Merge branch 'bug/JAL-2578' into develop

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

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index a15f605..9c2a1b9 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -112,7 +112,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
     adjusting = true;
 
-    setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
+    setAnnotations(new JComboBox<>(getAnnotationItems(false)));
     populateThresholdComboBox(threshold);
     AnnotationColumnChooser lastChooser = av
             .getAnnotationColumnSelectionState();
@@ -386,10 +386,13 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
     }
 
+    // show hidden columns here, before changing the column selection in
+    // filterAnnotations, because showing hidden columns has the side effect of
+    // adding them to the selection
+    av.showAllHiddenColumns();
     av.getColumnSelection().filterAnnotations(
             getCurrentAnnotation().annotations, filterParams);
 
-    av.showAllHiddenColumns();
     if (getActionOption() == ACTION_OPTION_HIDE)
     {
       av.hideSelectedColumns();