JAL-2480 include sequenceFeatureStore in createDatasetSequence

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 7ecb4ed..6c82bf3 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import jalview.datamodel.features.SequenceFeaturesI;
+
 import java.util.List;
 import java.util.Vector;
 
@@ -267,6 +269,13 @@ public interface SequenceI extends ASequenceI
   public SequenceFeature[] getSequenceFeatures();
 
   /**
+   * Answers the object holding features for the sequence
+   * 
+   * @return
+   */
+  SequenceFeaturesI getFeatures();
+
+  /**
    * Replaces the array of sequence features associated with this sequence with
    * a new array reference. If this sequence has a dataset sequence, then this
    * method will update the dataset sequence's feature array
@@ -339,7 +348,7 @@ public interface SequenceI extends ASequenceI
 
   /**
    * Adds the given sequence feature and returns true, or returns false if it is
-   * already present on the sequence
+   * already present on the sequence, or if the feature type is null.
    * 
    * @param sf
    * @return
@@ -477,13 +486,14 @@ public interface SequenceI extends ASequenceI
   public List<DBRefEntry> getPrimaryDBRefs();
 
   /**
-   * Returns a (possibly empty) list of sequence features of the given type that
-   * overlap the range from-to (inclusive)
+   * Returns a (possibly empty) list of sequence features that overlap the range
+   * from-to (inclusive), optionally restricted to one or more specified feature
+   * types
    * 
-   * @param type
    * @param from
    * @param to
+   * @param types
    * @return
    */
-  List<SequenceFeature> findFeatures(String type, int from, int to);
+  List<SequenceFeature> findFeatures(int from, int to, String... types);
 }