Merge branch 'develop' into feature/JAL-2759

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

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 84b2c6f..6924b63 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -36,7 +36,6 @@ import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.KeyEvent;
-import java.util.ArrayList;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBox;
@@ -241,20 +240,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       {
         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null)
-        {
-          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
-          for (int[] positions : regions)
-          {
-            av.hideColumns(positions[0], positions[1]);
-          }
-        }
-        // TODO not clear why we need to hide all the columns (above) if we are
-        // going to copy the hidden columns over wholesale anyway
         av.getAlignment().setHiddenColumns(oldHidden);
       }
       av.sendSelection();
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
   }
 
@@ -267,7 +256,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
       updateView();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
-      ap.paintAlignment(false);
+      ap.paintAlignment(false, false);
     }
   }
 
@@ -391,7 +380,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
     av.getColumnSelection().filterAnnotations(
             getCurrentAnnotation().annotations, filterParams);
 
-    if (getActionOption() == ACTION_OPTION_HIDE)
+    boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
+    if (hideCols)
     {
       av.hideSelectedColumns();
     }
@@ -399,7 +389,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
-    ap.paintAlignment(true);
+    // only update overview and structures if columns were hidden
+    ap.paintAlignment(hideCols, hideCols);
   }
 
   public HiddenColumns getOldHiddenColumns()