Merge branch 'alpha/JAL-3362_Jalview_212_alpha' into alpha/merge_212_JalviewJS_2112

[jalview.git] / src / jalview / datamodel / SequenceI.java

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 5cddade..72ce22c 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,8 +20,10 @@
  */
 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;
@@ -359,14 +361,17 @@ public interface SequenceI extends ASequenceI
   /**
    * 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
@@ -587,7 +592,9 @@ public interface SequenceI extends ASequenceI
    *          iterator over regions
    * @return first residue not contained in regions
    */
-  int firstResidueOutsideIterator(Iterator<int[]> it);
+
+  public int firstResidueOutsideIterator(Iterator<int[]> it);
+
 
   /**
    * Answers true if this sequence has an associated Hidden Markov Model
@@ -596,3 +603,4 @@ public interface SequenceI extends ASequenceI
    */
   boolean hasHMMProfile();
 }
+