X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;fp=src%2Fjalview%2Fapi%2FAlignViewControllerI.java;h=8ed2c95b6fc2d0b9fbb1ec2cd9af49a9263f0bfb;hb=9098789d536725881086f20aba4d430edfc148a7;hp=26966ba37711b7b6d09d5db66481fa22343a0e73;hpb=807cb3673fd8e34f4305e290e053c3d71fd773ee;p=jalview.git

diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java
index 26966ba..8ed2c95 100644
--- a/src/jalview/api/AlignViewControllerI.java
+++ b/src/jalview/api/AlignViewControllerI.java
@@ -97,4 +97,16 @@ public interface AlignViewControllerI
   public boolean parseFeaturesFile(String file, String protocol,
           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);
+
 }