Merge branch 'develop' into features/JAL-250_hideredundantseqs

diff --cc src/jalview/analysis/AlignSeq.java
Simple merge

diff --cc src/jalview/api/AlignViewControllerI.java
index 70ae61e,a7ec69e..04c1fd9
--- 1/src/jalview/api/AlignViewControllerI.java
--- 2/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@@ -20,7 -20,7 +20,8 @@@
   */
  package jalview.api;
  
 +import jalview.datamodel.SequenceGroup;
+ import jalview.io.DataSourceType;
  
  import java.util.List;
  
@@@ -100,11 -100,15 +101,23 @@@ public interface AlignViewController
            boolean relaxedIdMatching);
  
    /**
 +   * clear any group definitions in the current view and add a set of new group
 +   * definitions with randomly generated colours
 +   * 
 +   * @param gps
 +   */
 +  void showRandomColoursForGroups(List<SequenceGroup> gps);
 +
++  /**
+    * 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);
+ 
  }

diff --cc src/jalview/controller/AlignViewController.java
Simple merge