X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FAlignViewportI.java;h=d8ba30d007abda84883e1ef0f4ead7f8199c5e6e;hp=567ae837fe7c157080d23b408c85f1fb4748cfde;hb=5b977aa5b8443f3a5e1bfdc1ef84bf1c4b91631f;hpb=6b89b11e2e9b551714d3a3ff6dd7d6365556afc7

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 567ae83..d8ba30d 100644
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -22,6 +22,7 @@ package jalview.api;
 
 import java.awt.Color;
 import java.util.Hashtable;
+import java.util.List;
 import java.util.Map;
 
 import jalview.analysis.Conservation;
@@ -191,4 +192,12 @@ public interface AlignViewportI
 
   void setConservation(Conservation cons);
 
+  /**
+   * get a copy of the currently visible alignment annotation
+   * @param selectedOnly if true - trim to selected regions on the alignment
+   * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+   */
+  List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+          boolean selectedOnly);
+
 }