*/
package jalview.datamodel;
-import jalview.datamodel.Sequence.DBModList;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.MapList;
-import jalview.ws.params.InvalidArgumentException;
-
import java.util.BitSet;
import java.util.Iterator;
import java.util.List;
import java.util.Vector;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.datamodel.Sequence.DBModList;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.MapList;
+import jalview.ws.params.InvalidArgumentException;
/**
* Methods for manipulating a sequence, its metadata and related annotation in
* @author $author$
* @version $Revision$
*/
-public interface SequenceI extends ASequenceI
+public interface SequenceI extends ASequenceI, ContactMapHolderI
{
/**
* Set the display name for the sequence
/**
* Derive a sequence (using this one's dataset or as the dataset)
*
- * @return duplicate sequence with valid dataset sequence
+ * @return duplicate sequence and any annotation present with valid dataset sequence
*/
public SequenceI deriveSequence();
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
+ public void addContactListFor(AlignmentAnnotation annotation,
+ ContactMatrixI cm);
+
}