JAL-958 JAL-966 refactor group/alignment associated conservation, consensus and logo...

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

diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java
index 54a1d6f..61b2950 100644 (file)
--- a/src/jalview/api/AlignViewportI.java
+++ b/src/jalview/api/AlignViewportI.java
@@ -117,4 +117,14 @@ public interface AlignViewportI
   void setHiddenRepSequences(
           Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
 
+  /**
+   * hides or shows dynamic annotation rows based on groups and group and alignment associated auto-annotation state flags
+   * apply the current group/autoannotation settings to the alignment view. 
+   * Usually you should call the AlignmentViewPanel.adjustAnnotationHeight() method afterwards to ensure the annotation panel bounds are set correctly.
+   * @param applyGlobalSettings - apply to all autoannotation rows or just the ones associated with the current visible region
+   * @param preserveNewGroupSettings - don't apply global settings to groups which don't already have group associated annotation
+   */
+  void updateGroupAnnotationSettings(boolean applyGlobalSettings,
+          boolean preserveNewGroupSettings);
+
 }