X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=d379553563a2abbecc848371c7bd5ffcd8fe4166;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=090a8b50ed87597452bd0ef60305faf5a5952b64;hpb=770a6a7d91b1f46a7d0372b987f859b35f286ad8;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 090a8b5..d379553 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 2.9)
+ * Copyright (C) 2015 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();
@@ -62,15 +65,34 @@ public interface AlignViewControllerI<ViewportI>
           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
+   * 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
+   * 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);
 
+  /**
+   * 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
+   */
+  public boolean parseFeaturesFile(String file, String protocol,
+          boolean relaxedIdMatching);
+
 }