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.HiddenColumns;
  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 HiddenColumns oldHiddenColumns;
 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     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 139     if (anns == null)
 140     {
 141       return;
 142     }
 143     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 144     adjusting = true;
 145     Vector<String> list = new Vector<String>();
 146     int index = 1;
 147     for (int i = 0; i < anns.length; i++)
 148     {
 149       String label = anns[i].label;
 150       if (anns[i].sequenceRef != null)
 151       {
 152         label = label + "_" + anns[i].sequenceRef.getName();
 153       }
 154       if (!list.contains(label))
 155       {
 156         list.addElement(label);
 157       }
 158       else
 159       {
 160         list.addElement(label + "_" + (index++));
 161       }
 162     }
 163
 164     for (int i = 0; i < list.size(); i++)
 165     {
 166       annotations.addItem(list.elementAt(i).toString());
 167     }
 168
 169     populateThresholdComboBox(threshold);
 170     AnnotationColumnChooser lastChooser = av
 171             .getAnnotationColumnSelectionState();
 172     // restore Object state from the previous session if one exists
 173     if (lastChooser != null)
 174     {
 175       currentSearchPanel = lastChooser
 176               .getCurrentSearchPanel();
 177       currentStructureFilterPanel = lastChooser
 178               .getCurrentStructureFilterPanel();
 179       annotations.select(lastChooser
 180               .getAnnotations().getSelectedIndex());
 181       threshold.select(lastChooser
 182               .getThreshold().getSelectedIndex());
 183       actionOption = lastChooser
 184               .getActionOption();
 185       percentThreshold.setState(lastChooser.percentThreshold.getState());
 186     }
 187
 188     try
 189     {
 190       jbInit();
 191     } catch (Exception ex)
 192     {
 193     }
 194     adjusting = false;
 195
 196     updateView();
 197     frame.invalidate();
 198     frame.pack();
 199   }
 200
 201   private void jbInit() throws Exception
 202   {
 203     ok.setLabel(MessageManager.getString("action.ok"));
 204
 205     cancel.setLabel(MessageManager.getString("action.cancel"));
 206
 207     thresholdValue.setEnabled(false);
 208     thresholdValue.setColumns(7);
 209     thresholdValue.setCaretPosition(0);
 210
 211     ok.addActionListener(this);
 212     cancel.addActionListener(this);
 213     annotations.addItemListener(this);
 214     thresholdValue.addActionListener(this);
 215     threshold.addItemListener(this);
 216
 217     slider.setBackground(Color.white);
 218     slider.setEnabled(false);
 219     slider.setPreferredSize(new Dimension(100, 32));
 220
 221     thresholdPanel.setBackground(Color.white);
 222     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 223     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 224
 225     percentThreshold.setLabel("As percentage");
 226     percentThreshold.addItemListener(this);
 227
 228     actionPanel.setBackground(Color.white);
 229     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 230
 231     graphFilterView.setLayout(gBorderLayout);
 232     graphFilterView.setBackground(Color.white);
 233
 234     noGraphFilterView.setLayout(ngBorderLayout);
 235     noGraphFilterView.setBackground(Color.white);
 236
 237     annotationComboBoxPanel.setBackground(Color.white);
 238     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 239
 240     gSearchPanel = new SearchPanel(this);
 241     ngSearchPanel = new SearchPanel(this);
 242     gFurtherActionPanel = new FurtherActionPanel(this);
 243     ngFurtherActionPanel = new FurtherActionPanel(this);
 244     gStructureFilterPanel = new StructureFilterPanel(this);
 245     ngStructureFilterPanel = new StructureFilterPanel(this);
 246
 247     thresholdPanel.setTitle("Threshold Filter");
 248     thresholdPanel.add(getThreshold());
 249     thresholdPanel.add(slider);
 250     thresholdPanel.add(thresholdValue);
 251     thresholdPanel.add(percentThreshold);
 252
 253     actionPanel.add(ok);
 254     actionPanel.add(cancel);
 255
 256     Panel staticPanel = new Panel();
 257     staticPanel.setLayout(new BorderLayout());
 258     staticPanel.setBackground(Color.white);
 259
 260     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 261     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 262
 263     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 264     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 265     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 266
 267     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 268     noGraphFilterView.add(ngStructureFilterPanel,
 269             java.awt.BorderLayout.CENTER);
 270     noGraphFilterView.add(ngFurtherActionPanel,
 271             java.awt.BorderLayout.CENTER);
 272
 273     annotationComboBoxPanel.add(getAnnotations());
 274     switchableViewsPanel.add(noGraphFilterView,
 275             AnnotationColumnChooser.NO_GRAPH_VIEW);
 276     switchableViewsPanel.add(graphFilterView,
 277             AnnotationColumnChooser.GRAPH_VIEW);
 278
 279     this.setLayout(borderLayout1);
 280     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 281     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 282     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 283
 284     selectedAnnotationChanged();
 285     this.validate();
 286   }
 287
 288   @Override
 289   @SuppressWarnings("unchecked")
 290   public void reset()
 291   {
 292     if (this.getOldHiddenColumns() != null)
 293     {
 294       av.getColumnSelection().clear();
 295
 296       if (av.getAnnotationColumnSelectionState() != null)
 297       {
 298         HiddenColumns oldHidden = av
 299                 .getAnnotationColumnSelectionState()
 300                 .getOldHiddenColumns();
 301         if (oldHidden != null && oldHidden.getHiddenRegions() != null
 302                 && !oldHidden.getHiddenRegions().isEmpty())
 303         {
 304           for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
 305                   .iterator(); itr.hasNext();)
 306           {
 307             int positions[] = itr.next();
 308             av.hideColumns(positions[0], positions[1]);
 309           }
 310         }
 311         av.getAlignment().setHiddenColumns(oldHidden);
 312       }
 313       ap.paintAlignment(true);
 314     }
 315
 316   }
 317
 318   @Override
 319   public void adjustmentValueChanged(AdjustmentEvent evt)
 320   {
 321     if (!adjusting)
 322     {
 323       setThresholdValueText();
 324       valueChanged(!sliderDragging);
 325     }
 326   }
 327
 328   protected void addSliderMouseListeners()
 329   {
 330
 331     slider.addMouseListener(new MouseAdapter()
 332     {
 333       @Override
 334       public void mousePressed(MouseEvent e)
 335       {
 336         sliderDragging = true;
 337         super.mousePressed(e);
 338       }
 339
 340       @Override
 341       public void mouseDragged(MouseEvent e)
 342       {
 343         sliderDragging = true;
 344         super.mouseDragged(e);
 345       }
 346
 347       @Override
 348       public void mouseReleased(MouseEvent evt)
 349       {
 350         if (sliderDragging)
 351         {
 352           sliderDragging = false;
 353           valueChanged(true);
 354         }
 355         ap.paintAlignment(true);
 356       }
 357     });
 358   }
 359
 360   @Override
 361   public void valueChanged(boolean updateAllAnnotation)
 362   {
 363     if (slider.isEnabled())
 364     {
 365       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 366       updateView();
 367       ap.paintAlignment(false);
 368     }
 369   }
 370
 371   public Choice getThreshold()
 372   {
 373     return threshold;
 374   }
 375
 376   public void setThreshold(Choice threshold)
 377   {
 378     this.threshold = threshold;
 379   }
 380
 381   public Choice getAnnotations()
 382   {
 383     return annotations;
 384   }
 385
 386   public void setAnnotations(Choice annotations)
 387   {
 388     this.annotations = annotations;
 389   }
 390
 391   @Override
 392   public void updateView()
 393   {
 394     // Check if combobox is still adjusting
 395     if (adjusting)
 396     {
 397       return;
 398     }
 399
 400     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 401     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 402             .getSelectedIndex()]);
 403
 404     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 405             .getSelectedIndex());
 406
 407     slider.setEnabled(true);
 408     thresholdValue.setEnabled(true);
 409     percentThreshold.setEnabled(true);
 410
 411     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 412     {
 413       slider.setEnabled(false);
 414       thresholdValue.setEnabled(false);
 415       thresholdValue.setText("");
 416       percentThreshold.setEnabled(false);
 417       // build filter params
 418     }
 419     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 420     {
 421       if (getCurrentAnnotation().threshold == null)
 422       {
 423         getCurrentAnnotation()
 424                 .setThreshold(
 425                         new jalview.datamodel.GraphLine(
 426                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 427                                 "Threshold", Color.black));
 428       }
 429
 430       adjusting = true;
 431       float range = getCurrentAnnotation().graphMax * 1000
 432               - getCurrentAnnotation().graphMin * 1000;
 433
 434       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 435       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 436       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 437       setThresholdValueText();
 438       // slider.setMajorTickSpacing((int) (range / 10f));
 439       slider.setEnabled(true);
 440       thresholdValue.setEnabled(true);
 441       percentThreshold.setEnabled(true);
 442       adjusting = false;
 443
 444       // build filter params
 445       filterParams
 446               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 447       if (getCurrentAnnotation().isQuantitative())
 448       {
 449         filterParams
 450                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 451
 452         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 453         {
 454           filterParams
 455                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 456         }
 457         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 458         {
 459           filterParams
 460                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 461         }
 462       }
 463     }
 464
 465     if (currentStructureFilterPanel != null)
 466     {
 467       if (currentStructureFilterPanel.alphaHelix.getState())
 468       {
 469         filterParams.setFilterAlphaHelix(true);
 470       }
 471       if (currentStructureFilterPanel.betaStrand.getState())
 472       {
 473         filterParams.setFilterBetaSheet(true);
 474       }
 475       if (currentStructureFilterPanel.turn.getState())
 476       {
 477         filterParams.setFilterTurn(true);
 478       }
 479     }
 480
 481     if (currentSearchPanel != null)
 482     {
 483
 484       if (!currentSearchPanel.searchBox.getText().isEmpty())
 485       {
 486         currentSearchPanel.description.setEnabled(true);
 487         currentSearchPanel.displayName.setEnabled(true);
 488         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 489         if (currentSearchPanel.displayName.getState())
 490         {
 491           filterParams
 492                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 493         }
 494         if (currentSearchPanel.description.getState())
 495         {
 496           filterParams
 497                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 498         }
 499       }
 500       else
 501       {
 502         currentSearchPanel.description.setEnabled(false);
 503         currentSearchPanel.displayName.setEnabled(false);
 504       }
 505     }
 506
 507     av.getColumnSelection().filterAnnotations(
 508             getCurrentAnnotation().annotations, filterParams);
 509
 510     av.showAllHiddenColumns();
 511     if (getActionOption() == ACTION_OPTION_HIDE)
 512     {
 513       av.hideSelectedColumns();
 514     }
 515
 516     filterParams = null;
 517     av.setAnnotationColumnSelectionState(this);
 518     ap.paintAlignment(true);
 519   }
 520
 521   public HiddenColumns getOldHiddenColumns()
 522   {
 523     return oldHiddenColumns;
 524   }
 525
 526   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 527   {
 528     if (currentHiddenColumns != null)
 529     {
 530       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 531     }
 532   }
 533
 534   public FurtherActionPanel getCurrentFutherActionPanel()
 535   {
 536     return currentFurtherActionPanel;
 537   }
 538
 539   public void setCurrentFutherActionPanel(
 540           FurtherActionPanel currentFutherActionPanel)
 541   {
 542     this.currentFurtherActionPanel = currentFutherActionPanel;
 543   }
 544
 545   public SearchPanel getCurrentSearchPanel()
 546   {
 547     return currentSearchPanel;
 548   }
 549
 550   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 551   {
 552     this.currentSearchPanel = currentSearchPanel;
 553   }
 554
 555   public int getActionOption()
 556   {
 557     return actionOption;
 558   }
 559
 560   public void setActionOption(int actionOption)
 561   {
 562     this.actionOption = actionOption;
 563   }
 564
 565   public StructureFilterPanel getCurrentStructureFilterPanel()
 566   {
 567     return currentStructureFilterPanel;
 568   }
 569
 570   public void setCurrentStructureFilterPanel(
 571           StructureFilterPanel currentStructureFilterPanel)
 572   {
 573     this.currentStructureFilterPanel = currentStructureFilterPanel;
 574   }
 575
 576   @Override
 577   public void itemStateChanged(ItemEvent e)
 578   {
 579     if (e.getSource() == annotations)
 580     {
 581       selectedAnnotationChanged();
 582     }
 583     else if (e.getSource() == threshold)
 584     {
 585       threshold_actionPerformed(null);
 586     }
 587     else if (e.getSource() == percentThreshold)
 588     {
 589       if (!adjusting)
 590       {
 591         percentageValue_actionPerformed();
 592       }
 593
 594     }
 595   }
 596
 597   public void selectedAnnotationChanged()
 598   {
 599     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 600     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 601             .getSelectedIndex()].isQuantitative())
 602     {
 603       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 604     }
 605
 606     gSearchPanel.syncState();
 607     gFurtherActionPanel.syncState();
 608     gStructureFilterPanel.syncState();
 609
 610     ngSearchPanel.syncState();
 611     ngFurtherActionPanel.syncState();
 612     ngStructureFilterPanel.syncState();
 613
 614     switchableViewsLayout.show(switchableViewsPanel, currentView);
 615     updateView();
 616   }
 617
 618   public class FurtherActionPanel extends Panel implements ItemListener
 619   {
 620     private AnnotationColumnChooser aColChooser;
 621
 622     private Choice furtherAction = new Choice();
 623
 624     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 625     {
 626       this.aColChooser = aColChooser;
 627       furtherAction.addItem("Select");
 628       furtherAction.addItem("Hide");
 629       furtherAction.addItemListener(this);
 630       syncState();
 631
 632       // this.setTitle("Filter Actions");
 633       // this.setFont(JvSwingUtils.getLabelFont());
 634
 635       this.add(furtherAction);
 636     }
 637
 638     public void syncState()
 639     {
 640       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 641       {
 642         furtherAction.select("Hide");
 643       }
 644       else
 645       {
 646         furtherAction.select("Select");
 647       }
 648     }
 649
 650     @Override
 651     public void itemStateChanged(ItemEvent e)
 652     {
 653       aColChooser.setCurrentFutherActionPanel(this);
 654       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 655       {
 656         setActionOption(ACTION_OPTION_SELECT);
 657         updateView();
 658       }
 659       else
 660       {
 661         setActionOption(ACTION_OPTION_HIDE);
 662         updateView();
 663       }
 664
 665     }
 666   }
 667
 668   public class StructureFilterPanel extends TitledPanel implements
 669           ItemListener
 670   {
 671     private AnnotationColumnChooser aColChooser;
 672
 673     private Checkbox alphaHelix = new Checkbox();
 674
 675     private Checkbox betaStrand = new Checkbox();
 676
 677     private Checkbox turn = new Checkbox();
 678
 679     private Checkbox all = new Checkbox();
 680
 681     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 682     {
 683       this.aColChooser = aColChooser;
 684
 685       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 686       alphaHelix.setBackground(Color.white);
 687
 688       alphaHelix.addItemListener(this);
 689
 690       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 691       betaStrand.setBackground(Color.white);
 692       betaStrand.addItemListener(this);
 693
 694       turn.setLabel(MessageManager.getString("label.turn"));
 695       turn.setBackground(Color.white);
 696       turn.addItemListener(this);
 697
 698       all.setLabel(MessageManager.getString("label.select_all"));
 699       all.setBackground(Color.white);
 700       all.addItemListener(this);
 701
 702       this.setBackground(Color.white);
 703       this.setTitle("Structure Filter");
 704       // this.setFont(JvSwingUtils.getLabelFont());
 705
 706       this.add(all);
 707       this.add(alphaHelix);
 708       this.add(betaStrand);
 709       this.add(turn);
 710     }
 711
 712     public void alphaHelix_actionPerformed()
 713     {
 714       updateSelectAllState();
 715       aColChooser.setCurrentStructureFilterPanel(this);
 716       aColChooser.updateView();
 717     }
 718
 719     public void betaStrand_actionPerformed()
 720     {
 721       updateSelectAllState();
 722       aColChooser.setCurrentStructureFilterPanel(this);
 723       aColChooser.updateView();
 724     }
 725
 726     public void turn_actionPerformed()
 727     {
 728       updateSelectAllState();
 729       aColChooser.setCurrentStructureFilterPanel(this);
 730       aColChooser.updateView();
 731     }
 732
 733     public void all_actionPerformed()
 734     {
 735       if (all.getState())
 736       {
 737         alphaHelix.setState(true);
 738         betaStrand.setState(true);
 739         turn.setState(true);
 740       }
 741       else
 742       {
 743         alphaHelix.setState(false);
 744         betaStrand.setState(false);
 745         turn.setState(false);
 746       }
 747       aColChooser.setCurrentStructureFilterPanel(this);
 748       aColChooser.updateView();
 749     }
 750
 751     public void updateSelectAllState()
 752     {
 753       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 754       {
 755         all.setState(true);
 756       }
 757       else
 758       {
 759         all.setState(false);
 760       }
 761     }
 762
 763     public void syncState()
 764     {
 765       StructureFilterPanel sfp = aColChooser
 766               .getCurrentStructureFilterPanel();
 767       if (sfp != null)
 768       {
 769         alphaHelix.setState(sfp.alphaHelix.getState());
 770         betaStrand.setState(sfp.betaStrand.getState());
 771         turn.setState(sfp.turn.getState());
 772         if (sfp.all.getState())
 773         {
 774           all.setState(true);
 775           alphaHelix.setState(true);
 776           betaStrand.setState(true);
 777           turn.setState(true);
 778         }
 779       }
 780
 781     }
 782
 783     @Override
 784     public void itemStateChanged(ItemEvent e)
 785     {
 786       if (e.getSource() == alphaHelix)
 787       {
 788         alphaHelix_actionPerformed();
 789       }
 790       else if (e.getSource() == betaStrand)
 791       {
 792         betaStrand_actionPerformed();
 793       }
 794       else if (e.getSource() == turn)
 795       {
 796         turn_actionPerformed();
 797       }
 798       else if (e.getSource() == all)
 799       {
 800         all_actionPerformed();
 801       }
 802     }
 803   }
 804
 805   public class SearchPanel extends TitledPanel implements ItemListener
 806   {
 807     private AnnotationColumnChooser aColChooser;
 808
 809     private Checkbox displayName = new Checkbox();
 810
 811     private Checkbox description = new Checkbox();
 812
 813     private TextField searchBox = new TextField(10);
 814
 815     public SearchPanel(AnnotationColumnChooser aColChooser)
 816     {
 817
 818       this.aColChooser = aColChooser;
 819       searchBox.addTextListener(new TextListener()
 820       {
 821
 822         @Override
 823         public void textValueChanged(TextEvent e)
 824         {
 825           searchStringAction();
 826
 827         }
 828
 829       });
 830
 831       displayName.setLabel(MessageManager.getString("label.label"));
 832       displayName.setEnabled(false);
 833       displayName.addItemListener(this);
 834
 835       description.setLabel(MessageManager.getString("label.description"));
 836       description.setEnabled(false);
 837       description.addItemListener(this);
 838       this.setTitle("Search Filter");
 839       // this.setFont(JvSwingUtils.getLabelFont());
 840
 841       syncState();
 842       this.add(searchBox);
 843       this.add(displayName);
 844       this.add(description);
 845     }
 846
 847     public void displayNameCheckboxAction()
 848     {
 849       aColChooser.setCurrentSearchPanel(this);
 850       aColChooser.updateView();
 851     }
 852
 853     public void discriptionCheckboxAction()
 854     {
 855       aColChooser.setCurrentSearchPanel(this);
 856       aColChooser.updateView();
 857     }
 858
 859     public void searchStringAction()
 860     {
 861       aColChooser.setCurrentSearchPanel(this);
 862       aColChooser.updateView();
 863     }
 864
 865     public void syncState()
 866     {
 867       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 868       if (sp != null)
 869       {
 870         description.setEnabled(sp.description.isEnabled());
 871         description.setState(sp.description.getState());
 872
 873         displayName.setEnabled(sp.displayName.isEnabled());
 874         displayName.setState(sp.displayName.getState());
 875
 876         searchBox.setText(sp.searchBox.getText());
 877       }
 878     }
 879
 880     @Override
 881     public void itemStateChanged(ItemEvent e)
 882     {
 883       if (e.getSource() == displayName)
 884       {
 885         displayNameCheckboxAction();
 886       }
 887       else if (e.getSource() == description)
 888       {
 889         discriptionCheckboxAction();
 890       }
 891
 892     }
 893   }
 894
 895   @Override
 896   public void actionPerformed(ActionEvent evt)
 897   {
 898
 899     if (evt.getSource() == ok)
 900     {
 901       ok_actionPerformed(null);
 902     }
 903     else if (evt.getSource() == cancel)
 904     {
 905       cancel_actionPerformed(null);
 906     }
 907     else if (evt.getSource() == thresholdValue)
 908     {
 909       thresholdValue_actionPerformed(null);
 910     }
 911     else
 912     {
 913       updateView();
 914     }
 915   }
 916
 917   @Override
 918   public void mouseClicked(MouseEvent e)
 919   {
 920     // TODO Auto-generated method stub
 921
 922   }
 923
 924   @Override
 925   public void mousePressed(MouseEvent e)
 926   {
 927     if (e.getSource() == slider)
 928     {
 929       updateView();
 930     }
 931
 932   }
 933
 934   @Override
 935   public void mouseReleased(MouseEvent e)
 936   {
 937     if (e.getSource() == slider)
 938     {
 939       updateView();
 940     }
 941   }
 942
 943   @Override
 944   public void mouseEntered(MouseEvent e)
 945   {
 946     if (e.getSource() == slider)
 947     {
 948       updateView();
 949     }
 950   }
 951
 952   @Override
 953   public void mouseExited(MouseEvent e)
 954   {
 955     if (e.getSource() == slider)
 956     {
 957       updateView();
 958     }
 959   }
 960
 961 }