JAL-2089 Merge branch releases/Release_2_10_Branch to master

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

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 9f91eda..24020e5 100644 (file)
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -20,6 +20,8 @@
  */
 package jalview.api;
 
+import java.util.List;
+
 /**
  * prototype abstract controller for a Jalview alignment view
  * 
@@ -62,7 +64,7 @@ public interface AlignViewControllerI
    * @return true if operation affected state
    */
   boolean markColumnsContainingFeatures(boolean invert,
-          boolean extendCurrent, boolean clearColumns, String featureType);
+          boolean extendCurrent, boolean toggle, String featureType);
 
   /**
    * sort the alignment or current selection by average score over the given set
@@ -71,7 +73,7 @@ public interface AlignViewControllerI
    * @param typ
    *          list of feature names or null to use currently displayed features
    */
-  void sortAlignmentByFeatureScore(String[] typ);
+  void sortAlignmentByFeatureScore(List<String> typ);
 
   /**
    * sort the alignment or current selection by distribution of the given set of
@@ -80,7 +82,7 @@ public interface AlignViewControllerI
    * @param typ
    *          list of feature names or null to use currently displayed features
    */
-  void sortAlignmentByFeatureDensity(String[] typ);
+  void sortAlignmentByFeatureDensity(List<String> typ);
 
   /**
    * add a features file of some kind to the current view