X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=a7ec69e2480d835675999aeb540db278410744f6;hb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;hp=be845bc5e1666bf336e664f89349a65db2c5e2c4;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index be845bc..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 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -20,15 +20,24 @@
  */
 package jalview.api;
 
+import jalview.io.DataSourceType;
+
+import java.util.List;
+
 /**
  * prototype abstract controller for a Jalview alignment view
+ * 
  * @author jimp
  * 
- * All operations should return true if the view has changed as a result of the operation
- * @param <ViewportI>
- *
+ *         All operations should return true if the view has changed as a result
+ *         of the operation
+ * 
+ *         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();
@@ -39,16 +48,67 @@ public interface AlignViewControllerI<ViewportI>
 
   public boolean deleteGroups();
 
-  public void setViewportAndAlignmentPanel(AlignViewportI viewport, AlignmentViewPanel alignPanel);
+  public void setViewportAndAlignmentPanel(AlignViewportI viewport,
+          AlignmentViewPanel alignPanel);
 
   /**
-   * Mark columns in the current column selection according to positions of sequence features
-   * @param invert - when set, mark all but columns containing given type
-   * @param extendCurrent - when set, do not clear existing column selection
-   * @param toggle - rather than explicitly set, toggle selection state
-   * @param featureType - feature type string
+   * Mark columns in the current column selection according to positions of
+   * sequence features
+   * 
+   * @param invert
+   *          - when set, mark all but columns containing given type
+   * @param extendCurrent
+   *          - when set, do not clear existing column selection
+   * @param toggle
+   *          - rather than explicitly set, toggle selection state
+   * @param featureType
+   *          - feature type string
    * @return true if operation affected state
    */
-  boolean markColumnsContainingFeatures(boolean invert, boolean extendCurrent, boolean clearColumns, String featureType);
+  boolean markColumnsContainingFeatures(boolean invert,
+          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
+   */
+  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
+   */
+  void sortAlignmentByFeatureDensity(List<String> typ);
+
+  /**
+   * add a features file of some kind to the current view
+   * 
+   * @param file
+   * @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, 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);
 
 }