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.util.Platform;
  29 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.CardLayout;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.awt.event.FocusAdapter;
  38 import java.awt.event.FocusEvent;
  39 import java.awt.event.ItemEvent;
  40 import java.awt.event.ItemListener;
  41 import java.awt.event.KeyEvent;
  42
  43 import javax.swing.ButtonGroup;
  44 import javax.swing.JCheckBox;
  45 import javax.swing.JComboBox;
  46 import javax.swing.JInternalFrame;
  47 import javax.swing.JLayeredPane;
  48 import javax.swing.JPanel;
  49 import javax.swing.JRadioButton;
  50 import javax.swing.border.TitledBorder;
  51
  52 import net.miginfocom.swing.MigLayout;
  53
  54 @SuppressWarnings("serial")
  55 public class AnnotationColumnChooser extends AnnotationRowFilter
  56         implements ItemListener
  57 {
  58   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  59
  60   private JPanel annotationComboBoxPanel = new JPanel();
  61
  62   private StructureFilterPanel gStructureFilterPanel;
  63
  64   private StructureFilterPanel ngStructureFilterPanel;
  65
  66   private StructureFilterPanel currentStructureFilterPanel;
  67
  68   private SearchPanel currentSearchPanel;
  69
  70   private SearchPanel gSearchPanel;
  71
  72   private SearchPanel ngSearchPanel;
  73
  74   private FurtherActionPanel currentFurtherActionPanel;
  75
  76   private FurtherActionPanel gFurtherActionPanel;
  77
  78   private FurtherActionPanel ngFurtherActionPanel;
  79
  80   public static final int ACTION_OPTION_SELECT = 1;
  81
  82   public static int ACTION_OPTION_HIDE = 2;
  83
  84   public static String NO_GRAPH_VIEW = "0";
  85
  86   public static String GRAPH_VIEW = "1";
  87
  88   private int actionOption = ACTION_OPTION_SELECT;
  89
  90   private HiddenColumns oldHiddenColumns;
  91
  92   protected static int MIN_WIDTH = (Platform.isJS() ? 370 : 420);
  93   protected static int MIN_HEIGHT = (Platform.isJS() ? 370 : 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"), 0,
 103             0);
 104     // BH note: MIGLayout ignores this completely,
 105     // possibly creating a frame smaller than specified:
 106     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 107
 108     addSliderChangeListener();
 109     addSliderMouseListeners();
 110
 111     if (av.getAlignment().getAlignmentAnnotation() == null)
 112     {
 113       return;
 114     }
 115     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 116     adjusting = true;
 117
 118     setAnnotations(new JComboBox<>(getAnnotationItems(false)));
 119     populateThresholdComboBox(threshold);
 120     AnnotationColumnChooser lastChooser = av
 121             .getAnnotationColumnSelectionState();
 122     // restore Object state from the previous session if one exists
 123     if (lastChooser != null)
 124     {
 125       currentSearchPanel = lastChooser.getCurrentSearchPanel();
 126       currentStructureFilterPanel = lastChooser
 127               .getCurrentStructureFilterPanel();
 128       annotations.setSelectedIndex(
 129               lastChooser.getAnnotations().getSelectedIndex());
 130       threshold.setSelectedIndex(
 131               lastChooser.getThreshold().getSelectedIndex());
 132       actionOption = lastChooser.getActionOption();
 133       percentThreshold
 134               .setSelected(lastChooser.percentThreshold.isSelected());
 135     }
 136
 137     try
 138     {
 139       jbInit();
 140     } catch (Exception ex)
 141     {
 142     }
 143     adjusting = false;
 144
 145     updateView();
 146     frame.invalidate();
 147     frame.pack();
 148   }
 149
 150   @Override
 151   protected void jbInit()
 152   {
 153     super.jbInit();
 154
 155     JPanel thresholdPanel = new JPanel();
 156     thresholdPanel.setBorder(new TitledBorder(
 157             MessageManager.getString("label.threshold_filter")));
 158     thresholdPanel.setBackground(Color.white);
 159     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 160     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]") );
 161
 162     percentThreshold.setBackground(Color.white);
 163     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 164
 165     JPanel actionPanel = new JPanel();
 166     actionPanel.setBackground(Color.white);
 167     actionPanel.setFont(JvSwingUtils.getLabelFont());
 168
 169     JPanel graphFilterView = new JPanel();
 170     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 171     graphFilterView.setBackground(Color.white);
 172
 173     JPanel noGraphFilterView = new JPanel();
 174     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 175     noGraphFilterView.setBackground(Color.white);
 176
 177     annotationComboBoxPanel.setBackground(Color.white);
 178     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 179
 180     gSearchPanel = new SearchPanel(this);
 181     ngSearchPanel = new SearchPanel(this);
 182     gFurtherActionPanel = new FurtherActionPanel(this);
 183     ngFurtherActionPanel = new FurtherActionPanel(this);
 184     gStructureFilterPanel = new StructureFilterPanel(this);
 185     ngStructureFilterPanel = new StructureFilterPanel(this);
 186
 187     thresholdPanel.add(getThreshold());
 188     thresholdPanel.add(percentThreshold, "wrap");
 189     thresholdPanel.add(slider, "grow");
 190     thresholdPanel.add(thresholdValue, "span, wrap");
 191
 192     actionPanel.add(ok);
 193     actionPanel.add(cancel);
 194
 195     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 196     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 197     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 198     graphFilterView.add(gFurtherActionPanel);
 199
 200     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 201     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 202     noGraphFilterView.add(ngFurtherActionPanel);
 203
 204     annotationComboBoxPanel.add(getAnnotations());
 205     switchableViewsPanel.add(noGraphFilterView,
 206             AnnotationColumnChooser.NO_GRAPH_VIEW);
 207     switchableViewsPanel.add(graphFilterView,
 208             AnnotationColumnChooser.GRAPH_VIEW);
 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.getAnnotationColumnSelectionState()
 245                 .getOldHiddenColumns();
 246         av.getAlignment().setHiddenColumns(oldHidden);
 247       }
 248       av.sendSelection();
 249       ap.paintAlignment(true, true);
 250     }
 251   }
 252
 253   @Override
 254   public void valueChanged(boolean updateAllAnnotation)
 255   {
 256     if (slider.isEnabled())
 257     {
 258       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 259       updateView();
 260       propagateSeqAssociatedThreshold(updateAllAnnotation,
 261               getCurrentAnnotation());
 262       ap.paintAlignment(false, false);
 263     }
 264   }
 265
 266   @Override
 267   public void updateView()
 268   {
 269     // Check if combobox is still adjusting
 270     if (adjusting)
 271     {
 272       return;
 273     }
 274
 275     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 276
 277     setCurrentAnnotation(av.getAlignment()
 278             .getAlignmentAnnotation()[annmap[getAnnotations()
 279                     .getSelectedIndex()]]);
 280
 281     int selectedThresholdItem = getSelectedThresholdItem(
 282             getThreshold().getSelectedIndex());
 283
 284     slider.setEnabled(true);
 285     thresholdValue.setEnabled(true);
 286     percentThreshold.setEnabled(true);
 287
 288     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 289     {
 290       slider.setEnabled(false);
 291       thresholdValue.setEnabled(false);
 292       thresholdValue.setText("");
 293       percentThreshold.setEnabled(false);
 294       // build filter params
 295     }
 296     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 297     {
 298       if (getCurrentAnnotation().threshold == null)
 299       {
 300         getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
 301                 (getCurrentAnnotation().graphMax
 302                         - getCurrentAnnotation().graphMin) / 2f,
 303                 "Threshold", Color.black));
 304       }
 305
 306       adjusting = true;
 307       float range = getCurrentAnnotation().graphMax * 1000
 308               - getCurrentAnnotation().graphMin * 1000;
 309
 310       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 311       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 312       slider.setValue(
 313               (int) (getCurrentAnnotation().threshold.value * 1000));
 314
 315       setThresholdValueText();
 316
 317       slider.setMajorTickSpacing((int) (range / 10f));
 318       slider.setEnabled(true);
 319       thresholdValue.setEnabled(true);
 320       adjusting = false;
 321
 322       // build filter params
 323       filterParams.setThresholdType(
 324               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 325       if (getCurrentAnnotation().isQuantitative())
 326       {
 327         filterParams
 328                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 329
 330         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 331         {
 332           filterParams.setThresholdType(
 333                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 334         }
 335         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 336         {
 337           filterParams.setThresholdType(
 338                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 339         }
 340       }
 341     }
 342
 343     updateThresholdPanelToolTip();
 344     if (currentStructureFilterPanel != null)
 345     {
 346       if (currentStructureFilterPanel.alphaHelix.isSelected())
 347       {
 348         filterParams.setFilterAlphaHelix(true);
 349       }
 350       if (currentStructureFilterPanel.betaStrand.isSelected())
 351       {
 352         filterParams.setFilterBetaSheet(true);
 353       }
 354       if (currentStructureFilterPanel.turn.isSelected())
 355       {
 356         filterParams.setFilterTurn(true);
 357       }
 358     }
 359
 360     if (currentSearchPanel != null)
 361     {
 362       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
 363       {
 364         filterParams.setRegexString(
 365                 currentSearchPanel.searchBox.getUserInput());
 366         if (currentSearchPanel.displayName.isSelected())
 367         {
 368           filterParams.addRegexSearchField(
 369                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 370         }
 371         if (currentSearchPanel.description.isSelected())
 372         {
 373           filterParams.addRegexSearchField(
 374                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 375         }
 376       }
 377     }
 378
 379     // show hidden columns here, before changing the column selection in
 380     // filterAnnotations, because showing hidden columns has the side effect of
 381     // adding them to the selection
 382     av.showAllHiddenColumns();
 383     av.getColumnSelection().filterAnnotations(
 384             getCurrentAnnotation().annotations, filterParams);
 385
 386     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
 387     if (hideCols)
 388     {
 389       av.hideSelectedColumns();
 390     }
 391     av.sendSelection();
 392
 393     filterParams = null;
 394     av.setAnnotationColumnSelectionState(this);
 395     // only update overview and structures if columns were hidden
 396     ap.paintAlignment(hideCols, hideCols);
 397   }
 398
 399   public HiddenColumns getOldHiddenColumns()
 400   {
 401     return oldHiddenColumns;
 402   }
 403
 404   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 405   {
 406     if (currentHiddenColumns != null)
 407     {
 408       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 409     }
 410   }
 411
 412   public FurtherActionPanel getCurrentFutherActionPanel()
 413   {
 414     return currentFurtherActionPanel;
 415   }
 416
 417   public void setCurrentFutherActionPanel(
 418           FurtherActionPanel currentFutherActionPanel)
 419   {
 420     this.currentFurtherActionPanel = currentFutherActionPanel;
 421   }
 422
 423   public SearchPanel getCurrentSearchPanel()
 424   {
 425     return currentSearchPanel;
 426   }
 427
 428   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 429   {
 430     this.currentSearchPanel = currentSearchPanel;
 431   }
 432
 433   public int getActionOption()
 434   {
 435     return actionOption;
 436   }
 437
 438   public void setActionOption(int actionOption)
 439   {
 440     this.actionOption = actionOption;
 441   }
 442
 443   public StructureFilterPanel getCurrentStructureFilterPanel()
 444   {
 445     return currentStructureFilterPanel;
 446   }
 447
 448   public void setCurrentStructureFilterPanel(
 449           StructureFilterPanel currentStructureFilterPanel)
 450   {
 451     this.currentStructureFilterPanel = currentStructureFilterPanel;
 452   }
 453
 454   public void select_action(ActionEvent actionEvent)
 455   {
 456     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 457     if (radioButton.isSelected())
 458     {
 459       setActionOption(ACTION_OPTION_SELECT);
 460       updateView();
 461     }
 462   }
 463
 464   public void hide_action(ActionEvent actionEvent)
 465   {
 466     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 467     if (radioButton.isSelected())
 468     {
 469       setActionOption(ACTION_OPTION_HIDE);
 470       updateView();
 471     }
 472   }
 473
 474   @Override
 475   public void itemStateChanged(ItemEvent e)
 476   {
 477     selectedAnnotationChanged();
 478   }
 479
 480   @Override
 481   public void selectedAnnotationChanged()
 482   {
 483     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 484     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 485             .getSelectedIndex()]].isQuantitative())
 486     {
 487       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 488     }
 489     saveCache();
 490     gSearchPanel.syncState();
 491     gFurtherActionPanel.syncState();
 492     gStructureFilterPanel.syncState();
 493
 494     ngSearchPanel.syncState();
 495     ngFurtherActionPanel.syncState();
 496     ngStructureFilterPanel.syncState();
 497
 498     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 499             .getLayout();
 500         switchableViewsLayout.show(switchableViewsPanel, currentView);
 501     updateView();
 502   }
 503
 504   public class FurtherActionPanel extends JPanel
 505   {
 506     private AnnotationColumnChooser aColChooser;
 507
 508     private JRadioButton hideOption = new JRadioButton();
 509
 510     private JRadioButton selectOption = new JRadioButton();
 511
 512     private ButtonGroup optionsGroup = new ButtonGroup();
 513
 514     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 515     {
 516       this.aColChooser = aColChooser;
 517       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 518       selectOption.addActionListener(new ActionListener()
 519       {
 520         @Override
 521         public void actionPerformed(ActionEvent actionEvent)
 522         {
 523           selectRadioAction(actionEvent);
 524         }
 525       });
 526
 527       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 528       hideOption.addActionListener(new ActionListener()
 529       {
 530         @Override
 531         public void actionPerformed(ActionEvent actionEvent)
 532         {
 533           hideRadioAction(actionEvent);
 534         }
 535       });
 536
 537       optionsGroup.add(selectOption);
 538       optionsGroup.add(hideOption);
 539       optionsGroup.setSelected(selectOption.getModel(), true);
 540
 541       JvSwingUtils.jvInitComponent(this);
 542       syncState();
 543
 544       this.add(selectOption);
 545       this.add(hideOption);
 546     }
 547
 548     public void selectRadioAction(ActionEvent actionEvent)
 549     {
 550       aColChooser.setCurrentFutherActionPanel(this);
 551       aColChooser.select_action(actionEvent);
 552     }
 553
 554     public void hideRadioAction(ActionEvent actionEvent)
 555     {
 556       aColChooser.setCurrentFutherActionPanel(this);
 557       aColChooser.hide_action(actionEvent);
 558     }
 559
 560     public void syncState()
 561     {
 562       if (aColChooser
 563               .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 564       {
 565         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 566       }
 567       else
 568       {
 569         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 570       }
 571     }
 572   }
 573
 574   public class StructureFilterPanel extends JPanel
 575   {
 576     private AnnotationColumnChooser aColChooser;
 577
 578     private JCheckBox alphaHelix = new JCheckBox();
 579
 580     private JCheckBox betaStrand = new JCheckBox();
 581
 582     private JCheckBox turn = new JCheckBox();
 583
 584     private JCheckBox all = new JCheckBox();
 585
 586     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 587     {
 588       this.aColChooser = aColChooser;
 589
 590       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 591       alphaHelix.addActionListener(new ActionListener()
 592       {
 593         @Override
 594         public void actionPerformed(ActionEvent actionEvent)
 595         {
 596           alphaHelix_actionPerformed();
 597         }
 598       });
 599
 600       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 601       betaStrand.addActionListener(new ActionListener()
 602       {
 603         @Override
 604         public void actionPerformed(ActionEvent actionEvent)
 605         {
 606           betaStrand_actionPerformed();
 607         }
 608       });
 609
 610       JvSwingUtils.jvInitComponent(turn, "label.turn");
 611       turn.addActionListener(new ActionListener()
 612       {
 613         @Override
 614         public void actionPerformed(ActionEvent actionEvent)
 615         {
 616           turn_actionPerformed();
 617         }
 618       });
 619
 620       JvSwingUtils.jvInitComponent(all, "label.select_all");
 621       all.addActionListener(new ActionListener()
 622       {
 623         @Override
 624         public void actionPerformed(ActionEvent actionEvent)
 625         {
 626           all_actionPerformed();
 627         }
 628       });
 629
 630       this.setBorder(new TitledBorder(
 631               MessageManager.getString("label.structures_filter")));
 632       JvSwingUtils.jvInitComponent(this);
 633
 634       this.add(all);
 635       this.add(alphaHelix);
 636       this.add(betaStrand);
 637       this.add(turn);
 638     }
 639
 640     public void alphaHelix_actionPerformed()
 641     {
 642       updateSelectAllState();
 643       aColChooser.setCurrentStructureFilterPanel(this);
 644       aColChooser.updateView();
 645     }
 646
 647     public void betaStrand_actionPerformed()
 648     {
 649       updateSelectAllState();
 650       aColChooser.setCurrentStructureFilterPanel(this);
 651       aColChooser.updateView();
 652     }
 653
 654     public void turn_actionPerformed()
 655     {
 656       updateSelectAllState();
 657       aColChooser.setCurrentStructureFilterPanel(this);
 658       aColChooser.updateView();
 659     }
 660
 661     public void all_actionPerformed()
 662     {
 663       if (all.isSelected())
 664       {
 665         alphaHelix.setSelected(true);
 666         betaStrand.setSelected(true);
 667         turn.setSelected(true);
 668       }
 669       else
 670       {
 671         alphaHelix.setSelected(false);
 672         betaStrand.setSelected(false);
 673         turn.setSelected(false);
 674       }
 675       aColChooser.setCurrentStructureFilterPanel(this);
 676       aColChooser.updateView();
 677     }
 678
 679     public void updateSelectAllState()
 680     {
 681       if (alphaHelix.isSelected() && betaStrand.isSelected()
 682               && turn.isSelected())
 683       {
 684         all.setSelected(true);
 685       }
 686       else
 687       {
 688         all.setSelected(false);
 689       }
 690     }
 691
 692     public void syncState()
 693     {
 694       StructureFilterPanel sfp = aColChooser
 695               .getCurrentStructureFilterPanel();
 696       if (sfp != null)
 697       {
 698         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 699         betaStrand.setSelected(sfp.betaStrand.isSelected());
 700         turn.setSelected(sfp.turn.isSelected());
 701         if (sfp.all.isSelected())
 702         {
 703           all.setSelected(true);
 704           alphaHelix.setSelected(true);
 705           betaStrand.setSelected(true);
 706           turn.setSelected(true);
 707         }
 708       }
 709
 710     }
 711   }
 712
 713   public class SearchPanel extends JPanel
 714   {
 715     private AnnotationColumnChooser aColChooser;
 716
 717     private JCheckBox displayName = new JCheckBox();
 718
 719     private JCheckBox description = new JCheckBox();
 720
 721     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 722
 723     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
 724             FILTER_BY_ANN_CACHE_KEY);
 725
 726     public SearchPanel(AnnotationColumnChooser aColChooser)
 727     {
 728
 729       this.aColChooser = aColChooser;
 730       JvSwingUtils.jvInitComponent(this);
 731       this.setBorder(new TitledBorder(
 732               MessageManager.getString("label.search_filter")));
 733
 734       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
 735       searchBox.getComponent().setToolTipText(
 736               MessageManager.getString("info.enter_search_text_here"));
 737       searchBox.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.addFocusListener(new FocusAdapter()
 750       {
 751         @Override
 752         public void focusLost(FocusEvent e)
 753         {
 754           searchStringAction();
 755         }
 756       });
 757
 758       JvSwingUtils.jvInitComponent(displayName, "label.label");
 759       displayName.addActionListener(new ActionListener()
 760       {
 761         @Override
 762         public void actionPerformed(ActionEvent actionEvent)
 763         {
 764           displayNameCheckboxAction();
 765         }
 766       });
 767
 768       JvSwingUtils.jvInitComponent(description, "label.description");
 769       description.addActionListener(new ActionListener()
 770       {
 771         @Override
 772         public void actionPerformed(ActionEvent actionEvent)
 773         {
 774           descriptionCheckboxAction();
 775         }
 776       });
 777
 778       syncState();
 779       this.add(searchBox.getComponent());
 780       this.add(displayName);
 781       this.add(description);
 782     }
 783
 784     public void displayNameCheckboxAction()
 785     {
 786       aColChooser.setCurrentSearchPanel(this);
 787       aColChooser.updateView();
 788     }
 789
 790     public void descriptionCheckboxAction()
 791     {
 792       aColChooser.setCurrentSearchPanel(this);
 793       aColChooser.updateView();
 794     }
 795
 796     public void searchStringAction()
 797     {
 798       aColChooser.setCurrentSearchPanel(this);
 799       aColChooser.updateView();
 800       updateSearchPanelToolTips();
 801       searchBox.updateCache();
 802     }
 803
 804     public void syncState()
 805     {
 806       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 807       if (sp != null)
 808       {
 809         description.setEnabled(sp.description.isEnabled());
 810         description.setSelected(sp.description.isSelected());
 811
 812         displayName.setEnabled(sp.displayName.isEnabled());
 813         displayName.setSelected(sp.displayName.isSelected());
 814
 815         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 816       }
 817       updateSearchPanelToolTips();
 818     }
 819
 820     public void updateSearchPanelToolTips()
 821     {
 822       String defaultTtip = MessageManager
 823               .getString("info.enter_search_text_to_enable");
 824       String labelTtip = MessageManager.formatMessage(
 825               "info.search_in_annotation_label",
 826               annotations.getSelectedItem().toString());
 827       String descTtip = MessageManager.formatMessage(
 828               "info.search_in_annotation_description",
 829               annotations.getSelectedItem().toString());
 830       displayName.setToolTipText(
 831               displayName.isEnabled() ? labelTtip : defaultTtip);
 832       description.setToolTipText(
 833               description.isEnabled() ? descTtip : defaultTtip);
 834     }
 835   }
 836
 837   @Override
 838   public void ok_actionPerformed()
 839   {
 840     saveCache();
 841     super.ok_actionPerformed();
 842   }
 843
 844   @Override
 845   public void cancel_actionPerformed()
 846   {
 847     saveCache();
 848     super.cancel_actionPerformed();
 849   }
 850
 851   private void saveCache()
 852   {
 853     gSearchPanel.searchBox.persistCache();
 854     ngSearchPanel.searchBox.persistCache();
 855     gSearchPanel.searchBox.updateCache();
 856     ngSearchPanel.searchBox.updateCache();
 857   }
 858 }