X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=a7ec69e2480d835675999aeb540db278410744f6;hb=4d959452a9c486b6d94291d8e819036ec19b09ef;hp=b868ee5770fb5a732892f8e68ef6221c622d36e3;hpb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index b868ee5..a7ec69e 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -99,4 +99,16 @@ public interface AlignViewControllerI
   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);
+
 }