X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=26966ba37711b7b6d09d5db66481fa22343a0e73;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=235a656db81b761ee6ee8786dec943553c950581;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 235a656..26966ba 100644
--- 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
  * 
@@ -62,18 +64,37 @@ 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 of features
-   * @param typ list of feature names or null to use currently displayed features
+   * 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);
+  void sortAlignmentByFeatureScore(List<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
+   * 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(List<String> typ);
+
+  /**
+   * add a features file of some kind to the current view
+   * 
+   * @param file
+   * @param protocol
+   * @param relaxedIdMatching
+   *          if true, try harder to match up IDs with local sequence data
+   * @return true if parsing resulted in something being imported to the view or
+   *         dataset
    */
-  void sortAlignmentByFeatureDensity(String[] typ);
+  public boolean parseFeaturesFile(String file, String protocol,
+          boolean relaxedIdMatching);
 
 }