src/jalview/gui/AnnotationColumnChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.gui;
  23
  24 import jalview.datamodel.HiddenColumns;
  25 import jalview.io.cache.JvCacheableInputBox;
  26 import jalview.schemes.AnnotationColourGradient;
  27 import jalview.util.MessageManager;
  28 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.CardLayout;
  32 import java.awt.Color;
  33 import java.awt.Dimension;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.ItemEvent;
  37 import java.awt.event.ItemListener;
  38 import java.awt.event.KeyEvent;
  39 import java.util.Iterator;
  40
  41 import javax.swing.ButtonGroup;
  42 import javax.swing.JCheckBox;
  43 import javax.swing.JComboBox;
  44 import javax.swing.JInternalFrame;
  45 import javax.swing.JLayeredPane;
  46 import javax.swing.JPanel;
  47 import javax.swing.JRadioButton;
  48 import javax.swing.border.TitledBorder;
  49
  50 import net.miginfocom.swing.MigLayout;
  51
  52 @SuppressWarnings("serial")
  53 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  54         ItemListener
  55 {
  56   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  57
  58   private JPanel annotationComboBoxPanel = new JPanel();
  59
  60   private StructureFilterPanel gStructureFilterPanel;
  61
  62   private StructureFilterPanel ngStructureFilterPanel;
  63
  64   private StructureFilterPanel currentStructureFilterPanel;
  65
  66   private SearchPanel currentSearchPanel;
  67
  68   private SearchPanel gSearchPanel;
  69
  70   private SearchPanel ngSearchPanel;
  71
  72   private FurtherActionPanel currentFurtherActionPanel;
  73
  74   private FurtherActionPanel gFurtherActionPanel;
  75
  76   private FurtherActionPanel ngFurtherActionPanel;
  77
  78   public static final int ACTION_OPTION_SELECT = 1;
  79
  80   public static int ACTION_OPTION_HIDE = 2;
  81
  82   public static String NO_GRAPH_VIEW = "0";
  83
  84   public static String GRAPH_VIEW = "1";
  85
  86   private int actionOption = ACTION_OPTION_SELECT;
  87
  88   private HiddenColumns oldHiddenColumns;
  89
  90   protected int MIN_WIDTH = 420;
  91
  92   protected int MIN_HEIGHT = 430;
  93
  94   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  95   {
  96     super(av, ap);
  97     frame = new JInternalFrame();
  98     frame.setContentPane(this);
  99     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 100     Desktop.addInternalFrame(frame,
 101             MessageManager.getString("label.select_by_annotation"), 520,
 102             215);
 103     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 104
 105     addSliderChangeListener();
 106     addSliderMouseListeners();
 107
 108     if (av.getAlignment().getAlignmentAnnotation() == null)
 109     {
 110       return;
 111     }
 112     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 113     adjusting = true;
 114
 115     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 116     populateThresholdComboBox(threshold);
 117     AnnotationColumnChooser lastChooser = av
 118             .getAnnotationColumnSelectionState();
 119     // restore Object state from the previous session if one exists
 120     if (lastChooser != null)
 121     {
 122       currentSearchPanel = lastChooser
 123               .getCurrentSearchPanel();
 124       currentStructureFilterPanel = lastChooser
 125               .getCurrentStructureFilterPanel();
 126       annotations.setSelectedIndex(lastChooser
 127               .getAnnotations().getSelectedIndex());
 128       threshold.setSelectedIndex(lastChooser
 129               .getThreshold().getSelectedIndex());
 130       actionOption = lastChooser
 131               .getActionOption();
 132       percentThreshold.setSelected(lastChooser.percentThreshold
 133               .isSelected());
 134     }
 135
 136     try
 137     {
 138       jbInit();
 139     } catch (Exception ex)
 140     {
 141     }
 142     adjusting = false;
 143
 144     updateView();
 145     frame.invalidate();
 146     frame.pack();
 147   }
 148
 149   @Override
 150   protected void jbInit()
 151   {
 152     super.jbInit();
 153
 154     JPanel thresholdPanel = new JPanel();
 155     thresholdPanel.setBorder(new TitledBorder(MessageManager
 156             .getString("label.threshold_filter")));
 157     thresholdPanel.setBackground(Color.white);
 158     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 159     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 160
 161     percentThreshold.setBackground(Color.white);
 162     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 163
 164     JPanel actionPanel = new JPanel();
 165     actionPanel.setBackground(Color.white);
 166     actionPanel.setFont(JvSwingUtils.getLabelFont());
 167
 168     JPanel graphFilterView = new JPanel();
 169     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 170     graphFilterView.setBackground(Color.white);
 171
 172     JPanel noGraphFilterView = new JPanel();
 173     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 174     noGraphFilterView.setBackground(Color.white);
 175
 176     annotationComboBoxPanel.setBackground(Color.white);
 177     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 178
 179     gSearchPanel = new SearchPanel(this);
 180     ngSearchPanel = new SearchPanel(this);
 181     gFurtherActionPanel = new FurtherActionPanel(this);
 182     ngFurtherActionPanel = new FurtherActionPanel(this);
 183     gStructureFilterPanel = new StructureFilterPanel(this);
 184     ngStructureFilterPanel = new StructureFilterPanel(this);
 185
 186     thresholdPanel.add(getThreshold());
 187     thresholdPanel.add(percentThreshold, "wrap");
 188     thresholdPanel.add(slider, "grow");
 189     thresholdPanel.add(thresholdValue, "span, wrap");
 190
 191     actionPanel.add(ok);
 192     actionPanel.add(cancel);
 193
 194     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 195     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 196     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 197     graphFilterView.add(gFurtherActionPanel);
 198
 199     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 200     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 201     noGraphFilterView.add(ngFurtherActionPanel);
 202
 203     annotationComboBoxPanel.add(getAnnotations());
 204     switchableViewsPanel.add(noGraphFilterView,
 205             AnnotationColumnChooser.NO_GRAPH_VIEW);
 206     switchableViewsPanel.add(graphFilterView,
 207             AnnotationColumnChooser.GRAPH_VIEW);
 208
 209     this.setLayout(new BorderLayout());
 210     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 211     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 212     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 213
 214     selectedAnnotationChanged();
 215     updateThresholdPanelToolTip();
 216     this.validate();
 217   }
 218
 219   protected void updateThresholdPanelToolTip()
 220   {
 221     thresholdValue.setToolTipText("");
 222     slider.setToolTipText("");
 223
 224     String defaultTtip = MessageManager
 225             .getString("info.change_threshold_mode_to_enable");
 226
 227     String thresh = getThreshold().getSelectedItem().toString();
 228     if (thresh.equalsIgnoreCase("No Threshold"))
 229     {
 230       thresholdValue.setToolTipText(defaultTtip);
 231       slider.setToolTipText(defaultTtip);
 232     }
 233   }
 234
 235   @Override
 236   protected void reset()
 237   {
 238     if (this.getOldHiddenColumns() != null)
 239     {
 240       av.getColumnSelection().clear();
 241
 242       if (av.getAnnotationColumnSelectionState() != null)
 243       {
 244         HiddenColumns oldHidden = av
 245                 .getAnnotationColumnSelectionState()
 246                 .getOldHiddenColumns();
 247         if (oldHidden != null && oldHidden.getHiddenRegions() != null
 248                 && !oldHidden.getHiddenRegions().isEmpty())
 249         {
 250           for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
 251                   .iterator(); itr.hasNext();)
 252           {
 253             int positions[] = itr.next();
 254             av.hideColumns(positions[0], positions[1]);
 255           }
 256         }
 257         av.getAlignment().setHiddenColumns(oldHidden);
 258       }
 259       ap.paintAlignment(true);
 260     }
 261
 262   }
 263
 264   @Override
 265   public void valueChanged(boolean updateAllAnnotation)
 266   {
 267     if (slider.isEnabled())
 268     {
 269       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 270       updateView();
 271       propagateSeqAssociatedThreshold(updateAllAnnotation,
 272               getCurrentAnnotation());
 273       ap.paintAlignment(false);
 274     }
 275   }
 276
 277   @Override
 278   public void updateView()
 279   {
 280     // Check if combobox is still adjusting
 281     if (adjusting)
 282     {
 283       return;
 284     }
 285
 286     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 287
 288     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 289             .getSelectedIndex()]]);
 290
 291     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 292             .getSelectedIndex());
 293
 294     slider.setEnabled(true);
 295     thresholdValue.setEnabled(true);
 296     percentThreshold.setEnabled(true);
 297
 298     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 299     {
 300       slider.setEnabled(false);
 301       thresholdValue.setEnabled(false);
 302       thresholdValue.setText("");
 303       percentThreshold.setEnabled(false);
 304       // build filter params
 305     }
 306     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 307     {
 308       if (getCurrentAnnotation().threshold == null)
 309       {
 310         getCurrentAnnotation()
 311                 .setThreshold(
 312                         new jalview.datamodel.GraphLine(
 313                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 314                                 "Threshold", Color.black));
 315       }
 316
 317       adjusting = true;
 318       float range = getCurrentAnnotation().graphMax * 1000
 319               - getCurrentAnnotation().graphMin * 1000;
 320
 321       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 322       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 323       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 324
 325       setThresholdValueText();
 326
 327       slider.setMajorTickSpacing((int) (range / 10f));
 328       slider.setEnabled(true);
 329       thresholdValue.setEnabled(true);
 330       adjusting = false;
 331
 332       // build filter params
 333       filterParams
 334               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 335       if (getCurrentAnnotation().isQuantitative())
 336       {
 337         filterParams
 338                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 339
 340         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 341         {
 342           filterParams
 343                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 344         }
 345         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 346         {
 347           filterParams
 348                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 349         }
 350       }
 351     }
 352
 353     updateThresholdPanelToolTip();
 354     if (currentStructureFilterPanel != null)
 355     {
 356       if (currentStructureFilterPanel.alphaHelix.isSelected())
 357       {
 358         filterParams.setFilterAlphaHelix(true);
 359       }
 360       if (currentStructureFilterPanel.betaStrand.isSelected())
 361       {
 362         filterParams.setFilterBetaSheet(true);
 363       }
 364       if (currentStructureFilterPanel.turn.isSelected())
 365       {
 366         filterParams.setFilterTurn(true);
 367       }
 368     }
 369
 370     if (currentSearchPanel != null)
 371     {
 372       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
 373       {
 374         filterParams.setRegexString(currentSearchPanel.searchBox
 375                 .getUserInput());
 376         if (currentSearchPanel.displayName.isSelected())
 377         {
 378           filterParams
 379                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 380         }
 381         if (currentSearchPanel.description.isSelected())
 382         {
 383           filterParams
 384                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 385         }
 386       }
 387     }
 388
 389     av.getColumnSelection().filterAnnotations(
 390             getCurrentAnnotation().annotations, filterParams);
 391
 392     av.showAllHiddenColumns();
 393     if (getActionOption() == ACTION_OPTION_HIDE)
 394     {
 395       av.hideSelectedColumns();
 396     }
 397
 398     filterParams = null;
 399     av.setAnnotationColumnSelectionState(this);
 400     ap.paintAlignment(true);
 401   }
 402
 403   public HiddenColumns getOldHiddenColumns()
 404   {
 405     return oldHiddenColumns;
 406   }
 407
 408   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 409   {
 410     if (currentHiddenColumns != null)
 411     {
 412       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 413     }
 414   }
 415
 416   public FurtherActionPanel getCurrentFutherActionPanel()
 417   {
 418     return currentFurtherActionPanel;
 419   }
 420
 421   public void setCurrentFutherActionPanel(
 422           FurtherActionPanel currentFutherActionPanel)
 423   {
 424     this.currentFurtherActionPanel = currentFutherActionPanel;
 425   }
 426
 427   public SearchPanel getCurrentSearchPanel()
 428   {
 429     return currentSearchPanel;
 430   }
 431
 432   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 433   {
 434     this.currentSearchPanel = currentSearchPanel;
 435   }
 436
 437   public int getActionOption()
 438   {
 439     return actionOption;
 440   }
 441
 442   public void setActionOption(int actionOption)
 443   {
 444     this.actionOption = actionOption;
 445   }
 446
 447   public StructureFilterPanel getCurrentStructureFilterPanel()
 448   {
 449     return currentStructureFilterPanel;
 450   }
 451
 452   public void setCurrentStructureFilterPanel(
 453           StructureFilterPanel currentStructureFilterPanel)
 454   {
 455     this.currentStructureFilterPanel = currentStructureFilterPanel;
 456   }
 457
 458   public void select_action(ActionEvent actionEvent)
 459   {
 460     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 461     if (radioButton.isSelected())
 462     {
 463       setActionOption(ACTION_OPTION_SELECT);
 464       updateView();
 465     }
 466   }
 467
 468   public void hide_action(ActionEvent actionEvent)
 469   {
 470     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 471     if (radioButton.isSelected())
 472     {
 473       setActionOption(ACTION_OPTION_HIDE);
 474       updateView();
 475     }
 476   }
 477
 478   @Override
 479   public void itemStateChanged(ItemEvent e)
 480   {
 481     selectedAnnotationChanged();
 482   }
 483
 484   @Override
 485   public void selectedAnnotationChanged()
 486   {
 487     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 488     if (av.getAlignment()
 489             .getAlignmentAnnotation()[annmap[getAnnotations()
 490             .getSelectedIndex()]].isQuantitative())
 491     {
 492       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 493     }
 494     saveCache();
 495     gSearchPanel.syncState();
 496     gFurtherActionPanel.syncState();
 497     gStructureFilterPanel.syncState();
 498
 499     ngSearchPanel.syncState();
 500     ngFurtherActionPanel.syncState();
 501     ngStructureFilterPanel.syncState();
 502
 503     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 504             .getLayout();
 505     switchableViewsLayout.show(switchableViewsPanel, currentView);
 506     updateView();
 507   }
 508
 509   public class FurtherActionPanel extends JPanel
 510   {
 511     private AnnotationColumnChooser aColChooser;
 512
 513     private JRadioButton hideOption = new JRadioButton();
 514
 515     private JRadioButton selectOption = new JRadioButton();
 516
 517     private ButtonGroup optionsGroup = new ButtonGroup();
 518
 519     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 520     {
 521       this.aColChooser = aColChooser;
 522       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 523       selectOption.addActionListener(new ActionListener()
 524       {
 525         @Override
 526         public void actionPerformed(ActionEvent actionEvent)
 527         {
 528           selectRadioAction(actionEvent);
 529         }
 530       });
 531
 532       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 533       hideOption.addActionListener(new ActionListener()
 534       {
 535         @Override
 536         public void actionPerformed(ActionEvent actionEvent)
 537         {
 538           hideRadioAction(actionEvent);
 539         }
 540       });
 541
 542       optionsGroup.add(selectOption);
 543       optionsGroup.add(hideOption);
 544       optionsGroup.setSelected(selectOption.getModel(), true);
 545
 546       JvSwingUtils.jvInitComponent(this);
 547       syncState();
 548
 549       this.add(selectOption);
 550       this.add(hideOption);
 551     }
 552
 553     public void selectRadioAction(ActionEvent actionEvent)
 554     {
 555       aColChooser.setCurrentFutherActionPanel(this);
 556       aColChooser.select_action(actionEvent);
 557     }
 558
 559     public void hideRadioAction(ActionEvent actionEvent)
 560     {
 561       aColChooser.setCurrentFutherActionPanel(this);
 562       aColChooser.hide_action(actionEvent);
 563     }
 564
 565     public void syncState()
 566     {
 567       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 568       {
 569         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 570       }
 571       else
 572       {
 573         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 574       }
 575     }
 576   }
 577
 578   public class StructureFilterPanel extends JPanel
 579   {
 580     private AnnotationColumnChooser aColChooser;
 581
 582     private JCheckBox alphaHelix = new JCheckBox();
 583
 584     private JCheckBox betaStrand = new JCheckBox();
 585
 586     private JCheckBox turn = new JCheckBox();
 587
 588     private JCheckBox all = new JCheckBox();
 589
 590     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 591     {
 592       this.aColChooser = aColChooser;
 593
 594       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 595       alphaHelix.addActionListener(new ActionListener()
 596       {
 597         @Override
 598         public void actionPerformed(ActionEvent actionEvent)
 599         {
 600           alphaHelix_actionPerformed();
 601         }
 602       });
 603
 604       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 605       betaStrand.addActionListener(new ActionListener()
 606       {
 607         @Override
 608         public void actionPerformed(ActionEvent actionEvent)
 609         {
 610           betaStrand_actionPerformed();
 611         }
 612       });
 613
 614       JvSwingUtils.jvInitComponent(turn, "label.turn");
 615       turn.addActionListener(new ActionListener()
 616       {
 617         @Override
 618         public void actionPerformed(ActionEvent actionEvent)
 619         {
 620           turn_actionPerformed();
 621         }
 622       });
 623
 624       JvSwingUtils.jvInitComponent(all, "label.select_all");
 625       all.addActionListener(new ActionListener()
 626       {
 627         @Override
 628         public void actionPerformed(ActionEvent actionEvent)
 629         {
 630           all_actionPerformed();
 631         }
 632       });
 633
 634       this.setBorder(new TitledBorder(MessageManager
 635               .getString("label.structures_filter")));
 636       JvSwingUtils.jvInitComponent(this);
 637
 638       this.add(all);
 639       this.add(alphaHelix);
 640       this.add(betaStrand);
 641       this.add(turn);
 642     }
 643
 644     public void alphaHelix_actionPerformed()
 645     {
 646       updateSelectAllState();
 647       aColChooser.setCurrentStructureFilterPanel(this);
 648       aColChooser.updateView();
 649     }
 650
 651     public void betaStrand_actionPerformed()
 652     {
 653       updateSelectAllState();
 654       aColChooser.setCurrentStructureFilterPanel(this);
 655       aColChooser.updateView();
 656     }
 657
 658     public void turn_actionPerformed()
 659     {
 660       updateSelectAllState();
 661       aColChooser.setCurrentStructureFilterPanel(this);
 662       aColChooser.updateView();
 663     }
 664
 665     public void all_actionPerformed()
 666     {
 667       if (all.isSelected())
 668       {
 669         alphaHelix.setSelected(true);
 670         betaStrand.setSelected(true);
 671         turn.setSelected(true);
 672       }
 673       else
 674       {
 675         alphaHelix.setSelected(false);
 676         betaStrand.setSelected(false);
 677         turn.setSelected(false);
 678       }
 679       aColChooser.setCurrentStructureFilterPanel(this);
 680       aColChooser.updateView();
 681     }
 682
 683     public void updateSelectAllState()
 684     {
 685       if (alphaHelix.isSelected() && betaStrand.isSelected()
 686               && turn.isSelected())
 687       {
 688         all.setSelected(true);
 689       }
 690       else
 691       {
 692         all.setSelected(false);
 693       }
 694     }
 695
 696     public void syncState()
 697     {
 698       StructureFilterPanel sfp = aColChooser
 699               .getCurrentStructureFilterPanel();
 700       if (sfp != null)
 701       {
 702         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 703         betaStrand.setSelected(sfp.betaStrand.isSelected());
 704         turn.setSelected(sfp.turn.isSelected());
 705         if (sfp.all.isSelected())
 706         {
 707           all.setSelected(true);
 708           alphaHelix.setSelected(true);
 709           betaStrand.setSelected(true);
 710           turn.setSelected(true);
 711         }
 712       }
 713
 714     }
 715   }
 716
 717   public class SearchPanel extends JPanel
 718   {
 719     private AnnotationColumnChooser aColChooser;
 720
 721     private JCheckBox displayName = new JCheckBox();
 722
 723     private JCheckBox description = new JCheckBox();
 724
 725     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 726
 727     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<String>(
 728             FILTER_BY_ANN_CACHE_KEY);
 729
 730     public SearchPanel(AnnotationColumnChooser aColChooser)
 731     {
 732
 733       this.aColChooser = aColChooser;
 734       JvSwingUtils.jvInitComponent(this);
 735       this.setBorder(new TitledBorder(MessageManager
 736               .getString("label.search_filter")));
 737
 738       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
 739       searchBox.setToolTipText(MessageManager
 740               .getString("info.enter_search_text_here"));
 741       searchBox.getEditor().getEditorComponent()
 742               .addKeyListener(new java.awt.event.KeyAdapter()
 743               {
 744                 @Override
 745                 public void keyPressed(KeyEvent e)
 746                 {
 747                   if (e.getKeyCode() == KeyEvent.VK_ENTER)
 748                   {
 749                     e.consume();
 750                     searchStringAction();
 751                   }
 752                 }
 753               });
 754
 755
 756
 757       JvSwingUtils.jvInitComponent(displayName, "label.label");
 758       displayName.addActionListener(new ActionListener()
 759       {
 760         @Override
 761         public void actionPerformed(ActionEvent actionEvent)
 762         {
 763           displayNameCheckboxAction();
 764         }
 765       });
 766
 767       JvSwingUtils.jvInitComponent(description, "label.description");
 768       description.addActionListener(new ActionListener()
 769       {
 770         @Override
 771         public void actionPerformed(ActionEvent actionEvent)
 772         {
 773           discriptionCheckboxAction();
 774         }
 775       });
 776
 777       syncState();
 778       this.add(searchBox);
 779       this.add(displayName);
 780       this.add(description);
 781     }
 782
 783     public void displayNameCheckboxAction()
 784     {
 785       aColChooser.setCurrentSearchPanel(this);
 786       aColChooser.updateView();
 787     }
 788
 789     public void discriptionCheckboxAction()
 790     {
 791       aColChooser.setCurrentSearchPanel(this);
 792       aColChooser.updateView();
 793     }
 794
 795     public void searchStringAction()
 796     {
 797       aColChooser.setCurrentSearchPanel(this);
 798       aColChooser.updateView();
 799       updateSearchPanelToolTips();
 800       searchBox.updateCache();
 801     }
 802
 803     public void syncState()
 804     {
 805       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 806       if (sp != null)
 807       {
 808         description.setEnabled(sp.description.isEnabled());
 809         description.setSelected(sp.description.isSelected());
 810
 811         displayName.setEnabled(sp.displayName.isEnabled());
 812         displayName.setSelected(sp.displayName.isSelected());
 813
 814         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 815       }
 816       updateSearchPanelToolTips();
 817     }
 818
 819     public void updateSearchPanelToolTips()
 820     {
 821       String defaultTtip = MessageManager
 822               .getString("info.enter_search_text_to_enable");
 823       String labelTtip = MessageManager.formatMessage(
 824               "info.search_in_annotation_label", annotations
 825                       .getSelectedItem().toString());
 826       String descTtip = MessageManager.formatMessage(
 827               "info.search_in_annotation_description", annotations
 828                       .getSelectedItem().toString());
 829       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 830               : defaultTtip);
 831       description.setToolTipText(description.isEnabled() ? descTtip
 832               : defaultTtip);
 833     }
 834   }
 835
 836   @Override
 837   public void ok_actionPerformed()
 838   {
 839     saveCache();
 840     super.ok_actionPerformed();
 841   }
 842
 843   @Override
 844   public void cancel_actionPerformed()
 845   {
 846     saveCache();
 847     super.cancel_actionPerformed();
 848   }
 849
 850   private void saveCache()
 851   {
 852     gSearchPanel.searchBox.persistCache();
 853     ngSearchPanel.searchBox.persistCache();
 854     gSearchPanel.searchBox.updateCache();
 855     ngSearchPanel.searchBox.updateCache();
 856   }
 857 }