package jalview.datamodel;
import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
import java.util.BitSet;
import java.util.Iterator;
public int replace(char c1, char c2);
/**
+ * Answers the GeneLociI, or null if not known
+ *
+ * @return
+ */
+ GeneLociI getGeneLoci();
+
+ /**
+ * Sets the mapping to gene loci for the sequence
+ *
+ * @param speciesId
+ * @param assemblyId
+ * @param chromosomeId
+ * @param map
+ */
+ void setGeneLoci(String speciesId, String assemblyId,
+ String chromosomeId, MapList map);
+
+
+ /**
* 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
* @return a String corresponding to the sequence
*/
public String getSequenceStringFromIterator(Iterator<int[]> it);
+
+ /**
+ * Locate the first position in this sequence which is not contained in an
+ * iterator region. If no such position exists, return 0
+ *
+ * @param it
+ * iterator over regions
+ * @return first residue not contained in regions
+ */
+ public int firstResidueOutsideIterator(Iterator<int[]> it);
}