X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=d379553563a2abbecc848371c7bd5ffcd8fe4166;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=cac3776fa8cfaa19161227465e22f84047666838;hpb=5146792501661f7d07d4357651cb1b04fd4d9a46;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index cac3776..d379553 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -1,14 +1,39 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.api;
 
 /**
  * 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();
@@ -19,16 +44,55 @@ 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 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);
 
 }