JAL-1486 JAL-535 refactor code for trimming alignment annotation according to selecti...

[jalview.git] / src / jalview / api / AlignViewportI.java

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 567ae83..d8ba30d 100644 (file)
--- 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);
+
 }