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