+ /**
+ * @return The index (zero-based) on this sequence in the MSA. It returns
+ * {@code -1} if this information is not available.
+ */
+ public int getIndex()
+ {
+ return index;
+ }
+
+ /**
+ * Defines the position of this sequence in the MSA. Use the value {@code -1}
+ * if this information is undefined.
+ *
+ * @param The
+ * position for this sequence. This value is zero-based (zero for
+ * this first sequence)
+ */
+ public void setIndex(int value)
+ {
+ index = value;
+ }
+
+ public void setRNA(RNA r){rna=r;}
+
+ public RNA getRNA() { return rna; }
+