JAL-2577 mirror hide/select columns by annotation across split frame
[jalview.git] / src / jalview / gui / AnnotationColumnChooser.java
index 31b5b64..a95d0c0 100644 (file)
@@ -1,10 +1,31 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+
 package jalview.gui;
 
-import jalview.api.analysis.AnnotationFilterParameter;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.io.cache.JvCacheableInputBox;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.util.MessageManager;
+import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 
 import java.awt.BorderLayout;
 import java.awt.CardLayout;
@@ -14,21 +35,17 @@ 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;
-import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JInternalFrame;
-import javax.swing.JLabel;
 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;
 
@@ -36,34 +53,10 @@ import net.miginfocom.swing.MigLayout;
 public class AnnotationColumnChooser extends AnnotationRowFilter implements
         ItemListener
 {
-
-  private JComboBox<String> annotations;
-
-  private JButton ok = new JButton();
-
-  private JButton cancel = new JButton();
-
-  private JPanel actionPanel = new JPanel();
-
-  private JPanel thresholdPanel = new JPanel();
-
   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
 
-  private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
-          .getLayout());
-
-  private JPanel noGraphFilterView = new JPanel();
-
-  private JPanel graphFilterView = new JPanel();
-
   private JPanel annotationComboBoxPanel = new JPanel();
 
-  private JLabel annotationLabel = new JLabel();
-
-  private BorderLayout borderLayout1 = new BorderLayout();
-
-  private JComboBox<String> threshold = new JComboBox<String>();
-
   private StructureFilterPanel gStructureFilterPanel;
 
   private StructureFilterPanel ngStructureFilterPanel;
@@ -92,18 +85,11 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   private int actionOption = ACTION_OPTION_SELECT;
 
-  private ColumnSelection oldColumnSelection;
+  private HiddenColumns oldHiddenColumns;
 
-  public AnnotationColumnChooser()
-  {
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
+  protected int MIN_WIDTH = 420;
+
+  protected int MIN_HEIGHT = 430;
 
   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
   {
@@ -114,6 +100,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     Desktop.addInternalFrame(frame,
             MessageManager.getString("label.select_by_annotation"), 520,
             215);
+    frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 
     addSliderChangeListener();
     addSliderMouseListeners();
@@ -122,25 +109,28 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       return;
     }
-    setOldColumnSelection(av.getColumnSelection());
+    setOldHiddenColumns(av.getAlignment().getHiddenColumns());
     adjusting = true;
 
-    setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
+    setAnnotations(new JComboBox<>(getAnnotationItems(false)));
     populateThresholdComboBox(threshold);
-
+    AnnotationColumnChooser lastChooser = av
+            .getAnnotationColumnSelectionState();
     // restore Object state from the previous session if one exists
-    if (av.getAnnotationColumnSelectionState() != null)
+    if (lastChooser != null)
     {
-      currentSearchPanel = av.getAnnotationColumnSelectionState()
+      currentSearchPanel = lastChooser
               .getCurrentSearchPanel();
-      currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
+      currentStructureFilterPanel = lastChooser
               .getCurrentStructureFilterPanel();
-      annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
+      annotations.setSelectedIndex(lastChooser
               .getAnnotations().getSelectedIndex());
-      threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
+      threshold.setSelectedIndex(lastChooser
               .getThreshold().getSelectedIndex());
-      actionOption = av.getAnnotationColumnSelectionState()
+      actionOption = lastChooser
               .getActionOption();
+      percentThreshold.setSelected(lastChooser.percentThreshold
+              .isSelected());
     }
 
     try
@@ -156,75 +146,33 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     frame.pack();
   }
 
-  private void jbInit() throws Exception
+  @Override
+  protected void jbInit()
   {
-    ok.setOpaque(false);
-    ok.setText(MessageManager.getString("action.ok"));
-    ok.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-
-    cancel.setOpaque(false);
-    cancel.setText(MessageManager.getString("action.cancel"));
-    cancel.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-
-    annotations.addItemListener(this);
-    threshold.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed(e);
-      }
-    });
-
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(7);
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed(e);
-      }
-    });
-
-    slider.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(100, 32));
+    super.jbInit();
 
-    annotationLabel.setBackground(Color.white);
-    annotationLabel.setFont(JvSwingUtils.getLabelFont());
-    annotationLabel.setText("Select Annotation : ");
-
-    thresholdPanel.setBorder(new TitledBorder("Threshold Filter"));
+    JPanel thresholdPanel = new JPanel();
+    thresholdPanel.setBorder(new TitledBorder(MessageManager
+            .getString("label.threshold_filter")));
     thresholdPanel.setBackground(Color.white);
     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 
+    percentThreshold.setBackground(Color.white);
+    percentThreshold.setFont(JvSwingUtils.getLabelFont());
+
+    JPanel actionPanel = new JPanel();
     actionPanel.setBackground(Color.white);
     actionPanel.setFont(JvSwingUtils.getLabelFont());
 
+    JPanel graphFilterView = new JPanel();
     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
     graphFilterView.setBackground(Color.white);
 
+    JPanel noGraphFilterView = new JPanel();
     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
     noGraphFilterView.setBackground(Color.white);
+
     annotationComboBoxPanel.setBackground(Color.white);
     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 
@@ -236,8 +184,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ngStructureFilterPanel = new StructureFilterPanel(this);
 
     thresholdPanel.add(getThreshold());
-    thresholdPanel.add(thresholdValue, "wrap");
-    thresholdPanel.add(slider, "grow, span, wrap");
+    thresholdPanel.add(percentThreshold, "wrap");
+    thresholdPanel.add(slider, "grow");
+    thresholdPanel.add(thresholdValue, "span, wrap");
 
     actionPanel.add(ok);
     actionPanel.add(cancel);
@@ -257,44 +206,62 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     switchableViewsPanel.add(graphFilterView,
             AnnotationColumnChooser.GRAPH_VIEW);
 
-    this.setLayout(borderLayout1);
+    this.setLayout(new BorderLayout());
     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 
     selectedAnnotationChanged();
+    updateThresholdPanelToolTip();
     this.validate();
   }
 
-  @SuppressWarnings("unchecked")
-  public void reset()
+  protected void updateThresholdPanelToolTip()
+  {
+    thresholdValue.setToolTipText("");
+    slider.setToolTipText("");
+
+    String defaultTtip = MessageManager
+            .getString("info.change_threshold_mode_to_enable");
+
+    String thresh = getThreshold().getSelectedItem().toString();
+    if (thresh.equalsIgnoreCase("No Threshold"))
+    {
+      thresholdValue.setToolTipText(defaultTtip);
+      slider.setToolTipText(defaultTtip);
+    }
+  }
+
+  @Override
+  protected void reset()
   {
-    if (this.getOldColumnSelection() != null)
+    if (this.getOldHiddenColumns() != null)
     {
       av.getColumnSelection().clear();
 
       if (av.getAnnotationColumnSelectionState() != null)
       {
-        ColumnSelection oldSelection = av
+        HiddenColumns oldHidden = av
                 .getAnnotationColumnSelectionState()
-                .getOldColumnSelection();
-        if (oldSelection != null && oldSelection.getHiddenColumns() != null
-                && !oldSelection.getHiddenColumns().isEmpty())
+                .getOldHiddenColumns();
+        if (oldHidden != null && oldHidden.getHiddenRegions() != null
+                && !oldHidden.getHiddenRegions().isEmpty())
         {
-          for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
+          for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
                   .iterator(); itr.hasNext();)
           {
             int positions[] = itr.next();
             av.hideColumns(positions[0], positions[1]);
           }
         }
-        av.setColumnSelection(oldSelection);
+        av.getAlignment().setHiddenColumns(oldHidden);
       }
       ap.paintAlignment(true);
     }
 
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())
@@ -307,26 +274,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
   }
 
-  public JComboBox<String> getThreshold()
-  {
-    return threshold;
-  }
-
-  public void setThreshold(JComboBox<String> threshold)
-  {
-    this.threshold = threshold;
-  }
-
-  public JComboBox<String> getAnnotations()
-  {
-    return annotations;
-  }
-
-  public void setAnnotations(JComboBox<String> annotations)
-  {
-    this.annotations = annotations;
-  }
-
   @Override
   public void updateView()
   {
@@ -346,12 +293,14 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     slider.setEnabled(true);
     thresholdValue.setEnabled(true);
+    percentThreshold.setEnabled(true);
 
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
       thresholdValue.setEnabled(false);
       thresholdValue.setText("");
+      percentThreshold.setEnabled(false);
       // build filter params
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
@@ -372,7 +321,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
-      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+      
+      setThresholdValueText();
+
       slider.setMajorTickSpacing((int) (range / 10f));
       slider.setEnabled(true);
       thresholdValue.setEnabled(true);
@@ -381,8 +332,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       // build filter params
       filterParams
               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
-      if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
+      if (getCurrentAnnotation().isQuantitative())
       {
+        filterParams
+                .setThresholdValue(getCurrentAnnotation().threshold.value);
 
         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
         {
@@ -397,17 +350,18 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
     }
 
+    updateThresholdPanelToolTip();
     if (currentStructureFilterPanel != null)
     {
-      if (currentStructureFilterPanel.getAlphaHelix().isSelected())
+      if (currentStructureFilterPanel.alphaHelix.isSelected())
       {
         filterParams.setFilterAlphaHelix(true);
       }
-      if (currentStructureFilterPanel.getBetaStrand().isSelected())
+      if (currentStructureFilterPanel.betaStrand.isSelected())
       {
         filterParams.setFilterBetaSheet(true);
       }
-      if (currentStructureFilterPanel.getTurn().isSelected())
+      if (currentStructureFilterPanel.turn.isSelected())
       {
         filterParams.setFilterTurn(true);
       }
@@ -415,56 +369,96 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     if (currentSearchPanel != null)
     {
-      if (!currentSearchPanel.getSearchString().isEmpty())
+      if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
       {
-        currentSearchPanel.getDescription().setEnabled(true);
-        currentSearchPanel.getDisplayName().setEnabled(true);
-        filterParams.setRegexString(currentSearchPanel.getSearchString());
-        if (currentSearchPanel.isDisplayNameChecked())
+        filterParams.setRegexString(currentSearchPanel.searchBox
+                .getUserInput());
+        if (currentSearchPanel.displayName.isSelected())
         {
           filterParams
                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
         }
-        if (currentSearchPanel.isDescriptionChecked())
+        if (currentSearchPanel.description.isSelected())
         {
           filterParams
                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
         }
       }
-      else
-      {
-        currentSearchPanel.getDescription().setEnabled(false);
-        currentSearchPanel.getDisplayName().setEnabled(false);
-      }
     }
 
-    filterAnnotations(getCurrentAnnotation().annotations, filterParams,
-            av.getColumnSelection());
-
+    // 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);
+
     if (getActionOption() == ACTION_OPTION_HIDE)
     {
       av.hideSelectedColumns();
     }
+    av.sendSelection();
 
     filterParams = null;
     av.setAnnotationColumnSelectionState(this);
     ap.paintAlignment(true);
   }
 
-  public ColumnSelection getOldColumnSelection()
+  public HiddenColumns getOldHiddenColumns()
   {
-    return oldColumnSelection;
+    return oldHiddenColumns;
   }
 
-  public void setOldColumnSelection(ColumnSelection currentColumnSelection)
+  public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
   {
-    if (currentColumnSelection != null)
+    if (currentHiddenColumns != null)
     {
-      this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
+      this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
     }
   }
 
+  public FurtherActionPanel getCurrentFutherActionPanel()
+  {
+    return currentFurtherActionPanel;
+  }
+
+  public void setCurrentFutherActionPanel(
+          FurtherActionPanel currentFutherActionPanel)
+  {
+    this.currentFurtherActionPanel = currentFutherActionPanel;
+  }
+
+  public SearchPanel getCurrentSearchPanel()
+  {
+    return currentSearchPanel;
+  }
+
+  public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
+  {
+    this.currentSearchPanel = currentSearchPanel;
+  }
+
+  public int getActionOption()
+  {
+    return actionOption;
+  }
+
+  public void setActionOption(int actionOption)
+  {
+    this.actionOption = actionOption;
+  }
+
+  public StructureFilterPanel getCurrentStructureFilterPanel()
+  {
+    return currentStructureFilterPanel;
+  }
+
+  public void setCurrentStructureFilterPanel(
+          StructureFilterPanel currentStructureFilterPanel)
+  {
+    this.currentStructureFilterPanel = currentStructureFilterPanel;
+  }
+
   public void select_action(ActionEvent actionEvent)
   {
     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
@@ -491,15 +485,17 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     selectedAnnotationChanged();
   }
 
+  @Override
   public void selectedAnnotationChanged()
   {
     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
-    if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
-            .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
+    if (av.getAlignment()
+            .getAlignmentAnnotation()[annmap[getAnnotations()
+            .getSelectedIndex()]].isQuantitative())
     {
       currentView = AnnotationColumnChooser.GRAPH_VIEW;
     }
-
+    saveCache();
     gSearchPanel.syncState();
     gFurtherActionPanel.syncState();
     gStructureFilterPanel.syncState();
@@ -508,52 +504,12 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     ngFurtherActionPanel.syncState();
     ngStructureFilterPanel.syncState();
 
+    CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
+            .getLayout();
     switchableViewsLayout.show(switchableViewsPanel, currentView);
     updateView();
   }
 
-  public FurtherActionPanel getCurrentFutherActionPanel()
-  {
-    return currentFurtherActionPanel;
-  }
-
-  public void setCurrentFutherActionPanel(
-          FurtherActionPanel currentFutherActionPanel)
-  {
-    this.currentFurtherActionPanel = currentFutherActionPanel;
-  }
-
-  public SearchPanel getCurrentSearchPanel()
-  {
-    return currentSearchPanel;
-  }
-
-  public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
-  {
-    this.currentSearchPanel = currentSearchPanel;
-  }
-
-  public int getActionOption()
-  {
-    return actionOption;
-  }
-
-  public void setActionOption(int actionOption)
-  {
-    this.actionOption = actionOption;
-  }
-
-  public StructureFilterPanel getCurrentStructureFilterPanel()
-  {
-    return currentStructureFilterPanel;
-  }
-
-  public void setCurrentStructureFilterPanel(
-          StructureFilterPanel currentStructureFilterPanel)
-  {
-    this.currentStructureFilterPanel = currentStructureFilterPanel;
-  }
-
   public class FurtherActionPanel extends JPanel
   {
     private AnnotationColumnChooser aColChooser;
@@ -567,10 +523,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
     {
       this.aColChooser = aColChooser;
-      getSelectOption().setBackground(Color.white);
-      getSelectOption().setFont(JvSwingUtils.getLabelFont());
-      getSelectOption().setText("Select");
-      getSelectOption().addActionListener(new ActionListener()
+      JvSwingUtils.jvInitComponent(selectOption, "action.select");
+      selectOption.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent actionEvent)
@@ -579,10 +533,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      getHideOption().setBackground(Color.white);
-      getHideOption().setFont(JvSwingUtils.getLabelFont());
-      getHideOption().setText("Hide");
-      getHideOption().addActionListener(new ActionListener()
+      JvSwingUtils.jvInitComponent(hideOption, "action.hide");
+      hideOption.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent actionEvent)
@@ -591,16 +543,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      getOptionsGroup().add(getSelectOption());
-      getOptionsGroup().add(getHideOption());
-      getOptionsGroup().setSelected(getSelectOption().getModel(), true);
+      optionsGroup.add(selectOption);
+      optionsGroup.add(hideOption);
+      optionsGroup.setSelected(selectOption.getModel(), true);
 
-      this.setBackground(Color.white);
-      this.setFont(JvSwingUtils.getLabelFont());
+      JvSwingUtils.jvInitComponent(this);
       syncState();
 
-      this.add(getSelectOption());
-      this.add(getHideOption());
+      this.add(selectOption);
+      this.add(hideOption);
     }
 
     public void selectRadioAction(ActionEvent actionEvent)
@@ -615,47 +566,15 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       aColChooser.hide_action(actionEvent);
     }
 
-    public JRadioButton getHideOption()
-    {
-      return hideOption;
-    }
-
-    public void setHideOption(JRadioButton hideOption)
-    {
-      this.hideOption = hideOption;
-    }
-
-    public JRadioButton getSelectOption()
-    {
-      return selectOption;
-    }
-
-    public void setSelectOption(JRadioButton selectOption)
-    {
-      this.selectOption = selectOption;
-    }
-
-    public ButtonGroup getOptionsGroup()
-    {
-      return optionsGroup;
-    }
-
-    public void setOptionsGroup(ButtonGroup optionsGroup)
-    {
-      this.optionsGroup = optionsGroup;
-    }
-
     public void syncState()
     {
       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
       {
-        this.getOptionsGroup().setSelected(this.getHideOption().getModel(),
-                true);
+        this.optionsGroup.setSelected(this.hideOption.getModel(), true);
       }
       else
       {
-        this.getOptionsGroup().setSelected(
-                this.getSelectOption().getModel(), true);
+        this.optionsGroup.setSelected(this.selectOption.getModel(), true);
       }
     }
   }
@@ -676,9 +595,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       this.aColChooser = aColChooser;
 
-      alphaHelix.setBackground(Color.white);
-      alphaHelix.setFont(JvSwingUtils.getLabelFont());
-      alphaHelix.setText("Alpha Helix");
+      JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
       alphaHelix.addActionListener(new ActionListener()
       {
         @Override
@@ -688,9 +605,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      betaStrand.setBackground(Color.white);
-      betaStrand.setFont(JvSwingUtils.getLabelFont());
-      betaStrand.setText("Beta Strand");
+      JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
       betaStrand.addActionListener(new ActionListener()
       {
         @Override
@@ -700,9 +615,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      turn.setBackground(Color.white);
-      turn.setFont(JvSwingUtils.getLabelFont());
-      turn.setText("Turn");
+      JvSwingUtils.jvInitComponent(turn, "label.turn");
       turn.addActionListener(new ActionListener()
       {
         @Override
@@ -712,9 +625,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      all.setBackground(Color.white);
-      all.setFont(JvSwingUtils.getLabelFont());
-      all.setText("Select all");
+      JvSwingUtils.jvInitComponent(all, "label.select_all");
       all.addActionListener(new ActionListener()
       {
         @Override
@@ -724,9 +635,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      this.setBorder(new TitledBorder("Structures Filter"));
-      this.setBackground(Color.white);
-      this.setFont(JvSwingUtils.getLabelFont());
+      this.setBorder(new TitledBorder(MessageManager
+              .getString("label.structures_filter")));
+      JvSwingUtils.jvInitComponent(this);
 
       this.add(all);
       this.add(alphaHelix);
@@ -792,10 +703,10 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
               .getCurrentStructureFilterPanel();
       if (sfp != null)
       {
-        alphaHelix.setSelected(sfp.getAlphaHelix().isSelected());
-        betaStrand.setSelected(sfp.getBetaStrand().isSelected());
-        turn.setSelected(sfp.getTurn().isSelected());
-        if (sfp.getAll().isSelected())
+        alphaHelix.setSelected(sfp.alphaHelix.isSelected());
+        betaStrand.setSelected(sfp.betaStrand.isSelected());
+        turn.setSelected(sfp.turn.isSelected());
+        if (sfp.all.isSelected())
         {
           all.setSelected(true);
           alphaHelix.setSelected(true);
@@ -805,47 +716,6 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       }
 
     }
-
-    public JCheckBox getAlphaHelix()
-    {
-      return alphaHelix;
-    }
-
-    public void setAlphaHelix(JCheckBox alphaHelix)
-    {
-      this.alphaHelix = alphaHelix;
-    }
-
-    public JCheckBox getBetaStrand()
-    {
-      return betaStrand;
-    }
-
-    public void setBetaStrand(JCheckBox betaStrand)
-    {
-      this.betaStrand = betaStrand;
-    }
-
-    public JCheckBox getTurn()
-    {
-      return turn;
-    }
-
-    public void setTurn(JCheckBox turn)
-    {
-      this.turn = turn;
-    }
-
-    public JCheckBox getAll()
-    {
-      return all;
-    }
-
-    public void setAll(JCheckBox all)
-    {
-      this.all = all;
-
-    }
   }
 
   public class SearchPanel extends JPanel
@@ -856,47 +726,40 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
     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";
 
-    private JCheckBox structuresFilter = new JCheckBox();
+    public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(
+            FILTER_BY_ANN_CACHE_KEY);
 
     public SearchPanel(AnnotationColumnChooser aColChooser)
     {
 
       this.aColChooser = aColChooser;
-      this.setBorder(new TitledBorder("Search Filter"));
-      this.setBackground(Color.white);
-      this.setFont(JvSwingUtils.getLabelFont());
-
-      getSearchBox().setBackground(Color.white);
-      getSearchBox().setFont(JvSwingUtils.getLabelFont());
-      getSearchBox().getDocument().addDocumentListener(
-              new DocumentListener()
+      JvSwingUtils.jvInitComponent(this);
+      this.setBorder(new TitledBorder(MessageManager
+              .getString("label.search_filter")));
+
+      searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
+      searchBox.setToolTipText(MessageManager
+              .getString("info.enter_search_text_here"));
+      searchBox.getEditor().getEditorComponent()
+              .addKeyListener(new java.awt.event.KeyAdapter()
               {
                 @Override
-                public void insertUpdate(DocumentEvent e)
+                public void keyPressed(KeyEvent e)
                 {
-                  searchStringAction();
+                  if (e.getKeyCode() == KeyEvent.VK_ENTER)
+                  {
+                    e.consume();
+                    searchStringAction();
+                  }
                 }
+              });
 
-                @Override
-                public void removeUpdate(DocumentEvent e)
-                {
-                  searchStringAction();
-                }
 
-                @Override
-                public void changedUpdate(DocumentEvent e)
-                {
-                  searchStringAction();
-                }
-              });
 
-      getDisplayName().setBackground(Color.white);
-      getDisplayName().setFont(JvSwingUtils.getLabelFont());
-      getDisplayName().setText("Display Name");
-      getDisplayName().setEnabled(false);
-      getDisplayName().addActionListener(new ActionListener()
+      JvSwingUtils.jvInitComponent(displayName, "label.label");
+      displayName.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent actionEvent)
@@ -905,11 +768,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
         }
       });
 
-      getDescription().setBackground(Color.white);
-      getDescription().setFont(JvSwingUtils.getLabelFont());
-      getDescription().setText("Description");
-      getDescription().setEnabled(false);
-      getDescription().addActionListener(new ActionListener()
+      JvSwingUtils.jvInitComponent(description, "label.description");
+      description.addActionListener(new ActionListener()
       {
         @Override
         public void actionPerformed(ActionEvent actionEvent)
@@ -919,24 +779,9 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       });
 
       syncState();
-      this.add(getSearchBox());
-      this.add(getDisplayName());
-      this.add(getDescription());
-    }
-
-    public boolean isDescriptionChecked()
-    {
-      return getDescription().isSelected();
-    }
-
-    public boolean isDisplayNameChecked()
-    {
-      return getDisplayName().isSelected();
-    }
-
-    public String getSearchString()
-    {
-      return getSearchBox().getText();
+      this.add(searchBox);
+      this.add(displayName);
+      this.add(description);
     }
 
     public void displayNameCheckboxAction()
@@ -955,46 +800,8 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     {
       aColChooser.setCurrentSearchPanel(this);
       aColChooser.updateView();
-    }
-
-    public JCheckBox getDisplayName()
-    {
-      return displayName;
-    }
-
-    public void setDisplayName(JCheckBox displayName)
-    {
-      this.displayName = displayName;
-    }
-
-    public JCheckBox getDescription()
-    {
-      return description;
-    }
-
-    public void setDescription(JCheckBox description)
-    {
-      this.description = description;
-    }
-
-    public JTextField getSearchBox()
-    {
-      return searchBox;
-    }
-
-    public void setSearchBox(JTextField searchBox)
-    {
-      this.searchBox = searchBox;
-    }
-
-    public JCheckBox getStructuresFilter()
-    {
-      return structuresFilter;
-    }
-
-    public void setStructuresFilter(JCheckBox structuresFilter)
-    {
-      this.structuresFilter = structuresFilter;
+      updateSearchPanelToolTips();
+      searchBox.updateCache();
     }
 
     public void syncState()
@@ -1002,15 +809,53 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
       SearchPanel sp = aColChooser.getCurrentSearchPanel();
       if (sp != null)
       {
-        description.setEnabled(sp.getDescription().isEnabled());
-        description.setSelected(sp.getDescription().isSelected());
+        description.setEnabled(sp.description.isEnabled());
+        description.setSelected(sp.description.isSelected());
 
-        displayName.setEnabled(sp.getDisplayName().isEnabled());
-        displayName.setSelected(sp.getDisplayName().isSelected());
+        displayName.setEnabled(sp.displayName.isEnabled());
+        displayName.setSelected(sp.displayName.isSelected());
 
-        searchBox.setText(sp.getSearchBox().getText());
+        searchBox.setSelectedItem(sp.searchBox.getUserInput());
       }
+      updateSearchPanelToolTips();
+    }
+
+    public void updateSearchPanelToolTips()
+    {
+      String defaultTtip = MessageManager
+              .getString("info.enter_search_text_to_enable");
+      String labelTtip = MessageManager.formatMessage(
+              "info.search_in_annotation_label", annotations
+                      .getSelectedItem().toString());
+      String descTtip = MessageManager.formatMessage(
+              "info.search_in_annotation_description", annotations
+                      .getSelectedItem().toString());
+      displayName.setToolTipText(displayName.isEnabled() ? labelTtip
+              : defaultTtip);
+      description.setToolTipText(description.isEnabled() ? descTtip
+              : defaultTtip);
     }
   }
 
+  @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();
+  }
 }