X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=a7ec69e2480d835675999aeb540db278410744f6;hb=e07d62e6efbd954164c27e15eee49f57aa2e1b4c;hp=5e3cfca40a2a3f945e39f3e74f1ceec4f4f1d3ef;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 5e3cfca..a7ec69e 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 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,10 @@
  */
 package jalview.api;
 
+import jalview.io.DataSourceType;
+
+import java.util.List;
+
 /**
  * prototype abstract controller for a Jalview alignment view
  * 
@@ -62,7 +66,7 @@ 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 +75,7 @@ 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
@@ -80,19 +84,31 @@ 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
    * 
    * @param file
-   * @param protocol
+   * @param sourceType
    * @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,
+  public boolean parseFeaturesFile(String file, DataSourceType sourceType,
           boolean relaxedIdMatching);
 
+  /**
+   * mark columns containing highlighted regions (e.g. from search, structure
+   * highlight, or a mouse over event in another viewer)
+   * 
+   * @param invert
+   * @param extendCurrent
+   * @param toggle
+   * @return
+   */
+  boolean markHighlightedColumns(boolean invert, boolean extendCurrent,
+          boolean toggle);
+
 }