src/jalview/gui/AnnotationColumnChooser.java

   1 package jalview.gui;
   2
   3 import jalview.api.analysis.AnnotationFilterParameter;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.ColumnSelection;
   6 import jalview.schemes.AnnotationColourGradient;
   7 import jalview.util.MessageManager;
   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.JButton;
  21 import javax.swing.JCheckBox;
  22 import javax.swing.JComboBox;
  23 import javax.swing.JInternalFrame;
  24 import javax.swing.JLabel;
  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 JLabel annotationLabel = new JLabel();
  62
  63   private BorderLayout borderLayout1 = new BorderLayout();
  64
  65   private JComboBox<String> threshold = new JComboBox<String>();
  66
  67   private StructureFilterPanel gStructureFilterPanel;
  68
  69   private StructureFilterPanel ngStructureFilterPanel;
  70
  71   private StructureFilterPanel currentStructureFilterPanel;
  72
  73   private SearchPanel currentSearchPanel;
  74
  75   private SearchPanel gSearchPanel;
  76
  77   private SearchPanel ngSearchPanel;
  78
  79   private FurtherActionPanel currentFurtherActionPanel;
  80
  81   private FurtherActionPanel gFurtherActionPanel;
  82
  83   private FurtherActionPanel ngFurtherActionPanel;
  84
  85   public static final int ACTION_OPTION_SELECT = 1;
  86
  87   public static int ACTION_OPTION_HIDE = 2;
  88
  89   public static String NO_GRAPH_VIEW = "0";
  90
  91   public static String GRAPH_VIEW = "1";
  92
  93   private int actionOption = ACTION_OPTION_SELECT;
  94
  95   private ColumnSelection oldColumnSelection;
  96
  97   public AnnotationColumnChooser()
  98   {
  99     try
 100     {
 101       jbInit();
 102     } catch (Exception ex)
 103     {
 104       ex.printStackTrace();
 105     }
 106   }
 107
 108   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 109   {
 110     super(av, ap);
 111     frame = new JInternalFrame();
 112     frame.setContentPane(this);
 113     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 114     Desktop.addInternalFrame(frame,
 115             MessageManager.getString("label.select_by_annotation"), 520,
 116             215);
 117
 118     addSliderChangeListener();
 119     addSliderMouseListeners();
 120
 121     if (av.getAlignment().getAlignmentAnnotation() == null)
 122     {
 123       return;
 124     }
 125     setOldColumnSelection(av.getColumnSelection());
 126     adjusting = true;
 127
 128     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 129     populateThresholdComboBox(threshold);
 130
 131     // restore Object state from the previous session if one exists
 132     if (av.getAnnotationColumnSelectionState() != null)
 133     {
 134       currentSearchPanel = av.getAnnotationColumnSelectionState()
 135               .getCurrentSearchPanel();
 136       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 137               .getCurrentStructureFilterPanel();
 138       annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
 139               .getAnnotations().getSelectedIndex());
 140       threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
 141               .getThreshold().getSelectedIndex());
 142       actionOption = av.getAnnotationColumnSelectionState()
 143               .getActionOption();
 144     }
 145
 146     try
 147     {
 148       jbInit();
 149     } catch (Exception ex)
 150     {
 151     }
 152     adjusting = false;
 153
 154     updateView();
 155     frame.invalidate();
 156     frame.pack();
 157   }
 158
 159   private void jbInit() throws Exception
 160   {
 161     ok.setOpaque(false);
 162     ok.setText(MessageManager.getString("action.ok"));
 163     ok.addActionListener(new ActionListener()
 164     {
 165       @Override
 166       public void actionPerformed(ActionEvent e)
 167       {
 168         ok_actionPerformed(e);
 169       }
 170     });
 171
 172     cancel.setOpaque(false);
 173     cancel.setText(MessageManager.getString("action.cancel"));
 174     cancel.addActionListener(new ActionListener()
 175     {
 176       @Override
 177       public void actionPerformed(ActionEvent e)
 178       {
 179         cancel_actionPerformed(e);
 180       }
 181     });
 182
 183     annotations.addItemListener(this);
 184     threshold.addActionListener(new ActionListener()
 185     {
 186       @Override
 187       public void actionPerformed(ActionEvent e)
 188       {
 189         threshold_actionPerformed(e);
 190       }
 191     });
 192
 193     thresholdValue.setEnabled(false);
 194     thresholdValue.setColumns(7);
 195     thresholdValue.addActionListener(new ActionListener()
 196     {
 197       @Override
 198       public void actionPerformed(ActionEvent e)
 199       {
 200         thresholdValue_actionPerformed(e);
 201       }
 202     });
 203
 204     slider.setPaintLabels(false);
 205     slider.setPaintTicks(true);
 206     slider.setBackground(Color.white);
 207     slider.setEnabled(false);
 208     slider.setOpaque(false);
 209     slider.setPreferredSize(new Dimension(100, 32));
 210
 211     annotationLabel.setBackground(Color.white);
 212     annotationLabel.setFont(JvSwingUtils.getLabelFont());
 213     annotationLabel.setText("Select Annotation : ");
 214
 215     thresholdPanel.setBorder(new TitledBorder("Threshold Filter"));
 216     thresholdPanel.setBackground(Color.white);
 217     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 218     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 219
 220     actionPanel.setBackground(Color.white);
 221     actionPanel.setFont(JvSwingUtils.getLabelFont());
 222
 223     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 224     graphFilterView.setBackground(Color.white);
 225
 226     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 227     noGraphFilterView.setBackground(Color.white);
 228     annotationComboBoxPanel.setBackground(Color.white);
 229     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 230
 231     gSearchPanel = new SearchPanel(this);
 232     ngSearchPanel = new SearchPanel(this);
 233     gFurtherActionPanel = new FurtherActionPanel(this);
 234     ngFurtherActionPanel = new FurtherActionPanel(this);
 235     gStructureFilterPanel = new StructureFilterPanel(this);
 236     ngStructureFilterPanel = new StructureFilterPanel(this);
 237
 238     thresholdPanel.add(getThreshold());
 239     thresholdPanel.add(thresholdValue, "wrap");
 240     thresholdPanel.add(slider, "grow, span, wrap");
 241
 242     actionPanel.add(ok);
 243     actionPanel.add(cancel);
 244
 245     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 246     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 247     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 248     graphFilterView.add(gFurtherActionPanel);
 249
 250     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 251     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 252     noGraphFilterView.add(ngFurtherActionPanel);
 253
 254     annotationComboBoxPanel.add(getAnnotations());
 255     switchableViewsPanel.add(noGraphFilterView,
 256             AnnotationColumnChooser.NO_GRAPH_VIEW);
 257     switchableViewsPanel.add(graphFilterView,
 258             AnnotationColumnChooser.GRAPH_VIEW);
 259
 260     this.setLayout(borderLayout1);
 261     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 262     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 263     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 264
 265     selectedAnnotationChanged();
 266     this.validate();
 267   }
 268
 269   @SuppressWarnings("unchecked")
 270   public void reset()
 271   {
 272     if (this.getOldColumnSelection() != null)
 273     {
 274       av.getColumnSelection().clear();
 275
 276       if (av.getAnnotationColumnSelectionState() != null)
 277       {
 278         ColumnSelection oldSelection = av
 279                 .getAnnotationColumnSelectionState()
 280                 .getOldColumnSelection();
 281         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 282                 && !oldSelection.getHiddenColumns().isEmpty())
 283         {
 284           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 285                   .iterator(); itr.hasNext();)
 286           {
 287             int positions[] = itr.next();
 288             av.hideColumns(positions[0], positions[1]);
 289           }
 290         }
 291         av.setColumnSelection(oldSelection);
 292       }
 293       ap.paintAlignment(true);
 294     }
 295
 296   }
 297
 298   public void valueChanged(boolean updateAllAnnotation)
 299   {
 300     if (slider.isEnabled())
 301     {
 302       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 303       updateView();
 304       propagateSeqAssociatedThreshold(updateAllAnnotation,
 305               getCurrentAnnotation());
 306       ap.paintAlignment(false);
 307     }
 308   }
 309
 310   public JComboBox<String> getThreshold()
 311   {
 312     return threshold;
 313   }
 314
 315   public void setThreshold(JComboBox<String> threshold)
 316   {
 317     this.threshold = threshold;
 318   }
 319
 320   public JComboBox<String> getAnnotations()
 321   {
 322     return annotations;
 323   }
 324
 325   public void setAnnotations(JComboBox<String> annotations)
 326   {
 327     this.annotations = annotations;
 328   }
 329
 330   @Override
 331   public void updateView()
 332   {
 333     // Check if combobox is still adjusting
 334     if (adjusting)
 335     {
 336       return;
 337     }
 338
 339     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 340
 341     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 342             .getSelectedIndex()]]);
 343
 344     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 345             .getSelectedIndex());
 346
 347     slider.setEnabled(true);
 348     thresholdValue.setEnabled(true);
 349
 350     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 351     {
 352       slider.setEnabled(false);
 353       thresholdValue.setEnabled(false);
 354       thresholdValue.setText("");
 355       // build filter params
 356     }
 357     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 358     {
 359       if (getCurrentAnnotation().threshold == null)
 360       {
 361         getCurrentAnnotation()
 362                 .setThreshold(
 363                         new jalview.datamodel.GraphLine(
 364                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 365                                 "Threshold", Color.black));
 366       }
 367
 368       adjusting = true;
 369       float range = getCurrentAnnotation().graphMax * 1000
 370               - getCurrentAnnotation().graphMin * 1000;
 371
 372       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 373       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 374       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 375       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 376       slider.setMajorTickSpacing((int) (range / 10f));
 377       slider.setEnabled(true);
 378       thresholdValue.setEnabled(true);
 379       adjusting = false;
 380
 381       // build filter params
 382       filterParams
 383               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 384       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 385       {
 386
 387         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 388         {
 389           filterParams
 390                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 391         }
 392         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 393         {
 394           filterParams
 395                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 396         }
 397       }
 398     }
 399
 400     if (currentStructureFilterPanel != null)
 401     {
 402       if (currentStructureFilterPanel.getAlphaHelix().isSelected())
 403       {
 404         filterParams.setFilterAlphaHelix(true);
 405       }
 406       if (currentStructureFilterPanel.getBetaStrand().isSelected())
 407       {
 408         filterParams.setFilterBetaSheet(true);
 409       }
 410       if (currentStructureFilterPanel.getTurn().isSelected())
 411       {
 412         filterParams.setFilterTurn(true);
 413       }
 414     }
 415
 416     if (currentSearchPanel != null)
 417     {
 418       if (!currentSearchPanel.getSearchString().isEmpty())
 419       {
 420         currentSearchPanel.getDescription().setEnabled(true);
 421         currentSearchPanel.getDisplayName().setEnabled(true);
 422         filterParams.setRegexString(currentSearchPanel.getSearchString());
 423         if (currentSearchPanel.isDisplayNameChecked())
 424         {
 425           filterParams
 426                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 427         }
 428         if (currentSearchPanel.isDescriptionChecked())
 429         {
 430           filterParams
 431                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 432         }
 433       }
 434       else
 435       {
 436         currentSearchPanel.getDescription().setEnabled(false);
 437         currentSearchPanel.getDisplayName().setEnabled(false);
 438       }
 439     }
 440
 441     filterAnnotations(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 void select_action(ActionEvent actionEvent)
 469   {
 470     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 471     if (radioButton.isSelected())
 472     {
 473       setActionOption(ACTION_OPTION_SELECT);
 474       updateView();
 475     }
 476   }
 477
 478   public void hide_action(ActionEvent actionEvent)
 479   {
 480     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 481     if (radioButton.isSelected())
 482     {
 483       setActionOption(ACTION_OPTION_HIDE);
 484       updateView();
 485     }
 486   }
 487
 488   @Override
 489   public void itemStateChanged(ItemEvent e)
 490   {
 491     selectedAnnotationChanged();
 492   }
 493
 494   public void selectedAnnotationChanged()
 495   {
 496     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 497     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 498             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 499     {
 500       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 501     }
 502
 503     gSearchPanel.syncState();
 504     gFurtherActionPanel.syncState();
 505     gStructureFilterPanel.syncState();
 506
 507     ngSearchPanel.syncState();
 508     ngFurtherActionPanel.syncState();
 509     ngStructureFilterPanel.syncState();
 510
 511     switchableViewsLayout.show(switchableViewsPanel, currentView);
 512     updateView();
 513   }
 514
 515   public FurtherActionPanel getCurrentFutherActionPanel()
 516   {
 517     return currentFurtherActionPanel;
 518   }
 519
 520   public void setCurrentFutherActionPanel(
 521           FurtherActionPanel currentFutherActionPanel)
 522   {
 523     this.currentFurtherActionPanel = currentFutherActionPanel;
 524   }
 525
 526   public SearchPanel getCurrentSearchPanel()
 527   {
 528     return currentSearchPanel;
 529   }
 530
 531   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 532   {
 533     this.currentSearchPanel = currentSearchPanel;
 534   }
 535
 536   public int getActionOption()
 537   {
 538     return actionOption;
 539   }
 540
 541   public void setActionOption(int actionOption)
 542   {
 543     this.actionOption = actionOption;
 544   }
 545
 546   public StructureFilterPanel getCurrentStructureFilterPanel()
 547   {
 548     return currentStructureFilterPanel;
 549   }
 550
 551   public void setCurrentStructureFilterPanel(
 552           StructureFilterPanel currentStructureFilterPanel)
 553   {
 554     this.currentStructureFilterPanel = currentStructureFilterPanel;
 555   }
 556
 557   public class FurtherActionPanel extends JPanel
 558   {
 559     private AnnotationColumnChooser aColChooser;
 560
 561     private JRadioButton hideOption = new JRadioButton();
 562
 563     private JRadioButton selectOption = new JRadioButton();
 564
 565     private ButtonGroup optionsGroup = new ButtonGroup();
 566
 567     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 568     {
 569       this.aColChooser = aColChooser;
 570       getSelectOption().setBackground(Color.white);
 571       getSelectOption().setFont(JvSwingUtils.getLabelFont());
 572       getSelectOption().setText("Select");
 573       getSelectOption().addActionListener(new ActionListener()
 574       {
 575         @Override
 576         public void actionPerformed(ActionEvent actionEvent)
 577         {
 578           selectRadioAction(actionEvent);
 579         }
 580       });
 581
 582       getHideOption().setBackground(Color.white);
 583       getHideOption().setFont(JvSwingUtils.getLabelFont());
 584       getHideOption().setText("Hide");
 585       getHideOption().addActionListener(new ActionListener()
 586       {
 587         @Override
 588         public void actionPerformed(ActionEvent actionEvent)
 589         {
 590           hideRadioAction(actionEvent);
 591         }
 592       });
 593
 594       getOptionsGroup().add(getSelectOption());
 595       getOptionsGroup().add(getHideOption());
 596       getOptionsGroup().setSelected(getSelectOption().getModel(), true);
 597
 598       this.setBackground(Color.white);
 599       this.setFont(JvSwingUtils.getLabelFont());
 600       syncState();
 601
 602       this.add(getSelectOption());
 603       this.add(getHideOption());
 604     }
 605
 606     public void selectRadioAction(ActionEvent actionEvent)
 607     {
 608       aColChooser.setCurrentFutherActionPanel(this);
 609       aColChooser.select_action(actionEvent);
 610     }
 611
 612     public void hideRadioAction(ActionEvent actionEvent)
 613     {
 614       aColChooser.setCurrentFutherActionPanel(this);
 615       aColChooser.hide_action(actionEvent);
 616     }
 617
 618     public JRadioButton getHideOption()
 619     {
 620       return hideOption;
 621     }
 622
 623     public void setHideOption(JRadioButton hideOption)
 624     {
 625       this.hideOption = hideOption;
 626     }
 627
 628     public JRadioButton getSelectOption()
 629     {
 630       return selectOption;
 631     }
 632
 633     public void setSelectOption(JRadioButton selectOption)
 634     {
 635       this.selectOption = selectOption;
 636     }
 637
 638     public ButtonGroup getOptionsGroup()
 639     {
 640       return optionsGroup;
 641     }
 642
 643     public void setOptionsGroup(ButtonGroup optionsGroup)
 644     {
 645       this.optionsGroup = optionsGroup;
 646     }
 647
 648     public void syncState()
 649     {
 650       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 651       {
 652         this.getOptionsGroup().setSelected(this.getHideOption().getModel(),
 653                 true);
 654       }
 655       else
 656       {
 657         this.getOptionsGroup().setSelected(
 658                 this.getSelectOption().getModel(), true);
 659       }
 660     }
 661   }
 662
 663   public class StructureFilterPanel extends JPanel
 664   {
 665     private AnnotationColumnChooser aColChooser;
 666
 667     private JCheckBox alphaHelix = new JCheckBox();
 668
 669     private JCheckBox betaStrand = new JCheckBox();
 670
 671     private JCheckBox turn = new JCheckBox();
 672
 673     private JCheckBox all = new JCheckBox();
 674
 675     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 676     {
 677       this.aColChooser = aColChooser;
 678
 679       alphaHelix.setBackground(Color.white);
 680       alphaHelix.setFont(JvSwingUtils.getLabelFont());
 681       alphaHelix.setText("Alpha Helix");
 682       alphaHelix.addActionListener(new ActionListener()
 683       {
 684         @Override
 685         public void actionPerformed(ActionEvent actionEvent)
 686         {
 687           alphaHelix_actionPerformed();
 688         }
 689       });
 690
 691       betaStrand.setBackground(Color.white);
 692       betaStrand.setFont(JvSwingUtils.getLabelFont());
 693       betaStrand.setText("Beta Strand");
 694       betaStrand.addActionListener(new ActionListener()
 695       {
 696         @Override
 697         public void actionPerformed(ActionEvent actionEvent)
 698         {
 699           betaStrand_actionPerformed();
 700         }
 701       });
 702
 703       turn.setBackground(Color.white);
 704       turn.setFont(JvSwingUtils.getLabelFont());
 705       turn.setText("Turn");
 706       turn.addActionListener(new ActionListener()
 707       {
 708         @Override
 709         public void actionPerformed(ActionEvent actionEvent)
 710         {
 711           turn_actionPerformed();
 712         }
 713       });
 714
 715       all.setBackground(Color.white);
 716       all.setFont(JvSwingUtils.getLabelFont());
 717       all.setText("Select all");
 718       all.addActionListener(new ActionListener()
 719       {
 720         @Override
 721         public void actionPerformed(ActionEvent actionEvent)
 722         {
 723           all_actionPerformed();
 724         }
 725       });
 726
 727       this.setBorder(new TitledBorder("Structures Filter"));
 728       this.setBackground(Color.white);
 729       this.setFont(JvSwingUtils.getLabelFont());
 730
 731       this.add(all);
 732       this.add(alphaHelix);
 733       this.add(betaStrand);
 734       this.add(turn);
 735     }
 736
 737     public void alphaHelix_actionPerformed()
 738     {
 739       updateSelectAllState();
 740       aColChooser.setCurrentStructureFilterPanel(this);
 741       aColChooser.updateView();
 742     }
 743
 744     public void betaStrand_actionPerformed()
 745     {
 746       updateSelectAllState();
 747       aColChooser.setCurrentStructureFilterPanel(this);
 748       aColChooser.updateView();
 749     }
 750
 751     public void turn_actionPerformed()
 752     {
 753       updateSelectAllState();
 754       aColChooser.setCurrentStructureFilterPanel(this);
 755       aColChooser.updateView();
 756     }
 757
 758     public void all_actionPerformed()
 759     {
 760       if (all.isSelected())
 761       {
 762         alphaHelix.setSelected(true);
 763         betaStrand.setSelected(true);
 764         turn.setSelected(true);
 765       }
 766       else
 767       {
 768         alphaHelix.setSelected(false);
 769         betaStrand.setSelected(false);
 770         turn.setSelected(false);
 771       }
 772       aColChooser.setCurrentStructureFilterPanel(this);
 773       aColChooser.updateView();
 774     }
 775
 776     public void updateSelectAllState()
 777     {
 778       if (alphaHelix.isSelected() && betaStrand.isSelected()
 779               && turn.isSelected())
 780       {
 781         all.setSelected(true);
 782       }
 783       else
 784       {
 785         all.setSelected(false);
 786       }
 787     }
 788
 789     public void syncState()
 790     {
 791       StructureFilterPanel sfp = aColChooser
 792               .getCurrentStructureFilterPanel();
 793       if (sfp != null)
 794       {
 795         alphaHelix.setSelected(sfp.getAlphaHelix().isSelected());
 796         betaStrand.setSelected(sfp.getBetaStrand().isSelected());
 797         turn.setSelected(sfp.getTurn().isSelected());
 798         if (sfp.getAll().isSelected())
 799         {
 800           all.setSelected(true);
 801           alphaHelix.setSelected(true);
 802           betaStrand.setSelected(true);
 803           turn.setSelected(true);
 804         }
 805       }
 806
 807     }
 808
 809     public JCheckBox getAlphaHelix()
 810     {
 811       return alphaHelix;
 812     }
 813
 814     public void setAlphaHelix(JCheckBox alphaHelix)
 815     {
 816       this.alphaHelix = alphaHelix;
 817     }
 818
 819     public JCheckBox getBetaStrand()
 820     {
 821       return betaStrand;
 822     }
 823
 824     public void setBetaStrand(JCheckBox betaStrand)
 825     {
 826       this.betaStrand = betaStrand;
 827     }
 828
 829     public JCheckBox getTurn()
 830     {
 831       return turn;
 832     }
 833
 834     public void setTurn(JCheckBox turn)
 835     {
 836       this.turn = turn;
 837     }
 838
 839     public JCheckBox getAll()
 840     {
 841       return all;
 842     }
 843
 844     public void setAll(JCheckBox all)
 845     {
 846       this.all = all;
 847
 848     }
 849   }
 850
 851   public class SearchPanel extends JPanel
 852   {
 853     private AnnotationColumnChooser aColChooser;
 854
 855     private JCheckBox displayName = new JCheckBox();
 856
 857     private JCheckBox description = new JCheckBox();
 858
 859     private JTextField searchBox = new JTextField(10);
 860
 861     private JCheckBox structuresFilter = new JCheckBox();
 862
 863     public SearchPanel(AnnotationColumnChooser aColChooser)
 864     {
 865
 866       this.aColChooser = aColChooser;
 867       this.setBorder(new TitledBorder("Search Filter"));
 868       this.setBackground(Color.white);
 869       this.setFont(JvSwingUtils.getLabelFont());
 870
 871       getSearchBox().setBackground(Color.white);
 872       getSearchBox().setFont(JvSwingUtils.getLabelFont());
 873       getSearchBox().getDocument().addDocumentListener(
 874               new DocumentListener()
 875               {
 876                 @Override
 877                 public void insertUpdate(DocumentEvent e)
 878                 {
 879                   searchStringAction();
 880                 }
 881
 882                 @Override
 883                 public void removeUpdate(DocumentEvent e)
 884                 {
 885                   searchStringAction();
 886                 }
 887
 888                 @Override
 889                 public void changedUpdate(DocumentEvent e)
 890                 {
 891                   searchStringAction();
 892                 }
 893               });
 894
 895       getDisplayName().setBackground(Color.white);
 896       getDisplayName().setFont(JvSwingUtils.getLabelFont());
 897       getDisplayName().setText("Display Name");
 898       getDisplayName().setEnabled(false);
 899       getDisplayName().addActionListener(new ActionListener()
 900       {
 901         @Override
 902         public void actionPerformed(ActionEvent actionEvent)
 903         {
 904           displayNameCheckboxAction();
 905         }
 906       });
 907
 908       getDescription().setBackground(Color.white);
 909       getDescription().setFont(JvSwingUtils.getLabelFont());
 910       getDescription().setText("Description");
 911       getDescription().setEnabled(false);
 912       getDescription().addActionListener(new ActionListener()
 913       {
 914         @Override
 915         public void actionPerformed(ActionEvent actionEvent)
 916         {
 917           discriptionCheckboxAction();
 918         }
 919       });
 920
 921       syncState();
 922       this.add(getSearchBox());
 923       this.add(getDisplayName());
 924       this.add(getDescription());
 925     }
 926
 927     public boolean isDescriptionChecked()
 928     {
 929       return getDescription().isSelected();
 930     }
 931
 932     public boolean isDisplayNameChecked()
 933     {
 934       return getDisplayName().isSelected();
 935     }
 936
 937     public String getSearchString()
 938     {
 939       return getSearchBox().getText();
 940     }
 941
 942     public void displayNameCheckboxAction()
 943     {
 944       aColChooser.setCurrentSearchPanel(this);
 945       aColChooser.updateView();
 946     }
 947
 948     public void discriptionCheckboxAction()
 949     {
 950       aColChooser.setCurrentSearchPanel(this);
 951       aColChooser.updateView();
 952     }
 953
 954     public void searchStringAction()
 955     {
 956       aColChooser.setCurrentSearchPanel(this);
 957       aColChooser.updateView();
 958     }
 959
 960     public JCheckBox getDisplayName()
 961     {
 962       return displayName;
 963     }
 964
 965     public void setDisplayName(JCheckBox displayName)
 966     {
 967       this.displayName = displayName;
 968     }
 969
 970     public JCheckBox getDescription()
 971     {
 972       return description;
 973     }
 974
 975     public void setDescription(JCheckBox description)
 976     {
 977       this.description = description;
 978     }
 979
 980     public JTextField getSearchBox()
 981     {
 982       return searchBox;
 983     }
 984
 985     public void setSearchBox(JTextField searchBox)
 986     {
 987       this.searchBox = searchBox;
 988     }
 989
 990     public JCheckBox getStructuresFilter()
 991     {
 992       return structuresFilter;
 993     }
 994
 995     public void setStructuresFilter(JCheckBox structuresFilter)
 996     {
 997       this.structuresFilter = structuresFilter;
 998     }
 999
1000     public void syncState()
1001     {
1002       SearchPanel sp = aColChooser.getCurrentSearchPanel();
1003       if (sp != null)
1004       {
1005         description.setEnabled(sp.getDescription().isEnabled());
1006         description.setSelected(sp.getDescription().isSelected());
1007
1008         displayName.setEnabled(sp.getDisplayName().isEnabled());
1009         displayName.setSelected(sp.getDisplayName().isSelected());
1010
1011         searchBox.setText(sp.getSearchBox().getText());
1012       }
1013     }
1014   }
1015
1016 }