Merge branch 'bug/JAL-2578' into develop

diff --combined src/jalview/gui/AnnotationColumnChooser.java
index a15f605,7dafa7d..9c2a1b9
--- 1/src/jalview/gui/AnnotationColumnChooser.java
--- 2/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@@ -22,7 -22,6 +22,7 @@@
  package jalview.gui;
  
  import jalview.datamodel.HiddenColumns;
 +import jalview.io.cache.JvCacheableInputBox;
  import jalview.schemes.AnnotationColourGradient;
  import jalview.util.MessageManager;
  import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
@@@ -35,7 -34,6 +35,7 @@@ import java.awt.event.ActionEvent
  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 javax.swing.ButtonGroup;
@@@ -45,7 -43,10 +45,7 @@@ import javax.swing.JInternalFrame
  import javax.swing.JLayeredPane;
  import javax.swing.JPanel;
  import javax.swing.JRadioButton;
 -import javax.swing.JTextField;
  import javax.swing.border.TitledBorder;
 -import javax.swing.event.DocumentEvent;
 -import javax.swing.event.DocumentListener;
  
  import net.miginfocom.swing.MigLayout;
  
@@@ -112,7 -113,7 +112,7 @@@ public class AnnotationColumnChooser ex
      setOldHiddenColumns(av.getAlignment().getHiddenColumns());
      adjusting = true;
  
-     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
+     setAnnotations(new JComboBox<>(getAnnotationItems(false)));
      populateThresholdComboBox(threshold);
      AnnotationColumnChooser lastChooser = av
              .getAnnotationColumnSelectionState();
@@@ -369,10 -370,12 +369,10 @@@
  
      if (currentSearchPanel != null)
      {
 -
 -      if (!currentSearchPanel.searchBox.getText().isEmpty())
 +      if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
        {
 -        currentSearchPanel.description.setEnabled(true);
 -        currentSearchPanel.displayName.setEnabled(true);
 -        filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 +        filterParams.setRegexString(currentSearchPanel.searchBox
 +                .getUserInput());
          if (currentSearchPanel.displayName.isSelected())
          {
            filterParams
@@@ -384,12 -387,20 +384,15 @@@
                    .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
          }
        }
 -      else
 -      {
 -        currentSearchPanel.description.setEnabled(false);
 -        currentSearchPanel.displayName.setEnabled(false);
 -      }
      }
  
+     // 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();
@@@ -491,7 -502,7 +494,7 @@@
      {
        currentView = AnnotationColumnChooser.GRAPH_VIEW;
      }
 -
 +    saveCache();
      gSearchPanel.syncState();
      gFurtherActionPanel.syncState();
      gStructureFilterPanel.syncState();
@@@ -722,10 -733,7 +725,10 @@@
  
      private JCheckBox description = new JCheckBox();
  
 -    private JTextField searchBox = new JTextField(10);
 +    private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 +
 +    public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(
 +            FILTER_BY_ANN_CACHE_KEY);
  
      public SearchPanel(AnnotationColumnChooser aColChooser)
      {
@@@ -735,26 -743,32 +738,26 @@@
        this.setBorder(new TitledBorder(MessageManager
                .getString("label.search_filter")));
  
 -      JvSwingUtils.jvInitComponent(searchBox);
 +      searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
        searchBox.setToolTipText(MessageManager
                .getString("info.enter_search_text_here"));
 -      searchBox.getDocument().addDocumentListener(new DocumentListener()
 -      {
 -        @Override
 -        public void insertUpdate(DocumentEvent e)
 -        {
 -          searchStringAction();
 -        }
 +      searchBox.getEditor().getEditorComponent()
 +              .addKeyListener(new java.awt.event.KeyAdapter()
 +              {
 +                @Override
 +                public void keyPressed(KeyEvent e)
 +                {
 +                  if (e.getKeyCode() == KeyEvent.VK_ENTER)
 +                  {
 +                    e.consume();
 +                    searchStringAction();
 +                  }
 +                }
 +              });
  
 -        @Override
 -        public void removeUpdate(DocumentEvent e)
 -        {
 -          searchStringAction();
 -        }
  
 -        @Override
 -        public void changedUpdate(DocumentEvent e)
 -        {
 -          searchStringAction();
 -        }
 -      });
  
        JvSwingUtils.jvInitComponent(displayName, "label.label");
 -      displayName.setEnabled(false);
        displayName.addActionListener(new ActionListener()
        {
          @Override
@@@ -765,6 -779,7 +768,6 @@@
        });
  
        JvSwingUtils.jvInitComponent(description, "label.description");
 -      description.setEnabled(false);
        description.addActionListener(new ActionListener()
        {
          @Override
@@@ -797,7 -812,6 +800,7 @@@
        aColChooser.setCurrentSearchPanel(this);
        aColChooser.updateView();
        updateSearchPanelToolTips();
 +      searchBox.updateCache();
      }
  
      public void syncState()
@@@ -811,7 -825,7 +814,7 @@@
          displayName.setEnabled(sp.displayName.isEnabled());
          displayName.setSelected(sp.displayName.isSelected());
  
 -        searchBox.setText(sp.searchBox.getText());
 +        searchBox.setSelectedItem(sp.searchBox.getUserInput());
        }
        updateSearchPanelToolTips();
      }
@@@ -833,25 -847,4 +836,25 @@@
      }
    }
  
 +  @Override
 +  public void ok_actionPerformed()
 +  {
 +    saveCache();
 +    super.ok_actionPerformed();
 +  }
 +
 +  @Override
 +  public void cancel_actionPerformed()
 +  {
 +    saveCache();
 +    super.cancel_actionPerformed();
 +  }
 +
 +  private void saveCache()
 +  {
 +    gSearchPanel.searchBox.persistCache();
 +    ngSearchPanel.searchBox.persistCache();
 +    gSearchPanel.searchBox.updateCache();
 +    ngSearchPanel.searchBox.updateCache();
 +  }
  }