JAL-3081 is/setShowAutocalculatedAbove pulled up to interface

[jalview.git] / src / jalview / gui / AlignmentPanel.java

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 502ab9d..b27d66d 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.analysis.AnnotationSorter;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
@@ -821,14 +822,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   /**
-   * Sorts annotations according to currently selected preference
+   * Sorts annotations according to currently selected preferences. Does nothing
+   * if currently set to 'Custom' (manual) ordering.
    */
-  void sortAnnotations()
+  @Override
+  public void sortAnnotations(boolean autoCalcOnly)
   {
-    final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
-            av.isShowAutocalculatedAbove());
-    sorter.sort(getAlignment().getAlignmentAnnotation(),
-            av.getSortAnnotationsBy());
+    SequenceAnnotationOrder sortBy = av.getSortAnnotationsBy();
+    if (sortBy != SequenceAnnotationOrder.CUSTOM)
+    {
+      final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+              av.isShowAutocalculatedAbove(), autoCalcOnly);
+      sorter.sort(getAlignment().getAlignmentAnnotation(), sortBy);
+    }
   }
 
   /**