src/jalview/appletgui/AnnotationColumnChooser.java

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