X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=d379553563a2abbecc848371c7bd5ffcd8fe4166;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=8a4465b4a4b8822889129688c19c248a6d5a86ed;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 8a4465b..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 2.8.2b1)
- * 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.
  * 
@@ -64,4 +64,35 @@ public interface AlignViewControllerI
   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);
+
+  /**
+   * 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);
+
 }