X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;h=3a7188ea47d3aa8966a830ed9032bec812a17ad1;hb=9ba5a485b66e9c5a86b12dedc7b32616f3ef6db8;hp=c49a5f3b4ccdf8ca0b4c31ceb5ee105da457ec0c;hpb=5e8ec77d921ff2d604811e5e4ba7e9211b0f48de;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index c49a5f3..3a7188e 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -46,7 +46,7 @@ import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.TextEvent;
 import java.awt.event.TextListener;
-import java.util.Iterator;
+import java.util.ArrayList;
 import java.util.Vector;
 
 //import javax.swing.JPanel;
@@ -300,14 +300,17 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
                 .getOldHiddenColumns();
         if (oldHidden != null)
         {
-          for (Iterator<int[]> itr = oldHidden.iterator(); itr.hasNext();)
+          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
+          for (int[] positions : regions)
           {
-            int positions[] = itr.next();
             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);
     }
 
@@ -426,8 +429,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
 
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * 1000
-              - getCurrentAnnotation().graphMin * 1000;
+      // float range = getCurrentAnnotation().graphMax * 1000
+      // - getCurrentAnnotation().graphMin * 1000;
 
       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
@@ -502,10 +505,13 @@ 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();
@@ -513,6 +519,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
+    av.sendSelection();
     ap.paintAlignment(true);
   }