import jalview.datamodel.features.SequenceFeaturesI;
import java.util.BitSet;
+import java.util.Iterator;
import java.util.List;
import java.util.Vector;
* @param c2
*/
public int replace(char c1, char c2);
+
+ /**
+ * Returns the sequence string constructed from the substrings of a sequence
+ * defined by the int[] ranges provided by an iterator. E.g. the iterator
+ * could iterate over all visible regions of the alignment
+ *
+ * @param it
+ * the iterator to use
+ * @return a String corresponding to the sequence
+ */
+ public String getSequenceStringFromIterator(Iterator<int[]> it);
}