src/jalview/gui/AnnotationColumnChooser.java

   1 package jalview.gui;
   2
   3 import jalview.controller.AlignViewController;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.ColumnSelection;
   6 import jalview.schemes.AnnotationColourGradient;
   7 import jalview.util.MessageManager;
   8 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
   9
  10 import java.awt.BorderLayout;
  11 import java.awt.CardLayout;
  12 import java.awt.Color;
  13 import java.awt.Dimension;
  14 import java.awt.event.ActionEvent;
  15 import java.awt.event.ActionListener;
  16 import java.awt.event.ItemEvent;
  17 import java.awt.event.ItemListener;
  18 import java.util.Iterator;
  19
  20 import javax.swing.ButtonGroup;
  21 import javax.swing.JButton;
  22 import javax.swing.JCheckBox;
  23 import javax.swing.JComboBox;
  24 import javax.swing.JInternalFrame;
  25 import javax.swing.JLayeredPane;
  26 import javax.swing.JPanel;
  27 import javax.swing.JRadioButton;
  28 import javax.swing.JTextField;
  29 import javax.swing.border.TitledBorder;
  30 import javax.swing.event.DocumentEvent;
  31 import javax.swing.event.DocumentListener;
  32
  33 import net.miginfocom.swing.MigLayout;
  34
  35 @SuppressWarnings("serial")
  36 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  37         ItemListener
  38 {
  39
  40   private JComboBox<String> annotations;
  41
  42   private JButton ok = new JButton();
  43
  44   private JButton cancel = new JButton();
  45
  46   private JPanel actionPanel = new JPanel();
  47
  48   private JPanel thresholdPanel = new JPanel();
  49
  50   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  51
  52   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  53           .getLayout());
  54
  55   private JPanel noGraphFilterView = new JPanel();
  56
  57   private JPanel graphFilterView = new JPanel();
  58
  59   private JPanel annotationComboBoxPanel = new JPanel();
  60
  61   private BorderLayout borderLayout1 = new BorderLayout();
  62
  63   private JComboBox<String> threshold = new JComboBox<String>();
  64
  65   private StructureFilterPanel gStructureFilterPanel;
  66
  67   private StructureFilterPanel ngStructureFilterPanel;
  68
  69   private StructureFilterPanel currentStructureFilterPanel;
  70
  71   private SearchPanel currentSearchPanel;
  72
  73   private SearchPanel gSearchPanel;
  74
  75   private SearchPanel ngSearchPanel;
  76
  77   private FurtherActionPanel currentFurtherActionPanel;
  78
  79   private FurtherActionPanel gFurtherActionPanel;
  80
  81   private FurtherActionPanel ngFurtherActionPanel;
  82
  83   public static final int ACTION_OPTION_SELECT = 1;
  84
  85   public static int ACTION_OPTION_HIDE = 2;
  86
  87   public static String NO_GRAPH_VIEW = "0";
  88
  89   public static String GRAPH_VIEW = "1";
  90
  91   private int actionOption = ACTION_OPTION_SELECT;
  92
  93   private ColumnSelection oldColumnSelection;
  94
  95   public AnnotationColumnChooser()
  96   {
  97     try
  98     {
  99       jbInit();
 100     } catch (Exception ex)
 101     {
 102       ex.printStackTrace();
 103     }
 104   }
 105
 106   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 107   {
 108     super(av, ap);
 109     frame = new JInternalFrame();
 110     frame.setContentPane(this);
 111     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 112     Desktop.addInternalFrame(frame,
 113             MessageManager.getString("label.select_by_annotation"), 520,
 114             215);
 115
 116     addSliderChangeListener();
 117     addSliderMouseListeners();
 118
 119     if (av.getAlignment().getAlignmentAnnotation() == null)
 120     {
 121       return;
 122     }
 123     setOldColumnSelection(av.getColumnSelection());
 124     adjusting = true;
 125
 126     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 127     populateThresholdComboBox(threshold);
 128
 129     // restore Object state from the previous session if one exists
 130     if (av.getAnnotationColumnSelectionState() != null)
 131     {
 132       currentSearchPanel = av.getAnnotationColumnSelectionState()
 133               .getCurrentSearchPanel();
 134       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 135               .getCurrentStructureFilterPanel();
 136       annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
 137               .getAnnotations().getSelectedIndex());
 138       threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
 139               .getThreshold().getSelectedIndex());
 140       actionOption = av.getAnnotationColumnSelectionState()
 141               .getActionOption();
 142     }
 143
 144     try
 145     {
 146       jbInit();
 147     } catch (Exception ex)
 148     {
 149     }
 150     adjusting = false;
 151
 152     updateView();
 153     frame.invalidate();
 154     frame.pack();
 155   }
 156
 157   private void jbInit() throws Exception
 158   {
 159     ok.setOpaque(false);
 160     ok.setText(MessageManager.getString("action.ok"));
 161     ok.addActionListener(new ActionListener()
 162     {
 163       @Override
 164       public void actionPerformed(ActionEvent e)
 165       {
 166         ok_actionPerformed(e);
 167       }
 168     });
 169
 170     cancel.setOpaque(false);
 171     cancel.setText(MessageManager.getString("action.cancel"));
 172     cancel.addActionListener(new ActionListener()
 173     {
 174       @Override
 175       public void actionPerformed(ActionEvent e)
 176       {
 177         cancel_actionPerformed(e);
 178       }
 179     });
 180
 181     annotations.addItemListener(this);
 182     threshold.addActionListener(new ActionListener()
 183     {
 184       @Override
 185       public void actionPerformed(ActionEvent e)
 186       {
 187         threshold_actionPerformed(e);
 188       }
 189     });
 190
 191     thresholdValue.setEnabled(false);
 192     thresholdValue.setColumns(7);
 193     thresholdValue.addActionListener(new ActionListener()
 194     {
 195       @Override
 196       public void actionPerformed(ActionEvent e)
 197       {
 198         thresholdValue_actionPerformed(e);
 199       }
 200     });
 201
 202     slider.setPaintLabels(false);
 203     slider.setPaintTicks(true);
 204     slider.setBackground(Color.white);
 205     slider.setEnabled(false);
 206     slider.setOpaque(false);
 207     slider.setPreferredSize(new Dimension(100, 32));
 208
 209     thresholdPanel.setBorder(new TitledBorder(MessageManager
 210             .getString("label.threshold_filter")));
 211     thresholdPanel.setBackground(Color.white);
 212     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 213     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 214
 215     actionPanel.setBackground(Color.white);
 216     actionPanel.setFont(JvSwingUtils.getLabelFont());
 217
 218     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 219     graphFilterView.setBackground(Color.white);
 220
 221     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 222     noGraphFilterView.setBackground(Color.white);
 223
 224     annotationComboBoxPanel.setBackground(Color.white);
 225     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 226
 227     gSearchPanel = new SearchPanel(this);
 228     ngSearchPanel = new SearchPanel(this);
 229     gFurtherActionPanel = new FurtherActionPanel(this);
 230     ngFurtherActionPanel = new FurtherActionPanel(this);
 231     gStructureFilterPanel = new StructureFilterPanel(this);
 232     ngStructureFilterPanel = new StructureFilterPanel(this);
 233
 234     thresholdPanel.add(getThreshold());
 235     thresholdPanel.add(thresholdValue, "wrap");
 236     thresholdPanel.add(slider, "grow, span, wrap");
 237
 238     actionPanel.add(ok);
 239     actionPanel.add(cancel);
 240
 241     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 242     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 243     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 244     graphFilterView.add(gFurtherActionPanel);
 245
 246     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 247     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 248     noGraphFilterView.add(ngFurtherActionPanel);
 249
 250     annotationComboBoxPanel.add(getAnnotations());
 251     switchableViewsPanel.add(noGraphFilterView,
 252             AnnotationColumnChooser.NO_GRAPH_VIEW);
 253     switchableViewsPanel.add(graphFilterView,
 254             AnnotationColumnChooser.GRAPH_VIEW);
 255
 256     this.setLayout(borderLayout1);
 257     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 258     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 259     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 260
 261     selectedAnnotationChanged();
 262     this.validate();
 263   }
 264
 265   @SuppressWarnings("unchecked")
 266   public void reset()
 267   {
 268     if (this.getOldColumnSelection() != null)
 269     {
 270       av.getColumnSelection().clear();
 271
 272       if (av.getAnnotationColumnSelectionState() != null)
 273       {
 274         ColumnSelection oldSelection = av
 275                 .getAnnotationColumnSelectionState()
 276                 .getOldColumnSelection();
 277         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 278                 && !oldSelection.getHiddenColumns().isEmpty())
 279         {
 280           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 281                   .iterator(); itr.hasNext();)
 282           {
 283             int positions[] = itr.next();
 284             av.hideColumns(positions[0], positions[1]);
 285           }
 286         }
 287         av.setColumnSelection(oldSelection);
 288       }
 289       ap.paintAlignment(true);
 290     }
 291
 292   }
 293
 294   public void valueChanged(boolean updateAllAnnotation)
 295   {
 296     if (slider.isEnabled())
 297     {
 298       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 299       updateView();
 300       propagateSeqAssociatedThreshold(updateAllAnnotation,
 301               getCurrentAnnotation());
 302       ap.paintAlignment(false);
 303     }
 304   }
 305
 306   public JComboBox<String> getThreshold()
 307   {
 308     return threshold;
 309   }
 310
 311   public void setThreshold(JComboBox<String> threshold)
 312   {
 313     this.threshold = threshold;
 314   }
 315
 316   public JComboBox<String> getAnnotations()
 317   {
 318     return annotations;
 319   }
 320
 321   public void setAnnotations(JComboBox<String> annotations)
 322   {
 323     this.annotations = annotations;
 324   }
 325
 326   @Override
 327   public void updateView()
 328   {
 329     // Check if combobox is still adjusting
 330     if (adjusting)
 331     {
 332       return;
 333     }
 334
 335     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 336
 337     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 338             .getSelectedIndex()]]);
 339
 340     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 341             .getSelectedIndex());
 342
 343     slider.setEnabled(true);
 344     thresholdValue.setEnabled(true);
 345
 346     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 347     {
 348       slider.setEnabled(false);
 349       thresholdValue.setEnabled(false);
 350       thresholdValue.setText("");
 351       // build filter params
 352     }
 353     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 354     {
 355       if (getCurrentAnnotation().threshold == null)
 356       {
 357         getCurrentAnnotation()
 358                 .setThreshold(
 359                         new jalview.datamodel.GraphLine(
 360                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 361                                 "Threshold", Color.black));
 362       }
 363
 364       adjusting = true;
 365       float range = getCurrentAnnotation().graphMax * 1000
 366               - getCurrentAnnotation().graphMin * 1000;
 367
 368       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 369       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 370       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 371       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 372       slider.setMajorTickSpacing((int) (range / 10f));
 373       slider.setEnabled(true);
 374       thresholdValue.setEnabled(true);
 375       adjusting = false;
 376
 377       // build filter params
 378       filterParams
 379               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 380       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 381       {
 382         filterParams
 383                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 384
 385         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 386         {
 387           filterParams
 388                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 389         }
 390         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 391         {
 392           filterParams
 393                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 394         }
 395       }
 396     }
 397
 398     if (currentStructureFilterPanel != null)
 399     {
 400       if (currentStructureFilterPanel.alphaHelix.isSelected())
 401       {
 402         filterParams.setFilterAlphaHelix(true);
 403       }
 404       if (currentStructureFilterPanel.betaStrand.isSelected())
 405       {
 406         filterParams.setFilterBetaSheet(true);
 407       }
 408       if (currentStructureFilterPanel.turn.isSelected())
 409       {
 410         filterParams.setFilterTurn(true);
 411       }
 412     }
 413
 414     if (currentSearchPanel != null)
 415     {
 416
 417       if (!currentSearchPanel.searchBox.getText().isEmpty())
 418       {
 419         currentSearchPanel.description.setEnabled(true);
 420         currentSearchPanel.displayName.setEnabled(true);
 421         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 422         if (currentSearchPanel.displayName.isSelected())
 423         {
 424           filterParams
 425                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 426         }
 427         if (currentSearchPanel.description.isSelected())
 428         {
 429           filterParams
 430                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 431         }
 432       }
 433       else
 434       {
 435         currentSearchPanel.description.setEnabled(false);
 436         currentSearchPanel.displayName.setEnabled(false);
 437       }
 438     }
 439
 440     AlignViewController.filterAnnotations(
 441             getCurrentAnnotation().annotations, filterParams,
 442             av.getColumnSelection());
 443
 444     av.showAllHiddenColumns();
 445     if (getActionOption() == ACTION_OPTION_HIDE)
 446     {
 447       av.hideSelectedColumns();
 448     }
 449
 450     filterParams = null;
 451     av.setAnnotationColumnSelectionState(this);
 452     ap.paintAlignment(true);
 453   }
 454
 455   public ColumnSelection getOldColumnSelection()
 456   {
 457     return oldColumnSelection;
 458   }
 459
 460   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 461   {
 462     if (currentColumnSelection != null)
 463     {
 464       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 465     }
 466   }
 467
 468   public FurtherActionPanel getCurrentFutherActionPanel()
 469   {
 470     return currentFurtherActionPanel;
 471   }
 472
 473   public void setCurrentFutherActionPanel(
 474           FurtherActionPanel currentFutherActionPanel)
 475   {
 476     this.currentFurtherActionPanel = currentFutherActionPanel;
 477   }
 478
 479   public SearchPanel getCurrentSearchPanel()
 480   {
 481     return currentSearchPanel;
 482   }
 483
 484   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 485   {
 486     this.currentSearchPanel = currentSearchPanel;
 487   }
 488
 489   public int getActionOption()
 490   {
 491     return actionOption;
 492   }
 493
 494   public void setActionOption(int actionOption)
 495   {
 496     this.actionOption = actionOption;
 497   }
 498
 499   public StructureFilterPanel getCurrentStructureFilterPanel()
 500   {
 501     return currentStructureFilterPanel;
 502   }
 503
 504   public void setCurrentStructureFilterPanel(
 505           StructureFilterPanel currentStructureFilterPanel)
 506   {
 507     this.currentStructureFilterPanel = currentStructureFilterPanel;
 508   }
 509
 510   public void select_action(ActionEvent actionEvent)
 511   {
 512     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 513     if (radioButton.isSelected())
 514     {
 515       setActionOption(ACTION_OPTION_SELECT);
 516       updateView();
 517     }
 518   }
 519
 520   public void hide_action(ActionEvent actionEvent)
 521   {
 522     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 523     if (radioButton.isSelected())
 524     {
 525       setActionOption(ACTION_OPTION_HIDE);
 526       updateView();
 527     }
 528   }
 529
 530   @Override
 531   public void itemStateChanged(ItemEvent e)
 532   {
 533     selectedAnnotationChanged();
 534   }
 535
 536   public void selectedAnnotationChanged()
 537   {
 538     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 539     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 540             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 541     {
 542       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 543     }
 544
 545     gSearchPanel.syncState();
 546     gFurtherActionPanel.syncState();
 547     gStructureFilterPanel.syncState();
 548
 549     ngSearchPanel.syncState();
 550     ngFurtherActionPanel.syncState();
 551     ngStructureFilterPanel.syncState();
 552
 553     switchableViewsLayout.show(switchableViewsPanel, currentView);
 554     updateView();
 555   }
 556
 557
 558   public class FurtherActionPanel extends JPanel
 559   {
 560     private AnnotationColumnChooser aColChooser;
 561
 562     private JRadioButton hideOption = new JRadioButton();
 563
 564     private JRadioButton selectOption = new JRadioButton();
 565
 566     private ButtonGroup optionsGroup = new ButtonGroup();
 567
 568     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 569     {
 570       this.aColChooser = aColChooser;
 571       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 572       selectOption.addActionListener(new ActionListener()
 573       {
 574         @Override
 575         public void actionPerformed(ActionEvent actionEvent)
 576         {
 577           selectRadioAction(actionEvent);
 578         }
 579       });
 580
 581       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 582       hideOption.addActionListener(new ActionListener()
 583       {
 584         @Override
 585         public void actionPerformed(ActionEvent actionEvent)
 586         {
 587           hideRadioAction(actionEvent);
 588         }
 589       });
 590
 591       optionsGroup.add(selectOption);
 592       optionsGroup.add(hideOption);
 593       optionsGroup.setSelected(selectOption.getModel(), true);
 594
 595       JvSwingUtils.jvInitComponent(this);
 596       syncState();
 597
 598       this.add(selectOption);
 599       this.add(hideOption);
 600     }
 601
 602     public void selectRadioAction(ActionEvent actionEvent)
 603     {
 604       aColChooser.setCurrentFutherActionPanel(this);
 605       aColChooser.select_action(actionEvent);
 606     }
 607
 608     public void hideRadioAction(ActionEvent actionEvent)
 609     {
 610       aColChooser.setCurrentFutherActionPanel(this);
 611       aColChooser.hide_action(actionEvent);
 612     }
 613
 614     public void syncState()
 615     {
 616       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 617       {
 618         this.optionsGroup.setSelected(this.hideOption.getModel(),
 619                 true);
 620       }
 621       else
 622       {
 623         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 624       }
 625     }
 626   }
 627
 628   public class StructureFilterPanel extends JPanel
 629   {
 630     private AnnotationColumnChooser aColChooser;
 631
 632     private JCheckBox alphaHelix = new JCheckBox();
 633
 634     private JCheckBox betaStrand = new JCheckBox();
 635
 636     private JCheckBox turn = new JCheckBox();
 637
 638     private JCheckBox all = new JCheckBox();
 639
 640     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 641     {
 642       this.aColChooser = aColChooser;
 643
 644       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 645       alphaHelix.addActionListener(new ActionListener()
 646       {
 647         @Override
 648         public void actionPerformed(ActionEvent actionEvent)
 649         {
 650           alphaHelix_actionPerformed();
 651         }
 652       });
 653
 654       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 655       betaStrand.addActionListener(new ActionListener()
 656       {
 657         @Override
 658         public void actionPerformed(ActionEvent actionEvent)
 659         {
 660           betaStrand_actionPerformed();
 661         }
 662       });
 663
 664       JvSwingUtils.jvInitComponent(turn, "label.turn");
 665       turn.addActionListener(new ActionListener()
 666       {
 667         @Override
 668         public void actionPerformed(ActionEvent actionEvent)
 669         {
 670           turn_actionPerformed();
 671         }
 672       });
 673
 674       JvSwingUtils.jvInitComponent(all, "label.select_all");
 675       all.addActionListener(new ActionListener()
 676       {
 677         @Override
 678         public void actionPerformed(ActionEvent actionEvent)
 679         {
 680           all_actionPerformed();
 681         }
 682       });
 683
 684       this.setBorder(new TitledBorder(MessageManager
 685               .getString("label.structures_filter")));
 686       JvSwingUtils.jvInitComponent(this);
 687
 688       this.add(all);
 689       this.add(alphaHelix);
 690       this.add(betaStrand);
 691       this.add(turn);
 692     }
 693
 694     public void alphaHelix_actionPerformed()
 695     {
 696       updateSelectAllState();
 697       aColChooser.setCurrentStructureFilterPanel(this);
 698       aColChooser.updateView();
 699     }
 700
 701     public void betaStrand_actionPerformed()
 702     {
 703       updateSelectAllState();
 704       aColChooser.setCurrentStructureFilterPanel(this);
 705       aColChooser.updateView();
 706     }
 707
 708     public void turn_actionPerformed()
 709     {
 710       updateSelectAllState();
 711       aColChooser.setCurrentStructureFilterPanel(this);
 712       aColChooser.updateView();
 713     }
 714
 715     public void all_actionPerformed()
 716     {
 717       if (all.isSelected())
 718       {
 719         alphaHelix.setSelected(true);
 720         betaStrand.setSelected(true);
 721         turn.setSelected(true);
 722       }
 723       else
 724       {
 725         alphaHelix.setSelected(false);
 726         betaStrand.setSelected(false);
 727         turn.setSelected(false);
 728       }
 729       aColChooser.setCurrentStructureFilterPanel(this);
 730       aColChooser.updateView();
 731     }
 732
 733     public void updateSelectAllState()
 734     {
 735       if (alphaHelix.isSelected() && betaStrand.isSelected()
 736               && turn.isSelected())
 737       {
 738         all.setSelected(true);
 739       }
 740       else
 741       {
 742         all.setSelected(false);
 743       }
 744     }
 745
 746     public void syncState()
 747     {
 748       StructureFilterPanel sfp = aColChooser
 749               .getCurrentStructureFilterPanel();
 750       if (sfp != null)
 751       {
 752         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 753         betaStrand.setSelected(sfp.betaStrand.isSelected());
 754         turn.setSelected(sfp.turn.isSelected());
 755         if (sfp.all.isSelected())
 756         {
 757           all.setSelected(true);
 758           alphaHelix.setSelected(true);
 759           betaStrand.setSelected(true);
 760           turn.setSelected(true);
 761         }
 762       }
 763
 764     }
 765   }
 766
 767   public class SearchPanel extends JPanel
 768   {
 769     private AnnotationColumnChooser aColChooser;
 770
 771     private JCheckBox displayName = new JCheckBox();
 772
 773     private JCheckBox description = new JCheckBox();
 774
 775     private JTextField searchBox = new JTextField(10);
 776
 777     public SearchPanel(AnnotationColumnChooser aColChooser)
 778     {
 779
 780       this.aColChooser = aColChooser;
 781       JvSwingUtils.jvInitComponent(this);
 782       this.setBorder(new TitledBorder(MessageManager
 783               .getString("label.search_filter")));
 784
 785       JvSwingUtils.jvInitComponent(searchBox);
 786       searchBox.getDocument().addDocumentListener(
 787               new DocumentListener()
 788               {
 789                 @Override
 790                 public void insertUpdate(DocumentEvent e)
 791                 {
 792                   searchStringAction();
 793                 }
 794
 795                 @Override
 796                 public void removeUpdate(DocumentEvent e)
 797                 {
 798                   searchStringAction();
 799                 }
 800
 801                 @Override
 802                 public void changedUpdate(DocumentEvent e)
 803                 {
 804                   searchStringAction();
 805                 }
 806               });
 807
 808       JvSwingUtils.jvInitComponent(displayName, "label.display_name");
 809       displayName.setEnabled(false);
 810       displayName.addActionListener(new ActionListener()
 811       {
 812         @Override
 813         public void actionPerformed(ActionEvent actionEvent)
 814         {
 815           displayNameCheckboxAction();
 816         }
 817       });
 818
 819       JvSwingUtils.jvInitComponent(description, "label.description");
 820       description.setEnabled(false);
 821       description.addActionListener(new ActionListener()
 822       {
 823         @Override
 824         public void actionPerformed(ActionEvent actionEvent)
 825         {
 826           discriptionCheckboxAction();
 827         }
 828       });
 829
 830       syncState();
 831       this.add(searchBox);
 832       this.add(displayName);
 833       this.add(description);
 834     }
 835
 836     public void displayNameCheckboxAction()
 837     {
 838       aColChooser.setCurrentSearchPanel(this);
 839       aColChooser.updateView();
 840     }
 841
 842     public void discriptionCheckboxAction()
 843     {
 844       aColChooser.setCurrentSearchPanel(this);
 845       aColChooser.updateView();
 846     }
 847
 848     public void searchStringAction()
 849     {
 850       aColChooser.setCurrentSearchPanel(this);
 851       aColChooser.updateView();
 852     }
 853
 854     public void syncState()
 855     {
 856       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 857       if (sp != null)
 858       {
 859         description.setEnabled(sp.description.isEnabled());
 860         description.setSelected(sp.description.isSelected());
 861
 862         displayName.setEnabled(sp.displayName.isEnabled());
 863         displayName.setSelected(sp.displayName.isSelected());
 864
 865         searchBox.setText(sp.searchBox.getText());
 866       }
 867     }
 868   }
 869
 870 }