Merge branch 'features/JAL-1605_html-svg-export' into develop

[jalview.git] / src / jalview / api / AlignViewControllerI.java

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index fadc09e..9bd3f45 100644 (file)
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -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);
+
 }