /**
+ * @return The index of the sequence in the alignment
+ */
+ public int getIndex();
+
+ /**
+ * @return The RNA of the sequence in the alignment
+ */
+
+ public RNA getRNA();
+
+ /**
+ * @param rna
+ * The RNA.
+ */
+ public void setRNA(RNA rna);
+
+ /**
+ *
+ * @return list of insertions (gap characters) in sequence
+ */
+ public List<int[]> getInsertions();
+