X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;h=37b45f92a50f62bd5f74adbb459009292c7976ff;hb=56d72101b0584635cf539d5413db27abc8deb575;hp=b4c1d54dabea6c3d29ee229b3441a06567dbfb32;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index b4c1d54..37b45f9 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -20,12 +20,6 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.HiddenColumns;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.util.MessageManager;
-import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
-
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
 import java.awt.Checkbox;
@@ -46,9 +40,14 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
-import java.util.ArrayList;
 import java.util.Vector;
 
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.HiddenColumns;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
+
 //import javax.swing.JPanel;
 
 //import net.miginfocom.swing.MigLayout;
@@ -293,20 +292,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       {
         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);
     }
 
   }
@@ -348,7 +337,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
           sliderDragging = false;
           valueChanged(true);
         }
-        ap.paintAlignment(true);
+        ap.paintAlignment(true, true);
       }
     });
   }
@@ -359,8 +348,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     if (slider.isEnabled())
     {
       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
-      updateView();
-      ap.paintAlignment(false);
+      updateView(); // this also calls paintAlignment(true,true)
     }
   }
 
@@ -504,8 +492,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     // filterAnnotations, because showing hidden columns has the side effect of
     // adding them to the selection
     av.showAllHiddenColumns();
-    av.getColumnSelection().filterAnnotations(
-            getCurrentAnnotation().annotations, filterParams);
+    av.getColumnSelection().filterAnnotations(getCurrentAnnotation(),
+            filterParams);
 
     if (getActionOption() == ACTION_OPTION_HIDE)
     {
@@ -515,7 +503,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
     av.sendSelection();
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   public HiddenColumns getOldHiddenColumns()