X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeaturesI.java;h=7213cbaf47e5c4117cc61e536883119578f96d35;hb=refs%2Fheads%2Fspike%2Fclinvar;hp=c4233918030daa87c9abdb961ebb80c5f71264dd;hpb=c8863c027ddace3961405ed0051f104f1ec99581;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeaturesI.java b/src/jalview/datamodel/features/SequenceFeaturesI.java
index c423391..7213cba 100644
--- a/src/jalview/datamodel/features/SequenceFeaturesI.java
+++ b/src/jalview/datamodel/features/SequenceFeaturesI.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.features;
 
 import jalview.datamodel.SequenceFeature;
@@ -22,7 +42,8 @@ public interface SequenceFeaturesI
   /**
    * Returns a (possibly empty) list of features, optionally restricted to
    * specified types, which overlap the given (inclusive) sequence position
-   * range
+   * range. If types are specified, features are returned in the order of the
+   * types given.
    * 
    * @param from
    * @param to
@@ -62,9 +83,9 @@ 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
@@ -193,4 +214,19 @@ 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();
+}