X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=deed751ad8d4b4a9ec451bb57789b08d0eb3b9a8;hb=5b833c4ea17f7e45fe1532b36219fcbfba3c0e4a;hp=80c4f9a0dd125e7ebd9e5e2e261f4316dfaa7597;hpb=0dc22d603ad9d58a4ed951fc2146f7a027917a2c;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index 80c4f9a..deed751 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -82,9 +82,9 @@ public interface SequenceFeaturesI
           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.
+   * Answers a list of all features stored, whose type either matches, or is a
+   * specialisation (in the Sequence Ontology) of, one of the given terms.
+   * Results are returned in no particular order.
    * 
    * @param ontologyTerm
    * @return
@@ -215,10 +215,36 @@ public interface SequenceFeaturesI
   float getMaximumScore(String type, boolean positional);
 
   /**
-   * Adds the shift amount to the start and end of all positional features,
-   * returning true if at least one feature was shifted, else false
+   * 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 shift
+   * @param fromPosition
+   * @param shiftBy
    */
-  abstract boolean shiftFeatures(int shift);
-}
\ No newline at end of file
+  boolean shiftFeatures(int fromPosition, int shiftBy);
+
+  /**
+   * Deletes all positional and non-positional features
+   */
+  void deleteAll();
+
+  /**
+   * Point-specific parameter return for JavaScript
+   * 
+   * @param pos
+   * @param type
+   * @param result
+   * @return result (JavaScript) or new ArrayList (Java -- see FeatureRender)
+   * @author Bob Hanson 2019.07.30
+   */
+  List<SequenceFeature> findFeatures(int pos, String type, List<SequenceFeature> result);
+
+  /**
+   * @author Bob Hanson 2019.08.01
+   * 
+   * @param type
+   * @return true if this type is in featureStore
+   */
+  boolean hasFeatures(String type);
+}