X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=58beca25ffaef0422f6d60ff68bf8f8d7ba806b0;hb=8eaa775e59bf928f8899f9ada5c9811200c2853a;hp=ed966e7e5d64b32a71dd9ea46aaaefb4464df78e;hpb=87a85be7fc7678455c298287349b03fdd12fd3ad;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index ed966e7..58beca2 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -33,8 +33,12 @@ public interface SequenceFeaturesI
           String... type);
 
   /**
-   * Answers a list of all features stored, optionally restricted to specified
-   * types, in no particular guaranteed order
+   * Answers a list of all features stored, in no particular guaranteed order.
+   * Positional features may optionally be restricted to specified types, but
+   * all non-positional features (if any) are always returned.
+   * <p>
+   * To filter non-positional features by type, use
+   * getNonPositionalFeatures(type).
    * 
    * @param type
    * @return
@@ -42,6 +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.
@@ -173,4 +193,12 @@ public interface SequenceFeaturesI
    * @return
    */
   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
+   * 
+   * @param shift
+   */
+  abstract boolean shiftFeatures(int shift);
 }
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