JAL-2591 Further refactoring (still incomplete)

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

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index a15f605..311b9d5 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -36,7 +36,7 @@ import java.awt.event.ActionListener;
 import java.awt.event.ItemEvent;
 import java.awt.event.ItemListener;
 import java.awt.event.KeyEvent;
-import java.util.Iterator;
+import java.util.ArrayList;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBox;
@@ -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();
@@ -244,16 +244,16 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
                 .getOldHiddenColumns();
-        if (oldHidden != null && oldHidden.getHiddenRegions() != null
-                && !oldHidden.getHiddenRegions().isEmpty())
+        if (oldHidden != null)
         {
-          for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
-                  .iterator(); itr.hasNext();)
+          ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopyAsList();
+          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);
       }
       ap.paintAlignment(true);
@@ -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();
@@ -724,7 +727,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 
-    public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(
+    public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
             FILTER_BY_ANN_CACHE_KEY);
 
     public SearchPanel(AnnotationColumnChooser aColChooser)