X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=235a656db81b761ee6ee8786dec943553c950581;hb=2a42323bc7b92e39c676fc46768f28d032f2f686;hp=fadc09e20fd8e2ac2f64a2d5a304e1e87851d47a;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index fadc09e..235a656 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -27,10 +27,13 @@ package jalview.api;
  * 
  *         All operations should return true if the view has changed as a result
  *         of the operation
- * @param <ViewportI>
+ * 
+ *         The controller holds methods that operate on an alignment view,
+ *         modifying its state in some way that may result in side effects
+ *         reflected in an associated GUI
  * 
  */
-public interface AlignViewControllerI<ViewportI>
+public interface AlignViewControllerI
 {
 
   public boolean makeGroupsFromSelection();
@@ -61,4 +64,16 @@ public interface AlignViewControllerI<ViewportI>
   boolean markColumnsContainingFeatures(boolean invert,
           boolean extendCurrent, boolean clearColumns, String featureType);
 
+  /**
+   * sort the alignment or current selection by average score over the given set of features
+   * @param typ list of feature names or null to use currently displayed features
+   */
+  void sortAlignmentByFeatureScore(String[] typ);
+
+  /**
+   * sort the alignment or current selection by distribution of the given set of features
+   * @param typ list of feature names or null to use currently displayed features
+   */
+  void sortAlignmentByFeatureDensity(String[] typ);
+
 }