src/jalview/appletgui/AnnotationColumnChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.ColumnSelection;
  25 import jalview.schemes.AnnotationColourGradient;
  26 import jalview.util.MessageManager;
  27 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.CardLayout;
  31 import java.awt.Checkbox;
  32 import java.awt.Choice;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.Frame;
  36 import java.awt.Panel;
  37 import java.awt.TextField;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.AdjustmentEvent;
  41 import java.awt.event.AdjustmentListener;
  42 import java.awt.event.ItemEvent;
  43 import java.awt.event.ItemListener;
  44 import java.awt.event.MouseAdapter;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.event.MouseListener;
  47 import java.awt.event.TextEvent;
  48 import java.awt.event.TextListener;
  49 import java.util.Iterator;
  50 import java.util.Vector;
  51
  52 import javax.swing.JPanel;
  53
  54 //import net.miginfocom.swing.MigLayout;
  55
  56 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  57         ActionListener, AdjustmentListener, ItemListener, MouseListener
  58 {
  59
  60   private Choice annotations = new Choice();
  61
  62   private Panel actionPanel = new Panel();
  63
  64   private TitledPanel thresholdPanel = new TitledPanel();
  65
  66   private Panel switchableViewsPanel = new Panel(new CardLayout());
  67
  68   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  69           .getLayout());
  70
  71   private Panel noGraphFilterView = new Panel();
  72
  73   private Panel graphFilterView = new Panel();
  74
  75   private Panel annotationComboBoxPanel = new Panel();
  76
  77   private BorderLayout borderLayout1 = new BorderLayout();
  78
  79   private BorderLayout gBorderLayout = new BorderLayout();
  80
  81   private BorderLayout ngBorderLayout = new BorderLayout();
  82
  83   private Choice threshold = new Choice();
  84
  85   private StructureFilterPanel gStructureFilterPanel;
  86
  87   private StructureFilterPanel ngStructureFilterPanel;
  88
  89   private StructureFilterPanel currentStructureFilterPanel;
  90
  91   private SearchPanel currentSearchPanel;
  92
  93   private SearchPanel gSearchPanel;
  94
  95   private SearchPanel ngSearchPanel;
  96
  97   private FurtherActionPanel currentFurtherActionPanel;
  98
  99   private FurtherActionPanel gFurtherActionPanel;
 100
 101   private FurtherActionPanel ngFurtherActionPanel;
 102
 103   public static final int ACTION_OPTION_SELECT = 1;
 104
 105   public static int ACTION_OPTION_HIDE = 2;
 106
 107   public static String NO_GRAPH_VIEW = "0";
 108
 109   public static String GRAPH_VIEW = "1";
 110
 111   private int actionOption = ACTION_OPTION_SELECT;
 112
 113   private ColumnSelection oldColumnSelection;
 114
 115   public AnnotationColumnChooser()
 116   {
 117     try
 118     {
 119       jbInit();
 120     } catch (Exception ex)
 121     {
 122       ex.printStackTrace();
 123     }
 124   }
 125
 126   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 127   {
 128     super(av, ap);
 129     frame = new Frame();
 130     frame.add(this);
 131     jalview.bin.JalviewLite.addFrame(frame,
 132             MessageManager.getString("label.select_by_annotation"), 520,
 133             215);
 134
 135     slider.addAdjustmentListener(this);
 136     slider.addMouseListener(this);
 137
 138     if (av.getAlignment().getAlignmentAnnotation() == null)
 139     {
 140       return;
 141     }
 142     setOldColumnSelection(av.getColumnSelection());
 143     adjusting = true;
 144     Vector list = new Vector();
 145     int index = 1;
 146     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 147     {
 148       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 149       if (!list.contains(label))
 150       {
 151         list.addElement(label);
 152       }
 153       else
 154       {
 155         list.addElement(label + "_" + (index++));
 156       }
 157     }
 158
 159     for (int i = 0; i < list.size(); i++)
 160     {
 161       annotations.addItem(list.elementAt(i).toString());
 162     }
 163
 164     populateThresholdComboBox(threshold);
 165
 166     // restore Object state from the previous session if one exists
 167     if (av.getAnnotationColumnSelectionState() != null)
 168     {
 169       currentSearchPanel = av.getAnnotationColumnSelectionState()
 170               .getCurrentSearchPanel();
 171       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 172               .getCurrentStructureFilterPanel();
 173       annotations.select(av.getAnnotationColumnSelectionState()
 174               .getAnnotations().getSelectedIndex());
 175       threshold.select(av.getAnnotationColumnSelectionState()
 176               .getThreshold().getSelectedIndex());
 177       actionOption = av.getAnnotationColumnSelectionState()
 178               .getActionOption();
 179     }
 180
 181     try
 182     {
 183       jbInit();
 184     } catch (Exception ex)
 185     {
 186     }
 187     adjusting = false;
 188
 189     updateView();
 190     frame.invalidate();
 191     frame.pack();
 192   }
 193
 194   private void jbInit() throws Exception
 195   {
 196     ok.setLabel(MessageManager.getString("action.ok"));
 197
 198     cancel.setLabel(MessageManager.getString("action.cancel"));
 199
 200     thresholdValue.setEnabled(false);
 201     thresholdValue.setColumns(7);
 202
 203     ok.addActionListener(this);
 204     cancel.addActionListener(this);
 205     annotations.addItemListener(this);
 206     thresholdValue.addActionListener(this);
 207     threshold.addItemListener(this);
 208
 209     slider.setBackground(Color.white);
 210     slider.setEnabled(false);
 211     slider.setPreferredSize(new Dimension(100, 32));
 212
 213     thresholdPanel.setBackground(Color.white);
 214     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 215     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 216
 217     actionPanel.setBackground(Color.white);
 218     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 219
 220     graphFilterView.setLayout(gBorderLayout);
 221     graphFilterView.setBackground(Color.white);
 222
 223     noGraphFilterView.setLayout(ngBorderLayout);
 224     noGraphFilterView.setBackground(Color.white);
 225
 226     annotationComboBoxPanel.setBackground(Color.white);
 227     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 228
 229     gSearchPanel = new SearchPanel(this);
 230     ngSearchPanel = new SearchPanel(this);
 231     gFurtherActionPanel = new FurtherActionPanel(this);
 232     ngFurtherActionPanel = new FurtherActionPanel(this);
 233     gStructureFilterPanel = new StructureFilterPanel(this);
 234     ngStructureFilterPanel = new StructureFilterPanel(this);
 235
 236     thresholdPanel.setTitle("Threshold Filter");
 237     thresholdPanel.add(getThreshold());
 238     thresholdPanel.add(slider);
 239     thresholdPanel.add(thresholdValue);
 240
 241     actionPanel.add(ok);
 242     actionPanel.add(cancel);
 243
 244     JPanel staticPanel = new JPanel();
 245     staticPanel.setLayout(new BorderLayout());
 246     staticPanel.setBackground(Color.white);
 247
 248     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 249     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 250
 251     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 252     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 253     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 254
 255     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 256     noGraphFilterView.add(ngStructureFilterPanel,
 257             java.awt.BorderLayout.CENTER);
 258     noGraphFilterView.add(ngFurtherActionPanel,
 259             java.awt.BorderLayout.CENTER);
 260
 261     annotationComboBoxPanel.add(getAnnotations());
 262     switchableViewsPanel.add(noGraphFilterView,
 263             AnnotationColumnChooser.NO_GRAPH_VIEW);
 264     switchableViewsPanel.add(graphFilterView,
 265             AnnotationColumnChooser.GRAPH_VIEW);
 266
 267     this.setLayout(borderLayout1);
 268     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 269     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 270     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 271
 272     selectedAnnotationChanged();
 273     this.validate();
 274   }
 275
 276   @SuppressWarnings("unchecked")
 277   public void reset()
 278   {
 279     if (this.getOldColumnSelection() != null)
 280     {
 281       av.getColumnSelection().clear();
 282
 283       if (av.getAnnotationColumnSelectionState() != null)
 284       {
 285         ColumnSelection oldSelection = av
 286                 .getAnnotationColumnSelectionState()
 287                 .getOldColumnSelection();
 288         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 289                 && !oldSelection.getHiddenColumns().isEmpty())
 290         {
 291           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 292                   .iterator(); itr.hasNext();)
 293           {
 294             int positions[] = itr.next();
 295             av.hideColumns(positions[0], positions[1]);
 296           }
 297         }
 298         av.setColumnSelection(oldSelection);
 299       }
 300       ap.paintAlignment(true);
 301     }
 302
 303   }
 304
 305   public void adjustmentValueChanged(AdjustmentEvent evt)
 306   {
 307     if (!adjusting)
 308     {
 309       thresholdValue.setText((slider.getValue() / 1000f) + "");
 310       valueChanged(!sliderDragging);
 311     }
 312   }
 313
 314   protected void addSliderMouseListeners()
 315   {
 316
 317     slider.addMouseListener(new MouseAdapter()
 318     {
 319       @Override
 320       public void mousePressed(MouseEvent e)
 321       {
 322         sliderDragging = true;
 323         super.mousePressed(e);
 324       }
 325
 326       @Override
 327       public void mouseDragged(MouseEvent e)
 328       {
 329         sliderDragging = true;
 330         super.mouseDragged(e);
 331       }
 332
 333       @Override
 334       public void mouseReleased(MouseEvent evt)
 335       {
 336         if (sliderDragging)
 337         {
 338           sliderDragging = false;
 339           valueChanged(true);
 340         }
 341         ap.paintAlignment(true);
 342       }
 343     });
 344   }
 345
 346   public void valueChanged(boolean updateAllAnnotation)
 347   {
 348     if (slider.isEnabled())
 349     {
 350       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 351       updateView();
 352       ap.paintAlignment(false);
 353     }
 354   }
 355
 356   public Choice getThreshold()
 357   {
 358     return threshold;
 359   }
 360
 361   public void setThreshold(Choice threshold)
 362   {
 363     this.threshold = threshold;
 364   }
 365
 366   public Choice getAnnotations()
 367   {
 368     return annotations;
 369   }
 370
 371   public void setAnnotations(Choice annotations)
 372   {
 373     this.annotations = annotations;
 374   }
 375
 376   @Override
 377   public void updateView()
 378   {
 379     // Check if combobox is still adjusting
 380     if (adjusting)
 381     {
 382       return;
 383     }
 384
 385     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 386     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 387             .getSelectedIndex()]);
 388
 389     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 390             .getSelectedIndex());
 391
 392     slider.setEnabled(true);
 393     thresholdValue.setEnabled(true);
 394
 395     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 396     {
 397       slider.setEnabled(false);
 398       thresholdValue.setEnabled(false);
 399       thresholdValue.setText("");
 400       // build filter params
 401     }
 402     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 403     {
 404       if (getCurrentAnnotation().threshold == null)
 405       {
 406         getCurrentAnnotation()
 407                 .setThreshold(
 408                         new jalview.datamodel.GraphLine(
 409                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 410                                 "Threshold", Color.black));
 411       }
 412
 413       adjusting = true;
 414       float range = getCurrentAnnotation().graphMax * 1000
 415               - getCurrentAnnotation().graphMin * 1000;
 416
 417       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 418       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 419       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 420       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 421       // slider.setMajorTickSpacing((int) (range / 10f));
 422       slider.setEnabled(true);
 423       thresholdValue.setEnabled(true);
 424       adjusting = false;
 425
 426       // build filter params
 427       filterParams
 428               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 429       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 430       {
 431         filterParams
 432                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 433
 434         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 435         {
 436           filterParams
 437                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 438         }
 439         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 440         {
 441           filterParams
 442                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 443         }
 444       }
 445     }
 446
 447     if (currentStructureFilterPanel != null)
 448     {
 449       if (currentStructureFilterPanel.alphaHelix.getState())
 450       {
 451         filterParams.setFilterAlphaHelix(true);
 452       }
 453       if (currentStructureFilterPanel.betaStrand.getState())
 454       {
 455         filterParams.setFilterBetaSheet(true);
 456       }
 457       if (currentStructureFilterPanel.turn.getState())
 458       {
 459         filterParams.setFilterTurn(true);
 460       }
 461     }
 462
 463     if (currentSearchPanel != null)
 464     {
 465
 466       if (!currentSearchPanel.searchBox.getText().isEmpty())
 467       {
 468         currentSearchPanel.description.setEnabled(true);
 469         currentSearchPanel.displayName.setEnabled(true);
 470         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 471         if (currentSearchPanel.displayName.getState())
 472         {
 473           filterParams
 474                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 475         }
 476         if (currentSearchPanel.description.getState())
 477         {
 478           filterParams
 479                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 480         }
 481       }
 482       else
 483       {
 484         currentSearchPanel.description.setEnabled(false);
 485         currentSearchPanel.displayName.setEnabled(false);
 486       }
 487     }
 488
 489     av.getColumnSelection().filterAnnotations(
 490             getCurrentAnnotation().annotations, filterParams);
 491
 492     av.showAllHiddenColumns();
 493     if (getActionOption() == ACTION_OPTION_HIDE)
 494     {
 495       av.hideSelectedColumns();
 496     }
 497
 498     filterParams = null;
 499     av.setAnnotationColumnSelectionState(this);
 500     ap.paintAlignment(true);
 501   }
 502
 503   public ColumnSelection getOldColumnSelection()
 504   {
 505     return oldColumnSelection;
 506   }
 507
 508   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 509   {
 510     if (currentColumnSelection != null)
 511     {
 512       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 513     }
 514   }
 515
 516   public FurtherActionPanel getCurrentFutherActionPanel()
 517   {
 518     return currentFurtherActionPanel;
 519   }
 520
 521   public void setCurrentFutherActionPanel(
 522           FurtherActionPanel currentFutherActionPanel)
 523   {
 524     this.currentFurtherActionPanel = currentFutherActionPanel;
 525   }
 526
 527   public SearchPanel getCurrentSearchPanel()
 528   {
 529     return currentSearchPanel;
 530   }
 531
 532   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 533   {
 534     this.currentSearchPanel = currentSearchPanel;
 535   }
 536
 537   public int getActionOption()
 538   {
 539     return actionOption;
 540   }
 541
 542   public void setActionOption(int actionOption)
 543   {
 544     this.actionOption = actionOption;
 545   }
 546
 547   public StructureFilterPanel getCurrentStructureFilterPanel()
 548   {
 549     return currentStructureFilterPanel;
 550   }
 551
 552   public void setCurrentStructureFilterPanel(
 553           StructureFilterPanel currentStructureFilterPanel)
 554   {
 555     this.currentStructureFilterPanel = currentStructureFilterPanel;
 556   }
 557
 558   @Override
 559   public void itemStateChanged(ItemEvent e)
 560   {
 561     if (e.getSource() == annotations)
 562     {
 563       selectedAnnotationChanged();
 564     }
 565     else if (e.getSource() == threshold)
 566     {
 567       threshold_actionPerformed(null);
 568     }
 569   }
 570
 571   public void selectedAnnotationChanged()
 572   {
 573     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 574     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 575             .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
 576     {
 577       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 578     }
 579
 580     gSearchPanel.syncState();
 581     gFurtherActionPanel.syncState();
 582     gStructureFilterPanel.syncState();
 583
 584     ngSearchPanel.syncState();
 585     ngFurtherActionPanel.syncState();
 586     ngStructureFilterPanel.syncState();
 587
 588     switchableViewsLayout.show(switchableViewsPanel, currentView);
 589     updateView();
 590   }
 591
 592   public class FurtherActionPanel extends Panel implements ItemListener
 593   {
 594     private AnnotationColumnChooser aColChooser;
 595
 596     private Choice furtherAction = new Choice();
 597
 598     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 599     {
 600       this.aColChooser = aColChooser;
 601       furtherAction.addItem("Select");
 602       furtherAction.addItem("Hide");
 603       furtherAction.addItemListener(this);
 604       syncState();
 605
 606       // this.setTitle("Filter Actions");
 607       // this.setFont(JvSwingUtils.getLabelFont());
 608
 609       this.add(furtherAction);
 610     }
 611
 612     public void syncState()
 613     {
 614       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 615       {
 616         furtherAction.select("Hide");
 617       }
 618       else
 619       {
 620         furtherAction.select("Select");
 621       }
 622     }
 623
 624     @Override
 625     public void itemStateChanged(ItemEvent e)
 626     {
 627       aColChooser.setCurrentFutherActionPanel(this);
 628       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 629       {
 630         setActionOption(ACTION_OPTION_SELECT);
 631         updateView();
 632       }
 633       else
 634       {
 635         setActionOption(ACTION_OPTION_HIDE);
 636         updateView();
 637       }
 638
 639     }
 640   }
 641
 642   public class StructureFilterPanel extends TitledPanel implements
 643           ItemListener
 644   {
 645     private AnnotationColumnChooser aColChooser;
 646
 647     private Checkbox alphaHelix = new Checkbox();
 648
 649     private Checkbox betaStrand = new Checkbox();
 650
 651     private Checkbox turn = new Checkbox();
 652
 653     private Checkbox all = new Checkbox();
 654
 655     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 656     {
 657       this.aColChooser = aColChooser;
 658
 659       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 660       alphaHelix.setBackground(Color.white);
 661
 662       alphaHelix.addItemListener(this);
 663
 664       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 665       betaStrand.setBackground(Color.white);
 666       betaStrand.addItemListener(this);
 667
 668       turn.setLabel(MessageManager.getString("label.turn"));
 669       turn.setBackground(Color.white);
 670       turn.addItemListener(this);
 671
 672       all.setLabel(MessageManager.getString("label.select_all"));
 673       all.setBackground(Color.white);
 674       all.addItemListener(this);
 675
 676       this.setBackground(Color.white);
 677       this.setTitle("Structure Filter");
 678       // this.setFont(JvSwingUtils.getLabelFont());
 679
 680       this.add(all);
 681       this.add(alphaHelix);
 682       this.add(betaStrand);
 683       this.add(turn);
 684     }
 685
 686     public void alphaHelix_actionPerformed()
 687     {
 688       updateSelectAllState();
 689       aColChooser.setCurrentStructureFilterPanel(this);
 690       aColChooser.updateView();
 691     }
 692
 693     public void betaStrand_actionPerformed()
 694     {
 695       updateSelectAllState();
 696       aColChooser.setCurrentStructureFilterPanel(this);
 697       aColChooser.updateView();
 698     }
 699
 700     public void turn_actionPerformed()
 701     {
 702       updateSelectAllState();
 703       aColChooser.setCurrentStructureFilterPanel(this);
 704       aColChooser.updateView();
 705     }
 706
 707     public void all_actionPerformed()
 708     {
 709       if (all.getState())
 710       {
 711         alphaHelix.setState(true);
 712         betaStrand.setState(true);
 713         turn.setState(true);
 714       }
 715       else
 716       {
 717         alphaHelix.setState(false);
 718         betaStrand.setState(false);
 719         turn.setState(false);
 720       }
 721       aColChooser.setCurrentStructureFilterPanel(this);
 722       aColChooser.updateView();
 723     }
 724
 725     public void updateSelectAllState()
 726     {
 727       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 728       {
 729         all.setState(true);
 730       }
 731       else
 732       {
 733         all.setState(false);
 734       }
 735     }
 736
 737     public void syncState()
 738     {
 739       StructureFilterPanel sfp = aColChooser
 740               .getCurrentStructureFilterPanel();
 741       if (sfp != null)
 742       {
 743         alphaHelix.setState(sfp.alphaHelix.getState());
 744         betaStrand.setState(sfp.betaStrand.getState());
 745         turn.setState(sfp.turn.getState());
 746         if (sfp.all.getState())
 747         {
 748           all.setState(true);
 749           alphaHelix.setState(true);
 750           betaStrand.setState(true);
 751           turn.setState(true);
 752         }
 753       }
 754
 755     }
 756
 757     @Override
 758     public void itemStateChanged(ItemEvent e)
 759     {
 760       if (e.getSource() == alphaHelix)
 761       {
 762         alphaHelix_actionPerformed();
 763       }
 764       else if (e.getSource() == betaStrand)
 765       {
 766         betaStrand_actionPerformed();
 767       }
 768       else if (e.getSource() == turn)
 769       {
 770         turn_actionPerformed();
 771       }
 772       else if (e.getSource() == all)
 773       {
 774         all_actionPerformed();
 775       }
 776     }
 777   }
 778
 779   public class SearchPanel extends TitledPanel implements ItemListener
 780   {
 781     private AnnotationColumnChooser aColChooser;
 782
 783     private Checkbox displayName = new Checkbox();
 784
 785     private Checkbox description = new Checkbox();
 786
 787     private TextField searchBox = new TextField(10);
 788
 789     public SearchPanel(AnnotationColumnChooser aColChooser)
 790     {
 791
 792       this.aColChooser = aColChooser;
 793       searchBox.addTextListener(new TextListener()
 794       {
 795
 796         @Override
 797         public void textValueChanged(TextEvent e)
 798         {
 799           searchStringAction();
 800
 801         }
 802
 803       });
 804
 805       displayName.setLabel(MessageManager.getString("label.label"));
 806       displayName.setEnabled(false);
 807       displayName.addItemListener(this);
 808
 809       description.setLabel(MessageManager.getString("label.description"));
 810       description.setEnabled(false);
 811       description.addItemListener(this);
 812       this.setTitle("Search Filter");
 813       // this.setFont(JvSwingUtils.getLabelFont());
 814
 815       syncState();
 816       this.add(searchBox);
 817       this.add(displayName);
 818       this.add(description);
 819     }
 820
 821     public void displayNameCheckboxAction()
 822     {
 823       aColChooser.setCurrentSearchPanel(this);
 824       aColChooser.updateView();
 825     }
 826
 827     public void discriptionCheckboxAction()
 828     {
 829       aColChooser.setCurrentSearchPanel(this);
 830       aColChooser.updateView();
 831     }
 832
 833     public void searchStringAction()
 834     {
 835       aColChooser.setCurrentSearchPanel(this);
 836       aColChooser.updateView();
 837     }
 838
 839     public void syncState()
 840     {
 841       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 842       if (sp != null)
 843       {
 844         description.setEnabled(sp.description.isEnabled());
 845         description.setState(sp.description.getState());
 846
 847         displayName.setEnabled(sp.displayName.isEnabled());
 848         displayName.setState(sp.displayName.getState());
 849
 850         searchBox.setText(sp.searchBox.getText());
 851       }
 852     }
 853
 854     @Override
 855     public void itemStateChanged(ItemEvent e)
 856     {
 857       if (e.getSource() == displayName)
 858       {
 859         displayNameCheckboxAction();
 860       }
 861       else if (e.getSource() == description)
 862       {
 863         discriptionCheckboxAction();
 864       }
 865
 866     }
 867   }
 868
 869   public void actionPerformed(ActionEvent evt)
 870   {
 871     if (evt.getSource() == thresholdValue)
 872     {
 873       try
 874       {
 875         float f = new Float(thresholdValue.getText()).floatValue();
 876         slider.setValue((int) (f * 1000));
 877         adjustmentValueChanged(null);
 878       } catch (NumberFormatException ex)
 879       {
 880       }
 881     }
 882
 883     else if (evt.getSource() == ok)
 884     {
 885       ok_actionPerformed(null);
 886     }
 887     else if (evt.getSource() == cancel)
 888     {
 889       cancel_actionPerformed(null);
 890     }
 891     else if (evt.getSource() == thresholdValue)
 892     {
 893       thresholdValue_actionPerformed(null);
 894     }
 895     else
 896     {
 897       updateView();
 898     }
 899   }
 900
 901   @Override
 902   public void mouseClicked(MouseEvent e)
 903   {
 904     // TODO Auto-generated method stub
 905
 906   }
 907
 908   @Override
 909   public void mousePressed(MouseEvent e)
 910   {
 911     if (e.getSource() == slider)
 912     {
 913       updateView();
 914     }
 915
 916   }
 917
 918   @Override
 919   public void mouseReleased(MouseEvent e)
 920   {
 921     if (e.getSource() == slider)
 922     {
 923       updateView();
 924     }
 925   }
 926
 927   @Override
 928   public void mouseEntered(MouseEvent e)
 929   {
 930     if (e.getSource() == slider)
 931     {
 932       updateView();
 933     }
 934   }
 935
 936   @Override
 937   public void mouseExited(MouseEvent e)
 938   {
 939     if (e.getSource() == slider)
 940     {
 941       updateView();
 942     }
 943   }
 944
 945 }