src/jalview/gui/AnnotationColumnChooser.java

   1 package jalview.gui;
   2
   3 import jalview.datamodel.AlignmentAnnotation;
   4 import jalview.datamodel.ColumnSelection;
   5 import jalview.schemes.AnnotationColourGradient;
   6 import jalview.util.MessageManager;
   7 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
   8
   9 import java.awt.BorderLayout;
  10 import java.awt.CardLayout;
  11 import java.awt.Color;
  12 import java.awt.Dimension;
  13 import java.awt.event.ActionEvent;
  14 import java.awt.event.ActionListener;
  15 import java.awt.event.ItemEvent;
  16 import java.awt.event.ItemListener;
  17 import java.util.Iterator;
  18
  19 import javax.swing.ButtonGroup;
  20 import javax.swing.JCheckBox;
  21 import javax.swing.JComboBox;
  22 import javax.swing.JInternalFrame;
  23 import javax.swing.JLayeredPane;
  24 import javax.swing.JPanel;
  25 import javax.swing.JRadioButton;
  26 import javax.swing.JTextField;
  27 import javax.swing.border.TitledBorder;
  28 import javax.swing.event.DocumentEvent;
  29 import javax.swing.event.DocumentListener;
  30
  31 import net.miginfocom.swing.MigLayout;
  32
  33 @SuppressWarnings("serial")
  34 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  35         ItemListener
  36 {
  37
  38   private JComboBox<String> annotations;
  39
  40   // private JButton ok = new JButton();
  41   //
  42   // private JButton cancel = new JButton();
  43
  44   private JPanel actionPanel = new JPanel();
  45
  46   private JPanel thresholdPanel = new JPanel();
  47
  48   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  49
  50   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  51           .getLayout());
  52   private JPanel noGraphFilterView = new JPanel();
  53
  54   private JPanel graphFilterView = new JPanel();
  55
  56   private JPanel annotationComboBoxPanel = new JPanel();
  57
  58   private BorderLayout borderLayout1 = new BorderLayout();
  59
  60   private JComboBox<String> threshold = new JComboBox<String>();
  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 ColumnSelection oldColumnSelection;
  91
  92   public AnnotationColumnChooser()
  93   {
  94     try
  95     {
  96       jbInit();
  97     } catch (Exception ex)
  98     {
  99       ex.printStackTrace();
 100     }
 101   }
 102
 103   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 104   {
 105     super(av, ap);
 106     frame = new JInternalFrame();
 107     frame.setContentPane(this);
 108     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 109     Desktop.addInternalFrame(frame,
 110             MessageManager.getString("label.select_by_annotation"), 520,
 111             215);
 112
 113     addSliderChangeListener();
 114     addSliderMouseListeners();
 115
 116     if (av.getAlignment().getAlignmentAnnotation() == null)
 117     {
 118       return;
 119     }
 120     setOldColumnSelection(av.getColumnSelection());
 121     adjusting = true;
 122
 123     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 124     populateThresholdComboBox(threshold);
 125
 126     // restore Object state from the previous session if one exists
 127     if (av.getAnnotationColumnSelectionState() != null)
 128     {
 129       currentSearchPanel = av.getAnnotationColumnSelectionState()
 130               .getCurrentSearchPanel();
 131       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 132               .getCurrentStructureFilterPanel();
 133       annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
 134               .getAnnotations().getSelectedIndex());
 135       threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
 136               .getThreshold().getSelectedIndex());
 137       actionOption = av.getAnnotationColumnSelectionState()
 138               .getActionOption();
 139     }
 140
 141     try
 142     {
 143       jbInit();
 144     } catch (Exception ex)
 145     {
 146     }
 147     adjusting = false;
 148
 149     updateView();
 150     frame.invalidate();
 151     frame.pack();
 152   }
 153
 154   private void jbInit() throws Exception
 155   {
 156     ok.setOpaque(false);
 157     ok.setText(MessageManager.getString("action.ok"));
 158     ok.addActionListener(new ActionListener()
 159     {
 160       @Override
 161       public void actionPerformed(ActionEvent e)
 162       {
 163         ok_actionPerformed(e);
 164       }
 165     });
 166
 167     cancel.setOpaque(false);
 168     cancel.setText(MessageManager.getString("action.cancel"));
 169     cancel.addActionListener(new ActionListener()
 170     {
 171       @Override
 172       public void actionPerformed(ActionEvent e)
 173       {
 174         cancel_actionPerformed(e);
 175       }
 176     });
 177
 178     annotations.addItemListener(this);
 179     threshold.addActionListener(new ActionListener()
 180     {
 181       @Override
 182       public void actionPerformed(ActionEvent e)
 183       {
 184         threshold_actionPerformed(e);
 185       }
 186     });
 187
 188     thresholdValue.setEnabled(false);
 189     thresholdValue.setColumns(7);
 190     thresholdValue.addActionListener(new ActionListener()
 191     {
 192       @Override
 193       public void actionPerformed(ActionEvent e)
 194       {
 195         thresholdValue_actionPerformed(e);
 196       }
 197     });
 198
 199     slider.setPaintLabels(false);
 200     slider.setPaintTicks(true);
 201     slider.setBackground(Color.white);
 202     slider.setEnabled(false);
 203     slider.setOpaque(false);
 204     slider.setPreferredSize(new Dimension(100, 32));
 205
 206     thresholdPanel.setBorder(new TitledBorder(MessageManager
 207             .getString("label.threshold_filter")));
 208     thresholdPanel.setBackground(Color.white);
 209     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 210     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 211
 212     actionPanel.setBackground(Color.white);
 213     actionPanel.setFont(JvSwingUtils.getLabelFont());
 214
 215     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 216     graphFilterView.setBackground(Color.white);
 217
 218     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 219     noGraphFilterView.setBackground(Color.white);
 220
 221     annotationComboBoxPanel.setBackground(Color.white);
 222     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 223
 224     gSearchPanel = new SearchPanel(this);
 225     ngSearchPanel = new SearchPanel(this);
 226     gFurtherActionPanel = new FurtherActionPanel(this);
 227     ngFurtherActionPanel = new FurtherActionPanel(this);
 228     gStructureFilterPanel = new StructureFilterPanel(this);
 229     ngStructureFilterPanel = new StructureFilterPanel(this);
 230
 231     thresholdPanel.add(getThreshold());
 232     thresholdPanel.add(thresholdValue, "wrap");
 233     thresholdPanel.add(slider, "grow, span, wrap");
 234
 235     actionPanel.add(ok);
 236     actionPanel.add(cancel);
 237
 238     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 239     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 240     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 241     graphFilterView.add(gFurtherActionPanel);
 242
 243     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 244     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 245     noGraphFilterView.add(ngFurtherActionPanel);
 246
 247     annotationComboBoxPanel.add(getAnnotations());
 248     switchableViewsPanel.add(noGraphFilterView,
 249             AnnotationColumnChooser.NO_GRAPH_VIEW);
 250     switchableViewsPanel.add(graphFilterView,
 251             AnnotationColumnChooser.GRAPH_VIEW);
 252
 253     this.setLayout(borderLayout1);
 254     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 255     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 256     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 257
 258     selectedAnnotationChanged();
 259     this.validate();
 260   }
 261
 262   @SuppressWarnings("unchecked")
 263   public void reset()
 264   {
 265     if (this.getOldColumnSelection() != null)
 266     {
 267       av.getColumnSelection().clear();
 268
 269       if (av.getAnnotationColumnSelectionState() != null)
 270       {
 271         ColumnSelection oldSelection = av
 272                 .getAnnotationColumnSelectionState()
 273                 .getOldColumnSelection();
 274         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 275                 && !oldSelection.getHiddenColumns().isEmpty())
 276         {
 277           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 278                   .iterator(); itr.hasNext();)
 279           {
 280             int positions[] = itr.next();
 281             av.hideColumns(positions[0], positions[1]);
 282           }
 283         }
 284         av.setColumnSelection(oldSelection);
 285       }
 286       ap.paintAlignment(true);
 287     }
 288
 289   }
 290
 291   public void valueChanged(boolean updateAllAnnotation)
 292   {
 293     if (slider.isEnabled())
 294     {
 295       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 296       updateView();
 297       propagateSeqAssociatedThreshold(updateAllAnnotation,
 298               getCurrentAnnotation());
 299       ap.paintAlignment(false);
 300     }
 301   }
 302
 303   public JComboBox<String> getThreshold()
 304   {
 305     return threshold;
 306   }
 307
 308   public void setThreshold(JComboBox<String> threshold)
 309   {
 310     this.threshold = threshold;
 311   }
 312
 313   public JComboBox<String> getAnnotations()
 314   {
 315     return annotations;
 316   }
 317
 318   public void setAnnotations(JComboBox<String> annotations)
 319   {
 320     this.annotations = annotations;
 321   }
 322
 323   @Override
 324   public void updateView()
 325   {
 326     // Check if combobox is still adjusting
 327     if (adjusting)
 328     {
 329       return;
 330     }
 331
 332     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 333
 334     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 335             .getSelectedIndex()]]);
 336
 337     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 338             .getSelectedIndex());
 339
 340     slider.setEnabled(true);
 341     thresholdValue.setEnabled(true);
 342
 343     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 344     {
 345       slider.setEnabled(false);
 346       thresholdValue.setEnabled(false);
 347       thresholdValue.setText("");
 348       // build filter params
 349     }
 350     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 351     {
 352       if (getCurrentAnnotation().threshold == null)
 353       {
 354         getCurrentAnnotation()
 355                 .setThreshold(
 356                         new jalview.datamodel.GraphLine(
 357                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 358                                 "Threshold", Color.black));
 359       }
 360
 361       adjusting = true;
 362       float range = getCurrentAnnotation().graphMax * 1000
 363               - getCurrentAnnotation().graphMin * 1000;
 364
 365       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 366       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 367       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 368       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 369       slider.setMajorTickSpacing((int) (range / 10f));
 370       slider.setEnabled(true);
 371       thresholdValue.setEnabled(true);
 372       adjusting = false;
 373
 374       // build filter params
 375       filterParams
 376               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 377       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 378       {
 379         filterParams
 380                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 381
 382         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 383         {
 384           filterParams
 385                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 386         }
 387         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 388         {
 389           filterParams
 390                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 391         }
 392       }
 393     }
 394
 395     if (currentStructureFilterPanel != null)
 396     {
 397       if (currentStructureFilterPanel.alphaHelix.isSelected())
 398       {
 399         filterParams.setFilterAlphaHelix(true);
 400       }
 401       if (currentStructureFilterPanel.betaStrand.isSelected())
 402       {
 403         filterParams.setFilterBetaSheet(true);
 404       }
 405       if (currentStructureFilterPanel.turn.isSelected())
 406       {
 407         filterParams.setFilterTurn(true);
 408       }
 409     }
 410
 411     if (currentSearchPanel != null)
 412     {
 413
 414       if (!currentSearchPanel.searchBox.getText().isEmpty())
 415       {
 416         currentSearchPanel.description.setEnabled(true);
 417         currentSearchPanel.displayName.setEnabled(true);
 418         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 419         if (currentSearchPanel.displayName.isSelected())
 420         {
 421           filterParams
 422                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 423         }
 424         if (currentSearchPanel.description.isSelected())
 425         {
 426           filterParams
 427                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 428         }
 429       }
 430       else
 431       {
 432         currentSearchPanel.description.setEnabled(false);
 433         currentSearchPanel.displayName.setEnabled(false);
 434       }
 435     }
 436
 437     av.getColumnSelection().filterAnnotations(
 438             getCurrentAnnotation().annotations, filterParams);
 439
 440     av.showAllHiddenColumns();
 441     if (getActionOption() == ACTION_OPTION_HIDE)
 442     {
 443       av.hideSelectedColumns();
 444     }
 445
 446     filterParams = null;
 447     av.setAnnotationColumnSelectionState(this);
 448     ap.paintAlignment(true);
 449   }
 450
 451   public ColumnSelection getOldColumnSelection()
 452   {
 453     return oldColumnSelection;
 454   }
 455
 456   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 457   {
 458     if (currentColumnSelection != null)
 459     {
 460       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 461     }
 462   }
 463
 464   public FurtherActionPanel getCurrentFutherActionPanel()
 465   {
 466     return currentFurtherActionPanel;
 467   }
 468
 469   public void setCurrentFutherActionPanel(
 470           FurtherActionPanel currentFutherActionPanel)
 471   {
 472     this.currentFurtherActionPanel = currentFutherActionPanel;
 473   }
 474
 475   public SearchPanel getCurrentSearchPanel()
 476   {
 477     return currentSearchPanel;
 478   }
 479
 480   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 481   {
 482     this.currentSearchPanel = currentSearchPanel;
 483   }
 484
 485   public int getActionOption()
 486   {
 487     return actionOption;
 488   }
 489
 490   public void setActionOption(int actionOption)
 491   {
 492     this.actionOption = actionOption;
 493   }
 494
 495   public StructureFilterPanel getCurrentStructureFilterPanel()
 496   {
 497     return currentStructureFilterPanel;
 498   }
 499
 500   public void setCurrentStructureFilterPanel(
 501           StructureFilterPanel currentStructureFilterPanel)
 502   {
 503     this.currentStructureFilterPanel = currentStructureFilterPanel;
 504   }
 505
 506   public void select_action(ActionEvent actionEvent)
 507   {
 508     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 509     if (radioButton.isSelected())
 510     {
 511       setActionOption(ACTION_OPTION_SELECT);
 512       updateView();
 513     }
 514   }
 515
 516   public void hide_action(ActionEvent actionEvent)
 517   {
 518     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 519     if (radioButton.isSelected())
 520     {
 521       setActionOption(ACTION_OPTION_HIDE);
 522       updateView();
 523     }
 524   }
 525
 526   @Override
 527   public void itemStateChanged(ItemEvent e)
 528   {
 529     selectedAnnotationChanged();
 530   }
 531
 532   public void selectedAnnotationChanged()
 533   {
 534     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 535     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 536             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 537     {
 538       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 539     }
 540
 541     gSearchPanel.syncState();
 542     gFurtherActionPanel.syncState();
 543     gStructureFilterPanel.syncState();
 544
 545     ngSearchPanel.syncState();
 546     ngFurtherActionPanel.syncState();
 547     ngStructureFilterPanel.syncState();
 548
 549     switchableViewsLayout.show(switchableViewsPanel, currentView);
 550     updateView();
 551   }
 552
 553
 554   public class FurtherActionPanel extends JPanel
 555   {
 556     private AnnotationColumnChooser aColChooser;
 557
 558     private JRadioButton hideOption = new JRadioButton();
 559
 560     private JRadioButton selectOption = new JRadioButton();
 561
 562     private ButtonGroup optionsGroup = new ButtonGroup();
 563
 564     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 565     {
 566       this.aColChooser = aColChooser;
 567       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 568       selectOption.addActionListener(new ActionListener()
 569       {
 570         @Override
 571         public void actionPerformed(ActionEvent actionEvent)
 572         {
 573           selectRadioAction(actionEvent);
 574         }
 575       });
 576
 577       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 578       hideOption.addActionListener(new ActionListener()
 579       {
 580         @Override
 581         public void actionPerformed(ActionEvent actionEvent)
 582         {
 583           hideRadioAction(actionEvent);
 584         }
 585       });
 586
 587       optionsGroup.add(selectOption);
 588       optionsGroup.add(hideOption);
 589       optionsGroup.setSelected(selectOption.getModel(), true);
 590
 591       JvSwingUtils.jvInitComponent(this);
 592       syncState();
 593
 594       this.add(selectOption);
 595       this.add(hideOption);
 596     }
 597
 598     public void selectRadioAction(ActionEvent actionEvent)
 599     {
 600       aColChooser.setCurrentFutherActionPanel(this);
 601       aColChooser.select_action(actionEvent);
 602     }
 603
 604     public void hideRadioAction(ActionEvent actionEvent)
 605     {
 606       aColChooser.setCurrentFutherActionPanel(this);
 607       aColChooser.hide_action(actionEvent);
 608     }
 609
 610     public void syncState()
 611     {
 612       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 613       {
 614         this.optionsGroup.setSelected(this.hideOption.getModel(),
 615                 true);
 616       }
 617       else
 618       {
 619         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 620       }
 621     }
 622   }
 623
 624   public class StructureFilterPanel extends JPanel
 625   {
 626     private AnnotationColumnChooser aColChooser;
 627
 628     private JCheckBox alphaHelix = new JCheckBox();
 629
 630     private JCheckBox betaStrand = new JCheckBox();
 631
 632     private JCheckBox turn = new JCheckBox();
 633
 634     private JCheckBox all = new JCheckBox();
 635
 636     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 637     {
 638       this.aColChooser = aColChooser;
 639
 640       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 641       alphaHelix.addActionListener(new ActionListener()
 642       {
 643         @Override
 644         public void actionPerformed(ActionEvent actionEvent)
 645         {
 646           alphaHelix_actionPerformed();
 647         }
 648       });
 649
 650       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 651       betaStrand.addActionListener(new ActionListener()
 652       {
 653         @Override
 654         public void actionPerformed(ActionEvent actionEvent)
 655         {
 656           betaStrand_actionPerformed();
 657         }
 658       });
 659
 660       JvSwingUtils.jvInitComponent(turn, "label.turn");
 661       turn.addActionListener(new ActionListener()
 662       {
 663         @Override
 664         public void actionPerformed(ActionEvent actionEvent)
 665         {
 666           turn_actionPerformed();
 667         }
 668       });
 669
 670       JvSwingUtils.jvInitComponent(all, "label.select_all");
 671       all.addActionListener(new ActionListener()
 672       {
 673         @Override
 674         public void actionPerformed(ActionEvent actionEvent)
 675         {
 676           all_actionPerformed();
 677         }
 678       });
 679
 680       this.setBorder(new TitledBorder(MessageManager
 681               .getString("label.structures_filter")));
 682       JvSwingUtils.jvInitComponent(this);
 683
 684       this.add(all);
 685       this.add(alphaHelix);
 686       this.add(betaStrand);
 687       this.add(turn);
 688     }
 689
 690     public void alphaHelix_actionPerformed()
 691     {
 692       updateSelectAllState();
 693       aColChooser.setCurrentStructureFilterPanel(this);
 694       aColChooser.updateView();
 695     }
 696
 697     public void betaStrand_actionPerformed()
 698     {
 699       updateSelectAllState();
 700       aColChooser.setCurrentStructureFilterPanel(this);
 701       aColChooser.updateView();
 702     }
 703
 704     public void turn_actionPerformed()
 705     {
 706       updateSelectAllState();
 707       aColChooser.setCurrentStructureFilterPanel(this);
 708       aColChooser.updateView();
 709     }
 710
 711     public void all_actionPerformed()
 712     {
 713       if (all.isSelected())
 714       {
 715         alphaHelix.setSelected(true);
 716         betaStrand.setSelected(true);
 717         turn.setSelected(true);
 718       }
 719       else
 720       {
 721         alphaHelix.setSelected(false);
 722         betaStrand.setSelected(false);
 723         turn.setSelected(false);
 724       }
 725       aColChooser.setCurrentStructureFilterPanel(this);
 726       aColChooser.updateView();
 727     }
 728
 729     public void updateSelectAllState()
 730     {
 731       if (alphaHelix.isSelected() && betaStrand.isSelected()
 732               && turn.isSelected())
 733       {
 734         all.setSelected(true);
 735       }
 736       else
 737       {
 738         all.setSelected(false);
 739       }
 740     }
 741
 742     public void syncState()
 743     {
 744       StructureFilterPanel sfp = aColChooser
 745               .getCurrentStructureFilterPanel();
 746       if (sfp != null)
 747       {
 748         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 749         betaStrand.setSelected(sfp.betaStrand.isSelected());
 750         turn.setSelected(sfp.turn.isSelected());
 751         if (sfp.all.isSelected())
 752         {
 753           all.setSelected(true);
 754           alphaHelix.setSelected(true);
 755           betaStrand.setSelected(true);
 756           turn.setSelected(true);
 757         }
 758       }
 759
 760     }
 761   }
 762
 763   public class SearchPanel extends JPanel
 764   {
 765     private AnnotationColumnChooser aColChooser;
 766
 767     private JCheckBox displayName = new JCheckBox();
 768
 769     private JCheckBox description = new JCheckBox();
 770
 771     private JTextField searchBox = new JTextField(10);
 772
 773     public SearchPanel(AnnotationColumnChooser aColChooser)
 774     {
 775
 776       this.aColChooser = aColChooser;
 777       JvSwingUtils.jvInitComponent(this);
 778       this.setBorder(new TitledBorder(MessageManager
 779               .getString("label.search_filter")));
 780
 781       JvSwingUtils.jvInitComponent(searchBox);
 782       searchBox.getDocument().addDocumentListener(
 783               new DocumentListener()
 784               {
 785                 @Override
 786                 public void insertUpdate(DocumentEvent e)
 787                 {
 788                   searchStringAction();
 789                 }
 790
 791                 @Override
 792                 public void removeUpdate(DocumentEvent e)
 793                 {
 794                   searchStringAction();
 795                 }
 796
 797                 @Override
 798                 public void changedUpdate(DocumentEvent e)
 799                 {
 800                   searchStringAction();
 801                 }
 802               });
 803
 804       JvSwingUtils.jvInitComponent(displayName, "label.display_name");
 805       displayName.setEnabled(false);
 806       displayName.addActionListener(new ActionListener()
 807       {
 808         @Override
 809         public void actionPerformed(ActionEvent actionEvent)
 810         {
 811           displayNameCheckboxAction();
 812         }
 813       });
 814
 815       JvSwingUtils.jvInitComponent(description, "label.description");
 816       description.setEnabled(false);
 817       description.addActionListener(new ActionListener()
 818       {
 819         @Override
 820         public void actionPerformed(ActionEvent actionEvent)
 821         {
 822           discriptionCheckboxAction();
 823         }
 824       });
 825
 826       syncState();
 827       this.add(searchBox);
 828       this.add(displayName);
 829       this.add(description);
 830     }
 831
 832     public void displayNameCheckboxAction()
 833     {
 834       aColChooser.setCurrentSearchPanel(this);
 835       aColChooser.updateView();
 836     }
 837
 838     public void discriptionCheckboxAction()
 839     {
 840       aColChooser.setCurrentSearchPanel(this);
 841       aColChooser.updateView();
 842     }
 843
 844     public void searchStringAction()
 845     {
 846       aColChooser.setCurrentSearchPanel(this);
 847       aColChooser.updateView();
 848     }
 849
 850     public void syncState()
 851     {
 852       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 853       if (sp != null)
 854       {
 855         description.setEnabled(sp.description.isEnabled());
 856         description.setSelected(sp.description.isSelected());
 857
 858         displayName.setEnabled(sp.displayName.isEnabled());
 859         displayName.setSelected(sp.displayName.isSelected());
 860
 861         searchBox.setText(sp.searchBox.getText());
 862       }
 863     }
 864   }
 865
 866 }