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.FocusAdapter;
  37 import java.awt.event.FocusEvent;
  38 import java.awt.event.ItemEvent;
  39 import java.awt.event.ItemListener;
  40 import java.awt.event.KeyEvent;
  41
  42 import javax.swing.ButtonGroup;
  43 import javax.swing.JCheckBox;
  44 import javax.swing.JComboBox;
  45 import javax.swing.JInternalFrame;
  46 import javax.swing.JLayeredPane;
  47 import javax.swing.JPanel;
  48 import javax.swing.JRadioButton;
  49 import javax.swing.border.TitledBorder;
  50
  51 import net.miginfocom.swing.MigLayout;
  52
  53 @SuppressWarnings("serial")
  54 public class AnnotationColumnChooser extends AnnotationRowFilter
  55         implements ItemListener
  56 {
  57   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  58
  59   private JPanel annotationComboBoxPanel = new JPanel();
  60
  61   private StructureFilterPanel gStructureFilterPanel;
  62
  63   private StructureFilterPanel ngStructureFilterPanel;
  64
  65   private StructureFilterPanel currentStructureFilterPanel;
  66
  67   private SearchPanel currentSearchPanel;
  68
  69   private SearchPanel gSearchPanel;
  70
  71   private SearchPanel ngSearchPanel;
  72
  73   private FurtherActionPanel currentFurtherActionPanel;
  74
  75   private FurtherActionPanel gFurtherActionPanel;
  76
  77   private FurtherActionPanel ngFurtherActionPanel;
  78
  79   public static final int ACTION_OPTION_SELECT = 1;
  80
  81   public static int ACTION_OPTION_HIDE = 2;
  82
  83   public static String NO_GRAPH_VIEW = "0";
  84
  85   public static String GRAPH_VIEW = "1";
  86
  87   private int actionOption = ACTION_OPTION_SELECT;
  88
  89   private HiddenColumns oldHiddenColumns;
  90
  91   protected int MIN_WIDTH = 420;
  92
  93   protected int MIN_HEIGHT = 430;
  94
  95   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  96   {
  97     super(av, ap);
  98     frame = new JInternalFrame();
  99     frame.setContentPane(this);
 100     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 101     Desktop.addInternalFrame(frame,
 102             MessageManager.getString("label.select_by_annotation"), 520,
 103             215);
 104     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 105
 106     addSliderChangeListener();
 107     addSliderMouseListeners();
 108
 109     if (av.getAlignment().getAlignmentAnnotation() == null)
 110     {
 111       return;
 112     }
 113     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 114     adjusting = true;
 115
 116     setAnnotations(new JComboBox<>(getAnnotationItems(false)));
 117     populateThresholdComboBox(threshold);
 118     AnnotationColumnChooser lastChooser = av
 119             .getAnnotationColumnSelectionState();
 120     // restore Object state from the previous session if one exists
 121     if (lastChooser != null)
 122     {
 123       currentSearchPanel = lastChooser.getCurrentSearchPanel();
 124       currentStructureFilterPanel = lastChooser
 125               .getCurrentStructureFilterPanel();
 126       annotations.setSelectedIndex(
 127               lastChooser.getAnnotations().getSelectedIndex());
 128       threshold.setSelectedIndex(
 129               lastChooser.getThreshold().getSelectedIndex());
 130       actionOption = lastChooser.getActionOption();
 131       percentThreshold
 132               .setSelected(lastChooser.percentThreshold.isSelected());
 133     }
 134
 135     try
 136     {
 137       jbInit();
 138     } catch (Exception ex)
 139     {
 140     }
 141     adjusting = false;
 142
 143     updateView();
 144     frame.invalidate();
 145     frame.pack();
 146   }
 147
 148   @Override
 149   protected void jbInit()
 150   {
 151     super.jbInit();
 152
 153     JPanel thresholdPanel = new JPanel();
 154     thresholdPanel.setBorder(new TitledBorder(
 155             MessageManager.getString("label.threshold_filter")));
 156     thresholdPanel.setBackground(Color.white);
 157     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 158     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 159
 160     percentThreshold.setBackground(Color.white);
 161     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 162
 163     JPanel actionPanel = new JPanel();
 164     actionPanel.setBackground(Color.white);
 165     actionPanel.setFont(JvSwingUtils.getLabelFont());
 166
 167     JPanel graphFilterView = new JPanel();
 168     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 169     graphFilterView.setBackground(Color.white);
 170
 171     JPanel noGraphFilterView = new JPanel();
 172     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 173     noGraphFilterView.setBackground(Color.white);
 174
 175     annotationComboBoxPanel.setBackground(Color.white);
 176     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 177
 178     gSearchPanel = new SearchPanel(this);
 179     ngSearchPanel = new SearchPanel(this);
 180     gFurtherActionPanel = new FurtherActionPanel(this);
 181     ngFurtherActionPanel = new FurtherActionPanel(this);
 182     gStructureFilterPanel = new StructureFilterPanel(this);
 183     ngStructureFilterPanel = new StructureFilterPanel(this);
 184
 185     thresholdPanel.add(getThreshold());
 186     thresholdPanel.add(percentThreshold, "wrap");
 187     thresholdPanel.add(slider, "grow");
 188     thresholdPanel.add(thresholdValue, "span, wrap");
 189
 190     actionPanel.add(ok);
 191     actionPanel.add(cancel);
 192
 193     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 194     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 195     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 196     graphFilterView.add(gFurtherActionPanel);
 197
 198     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 199     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 200     noGraphFilterView.add(ngFurtherActionPanel);
 201
 202     annotationComboBoxPanel.add(getAnnotations());
 203     switchableViewsPanel.add(noGraphFilterView,
 204             AnnotationColumnChooser.NO_GRAPH_VIEW);
 205     switchableViewsPanel.add(graphFilterView,
 206             AnnotationColumnChooser.GRAPH_VIEW);
 207
 208     this.setLayout(new BorderLayout());
 209     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 210     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 211     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 212
 213     selectedAnnotationChanged();
 214     updateThresholdPanelToolTip();
 215     this.validate();
 216   }
 217
 218   protected void updateThresholdPanelToolTip()
 219   {
 220     thresholdValue.setToolTipText("");
 221     slider.setToolTipText("");
 222
 223     String defaultTtip = MessageManager
 224             .getString("info.change_threshold_mode_to_enable");
 225
 226     String thresh = getThreshold().getSelectedItem().toString();
 227     if (thresh.equalsIgnoreCase("No Threshold"))
 228     {
 229       thresholdValue.setToolTipText(defaultTtip);
 230       slider.setToolTipText(defaultTtip);
 231     }
 232   }
 233
 234   @Override
 235   protected void reset()
 236   {
 237     if (this.getOldHiddenColumns() != null)
 238     {
 239       av.getColumnSelection().clear();
 240
 241       if (av.getAnnotationColumnSelectionState() != null)
 242       {
 243         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
 244                 .getOldHiddenColumns();
 245         av.getAlignment().setHiddenColumns(oldHidden);
 246       }
 247       av.sendSelection();
 248       ap.paintAlignment(true, true);
 249     }
 250   }
 251
 252   @Override
 253   public void valueChanged(boolean updateAllAnnotation)
 254   {
 255     if (slider.isEnabled())
 256     {
 257       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 258       updateView();
 259       propagateSeqAssociatedThreshold(updateAllAnnotation,
 260               getCurrentAnnotation());
 261       ap.paintAlignment(false, false);
 262     }
 263   }
 264
 265   @Override
 266   public void updateView()
 267   {
 268     // Check if combobox is still adjusting
 269     if (adjusting)
 270     {
 271       return;
 272     }
 273
 274     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 275
 276     setCurrentAnnotation(av.getAlignment()
 277             .getAlignmentAnnotation()[annmap[getAnnotations()
 278                     .getSelectedIndex()]]);
 279
 280     int selectedThresholdItem = getSelectedThresholdItem(
 281             getThreshold().getSelectedIndex());
 282
 283     slider.setEnabled(true);
 284     thresholdValue.setEnabled(true);
 285     percentThreshold.setEnabled(true);
 286
 287     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 288     {
 289       slider.setEnabled(false);
 290       thresholdValue.setEnabled(false);
 291       thresholdValue.setText("");
 292       percentThreshold.setEnabled(false);
 293       // build filter params
 294     }
 295     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 296     {
 297       if (getCurrentAnnotation().threshold == null)
 298       {
 299         getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
 300                 (getCurrentAnnotation().graphMax
 301                         - getCurrentAnnotation().graphMin) / 2f,
 302                 "Threshold", Color.black));
 303       }
 304
 305       adjusting = true;
 306       float range = getCurrentAnnotation().graphMax * 1000
 307               - getCurrentAnnotation().graphMin * 1000;
 308
 309       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 310       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 311       slider.setValue(
 312               (int) (getCurrentAnnotation().threshold.value * 1000));
 313
 314       setThresholdValueText();
 315
 316       slider.setMajorTickSpacing((int) (range / 10f));
 317       slider.setEnabled(true);
 318       thresholdValue.setEnabled(true);
 319       adjusting = false;
 320
 321       // build filter params
 322       filterParams.setThresholdType(
 323               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 324       if (getCurrentAnnotation().isQuantitative())
 325       {
 326         filterParams
 327                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 328
 329         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 330         {
 331           filterParams.setThresholdType(
 332                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 333         }
 334         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 335         {
 336           filterParams.setThresholdType(
 337                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 338         }
 339       }
 340     }
 341
 342     updateThresholdPanelToolTip();
 343     if (currentStructureFilterPanel != null)
 344     {
 345       if (currentStructureFilterPanel.alphaHelix.isSelected())
 346       {
 347         filterParams.setFilterAlphaHelix(true);
 348       }
 349       if (currentStructureFilterPanel.betaStrand.isSelected())
 350       {
 351         filterParams.setFilterBetaSheet(true);
 352       }
 353       if (currentStructureFilterPanel.turn.isSelected())
 354       {
 355         filterParams.setFilterTurn(true);
 356       }
 357     }
 358
 359     if (currentSearchPanel != null)
 360     {
 361       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
 362       {
 363         filterParams.setRegexString(
 364                 currentSearchPanel.searchBox.getUserInput());
 365         if (currentSearchPanel.displayName.isSelected())
 366         {
 367           filterParams.addRegexSearchField(
 368                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 369         }
 370         if (currentSearchPanel.description.isSelected())
 371         {
 372           filterParams.addRegexSearchField(
 373                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 374         }
 375       }
 376     }
 377
 378     // show hidden columns here, before changing the column selection in
 379     // filterAnnotations, because showing hidden columns has the side effect of
 380     // adding them to the selection
 381     av.showAllHiddenColumns();
 382     av.getColumnSelection().filterAnnotations(
 383             getCurrentAnnotation().annotations, filterParams);
 384
 385     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
 386     if (hideCols)
 387     {
 388       av.hideSelectedColumns();
 389     }
 390     av.sendSelection();
 391
 392     filterParams = null;
 393     av.setAnnotationColumnSelectionState(this);
 394     // only update overview and structures if columns were hidden
 395     ap.paintAlignment(hideCols, hideCols);
 396   }
 397
 398   public HiddenColumns getOldHiddenColumns()
 399   {
 400     return oldHiddenColumns;
 401   }
 402
 403   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 404   {
 405     if (currentHiddenColumns != null)
 406     {
 407       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 408     }
 409   }
 410
 411   public FurtherActionPanel getCurrentFutherActionPanel()
 412   {
 413     return currentFurtherActionPanel;
 414   }
 415
 416   public void setCurrentFutherActionPanel(
 417           FurtherActionPanel currentFutherActionPanel)
 418   {
 419     this.currentFurtherActionPanel = currentFutherActionPanel;
 420   }
 421
 422   public SearchPanel getCurrentSearchPanel()
 423   {
 424     return currentSearchPanel;
 425   }
 426
 427   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 428   {
 429     this.currentSearchPanel = currentSearchPanel;
 430   }
 431
 432   public int getActionOption()
 433   {
 434     return actionOption;
 435   }
 436
 437   public void setActionOption(int actionOption)
 438   {
 439     this.actionOption = actionOption;
 440   }
 441
 442   public StructureFilterPanel getCurrentStructureFilterPanel()
 443   {
 444     return currentStructureFilterPanel;
 445   }
 446
 447   public void setCurrentStructureFilterPanel(
 448           StructureFilterPanel currentStructureFilterPanel)
 449   {
 450     this.currentStructureFilterPanel = currentStructureFilterPanel;
 451   }
 452
 453   public void select_action(ActionEvent actionEvent)
 454   {
 455     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 456     if (radioButton.isSelected())
 457     {
 458       setActionOption(ACTION_OPTION_SELECT);
 459       updateView();
 460     }
 461   }
 462
 463   public void hide_action(ActionEvent actionEvent)
 464   {
 465     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 466     if (radioButton.isSelected())
 467     {
 468       setActionOption(ACTION_OPTION_HIDE);
 469       updateView();
 470     }
 471   }
 472
 473   @Override
 474   public void itemStateChanged(ItemEvent e)
 475   {
 476     selectedAnnotationChanged();
 477   }
 478
 479   @Override
 480   public void selectedAnnotationChanged()
 481   {
 482     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 483     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 484             .getSelectedIndex()]].isQuantitative())
 485     {
 486       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 487     }
 488     saveCache();
 489     gSearchPanel.syncState();
 490     gFurtherActionPanel.syncState();
 491     gStructureFilterPanel.syncState();
 492
 493     ngSearchPanel.syncState();
 494     ngFurtherActionPanel.syncState();
 495     ngStructureFilterPanel.syncState();
 496
 497     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 498             .getLayout();
 499     switchableViewsLayout.show(switchableViewsPanel, currentView);
 500     updateView();
 501   }
 502
 503   public class FurtherActionPanel extends JPanel
 504   {
 505     private AnnotationColumnChooser aColChooser;
 506
 507     private JRadioButton hideOption = new JRadioButton();
 508
 509     private JRadioButton selectOption = new JRadioButton();
 510
 511     private ButtonGroup optionsGroup = new ButtonGroup();
 512
 513     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 514     {
 515       this.aColChooser = aColChooser;
 516       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 517       selectOption.addActionListener(new ActionListener()
 518       {
 519         @Override
 520         public void actionPerformed(ActionEvent actionEvent)
 521         {
 522           selectRadioAction(actionEvent);
 523         }
 524       });
 525
 526       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 527       hideOption.addActionListener(new ActionListener()
 528       {
 529         @Override
 530         public void actionPerformed(ActionEvent actionEvent)
 531         {
 532           hideRadioAction(actionEvent);
 533         }
 534       });
 535
 536       optionsGroup.add(selectOption);
 537       optionsGroup.add(hideOption);
 538       optionsGroup.setSelected(selectOption.getModel(), true);
 539
 540       JvSwingUtils.jvInitComponent(this);
 541       syncState();
 542
 543       this.add(selectOption);
 544       this.add(hideOption);
 545     }
 546
 547     public void selectRadioAction(ActionEvent actionEvent)
 548     {
 549       aColChooser.setCurrentFutherActionPanel(this);
 550       aColChooser.select_action(actionEvent);
 551     }
 552
 553     public void hideRadioAction(ActionEvent actionEvent)
 554     {
 555       aColChooser.setCurrentFutherActionPanel(this);
 556       aColChooser.hide_action(actionEvent);
 557     }
 558
 559     public void syncState()
 560     {
 561       if (aColChooser
 562               .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 563       {
 564         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 565       }
 566       else
 567       {
 568         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 569       }
 570     }
 571   }
 572
 573   public class StructureFilterPanel extends JPanel
 574   {
 575     private AnnotationColumnChooser aColChooser;
 576
 577     private JCheckBox alphaHelix = new JCheckBox();
 578
 579     private JCheckBox betaStrand = new JCheckBox();
 580
 581     private JCheckBox turn = new JCheckBox();
 582
 583     private JCheckBox all = new JCheckBox();
 584
 585     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 586     {
 587       this.aColChooser = aColChooser;
 588
 589       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 590       alphaHelix.addActionListener(new ActionListener()
 591       {
 592         @Override
 593         public void actionPerformed(ActionEvent actionEvent)
 594         {
 595           alphaHelix_actionPerformed();
 596         }
 597       });
 598
 599       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 600       betaStrand.addActionListener(new ActionListener()
 601       {
 602         @Override
 603         public void actionPerformed(ActionEvent actionEvent)
 604         {
 605           betaStrand_actionPerformed();
 606         }
 607       });
 608
 609       JvSwingUtils.jvInitComponent(turn, "label.turn");
 610       turn.addActionListener(new ActionListener()
 611       {
 612         @Override
 613         public void actionPerformed(ActionEvent actionEvent)
 614         {
 615           turn_actionPerformed();
 616         }
 617       });
 618
 619       JvSwingUtils.jvInitComponent(all, "label.select_all");
 620       all.addActionListener(new ActionListener()
 621       {
 622         @Override
 623         public void actionPerformed(ActionEvent actionEvent)
 624         {
 625           all_actionPerformed();
 626         }
 627       });
 628
 629       this.setBorder(new TitledBorder(
 630               MessageManager.getString("label.structures_filter")));
 631       JvSwingUtils.jvInitComponent(this);
 632
 633       this.add(all);
 634       this.add(alphaHelix);
 635       this.add(betaStrand);
 636       this.add(turn);
 637     }
 638
 639     public void alphaHelix_actionPerformed()
 640     {
 641       updateSelectAllState();
 642       aColChooser.setCurrentStructureFilterPanel(this);
 643       aColChooser.updateView();
 644     }
 645
 646     public void betaStrand_actionPerformed()
 647     {
 648       updateSelectAllState();
 649       aColChooser.setCurrentStructureFilterPanel(this);
 650       aColChooser.updateView();
 651     }
 652
 653     public void turn_actionPerformed()
 654     {
 655       updateSelectAllState();
 656       aColChooser.setCurrentStructureFilterPanel(this);
 657       aColChooser.updateView();
 658     }
 659
 660     public void all_actionPerformed()
 661     {
 662       if (all.isSelected())
 663       {
 664         alphaHelix.setSelected(true);
 665         betaStrand.setSelected(true);
 666         turn.setSelected(true);
 667       }
 668       else
 669       {
 670         alphaHelix.setSelected(false);
 671         betaStrand.setSelected(false);
 672         turn.setSelected(false);
 673       }
 674       aColChooser.setCurrentStructureFilterPanel(this);
 675       aColChooser.updateView();
 676     }
 677
 678     public void updateSelectAllState()
 679     {
 680       if (alphaHelix.isSelected() && betaStrand.isSelected()
 681               && turn.isSelected())
 682       {
 683         all.setSelected(true);
 684       }
 685       else
 686       {
 687         all.setSelected(false);
 688       }
 689     }
 690
 691     public void syncState()
 692     {
 693       StructureFilterPanel sfp = aColChooser
 694               .getCurrentStructureFilterPanel();
 695       if (sfp != null)
 696       {
 697         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 698         betaStrand.setSelected(sfp.betaStrand.isSelected());
 699         turn.setSelected(sfp.turn.isSelected());
 700         if (sfp.all.isSelected())
 701         {
 702           all.setSelected(true);
 703           alphaHelix.setSelected(true);
 704           betaStrand.setSelected(true);
 705           turn.setSelected(true);
 706         }
 707       }
 708
 709     }
 710   }
 711
 712   public class SearchPanel extends JPanel
 713   {
 714     private AnnotationColumnChooser aColChooser;
 715
 716     private JCheckBox displayName = new JCheckBox();
 717
 718     private JCheckBox description = new JCheckBox();
 719
 720     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 721
 722     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
 723             FILTER_BY_ANN_CACHE_KEY);
 724
 725     public SearchPanel(AnnotationColumnChooser aColChooser)
 726     {
 727
 728       this.aColChooser = aColChooser;
 729       JvSwingUtils.jvInitComponent(this);
 730       this.setBorder(new TitledBorder(
 731               MessageManager.getString("label.search_filter")));
 732
 733       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
 734       searchBox.setToolTipText(
 735               MessageManager.getString("info.enter_search_text_here"));
 736       searchBox.getEditor().getEditorComponent()
 737               .addKeyListener(new java.awt.event.KeyAdapter()
 738               {
 739                 @Override
 740                 public void keyPressed(KeyEvent e)
 741                 {
 742                   if (e.getKeyCode() == KeyEvent.VK_ENTER)
 743                   {
 744                     e.consume();
 745                     searchStringAction();
 746                   }
 747                 }
 748               });
 749       searchBox.getEditor().getEditorComponent()
 750               .addFocusListener(new FocusAdapter()
 751       {
 752         @Override
 753         public void focusLost(FocusEvent e)
 754         {
 755           searchStringAction();
 756         }
 757       });
 758
 759       JvSwingUtils.jvInitComponent(displayName, "label.label");
 760       displayName.addActionListener(new ActionListener()
 761       {
 762         @Override
 763         public void actionPerformed(ActionEvent actionEvent)
 764         {
 765           displayNameCheckboxAction();
 766         }
 767       });
 768
 769       JvSwingUtils.jvInitComponent(description, "label.description");
 770       description.addActionListener(new ActionListener()
 771       {
 772         @Override
 773         public void actionPerformed(ActionEvent actionEvent)
 774         {
 775           descriptionCheckboxAction();
 776         }
 777       });
 778
 779       syncState();
 780       this.add(searchBox);
 781       this.add(displayName);
 782       this.add(description);
 783     }
 784
 785     public void displayNameCheckboxAction()
 786     {
 787       aColChooser.setCurrentSearchPanel(this);
 788       aColChooser.updateView();
 789     }
 790
 791     public void descriptionCheckboxAction()
 792     {
 793       aColChooser.setCurrentSearchPanel(this);
 794       aColChooser.updateView();
 795     }
 796
 797     public void searchStringAction()
 798     {
 799       aColChooser.setCurrentSearchPanel(this);
 800       aColChooser.updateView();
 801       updateSearchPanelToolTips();
 802       searchBox.updateCache();
 803     }
 804
 805     public void syncState()
 806     {
 807       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 808       if (sp != null)
 809       {
 810         description.setEnabled(sp.description.isEnabled());
 811         description.setSelected(sp.description.isSelected());
 812
 813         displayName.setEnabled(sp.displayName.isEnabled());
 814         displayName.setSelected(sp.displayName.isSelected());
 815
 816         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 817       }
 818       updateSearchPanelToolTips();
 819     }
 820
 821     public void updateSearchPanelToolTips()
 822     {
 823       String defaultTtip = MessageManager
 824               .getString("info.enter_search_text_to_enable");
 825       String labelTtip = MessageManager.formatMessage(
 826               "info.search_in_annotation_label",
 827               annotations.getSelectedItem().toString());
 828       String descTtip = MessageManager.formatMessage(
 829               "info.search_in_annotation_description",
 830               annotations.getSelectedItem().toString());
 831       displayName.setToolTipText(
 832               displayName.isEnabled() ? labelTtip : defaultTtip);
 833       description.setToolTipText(
 834               description.isEnabled() ? descTtip : defaultTtip);
 835     }
 836   }
 837
 838   @Override
 839   public void ok_actionPerformed()
 840   {
 841     saveCache();
 842     super.ok_actionPerformed();
 843   }
 844
 845   @Override
 846   public void cancel_actionPerformed()
 847   {
 848     saveCache();
 849     super.cancel_actionPerformed();
 850   }
 851
 852   private void saveCache()
 853   {
 854     gSearchPanel.searchBox.persistCache();
 855     ngSearchPanel.searchBox.persistCache();
 856     gSearchPanel.searchBox.updateCache();
 857     ngSearchPanel.searchBox.updateCache();
 858   }
 859 }