*/
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;
/**
* set the array of Database references for the sequence.
*
+ * BH 2019.02.04 changes param to DBModlist
+ *
* @param dbs
* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
* set are not normalised.
+ * @throws InvalidArgumentException if the is not one created by Sequence itself
*/
@Deprecated
- public void setDBRefs(DBRefEntry[] dbs);
+ public void setDBRefs(DBModList<DBRefEntry> dbs);
- public DBRefEntry[] getDBRefs();
+ public DBModList<DBRefEntry> getDBRefs();
/**
* add the given entry to the list of DBRefs for this sequence, or replace a
*/
public boolean addSequenceFeature(SequenceFeature sf);
+ /**
+ * Deletes the feature from the sequence (if found). To be precise, deletes
+ * the first feature {@code f} found where {@code f.equals(sf)}.
+ *
+ * @param sf
+ */
public void deleteFeature(SequenceFeature sf);
public void setDatasetSequence(SequenceI seq);
* @return first residue not contained in regions
*/
public int firstResidueOutsideIterator(Iterator<int[]> it);
+
+ /**
+ * Answers a (possibly empty) list of features of the specified type that
+ * overlap the specified column position. If parameter {@code result} is not
+ * null, features are appended to it and the (possibly extended) list is
+ * returned.
+ */
+ List<SequenceFeature> findFeatures(int column, String type,
+ List<SequenceFeature> result);
+
+ /**
+ * Answers true if this store contains at least one feature, else false
+ *
+ * @return
+ */
+ public boolean hasFeatures(String type);
+
}
+