unused/appletgui/AnnotationColumnChooser.java

   1 package jalview.appletgui;
   2
   3 import jalview.bin.JalviewLite;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.ColumnSelection;
   6 import jalview.datamodel.GraphLine;
   7 import jalview.schemes.AnnotationColourGradient;
   8 import jalview.util.MessageManager;
   9 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  10
  11 import java.awt.BorderLayout;
  12 import java.awt.CardLayout;
  13 import java.awt.Checkbox;
  14 import java.awt.Choice;
  15 import java.awt.Color;
  16 import java.awt.Dimension;
  17 import java.awt.Frame;
  18 import java.awt.Panel;
  19 import java.awt.TextField;
  20 import java.awt.event.ActionEvent;
  21 import java.awt.event.ActionListener;
  22 import java.awt.event.AdjustmentEvent;
  23 import java.awt.event.AdjustmentListener;
  24 import java.awt.event.ItemEvent;
  25 import java.awt.event.ItemListener;
  26 import java.awt.event.MouseAdapter;
  27 import java.awt.event.MouseEvent;
  28 import java.awt.event.MouseListener;
  29 import java.awt.event.TextEvent;
  30 import java.awt.event.TextListener;
  31 import java.util.Iterator;
  32 import java.util.Vector;
  33
  34 import javax.swing.JPanel;
  35
  36 //import net.miginfocom.swing.MigLayout;
  37
  38 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  39         ActionListener, AdjustmentListener, ItemListener, MouseListener
  40 {
  41
  42   private Choice annotations = new Choice();
  43
  44   private Panel actionPanel = new Panel();
  45
  46   private TitledPanel thresholdPanel = new TitledPanel();
  47
  48   private Panel switchableViewsPanel = new Panel(new CardLayout());
  49
  50   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  51           .getLayout());
  52
  53   private Panel noGraphFilterView = new Panel();
  54
  55   private Panel graphFilterView = new Panel();
  56
  57   private Panel annotationComboBoxPanel = new Panel();
  58
  59   private BorderLayout borderLayout1 = new BorderLayout();
  60
  61   private BorderLayout gBorderLayout = new BorderLayout();
  62
  63   private BorderLayout ngBorderLayout = new BorderLayout();
  64
  65   private Choice threshold = new Choice();
  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 JFrame();
 112     frame.add(this);
 113     JalviewLite.addFrame(frame,
 114             MessageManager.getString("label.select_by_annotation"), 520,
 115             215);
 116
 117     slider.addAdjustmentListener(this);
 118     slider.addMouseListener(this);
 119
 120     if (av.getAlignment().getAlignmentAnnotation() == null)
 121     {
 122       return;
 123     }
 124     setOldColumnSelection(av.getColumnSelection());
 125     adjusting = true;
 126     Vector list = new Vector();
 127     int index = 1;
 128     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 129     {
 130       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 131       if (!list.contains(label))
 132       {
 133         list.addElement(label);
 134       }
 135       else
 136       {
 137         list.addElement(label + "_" + (index++));
 138       }
 139     }
 140
 141     for (int i = 0; i < list.size(); i++)
 142     {
 143       annotations.addItem(list.elementAt(i).toString());
 144     }
 145
 146     populateThresholdComboBox(threshold);
 147
 148     // restore Object state from the previous session if one exists
 149     if (av.getAnnotationColumnSelectionState() != null)
 150     {
 151       currentSearchPanel = av.getAnnotationColumnSelectionState()
 152               .getCurrentSearchPanel();
 153       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 154               .getCurrentStructureFilterPanel();
 155       annotations.select(av.getAnnotationColumnSelectionState()
 156               .getAnnotations().getSelectedIndex());
 157       threshold.select(av.getAnnotationColumnSelectionState()
 158               .getThreshold().getSelectedIndex());
 159       actionOption = av.getAnnotationColumnSelectionState()
 160               .getActionOption();
 161     }
 162
 163     try
 164     {
 165       jbInit();
 166     } catch (Exception ex)
 167     {
 168     }
 169     adjusting = false;
 170
 171     updateView();
 172     frame.invalidate();
 173     frame.pack();
 174   }
 175
 176   private void jbInit() throws Exception
 177   {
 178     ok.setLabel(MessageManager.getString("action.ok"));
 179
 180     cancel.setLabel(MessageManager.getString("action.cancel"));
 181
 182     thresholdValue.setEnabled(false);
 183     thresholdValue.setColumns(7);
 184
 185     ok.addActionListener(this);
 186     cancel.addActionListener(this);
 187     annotations.addItemListener(this);
 188     thresholdValue.addActionListener(this);
 189     threshold.addItemListener(this);
 190
 191     slider.setBackground(Color.white);
 192     slider.setEnabled(false);
 193     slider.setPreferredSize(new Dimension(100, 32));
 194
 195     thresholdPanel.setBackground(Color.white);
 196     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 197     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 198
 199     actionPanel.setBackground(Color.white);
 200     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 201
 202     graphFilterView.setLayout(gBorderLayout);
 203     graphFilterView.setBackground(Color.white);
 204
 205     noGraphFilterView.setLayout(ngBorderLayout);
 206     noGraphFilterView.setBackground(Color.white);
 207
 208     annotationComboBoxPanel.setBackground(Color.white);
 209     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 210
 211     gSearchPanel = new SearchPanel(this);
 212     ngSearchPanel = new SearchPanel(this);
 213     gFurtherActionPanel = new FurtherActionPanel(this);
 214     ngFurtherActionPanel = new FurtherActionPanel(this);
 215     gStructureFilterPanel = new StructureFilterPanel(this);
 216     ngStructureFilterPanel = new StructureFilterPanel(this);
 217
 218     thresholdPanel.setTitle("Threshold Filter");
 219     thresholdPanel.add(getThreshold());
 220     thresholdPanel.add(slider);
 221     thresholdPanel.add(thresholdValue);
 222
 223     actionPanel.add(ok);
 224     actionPanel.add(cancel);
 225
 226     JPanel staticPanel = new JPanel();
 227     staticPanel.setLayout(new BorderLayout());
 228     staticPanel.setBackground(Color.white);
 229
 230     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 231     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 232
 233     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 234     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 235     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 236
 237     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 238     noGraphFilterView.add(ngStructureFilterPanel,
 239             java.awt.BorderLayout.CENTER);
 240     noGraphFilterView.add(ngFurtherActionPanel,
 241             java.awt.BorderLayout.CENTER);
 242
 243     annotationComboBoxPanel.add(getAnnotations());
 244     switchableViewsPanel.add(noGraphFilterView,
 245             AnnotationColumnChooser.NO_GRAPH_VIEW);
 246     switchableViewsPanel.add(graphFilterView,
 247             AnnotationColumnChooser.GRAPH_VIEW);
 248
 249     this.setLayout(borderLayout1);
 250     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 251     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 252     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 253
 254     selectedAnnotationChanged();
 255     this.validate();
 256   }
 257
 258   @SuppressWarnings("unchecked")
 259   public void reset()
 260   {
 261     if (this.getOldColumnSelection() != null)
 262     {
 263       av.getColumnSelection().clear();
 264
 265       if (av.getAnnotationColumnSelectionState() != null)
 266       {
 267         ColumnSelection oldSelection = av
 268                 .getAnnotationColumnSelectionState()
 269                 .getOldColumnSelection();
 270         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 271                 && !oldSelection.getHiddenColumns().isEmpty())
 272         {
 273           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 274                   .iterator(); itr.hasNext();)
 275           {
 276             int positions[] = itr.next();
 277             av.hideColumns(positions[0], positions[1]);
 278           }
 279         }
 280         av.setColumnSelection(oldSelection);
 281       }
 282       ap.paintAlignment(true);
 283     }
 284
 285   }
 286
 287   public void adjustmentValueChanged(AdjustmentEvent evt)
 288   {
 289     if (!adjusting)
 290     {
 291       thresholdValue.setText((slider.getValue() / 1000f) + "");
 292       valueChanged(!sliderDragging);
 293     }
 294   }
 295
 296   protected void addSliderMouseListeners()
 297   {
 298
 299     slider.addMouseListener(new MouseAdapter()
 300     {
 301       @Override
 302       public void mousePressed(MouseEvent e)
 303       {
 304         sliderDragging = true;
 305         super.mousePressed(e);
 306       }
 307
 308       @Override
 309       public void mouseDragged(MouseEvent e)
 310       {
 311         sliderDragging = true;
 312         super.mouseDragged(e);
 313       }
 314
 315       @Override
 316       public void mouseReleased(MouseEvent evt)
 317       {
 318         if (sliderDragging)
 319         {
 320           sliderDragging = false;
 321           valueChanged(true);
 322         }
 323         ap.paintAlignment(true);
 324       }
 325     });
 326   }
 327
 328   public void valueChanged(boolean updateAllAnnotation)
 329   {
 330     if (slider.isEnabled())
 331     {
 332       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 333       updateView();
 334       ap.paintAlignment(false);
 335     }
 336   }
 337
 338   public Choice getThreshold()
 339   {
 340     return threshold;
 341   }
 342
 343   public void setThreshold(Choice threshold)
 344   {
 345     this.threshold = threshold;
 346   }
 347
 348   public Choice getAnnotations()
 349   {
 350     return annotations;
 351   }
 352
 353   public void setAnnotations(Choice annotations)
 354   {
 355     this.annotations = annotations;
 356   }
 357
 358   @Override
 359   public void updateView()
 360   {
 361     // Check if combobox is still adjusting
 362     if (adjusting)
 363     {
 364       return;
 365     }
 366
 367     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 368     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 369             .getSelectedIndex()]);
 370
 371     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 372             .getSelectedIndex());
 373
 374     slider.setEnabled(true);
 375     thresholdValue.setEnabled(true);
 376
 377     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 378     {
 379       slider.setEnabled(false);
 380       thresholdValue.setEnabled(false);
 381       thresholdValue.setText("");
 382       // build filter params
 383     }
 384     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 385     {
 386       if (getCurrentAnnotation().threshold == null)
 387       {
 388         getCurrentAnnotation()
 389                 .setThreshold(
 390                         new GraphLine(
 391                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 392                                 "Threshold", Color.black));
 393       }
 394
 395       adjusting = true;
 396       float range = getCurrentAnnotation().graphMax * 1000
 397               - getCurrentAnnotation().graphMin * 1000;
 398
 399       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 400       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 401       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 402       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 403       // slider.setMajorTickSpacing((int) (range / 10f));
 404       slider.setEnabled(true);
 405       thresholdValue.setEnabled(true);
 406       adjusting = false;
 407
 408       // build filter params
 409       filterParams
 410               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 411       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 412       {
 413         filterParams
 414                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 415
 416         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 417         {
 418           filterParams
 419                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 420         }
 421         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 422         {
 423           filterParams
 424                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 425         }
 426       }
 427     }
 428
 429     if (currentStructureFilterPanel != null)
 430     {
 431       if (currentStructureFilterPanel.alphaHelix.getState())
 432       {
 433         filterParams.setFilterAlphaHelix(true);
 434       }
 435       if (currentStructureFilterPanel.betaStrand.getState())
 436       {
 437         filterParams.setFilterBetaSheet(true);
 438       }
 439       if (currentStructureFilterPanel.turn.getState())
 440       {
 441         filterParams.setFilterTurn(true);
 442       }
 443     }
 444
 445     if (currentSearchPanel != null)
 446     {
 447
 448       if (!currentSearchPanel.searchBox.getText().isEmpty())
 449       {
 450         currentSearchPanel.description.setEnabled(true);
 451         currentSearchPanel.displayName.setEnabled(true);
 452         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 453         if (currentSearchPanel.displayName.getState())
 454         {
 455           filterParams
 456                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 457         }
 458         if (currentSearchPanel.description.getState())
 459         {
 460           filterParams
 461                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 462         }
 463       }
 464       else
 465       {
 466         currentSearchPanel.description.setEnabled(false);
 467         currentSearchPanel.displayName.setEnabled(false);
 468       }
 469     }
 470
 471     av.getColumnSelection().filterAnnotations(
 472             getCurrentAnnotation().annotations, filterParams);
 473
 474     av.showAllHiddenColumns();
 475     if (getActionOption() == ACTION_OPTION_HIDE)
 476     {
 477       av.hideSelectedColumns();
 478     }
 479
 480     filterParams = null;
 481     av.setAnnotationColumnSelectionState(this);
 482     ap.paintAlignment(true);
 483   }
 484
 485   public ColumnSelection getOldColumnSelection()
 486   {
 487     return oldColumnSelection;
 488   }
 489
 490   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 491   {
 492     if (currentColumnSelection != null)
 493     {
 494       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 495     }
 496   }
 497
 498   public FurtherActionPanel getCurrentFutherActionPanel()
 499   {
 500     return currentFurtherActionPanel;
 501   }
 502
 503   public void setCurrentFutherActionPanel(
 504           FurtherActionPanel currentFutherActionPanel)
 505   {
 506     this.currentFurtherActionPanel = currentFutherActionPanel;
 507   }
 508
 509   public SearchPanel getCurrentSearchPanel()
 510   {
 511     return currentSearchPanel;
 512   }
 513
 514   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 515   {
 516     this.currentSearchPanel = currentSearchPanel;
 517   }
 518
 519   public int getActionOption()
 520   {
 521     return actionOption;
 522   }
 523
 524   public void setActionOption(int actionOption)
 525   {
 526     this.actionOption = actionOption;
 527   }
 528
 529   public StructureFilterPanel getCurrentStructureFilterPanel()
 530   {
 531     return currentStructureFilterPanel;
 532   }
 533
 534   public void setCurrentStructureFilterPanel(
 535           StructureFilterPanel currentStructureFilterPanel)
 536   {
 537     this.currentStructureFilterPanel = currentStructureFilterPanel;
 538   }
 539
 540   @Override
 541   public void itemStateChanged(ItemEvent e)
 542   {
 543     if (e.getSource() == annotations)
 544     {
 545       selectedAnnotationChanged();
 546     }
 547     else if (e.getSource() == threshold)
 548     {
 549       threshold_actionPerformed(null);
 550     }
 551   }
 552
 553   public void selectedAnnotationChanged()
 554   {
 555     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 556     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 557             .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
 558     {
 559       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 560     }
 561
 562     gSearchPanel.syncState();
 563     gFurtherActionPanel.syncState();
 564     gStructureFilterPanel.syncState();
 565
 566     ngSearchPanel.syncState();
 567     ngFurtherActionPanel.syncState();
 568     ngStructureFilterPanel.syncState();
 569
 570     switchableViewsLayout.show(switchableViewsPanel, currentView);
 571     updateView();
 572   }
 573
 574   public class FurtherActionPanel extends Panel implements
 575           ItemListener
 576   {
 577     private AnnotationColumnChooser aColChooser;
 578
 579     private Choice furtherAction = new Choice();
 580
 581     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 582     {
 583       this.aColChooser = aColChooser;
 584       furtherAction.addItem("Select");
 585       furtherAction.addItem("Hide");
 586       furtherAction.addItemListener(this);
 587       syncState();
 588
 589       // this.setTitle("Filter Actions");
 590       // this.setFont(JvSwingUtils.getLabelFont());
 591
 592       this.add(furtherAction);
 593     }
 594
 595     public void syncState()
 596     {
 597       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 598       {
 599         furtherAction.select("Hide");
 600       }
 601       else
 602       {
 603         furtherAction.select("Select");
 604       }
 605     }
 606
 607     @Override
 608     public void itemStateChanged(ItemEvent e)
 609     {
 610       aColChooser.setCurrentFutherActionPanel(this);
 611       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 612       {
 613         setActionOption(ACTION_OPTION_SELECT);
 614         updateView();
 615       }
 616       else
 617       {
 618         setActionOption(ACTION_OPTION_HIDE);
 619         updateView();
 620       }
 621
 622     }
 623   }
 624
 625   public class StructureFilterPanel extends TitledPanel implements
 626           ItemListener
 627   {
 628     private AnnotationColumnChooser aColChooser;
 629
 630     private Checkbox alphaHelix = new Checkbox();
 631
 632     private Checkbox betaStrand = new Checkbox();
 633
 634     private Checkbox turn = new Checkbox();
 635
 636     private Checkbox all = new Checkbox();
 637
 638     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 639     {
 640       this.aColChooser = aColChooser;
 641
 642       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 643       alphaHelix.setBackground(Color.white);
 644
 645       alphaHelix.addItemListener(this);
 646
 647       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 648       betaStrand.setBackground(Color.white);
 649       betaStrand.addItemListener(this);
 650
 651       turn.setLabel(MessageManager.getString("label.turn"));
 652       turn.setBackground(Color.white);
 653       turn.addItemListener(this);
 654
 655       all.setLabel(MessageManager.getString("label.select_all"));
 656       all.setBackground(Color.white);
 657       all.addItemListener(this);
 658
 659       this.setBackground(Color.white);
 660       this.setTitle("Structure Filter");
 661       // this.setFont(JvSwingUtils.getLabelFont());
 662
 663       this.add(all);
 664       this.add(alphaHelix);
 665       this.add(betaStrand);
 666       this.add(turn);
 667     }
 668
 669     public void alphaHelix_actionPerformed()
 670     {
 671       updateSelectAllState();
 672       aColChooser.setCurrentStructureFilterPanel(this);
 673       aColChooser.updateView();
 674     }
 675
 676     public void betaStrand_actionPerformed()
 677     {
 678       updateSelectAllState();
 679       aColChooser.setCurrentStructureFilterPanel(this);
 680       aColChooser.updateView();
 681     }
 682
 683     public void turn_actionPerformed()
 684     {
 685       updateSelectAllState();
 686       aColChooser.setCurrentStructureFilterPanel(this);
 687       aColChooser.updateView();
 688     }
 689
 690     public void all_actionPerformed()
 691     {
 692       if (all.getState())
 693       {
 694         alphaHelix.setState(true);
 695         betaStrand.setState(true);
 696         turn.setState(true);
 697       }
 698       else
 699       {
 700         alphaHelix.setState(false);
 701         betaStrand.setState(false);
 702         turn.setState(false);
 703       }
 704       aColChooser.setCurrentStructureFilterPanel(this);
 705       aColChooser.updateView();
 706     }
 707
 708     public void updateSelectAllState()
 709     {
 710       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 711       {
 712         all.setState(true);
 713       }
 714       else
 715       {
 716         all.setState(false);
 717       }
 718     }
 719
 720     public void syncState()
 721     {
 722       StructureFilterPanel sfp = aColChooser
 723               .getCurrentStructureFilterPanel();
 724       if (sfp != null)
 725       {
 726         alphaHelix.setState(sfp.alphaHelix.getState());
 727         betaStrand.setState(sfp.betaStrand.getState());
 728         turn.setState(sfp.turn.getState());
 729         if (sfp.all.getState())
 730         {
 731           all.setState(true);
 732           alphaHelix.setState(true);
 733           betaStrand.setState(true);
 734           turn.setState(true);
 735         }
 736       }
 737
 738     }
 739
 740     @Override
 741     public void itemStateChanged(ItemEvent e)
 742     {
 743       if (e.getSource() == alphaHelix)
 744       {
 745         alphaHelix_actionPerformed();
 746       }
 747       else if (e.getSource() == betaStrand)
 748       {
 749         betaStrand_actionPerformed();
 750       }
 751       else if (e.getSource() == turn)
 752       {
 753         turn_actionPerformed();
 754       }
 755       else if (e.getSource() == all)
 756       {
 757         all_actionPerformed();
 758       }
 759     }
 760   }
 761
 762   public class SearchPanel extends TitledPanel implements ItemListener
 763   {
 764     private AnnotationColumnChooser aColChooser;
 765
 766     private Checkbox displayName = new Checkbox();
 767
 768     private Checkbox description = new Checkbox();
 769
 770     private TextField searchBox = new TextField(10);
 771
 772     public SearchPanel(AnnotationColumnChooser aColChooser)
 773     {
 774
 775       this.aColChooser = aColChooser;
 776       searchBox.addTextListener(new TextListener()
 777       {
 778
 779         @Override
 780         public void textValueChanged(TextEvent e)
 781         {
 782           searchStringAction();
 783
 784         }
 785
 786       });
 787
 788       displayName.setLabel(MessageManager.getString("label.display_name"));
 789       displayName.setEnabled(false);
 790       displayName.addItemListener(this);
 791
 792       description.setLabel(MessageManager.getString("label.description"));
 793       description.setEnabled(false);
 794       description.addItemListener(this);
 795       this.setTitle("Search Filter");
 796       // this.setFont(JvSwingUtils.getLabelFont());
 797
 798       syncState();
 799       this.add(searchBox);
 800       this.add(displayName);
 801       this.add(description);
 802     }
 803
 804     public void displayNameCheckboxAction()
 805     {
 806       aColChooser.setCurrentSearchPanel(this);
 807       aColChooser.updateView();
 808     }
 809
 810     public void discriptionCheckboxAction()
 811     {
 812       aColChooser.setCurrentSearchPanel(this);
 813       aColChooser.updateView();
 814     }
 815
 816     public void searchStringAction()
 817     {
 818       aColChooser.setCurrentSearchPanel(this);
 819       aColChooser.updateView();
 820     }
 821
 822     public void syncState()
 823     {
 824       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 825       if (sp != null)
 826       {
 827         description.setEnabled(sp.description.isEnabled());
 828         description.setState(sp.description.getState());
 829
 830         displayName.setEnabled(sp.displayName.isEnabled());
 831         displayName.setState(sp.displayName.getState());
 832
 833         searchBox.setText(sp.searchBox.getText());
 834       }
 835     }
 836
 837     @Override
 838     public void itemStateChanged(ItemEvent e)
 839     {
 840       if (e.getSource() == displayName)
 841       {
 842         displayNameCheckboxAction();
 843       }
 844       else if (e.getSource() == description)
 845       {
 846         discriptionCheckboxAction();
 847       }
 848
 849     }
 850   }
 851
 852   public void actionPerformed(ActionEvent evt)
 853   {
 854     if (evt.getSource() == thresholdValue)
 855     {
 856       try
 857       {
 858         float f = new Float(thresholdValue.getText()).floatValue();
 859         slider.setValue((int) (f * 1000));
 860         adjustmentValueChanged(null);
 861       } catch (NumberFormatException ex)
 862       {
 863       }
 864     }
 865
 866     else if (evt.getSource() == ok)
 867     {
 868       ok_actionPerformed(null);
 869     }
 870     else if (evt.getSource() == cancel)
 871     {
 872       cancel_actionPerformed(null);
 873     }
 874     else if (evt.getSource() == thresholdValue)
 875     {
 876       thresholdValue_actionPerformed(null);
 877     }
 878     else
 879     {
 880       updateView();
 881     }
 882   }
 883
 884   @Override
 885   public void mouseClicked(MouseEvent e)
 886   {
 887     // TODO Auto-generated method stub
 888
 889   }
 890
 891   @Override
 892   public void mousePressed(MouseEvent e)
 893   {
 894     if (e.getSource() == slider)
 895     {
 896       updateView();
 897     }
 898
 899   }
 900
 901   @Override
 902   public void mouseReleased(MouseEvent e)
 903   {
 904     if (e.getSource() == slider)
 905     {
 906       updateView();
 907     }
 908   }
 909
 910   @Override
 911   public void mouseEntered(MouseEvent e)
 912   {
 913     if (e.getSource() == slider)
 914     {
 915       updateView();
 916     }
 917   }
 918
 919   @Override
 920   public void mouseExited(MouseEvent e)
 921   {
 922     if (e.getSource() == slider)
 923     {
 924       updateView();
 925     }
 926   }
 927
 928 }