X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=8c30dceaa5e95e5b06806a8932a75fc60f43c87e;hb=c8e86c8d3d346840e826942470784b0fec66d439;hp=281743eb433cb03235bb675a6cec336461037955;hpb=f782e40f6f1b3f2bb22927891493c5faf318625b;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index 281743e..8c30dce 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -46,6 +46,22 @@ public interface SequenceFeaturesI
   List<SequenceFeature> getAllFeatures(String... type);
 
   /**
+   * Answers a list of all positional (or non-positional) features which are in
+   * the specified feature group, optionally restricted to features of specified
+   * types.
+   * 
+   * @param positional
+   *          if true returns positional features, else non-positional features
+   * @param group
+   *          the feature group to be matched (which may be null)
+   * @param type
+   *          optional feature types to filter by
+   * @return
+   */
+  List<SequenceFeature> getFeaturesForGroup(boolean positional,
+          String group, String... type);
+
+  /**
    * Answers a list of all features stored, whose type either matches one of the
    * given ontology terms, or is a specialisation of a term in the Sequence
    * Ontology. Results are returned in no particular guaranteed order.
@@ -177,4 +193,19 @@ public interface SequenceFeaturesI
    * @return
    */
   float getMaximumScore(String type, boolean positional);
-}
\ No newline at end of file
+
+  /**
+   * Adds the shift amount to the start and end of all positional features whose
+   * start position is at or after fromPosition. Returns true if at least one
+   * feature was shifted, else false.
+   * 
+   * @param fromPosition
+   * @param shiftBy
+   */
+  boolean shiftFeatures(int fromPosition, int shiftBy);
+
+  /**
+   * Deletes all positional and non-positional features
+   */
+  void deleteAll();
+}