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.Vector;
  50
  51 //import javax.swing.JPanel;
  52
  53 //import net.miginfocom.swing.MigLayout;
  54
  55 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  56         ActionListener, AdjustmentListener, ItemListener, MouseListener
  57 {
  58
  59   private Choice annotations = new Choice();
  60
  61   private Panel actionPanel = new Panel();
  62
  63   private TitledPanel thresholdPanel = new TitledPanel();
  64
  65   private Panel switchableViewsPanel = new Panel(new CardLayout());
  66
  67   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  68           .getLayout());
  69
  70   private Panel noGraphFilterView = new Panel();
  71
  72   private Panel graphFilterView = new Panel();
  73
  74   private Panel annotationComboBoxPanel = new Panel();
  75
  76   private BorderLayout borderLayout1 = new BorderLayout();
  77
  78   private BorderLayout gBorderLayout = new BorderLayout();
  79
  80   private BorderLayout ngBorderLayout = new BorderLayout();
  81
  82   private Choice threshold = new Choice();
  83
  84   private StructureFilterPanel gStructureFilterPanel;
  85
  86   private StructureFilterPanel ngStructureFilterPanel;
  87
  88   private StructureFilterPanel currentStructureFilterPanel;
  89
  90   private SearchPanel currentSearchPanel;
  91
  92   private SearchPanel gSearchPanel;
  93
  94   private SearchPanel ngSearchPanel;
  95
  96   private FurtherActionPanel currentFurtherActionPanel;
  97
  98   private FurtherActionPanel gFurtherActionPanel;
  99
 100   private FurtherActionPanel ngFurtherActionPanel;
 101
 102   public static final int ACTION_OPTION_SELECT = 1;
 103
 104   public static int ACTION_OPTION_HIDE = 2;
 105
 106   public static String NO_GRAPH_VIEW = "0";
 107
 108   public static String GRAPH_VIEW = "1";
 109
 110   private int actionOption = ACTION_OPTION_SELECT;
 111
 112   private HiddenColumns oldHiddenColumns;
 113
 114   public AnnotationColumnChooser()
 115   {
 116     try
 117     {
 118       jbInit();
 119     } catch (Exception ex)
 120     {
 121       ex.printStackTrace();
 122     }
 123   }
 124
 125   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 126   {
 127     super(av, ap);
 128     frame = new Frame();
 129     frame.add(this);
 130     jalview.bin.JalviewLite.addFrame(frame,
 131             MessageManager.getString("label.select_by_annotation"), 520,
 132             215);
 133
 134     slider.addAdjustmentListener(this);
 135     slider.addMouseListener(this);
 136
 137     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 138     if (anns == null)
 139     {
 140       return;
 141     }
 142     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 143     adjusting = true;
 144     Vector<String> list = new Vector<>();
 145     int index = 1;
 146     for (int i = 0; i < anns.length; i++)
 147     {
 148       String label = anns[i].label;
 149       if (anns[i].sequenceRef != null)
 150       {
 151         label = label + "_" + anns[i].sequenceRef.getName();
 152       }
 153       if (!list.contains(label))
 154       {
 155         list.addElement(label);
 156       }
 157       else
 158       {
 159         list.addElement(label + "_" + (index++));
 160       }
 161     }
 162
 163     for (int i = 0; i < list.size(); i++)
 164     {
 165       annotations.addItem(list.elementAt(i).toString());
 166     }
 167
 168     populateThresholdComboBox(threshold);
 169     AnnotationColumnChooser lastChooser = av
 170             .getAnnotationColumnSelectionState();
 171     // restore Object state from the previous session if one exists
 172     if (lastChooser != null)
 173     {
 174       currentSearchPanel = lastChooser.getCurrentSearchPanel();
 175       currentStructureFilterPanel = lastChooser
 176               .getCurrentStructureFilterPanel();
 177       annotations.select(lastChooser.getAnnotations().getSelectedIndex());
 178       threshold.select(lastChooser.getThreshold().getSelectedIndex());
 179       actionOption = lastChooser.getActionOption();
 180       percentThreshold.setState(lastChooser.percentThreshold.getState());
 181     }
 182
 183     try
 184     {
 185       jbInit();
 186     } catch (Exception ex)
 187     {
 188     }
 189     adjusting = false;
 190
 191     updateView();
 192     frame.invalidate();
 193     frame.pack();
 194   }
 195
 196   private void jbInit() throws Exception
 197   {
 198     ok.setLabel(MessageManager.getString("action.ok"));
 199
 200     cancel.setLabel(MessageManager.getString("action.cancel"));
 201
 202     thresholdValue.setEnabled(false);
 203     thresholdValue.setColumns(7);
 204     thresholdValue.setCaretPosition(0);
 205
 206     ok.addActionListener(this);
 207     cancel.addActionListener(this);
 208     annotations.addItemListener(this);
 209     thresholdValue.addActionListener(this);
 210     threshold.addItemListener(this);
 211
 212     slider.setBackground(Color.white);
 213     slider.setEnabled(false);
 214     slider.setPreferredSize(new Dimension(100, 32));
 215
 216     thresholdPanel.setBackground(Color.white);
 217     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 218     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 219
 220     percentThreshold.setLabel("As percentage");
 221     percentThreshold.addItemListener(this);
 222
 223     actionPanel.setBackground(Color.white);
 224     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 225
 226     graphFilterView.setLayout(gBorderLayout);
 227     graphFilterView.setBackground(Color.white);
 228
 229     noGraphFilterView.setLayout(ngBorderLayout);
 230     noGraphFilterView.setBackground(Color.white);
 231
 232     annotationComboBoxPanel.setBackground(Color.white);
 233     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 234
 235     gSearchPanel = new SearchPanel(this);
 236     ngSearchPanel = new SearchPanel(this);
 237     gFurtherActionPanel = new FurtherActionPanel(this);
 238     ngFurtherActionPanel = new FurtherActionPanel(this);
 239     gStructureFilterPanel = new StructureFilterPanel(this);
 240     ngStructureFilterPanel = new StructureFilterPanel(this);
 241
 242     thresholdPanel.setTitle("Threshold Filter");
 243     thresholdPanel.add(getThreshold());
 244     thresholdPanel.add(slider);
 245     thresholdPanel.add(thresholdValue);
 246     thresholdPanel.add(percentThreshold);
 247
 248     actionPanel.add(ok);
 249     actionPanel.add(cancel);
 250
 251     Panel staticPanel = new Panel();
 252     staticPanel.setLayout(new BorderLayout());
 253     staticPanel.setBackground(Color.white);
 254
 255     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 256     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 257
 258     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 259     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 260     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 261
 262     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 263     noGraphFilterView.add(ngStructureFilterPanel,
 264             java.awt.BorderLayout.CENTER);
 265     noGraphFilterView.add(ngFurtherActionPanel,
 266             java.awt.BorderLayout.CENTER);
 267
 268     annotationComboBoxPanel.add(getAnnotations());
 269     switchableViewsPanel.add(noGraphFilterView,
 270             AnnotationColumnChooser.NO_GRAPH_VIEW);
 271     switchableViewsPanel.add(graphFilterView,
 272             AnnotationColumnChooser.GRAPH_VIEW);
 273
 274     this.setLayout(borderLayout1);
 275     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 276     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 277     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 278
 279     selectedAnnotationChanged();
 280     this.validate();
 281   }
 282
 283   @Override
 284   @SuppressWarnings("unchecked")
 285   public void reset()
 286   {
 287     if (this.getOldHiddenColumns() != null)
 288     {
 289       av.getColumnSelection().clear();
 290
 291       if (av.getAnnotationColumnSelectionState() != null)
 292       {
 293         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
 294                 .getOldHiddenColumns();
 295         av.getAlignment().setHiddenColumns(oldHidden);
 296       }
 297       av.sendSelection();
 298       ap.paintAlignment(true);
 299     }
 300
 301   }
 302
 303   @Override
 304   public void adjustmentValueChanged(AdjustmentEvent evt)
 305   {
 306     if (!adjusting)
 307     {
 308       setThresholdValueText();
 309       valueChanged(!sliderDragging);
 310     }
 311   }
 312
 313   protected void addSliderMouseListeners()
 314   {
 315
 316     slider.addMouseListener(new MouseAdapter()
 317     {
 318       @Override
 319       public void mousePressed(MouseEvent e)
 320       {
 321         sliderDragging = true;
 322         super.mousePressed(e);
 323       }
 324
 325       @Override
 326       public void mouseDragged(MouseEvent e)
 327       {
 328         sliderDragging = true;
 329         super.mouseDragged(e);
 330       }
 331
 332       @Override
 333       public void mouseReleased(MouseEvent evt)
 334       {
 335         if (sliderDragging)
 336         {
 337           sliderDragging = false;
 338           valueChanged(true);
 339         }
 340         ap.paintAlignment(true);
 341       }
 342     });
 343   }
 344
 345   @Override
 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()
 387             .getAlignmentAnnotation()[getAnnotations().getSelectedIndex()]);
 388
 389     int selectedThresholdItem = getSelectedThresholdItem(
 390             getThreshold().getSelectedIndex());
 391
 392     slider.setEnabled(true);
 393     thresholdValue.setEnabled(true);
 394     percentThreshold.setEnabled(true);
 395
 396     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 397     {
 398       slider.setEnabled(false);
 399       thresholdValue.setEnabled(false);
 400       thresholdValue.setText("");
 401       percentThreshold.setEnabled(false);
 402       // build filter params
 403     }
 404     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 405     {
 406       if (getCurrentAnnotation().threshold == null)
 407       {
 408         getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
 409                 (getCurrentAnnotation().graphMax
 410                         - getCurrentAnnotation().graphMin) / 2f,
 411                 "Threshold", Color.black));
 412       }
 413
 414       adjusting = true;
 415       // float range = getCurrentAnnotation().graphMax * 1000
 416       // - getCurrentAnnotation().graphMin * 1000;
 417
 418       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 419       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 420       slider.setValue(
 421               (int) (getCurrentAnnotation().threshold.value * 1000));
 422       setThresholdValueText();
 423       // slider.setMajorTickSpacing((int) (range / 10f));
 424       slider.setEnabled(true);
 425       thresholdValue.setEnabled(true);
 426       percentThreshold.setEnabled(true);
 427       adjusting = false;
 428
 429       // build filter params
 430       filterParams.setThresholdType(
 431               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 432       if (getCurrentAnnotation().isQuantitative())
 433       {
 434         filterParams
 435                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 436
 437         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 438         {
 439           filterParams.setThresholdType(
 440                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 441         }
 442         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 443         {
 444           filterParams.setThresholdType(
 445                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 446         }
 447       }
 448     }
 449
 450     if (currentStructureFilterPanel != null)
 451     {
 452       if (currentStructureFilterPanel.alphaHelix.getState())
 453       {
 454         filterParams.setFilterAlphaHelix(true);
 455       }
 456       if (currentStructureFilterPanel.betaStrand.getState())
 457       {
 458         filterParams.setFilterBetaSheet(true);
 459       }
 460       if (currentStructureFilterPanel.turn.getState())
 461       {
 462         filterParams.setFilterTurn(true);
 463       }
 464     }
 465
 466     if (currentSearchPanel != null)
 467     {
 468
 469       if (!currentSearchPanel.searchBox.getText().isEmpty())
 470       {
 471         currentSearchPanel.description.setEnabled(true);
 472         currentSearchPanel.displayName.setEnabled(true);
 473         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 474         if (currentSearchPanel.displayName.getState())
 475         {
 476           filterParams.addRegexSearchField(
 477                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 478         }
 479         if (currentSearchPanel.description.getState())
 480         {
 481           filterParams.addRegexSearchField(
 482                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 483         }
 484       }
 485       else
 486       {
 487         currentSearchPanel.description.setEnabled(false);
 488         currentSearchPanel.displayName.setEnabled(false);
 489       }
 490     }
 491
 492     // show hidden columns here, before changing the column selection in
 493     // filterAnnotations, because showing hidden columns has the side effect of
 494     // adding them to the selection
 495     av.showAllHiddenColumns();
 496     av.getColumnSelection().filterAnnotations(
 497             getCurrentAnnotation().annotations, filterParams);
 498
 499     if (getActionOption() == ACTION_OPTION_HIDE)
 500     {
 501       av.hideSelectedColumns();
 502     }
 503
 504     filterParams = null;
 505     av.setAnnotationColumnSelectionState(this);
 506     av.sendSelection();
 507     ap.paintAlignment(true);
 508   }
 509
 510   public HiddenColumns getOldHiddenColumns()
 511   {
 512     return oldHiddenColumns;
 513   }
 514
 515   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 516   {
 517     if (currentHiddenColumns != null)
 518     {
 519       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 520     }
 521   }
 522
 523   public FurtherActionPanel getCurrentFutherActionPanel()
 524   {
 525     return currentFurtherActionPanel;
 526   }
 527
 528   public void setCurrentFutherActionPanel(
 529           FurtherActionPanel currentFutherActionPanel)
 530   {
 531     this.currentFurtherActionPanel = currentFutherActionPanel;
 532   }
 533
 534   public SearchPanel getCurrentSearchPanel()
 535   {
 536     return currentSearchPanel;
 537   }
 538
 539   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 540   {
 541     this.currentSearchPanel = currentSearchPanel;
 542   }
 543
 544   public int getActionOption()
 545   {
 546     return actionOption;
 547   }
 548
 549   public void setActionOption(int actionOption)
 550   {
 551     this.actionOption = actionOption;
 552   }
 553
 554   public StructureFilterPanel getCurrentStructureFilterPanel()
 555   {
 556     return currentStructureFilterPanel;
 557   }
 558
 559   public void setCurrentStructureFilterPanel(
 560           StructureFilterPanel currentStructureFilterPanel)
 561   {
 562     this.currentStructureFilterPanel = currentStructureFilterPanel;
 563   }
 564
 565   @Override
 566   public void itemStateChanged(ItemEvent e)
 567   {
 568     if (e.getSource() == annotations)
 569     {
 570       selectedAnnotationChanged();
 571     }
 572     else if (e.getSource() == threshold)
 573     {
 574       threshold_actionPerformed(null);
 575     }
 576     else if (e.getSource() == percentThreshold)
 577     {
 578       if (!adjusting)
 579       {
 580         percentageValue_actionPerformed();
 581       }
 582
 583     }
 584   }
 585
 586   public void selectedAnnotationChanged()
 587   {
 588     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 589     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 590             .getSelectedIndex()].isQuantitative())
 591     {
 592       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 593     }
 594
 595     gSearchPanel.syncState();
 596     gFurtherActionPanel.syncState();
 597     gStructureFilterPanel.syncState();
 598
 599     ngSearchPanel.syncState();
 600     ngFurtherActionPanel.syncState();
 601     ngStructureFilterPanel.syncState();
 602
 603     switchableViewsLayout.show(switchableViewsPanel, currentView);
 604     updateView();
 605   }
 606
 607   public class FurtherActionPanel extends Panel implements ItemListener
 608   {
 609     private AnnotationColumnChooser aColChooser;
 610
 611     private Choice furtherAction = new Choice();
 612
 613     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 614     {
 615       this.aColChooser = aColChooser;
 616       furtherAction.addItem("Select");
 617       furtherAction.addItem("Hide");
 618       furtherAction.addItemListener(this);
 619       syncState();
 620
 621       // this.setTitle("Filter Actions");
 622       // this.setFont(JvSwingUtils.getLabelFont());
 623
 624       this.add(furtherAction);
 625     }
 626
 627     public void syncState()
 628     {
 629       if (aColChooser
 630               .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 631       {
 632         furtherAction.select("Hide");
 633       }
 634       else
 635       {
 636         furtherAction.select("Select");
 637       }
 638     }
 639
 640     @Override
 641     public void itemStateChanged(ItemEvent e)
 642     {
 643       aColChooser.setCurrentFutherActionPanel(this);
 644       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 645       {
 646         setActionOption(ACTION_OPTION_SELECT);
 647         updateView();
 648       }
 649       else
 650       {
 651         setActionOption(ACTION_OPTION_HIDE);
 652         updateView();
 653       }
 654
 655     }
 656   }
 657
 658   public class StructureFilterPanel extends TitledPanel
 659           implements ItemListener
 660   {
 661     private AnnotationColumnChooser aColChooser;
 662
 663     private Checkbox alphaHelix = new Checkbox();
 664
 665     private Checkbox betaStrand = new Checkbox();
 666
 667     private Checkbox turn = new Checkbox();
 668
 669     private Checkbox all = new Checkbox();
 670
 671     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 672     {
 673       this.aColChooser = aColChooser;
 674
 675       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 676       alphaHelix.setBackground(Color.white);
 677
 678       alphaHelix.addItemListener(this);
 679
 680       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 681       betaStrand.setBackground(Color.white);
 682       betaStrand.addItemListener(this);
 683
 684       turn.setLabel(MessageManager.getString("label.turn"));
 685       turn.setBackground(Color.white);
 686       turn.addItemListener(this);
 687
 688       all.setLabel(MessageManager.getString("label.select_all"));
 689       all.setBackground(Color.white);
 690       all.addItemListener(this);
 691
 692       this.setBackground(Color.white);
 693       this.setTitle("Structure Filter");
 694       // this.setFont(JvSwingUtils.getLabelFont());
 695
 696       this.add(all);
 697       this.add(alphaHelix);
 698       this.add(betaStrand);
 699       this.add(turn);
 700     }
 701
 702     public void alphaHelix_actionPerformed()
 703     {
 704       updateSelectAllState();
 705       aColChooser.setCurrentStructureFilterPanel(this);
 706       aColChooser.updateView();
 707     }
 708
 709     public void betaStrand_actionPerformed()
 710     {
 711       updateSelectAllState();
 712       aColChooser.setCurrentStructureFilterPanel(this);
 713       aColChooser.updateView();
 714     }
 715
 716     public void turn_actionPerformed()
 717     {
 718       updateSelectAllState();
 719       aColChooser.setCurrentStructureFilterPanel(this);
 720       aColChooser.updateView();
 721     }
 722
 723     public void all_actionPerformed()
 724     {
 725       if (all.getState())
 726       {
 727         alphaHelix.setState(true);
 728         betaStrand.setState(true);
 729         turn.setState(true);
 730       }
 731       else
 732       {
 733         alphaHelix.setState(false);
 734         betaStrand.setState(false);
 735         turn.setState(false);
 736       }
 737       aColChooser.setCurrentStructureFilterPanel(this);
 738       aColChooser.updateView();
 739     }
 740
 741     public void updateSelectAllState()
 742     {
 743       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 744       {
 745         all.setState(true);
 746       }
 747       else
 748       {
 749         all.setState(false);
 750       }
 751     }
 752
 753     public void syncState()
 754     {
 755       StructureFilterPanel sfp = aColChooser
 756               .getCurrentStructureFilterPanel();
 757       if (sfp != null)
 758       {
 759         alphaHelix.setState(sfp.alphaHelix.getState());
 760         betaStrand.setState(sfp.betaStrand.getState());
 761         turn.setState(sfp.turn.getState());
 762         if (sfp.all.getState())
 763         {
 764           all.setState(true);
 765           alphaHelix.setState(true);
 766           betaStrand.setState(true);
 767           turn.setState(true);
 768         }
 769       }
 770
 771     }
 772
 773     @Override
 774     public void itemStateChanged(ItemEvent e)
 775     {
 776       if (e.getSource() == alphaHelix)
 777       {
 778         alphaHelix_actionPerformed();
 779       }
 780       else if (e.getSource() == betaStrand)
 781       {
 782         betaStrand_actionPerformed();
 783       }
 784       else if (e.getSource() == turn)
 785       {
 786         turn_actionPerformed();
 787       }
 788       else if (e.getSource() == all)
 789       {
 790         all_actionPerformed();
 791       }
 792     }
 793   }
 794
 795   public class SearchPanel extends TitledPanel implements ItemListener
 796   {
 797     private AnnotationColumnChooser aColChooser;
 798
 799     private Checkbox displayName = new Checkbox();
 800
 801     private Checkbox description = new Checkbox();
 802
 803     private TextField searchBox = new TextField(10);
 804
 805     public SearchPanel(AnnotationColumnChooser aColChooser)
 806     {
 807
 808       this.aColChooser = aColChooser;
 809       searchBox.addTextListener(new TextListener()
 810       {
 811
 812         @Override
 813         public void textValueChanged(TextEvent e)
 814         {
 815           searchStringAction();
 816
 817         }
 818
 819       });
 820
 821       displayName.setLabel(MessageManager.getString("label.label"));
 822       displayName.setEnabled(false);
 823       displayName.addItemListener(this);
 824
 825       description.setLabel(MessageManager.getString("label.description"));
 826       description.setEnabled(false);
 827       description.addItemListener(this);
 828       this.setTitle("Search Filter");
 829       // this.setFont(JvSwingUtils.getLabelFont());
 830
 831       syncState();
 832       this.add(searchBox);
 833       this.add(displayName);
 834       this.add(description);
 835     }
 836
 837     public void displayNameCheckboxAction()
 838     {
 839       aColChooser.setCurrentSearchPanel(this);
 840       aColChooser.updateView();
 841     }
 842
 843     public void discriptionCheckboxAction()
 844     {
 845       aColChooser.setCurrentSearchPanel(this);
 846       aColChooser.updateView();
 847     }
 848
 849     public void searchStringAction()
 850     {
 851       aColChooser.setCurrentSearchPanel(this);
 852       aColChooser.updateView();
 853     }
 854
 855     public void syncState()
 856     {
 857       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 858       if (sp != null)
 859       {
 860         description.setEnabled(sp.description.isEnabled());
 861         description.setState(sp.description.getState());
 862
 863         displayName.setEnabled(sp.displayName.isEnabled());
 864         displayName.setState(sp.displayName.getState());
 865
 866         searchBox.setText(sp.searchBox.getText());
 867       }
 868     }
 869
 870     @Override
 871     public void itemStateChanged(ItemEvent e)
 872     {
 873       if (e.getSource() == displayName)
 874       {
 875         displayNameCheckboxAction();
 876       }
 877       else if (e.getSource() == description)
 878       {
 879         discriptionCheckboxAction();
 880       }
 881
 882     }
 883   }
 884
 885   @Override
 886   public void actionPerformed(ActionEvent evt)
 887   {
 888
 889     if (evt.getSource() == ok)
 890     {
 891       ok_actionPerformed(null);
 892     }
 893     else if (evt.getSource() == cancel)
 894     {
 895       cancel_actionPerformed(null);
 896     }
 897     else if (evt.getSource() == thresholdValue)
 898     {
 899       thresholdValue_actionPerformed(null);
 900     }
 901     else
 902     {
 903       updateView();
 904     }
 905   }
 906
 907   @Override
 908   public void mouseClicked(MouseEvent e)
 909   {
 910     // TODO Auto-generated method stub
 911
 912   }
 913
 914   @Override
 915   public void mousePressed(MouseEvent e)
 916   {
 917     if (e.getSource() == slider)
 918     {
 919       updateView();
 920     }
 921
 922   }
 923
 924   @Override
 925   public void mouseReleased(MouseEvent e)
 926   {
 927     if (e.getSource() == slider)
 928     {
 929       updateView();
 930     }
 931   }
 932
 933   @Override
 934   public void mouseEntered(MouseEvent e)
 935   {
 936     if (e.getSource() == slider)
 937     {
 938       updateView();
 939     }
 940   }
 941
 942   @Override
 943   public void mouseExited(MouseEvent e)
 944   {
 945     if (e.getSource() == slider)
 946     {
 947       updateView();
 948     }
 949   }
 950
 951 }