src/jalview/appletgui/AnnotationColumnChooser.java

   1 package jalview.appletgui;
   2
   3 import jalview.datamodel.AlignmentAnnotation;
   4 import jalview.datamodel.ColumnSelection;
   5 import jalview.gui.JvSwingUtils;
   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.Checkbox;
  13 import java.awt.Choice;
  14 import java.awt.Color;
  15 import java.awt.Dimension;
  16 import java.awt.Frame;
  17 import java.awt.Panel;
  18 import java.awt.TextField;
  19 import java.awt.event.ActionEvent;
  20 import java.awt.event.ActionListener;
  21 import java.awt.event.AdjustmentEvent;
  22 import java.awt.event.AdjustmentListener;
  23 import java.awt.event.ItemEvent;
  24 import java.awt.event.ItemListener;
  25 import java.awt.event.MouseAdapter;
  26 import java.awt.event.MouseEvent;
  27 import java.awt.event.MouseListener;
  28 import java.awt.event.TextEvent;
  29 import java.awt.event.TextListener;
  30 import java.util.Iterator;
  31 import java.util.Vector;
  32
  33 import javax.swing.JPanel;
  34
  35 //import net.miginfocom.swing.MigLayout;
  36
  37 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  38         ActionListener, AdjustmentListener, ItemListener, MouseListener
  39 {
  40
  41   private Choice annotations = new Choice();
  42
  43   private Panel actionPanel = new Panel();
  44
  45   private TitledPanel thresholdPanel = new TitledPanel();
  46
  47   private Panel switchableViewsPanel = new Panel(new CardLayout());
  48
  49   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  50           .getLayout());
  51
  52   private Panel noGraphFilterView = new Panel();
  53
  54   private Panel graphFilterView = new Panel();
  55
  56   private Panel annotationComboBoxPanel = new Panel();
  57
  58   private BorderLayout borderLayout1 = new BorderLayout();
  59
  60   private BorderLayout gBorderLayout = new BorderLayout();
  61
  62   private BorderLayout ngBorderLayout = new BorderLayout();
  63
  64   private Choice threshold = new Choice();
  65
  66   private StructureFilterPanel gStructureFilterPanel;
  67
  68   private StructureFilterPanel ngStructureFilterPanel;
  69
  70   private StructureFilterPanel currentStructureFilterPanel;
  71
  72   private SearchPanel currentSearchPanel;
  73
  74   private SearchPanel gSearchPanel;
  75
  76   private SearchPanel ngSearchPanel;
  77
  78   private FurtherActionPanel currentFurtherActionPanel;
  79
  80   private FurtherActionPanel gFurtherActionPanel;
  81
  82   private FurtherActionPanel ngFurtherActionPanel;
  83
  84   public static final int ACTION_OPTION_SELECT = 1;
  85
  86   public static int ACTION_OPTION_HIDE = 2;
  87
  88   public static String NO_GRAPH_VIEW = "0";
  89
  90   public static String GRAPH_VIEW = "1";
  91
  92   private int actionOption = ACTION_OPTION_SELECT;
  93
  94   private ColumnSelection oldColumnSelection;
  95
  96   public AnnotationColumnChooser()
  97   {
  98     try
  99     {
 100       jbInit();
 101     } catch (Exception ex)
 102     {
 103       ex.printStackTrace();
 104     }
 105   }
 106
 107   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 108   {
 109     super(av, ap);
 110     frame = new Frame();
 111     frame.add(this);
 112     jalview.bin.JalviewLite.addFrame(frame,
 113             MessageManager.getString("label.select_by_annotation"), 520,
 114             215);
 115
 116     slider.addAdjustmentListener(this);
 117     slider.addMouseListener(this);
 118
 119     if (av.getAlignment().getAlignmentAnnotation() == null)
 120     {
 121       return;
 122     }
 123     setOldColumnSelection(av.getColumnSelection());
 124     adjusting = true;
 125     Vector list = new Vector();
 126     int index = 1;
 127     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 128     {
 129       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 130       if (!list.contains(label))
 131       {
 132         list.addElement(label);
 133       }
 134       else
 135       {
 136         list.addElement(label + "_" + (index++));
 137       }
 138     }
 139
 140     for (int i = 0; i < list.size(); i++)
 141     {
 142       annotations.addItem(list.elementAt(i).toString());
 143     }
 144
 145     populateThresholdComboBox(threshold);
 146
 147     // restore Object state from the previous session if one exists
 148     if (av.getAnnotationColumnSelectionState() != null)
 149     {
 150       currentSearchPanel = av.getAnnotationColumnSelectionState()
 151               .getCurrentSearchPanel();
 152       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 153               .getCurrentStructureFilterPanel();
 154       annotations.select(av.getAnnotationColumnSelectionState()
 155               .getAnnotations().getSelectedIndex());
 156       threshold.select(av.getAnnotationColumnSelectionState()
 157               .getThreshold().getSelectedIndex());
 158       actionOption = av.getAnnotationColumnSelectionState()
 159               .getActionOption();
 160     }
 161
 162     try
 163     {
 164       jbInit();
 165     } catch (Exception ex)
 166     {
 167     }
 168     adjusting = false;
 169
 170     updateView();
 171     frame.invalidate();
 172     frame.pack();
 173   }
 174
 175   private void jbInit() throws Exception
 176   {
 177     ok.setLabel(MessageManager.getString("action.ok"));
 178
 179     cancel.setLabel(MessageManager.getString("action.cancel"));
 180
 181     thresholdValue.setEnabled(false);
 182     thresholdValue.setColumns(7);
 183
 184     ok.addActionListener(this);
 185     cancel.addActionListener(this);
 186     annotations.addItemListener(this);
 187     thresholdValue.addActionListener(this);
 188     threshold.addItemListener(this);
 189
 190     slider.setBackground(Color.white);
 191     slider.setEnabled(false);
 192     slider.setPreferredSize(new Dimension(100, 32));
 193
 194     thresholdPanel.setBackground(Color.white);
 195     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 196     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 197
 198     actionPanel.setBackground(Color.white);
 199     actionPanel.setFont(JvSwingUtils.getLabelFont());
 200
 201     graphFilterView.setLayout(gBorderLayout);
 202     graphFilterView.setBackground(Color.white);
 203
 204     noGraphFilterView.setLayout(ngBorderLayout);
 205     noGraphFilterView.setBackground(Color.white);
 206
 207     annotationComboBoxPanel.setBackground(Color.white);
 208     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 209
 210     gSearchPanel = new SearchPanel(this);
 211     ngSearchPanel = new SearchPanel(this);
 212     gFurtherActionPanel = new FurtherActionPanel(this);
 213     ngFurtherActionPanel = new FurtherActionPanel(this);
 214     gStructureFilterPanel = new StructureFilterPanel(this);
 215     ngStructureFilterPanel = new StructureFilterPanel(this);
 216
 217     thresholdPanel.setTitle("Threshold Filter");
 218     thresholdPanel.add(getThreshold());
 219     thresholdPanel.add(slider);
 220     thresholdPanel.add(thresholdValue);
 221
 222     actionPanel.add(ok);
 223     actionPanel.add(cancel);
 224
 225     JPanel staticPanel = new JPanel();
 226     staticPanel.setLayout(new BorderLayout());
 227     staticPanel.setBackground(Color.white);
 228
 229     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 230     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 231
 232     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 233     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 234     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 235
 236     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 237     noGraphFilterView.add(ngStructureFilterPanel,
 238             java.awt.BorderLayout.CENTER);
 239     noGraphFilterView.add(ngFurtherActionPanel,
 240             java.awt.BorderLayout.CENTER);
 241
 242     annotationComboBoxPanel.add(getAnnotations());
 243     switchableViewsPanel.add(noGraphFilterView,
 244             AnnotationColumnChooser.NO_GRAPH_VIEW);
 245     switchableViewsPanel.add(graphFilterView,
 246             AnnotationColumnChooser.GRAPH_VIEW);
 247
 248     this.setLayout(borderLayout1);
 249     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 250     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 251     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 252
 253     selectedAnnotationChanged();
 254     this.validate();
 255   }
 256
 257   @SuppressWarnings("unchecked")
 258   public void reset()
 259   {
 260     if (this.getOldColumnSelection() != null)
 261     {
 262       av.getColumnSelection().clear();
 263
 264       if (av.getAnnotationColumnSelectionState() != null)
 265       {
 266         ColumnSelection oldSelection = av
 267                 .getAnnotationColumnSelectionState()
 268                 .getOldColumnSelection();
 269         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 270                 && !oldSelection.getHiddenColumns().isEmpty())
 271         {
 272           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 273                   .iterator(); itr.hasNext();)
 274           {
 275             int positions[] = itr.next();
 276             av.hideColumns(positions[0], positions[1]);
 277           }
 278         }
 279         av.setColumnSelection(oldSelection);
 280       }
 281       ap.paintAlignment(true);
 282     }
 283
 284   }
 285
 286   public void adjustmentValueChanged(AdjustmentEvent evt)
 287   {
 288     if (!adjusting)
 289     {
 290       thresholdValue.setText((slider.getValue() / 1000f) + "");
 291       valueChanged(!sliderDragging);
 292     }
 293   }
 294
 295   protected void addSliderMouseListeners()
 296   {
 297
 298     slider.addMouseListener(new MouseAdapter()
 299     {
 300       @Override
 301       public void mousePressed(MouseEvent e)
 302       {
 303         sliderDragging = true;
 304         super.mousePressed(e);
 305       }
 306
 307       @Override
 308       public void mouseDragged(MouseEvent e)
 309       {
 310         sliderDragging = true;
 311         super.mouseDragged(e);
 312       }
 313
 314       @Override
 315       public void mouseReleased(MouseEvent evt)
 316       {
 317         if (sliderDragging)
 318         {
 319           sliderDragging = false;
 320           valueChanged(true);
 321         }
 322         ap.paintAlignment(true);
 323       }
 324     });
 325   }
 326
 327   public void valueChanged(boolean updateAllAnnotation)
 328   {
 329     if (slider.isEnabled())
 330     {
 331       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 332       updateView();
 333       ap.paintAlignment(false);
 334     }
 335   }
 336
 337   public Choice getThreshold()
 338   {
 339     return threshold;
 340   }
 341
 342   public void setThreshold(Choice threshold)
 343   {
 344     this.threshold = threshold;
 345   }
 346
 347   public Choice getAnnotations()
 348   {
 349     return annotations;
 350   }
 351
 352   public void setAnnotations(Choice annotations)
 353   {
 354     this.annotations = annotations;
 355   }
 356
 357   @Override
 358   public void updateView()
 359   {
 360     // Check if combobox is still adjusting
 361     if (adjusting)
 362     {
 363       return;
 364     }
 365
 366     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 367     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 368             .getSelectedIndex()]);
 369
 370     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 371             .getSelectedIndex());
 372
 373     slider.setEnabled(true);
 374     thresholdValue.setEnabled(true);
 375
 376     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 377     {
 378       slider.setEnabled(false);
 379       thresholdValue.setEnabled(false);
 380       thresholdValue.setText("");
 381       // build filter params
 382     }
 383     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 384     {
 385       if (getCurrentAnnotation().threshold == null)
 386       {
 387         getCurrentAnnotation()
 388                 .setThreshold(
 389                         new jalview.datamodel.GraphLine(
 390                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 391                                 "Threshold", Color.black));
 392       }
 393
 394       adjusting = true;
 395       float range = getCurrentAnnotation().graphMax * 1000
 396               - getCurrentAnnotation().graphMin * 1000;
 397
 398       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 399       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 400       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 401       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 402       // slider.setMajorTickSpacing((int) (range / 10f));
 403       slider.setEnabled(true);
 404       thresholdValue.setEnabled(true);
 405       adjusting = false;
 406
 407       // build filter params
 408       filterParams
 409               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 410       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 411       {
 412         filterParams
 413                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 414
 415         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 416         {
 417           filterParams
 418                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 419         }
 420         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 421         {
 422           filterParams
 423                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 424         }
 425       }
 426     }
 427
 428     if (currentStructureFilterPanel != null)
 429     {
 430       if (currentStructureFilterPanel.alphaHelix.getState())
 431       {
 432         filterParams.setFilterAlphaHelix(true);
 433       }
 434       if (currentStructureFilterPanel.betaStrand.getState())
 435       {
 436         filterParams.setFilterBetaSheet(true);
 437       }
 438       if (currentStructureFilterPanel.turn.getState())
 439       {
 440         filterParams.setFilterTurn(true);
 441       }
 442     }
 443
 444     if (currentSearchPanel != null)
 445     {
 446
 447       if (!currentSearchPanel.searchBox.getText().isEmpty())
 448       {
 449         currentSearchPanel.description.setEnabled(true);
 450         currentSearchPanel.displayName.setEnabled(true);
 451         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 452         if (currentSearchPanel.displayName.getState())
 453         {
 454           filterParams
 455                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 456         }
 457         if (currentSearchPanel.description.getState())
 458         {
 459           filterParams
 460                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 461         }
 462       }
 463       else
 464       {
 465         currentSearchPanel.description.setEnabled(false);
 466         currentSearchPanel.displayName.setEnabled(false);
 467       }
 468     }
 469
 470     av.getColumnSelection().filterAnnotations(
 471             getCurrentAnnotation().annotations, filterParams);
 472
 473     av.showAllHiddenColumns();
 474     if (getActionOption() == ACTION_OPTION_HIDE)
 475     {
 476       av.hideSelectedColumns();
 477     }
 478
 479     filterParams = null;
 480     av.setAnnotationColumnSelectionState(this);
 481     ap.paintAlignment(true);
 482   }
 483
 484   public ColumnSelection getOldColumnSelection()
 485   {
 486     return oldColumnSelection;
 487   }
 488
 489   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 490   {
 491     if (currentColumnSelection != null)
 492     {
 493       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 494     }
 495   }
 496
 497   public FurtherActionPanel getCurrentFutherActionPanel()
 498   {
 499     return currentFurtherActionPanel;
 500   }
 501
 502   public void setCurrentFutherActionPanel(
 503           FurtherActionPanel currentFutherActionPanel)
 504   {
 505     this.currentFurtherActionPanel = currentFutherActionPanel;
 506   }
 507
 508   public SearchPanel getCurrentSearchPanel()
 509   {
 510     return currentSearchPanel;
 511   }
 512
 513   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 514   {
 515     this.currentSearchPanel = currentSearchPanel;
 516   }
 517
 518   public int getActionOption()
 519   {
 520     return actionOption;
 521   }
 522
 523   public void setActionOption(int actionOption)
 524   {
 525     this.actionOption = actionOption;
 526   }
 527
 528   public StructureFilterPanel getCurrentStructureFilterPanel()
 529   {
 530     return currentStructureFilterPanel;
 531   }
 532
 533   public void setCurrentStructureFilterPanel(
 534           StructureFilterPanel currentStructureFilterPanel)
 535   {
 536     this.currentStructureFilterPanel = currentStructureFilterPanel;
 537   }
 538
 539   @Override
 540   public void itemStateChanged(ItemEvent e)
 541   {
 542     if (e.getSource() == annotations)
 543     {
 544       selectedAnnotationChanged();
 545     }
 546     else if (e.getSource() == threshold)
 547     {
 548       threshold_actionPerformed(null);
 549     }
 550   }
 551
 552   public void selectedAnnotationChanged()
 553   {
 554     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 555     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 556             .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
 557     {
 558       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 559     }
 560
 561     gSearchPanel.syncState();
 562     gFurtherActionPanel.syncState();
 563     gStructureFilterPanel.syncState();
 564
 565     ngSearchPanel.syncState();
 566     ngFurtherActionPanel.syncState();
 567     ngStructureFilterPanel.syncState();
 568
 569     switchableViewsLayout.show(switchableViewsPanel, currentView);
 570     updateView();
 571   }
 572
 573   public class FurtherActionPanel extends Panel implements
 574           ItemListener
 575   {
 576     private AnnotationColumnChooser aColChooser;
 577
 578     private Choice furtherAction = new Choice();
 579
 580     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 581     {
 582       this.aColChooser = aColChooser;
 583       furtherAction.addItem("Select");
 584       furtherAction.addItem("Hide");
 585       furtherAction.addItemListener(this);
 586       syncState();
 587
 588       // this.setTitle("Filter Actions");
 589       // this.setFont(JvSwingUtils.getLabelFont());
 590
 591       this.add(furtherAction);
 592     }
 593
 594     public void syncState()
 595     {
 596       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 597       {
 598         furtherAction.select("Hide");
 599       }
 600       else
 601       {
 602         furtherAction.select("Select");
 603       }
 604     }
 605
 606     @Override
 607     public void itemStateChanged(ItemEvent e)
 608     {
 609       aColChooser.setCurrentFutherActionPanel(this);
 610       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 611       {
 612         setActionOption(ACTION_OPTION_SELECT);
 613         updateView();
 614       }
 615       else
 616       {
 617         setActionOption(ACTION_OPTION_HIDE);
 618         updateView();
 619       }
 620
 621     }
 622   }
 623
 624   public class StructureFilterPanel extends TitledPanel implements
 625           ItemListener
 626   {
 627     private AnnotationColumnChooser aColChooser;
 628
 629     private Checkbox alphaHelix = new Checkbox();
 630
 631     private Checkbox betaStrand = new Checkbox();
 632
 633     private Checkbox turn = new Checkbox();
 634
 635     private Checkbox all = new Checkbox();
 636
 637     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 638     {
 639       this.aColChooser = aColChooser;
 640
 641       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 642       alphaHelix.setBackground(Color.white);
 643
 644       alphaHelix.addItemListener(this);
 645
 646       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 647       betaStrand.setBackground(Color.white);
 648       betaStrand.addItemListener(this);
 649
 650       turn.setLabel(MessageManager.getString("label.turn"));
 651       turn.setBackground(Color.white);
 652       turn.addItemListener(this);
 653
 654       all.setLabel(MessageManager.getString("label.select_all"));
 655       all.setBackground(Color.white);
 656       all.addItemListener(this);
 657
 658       this.setBackground(Color.white);
 659       this.setTitle("Structure Filter");
 660       this.setFont(JvSwingUtils.getLabelFont());
 661
 662       this.add(all);
 663       this.add(alphaHelix);
 664       this.add(betaStrand);
 665       this.add(turn);
 666     }
 667
 668     public void alphaHelix_actionPerformed()
 669     {
 670       updateSelectAllState();
 671       aColChooser.setCurrentStructureFilterPanel(this);
 672       aColChooser.updateView();
 673     }
 674
 675     public void betaStrand_actionPerformed()
 676     {
 677       updateSelectAllState();
 678       aColChooser.setCurrentStructureFilterPanel(this);
 679       aColChooser.updateView();
 680     }
 681
 682     public void turn_actionPerformed()
 683     {
 684       updateSelectAllState();
 685       aColChooser.setCurrentStructureFilterPanel(this);
 686       aColChooser.updateView();
 687     }
 688
 689     public void all_actionPerformed()
 690     {
 691       if (all.getState())
 692       {
 693         alphaHelix.setState(true);
 694         betaStrand.setState(true);
 695         turn.setState(true);
 696       }
 697       else
 698       {
 699         alphaHelix.setState(false);
 700         betaStrand.setState(false);
 701         turn.setState(false);
 702       }
 703       aColChooser.setCurrentStructureFilterPanel(this);
 704       aColChooser.updateView();
 705     }
 706
 707     public void updateSelectAllState()
 708     {
 709       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 710       {
 711         all.setState(true);
 712       }
 713       else
 714       {
 715         all.setState(false);
 716       }
 717     }
 718
 719     public void syncState()
 720     {
 721       StructureFilterPanel sfp = aColChooser
 722               .getCurrentStructureFilterPanel();
 723       if (sfp != null)
 724       {
 725         alphaHelix.setState(sfp.alphaHelix.getState());
 726         betaStrand.setState(sfp.betaStrand.getState());
 727         turn.setState(sfp.turn.getState());
 728         if (sfp.all.getState())
 729         {
 730           all.setState(true);
 731           alphaHelix.setState(true);
 732           betaStrand.setState(true);
 733           turn.setState(true);
 734         }
 735       }
 736
 737     }
 738
 739     @Override
 740     public void itemStateChanged(ItemEvent e)
 741     {
 742       if (e.getSource() == alphaHelix)
 743       {
 744         alphaHelix_actionPerformed();
 745       }
 746       else if (e.getSource() == betaStrand)
 747       {
 748         betaStrand_actionPerformed();
 749       }
 750       else if (e.getSource() == turn)
 751       {
 752         turn_actionPerformed();
 753       }
 754       else if (e.getSource() == all)
 755       {
 756         all_actionPerformed();
 757       }
 758     }
 759   }
 760
 761   public class SearchPanel extends TitledPanel implements ItemListener
 762   {
 763     private AnnotationColumnChooser aColChooser;
 764
 765     private Checkbox displayName = new Checkbox();
 766
 767     private Checkbox description = new Checkbox();
 768
 769     private TextField searchBox = new TextField(10);
 770
 771     public SearchPanel(AnnotationColumnChooser aColChooser)
 772     {
 773
 774       this.aColChooser = aColChooser;
 775       searchBox.addTextListener(new TextListener()
 776       {
 777
 778         @Override
 779         public void textValueChanged(TextEvent e)
 780         {
 781           searchStringAction();
 782
 783         }
 784
 785       });
 786
 787       displayName.setLabel(MessageManager.getString("label.display_name"));
 788       displayName.setEnabled(false);
 789       displayName.addItemListener(this);
 790
 791       description.setLabel(MessageManager.getString("label.description"));
 792       description.setEnabled(false);
 793       description.addItemListener(this);
 794       this.setTitle("Search Filter");
 795       this.setFont(JvSwingUtils.getLabelFont());
 796
 797       syncState();
 798       this.add(searchBox);
 799       this.add(displayName);
 800       this.add(description);
 801     }
 802
 803     public void displayNameCheckboxAction()
 804     {
 805       aColChooser.setCurrentSearchPanel(this);
 806       aColChooser.updateView();
 807     }
 808
 809     public void discriptionCheckboxAction()
 810     {
 811       aColChooser.setCurrentSearchPanel(this);
 812       aColChooser.updateView();
 813     }
 814
 815     public void searchStringAction()
 816     {
 817       aColChooser.setCurrentSearchPanel(this);
 818       aColChooser.updateView();
 819     }
 820
 821     public void syncState()
 822     {
 823       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 824       if (sp != null)
 825       {
 826         description.setEnabled(sp.description.isEnabled());
 827         description.setState(sp.description.getState());
 828
 829         displayName.setEnabled(sp.displayName.isEnabled());
 830         displayName.setState(sp.displayName.getState());
 831
 832         searchBox.setText(sp.searchBox.getText());
 833       }
 834     }
 835
 836     @Override
 837     public void itemStateChanged(ItemEvent e)
 838     {
 839       if (e.getSource() == displayName)
 840       {
 841         displayNameCheckboxAction();
 842       }
 843       else if (e.getSource() == description)
 844       {
 845         discriptionCheckboxAction();
 846       }
 847
 848     }
 849   }
 850
 851   public void actionPerformed(ActionEvent evt)
 852   {
 853     if (evt.getSource() == thresholdValue)
 854     {
 855       try
 856       {
 857         float f = new Float(thresholdValue.getText()).floatValue();
 858         slider.setValue((int) (f * 1000));
 859         adjustmentValueChanged(null);
 860       } catch (NumberFormatException ex)
 861       {
 862       }
 863     }
 864
 865     else if (evt.getSource() == ok)
 866     {
 867       ok_actionPerformed(null);
 868     }
 869     else if (evt.getSource() == cancel)
 870     {
 871       cancel_actionPerformed(null);
 872     }
 873     else if (evt.getSource() == thresholdValue)
 874     {
 875       thresholdValue_actionPerformed(null);
 876     }
 877     else
 878     {
 879       updateView();
 880     }
 881   }
 882
 883   @Override
 884   public void mouseClicked(MouseEvent e)
 885   {
 886     // TODO Auto-generated method stub
 887
 888   }
 889
 890   @Override
 891   public void mousePressed(MouseEvent e)
 892   {
 893     if (e.getSource() == slider)
 894     {
 895       updateView();
 896     }
 897
 898   }
 899
 900   @Override
 901   public void mouseReleased(MouseEvent e)
 902   {
 903     if (e.getSource() == slider)
 904     {
 905       updateView();
 906     }
 907   }
 908
 909   @Override
 910   public void mouseEntered(MouseEvent e)
 911   {
 912     if (e.getSource() == slider)
 913     {
 914       updateView();
 915     }
 916   }
 917
 918   @Override
 919   public void mouseExited(MouseEvent e)
 920   {
 921     if (e.getSource() == slider)
 922     {
 923       updateView();
 924     }
 925   }
 926
 927 }