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, 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, 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(); // this also calls paintAlignment(true,true)
 352     }
 353   }
 354
 355   public Choice getThreshold()
 356   {
 357     return threshold;
 358   }
 359
 360   public void setThreshold(Choice threshold)
 361   {
 362     this.threshold = threshold;
 363   }
 364
 365   public Choice getAnnotations()
 366   {
 367     return annotations;
 368   }
 369
 370   public void setAnnotations(Choice annotations)
 371   {
 372     this.annotations = annotations;
 373   }
 374
 375   @Override
 376   public void updateView()
 377   {
 378     // Check if combobox is still adjusting
 379     if (adjusting)
 380     {
 381       return;
 382     }
 383
 384     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 385     setCurrentAnnotation(av.getAlignment()
 386             .getAlignmentAnnotation()[getAnnotations().getSelectedIndex()]);
 387
 388     int selectedThresholdItem = getSelectedThresholdItem(
 389             getThreshold().getSelectedIndex());
 390
 391     slider.setEnabled(true);
 392     thresholdValue.setEnabled(true);
 393     percentThreshold.setEnabled(true);
 394
 395     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 396     {
 397       slider.setEnabled(false);
 398       thresholdValue.setEnabled(false);
 399       thresholdValue.setText("");
 400       percentThreshold.setEnabled(false);
 401       // build filter params
 402     }
 403     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 404     {
 405       if (getCurrentAnnotation().threshold == null)
 406       {
 407         getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
 408                 (getCurrentAnnotation().graphMax
 409                         - 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(
 420               (int) (getCurrentAnnotation().threshold.value * 1000));
 421       setThresholdValueText();
 422       // slider.setMajorTickSpacing((int) (range / 10f));
 423       slider.setEnabled(true);
 424       thresholdValue.setEnabled(true);
 425       percentThreshold.setEnabled(true);
 426       adjusting = false;
 427
 428       // build filter params
 429       filterParams.setThresholdType(
 430               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 431       if (getCurrentAnnotation().isQuantitative())
 432       {
 433         filterParams
 434                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 435
 436         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 437         {
 438           filterParams.setThresholdType(
 439                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 440         }
 441         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 442         {
 443           filterParams.setThresholdType(
 444                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 445         }
 446       }
 447     }
 448
 449     if (currentStructureFilterPanel != null)
 450     {
 451       if (currentStructureFilterPanel.alphaHelix.getState())
 452       {
 453         filterParams.setFilterAlphaHelix(true);
 454       }
 455       if (currentStructureFilterPanel.betaStrand.getState())
 456       {
 457         filterParams.setFilterBetaSheet(true);
 458       }
 459       if (currentStructureFilterPanel.turn.getState())
 460       {
 461         filterParams.setFilterTurn(true);
 462       }
 463     }
 464
 465     if (currentSearchPanel != null)
 466     {
 467
 468       if (!currentSearchPanel.searchBox.getText().isEmpty())
 469       {
 470         currentSearchPanel.description.setEnabled(true);
 471         currentSearchPanel.displayName.setEnabled(true);
 472         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 473         if (currentSearchPanel.displayName.getState())
 474         {
 475           filterParams.addRegexSearchField(
 476                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 477         }
 478         if (currentSearchPanel.description.getState())
 479         {
 480           filterParams.addRegexSearchField(
 481                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 482         }
 483       }
 484       else
 485       {
 486         currentSearchPanel.description.setEnabled(false);
 487         currentSearchPanel.displayName.setEnabled(false);
 488       }
 489     }
 490
 491     // show hidden columns here, before changing the column selection in
 492     // filterAnnotations, because showing hidden columns has the side effect of
 493     // adding them to the selection
 494     av.showAllHiddenColumns();
 495     av.getColumnSelection().filterAnnotations(
 496             getCurrentAnnotation().annotations, filterParams);
 497
 498     if (getActionOption() == ACTION_OPTION_HIDE)
 499     {
 500       av.hideSelectedColumns();
 501     }
 502
 503     filterParams = null;
 504     av.setAnnotationColumnSelectionState(this);
 505     av.sendSelection();
 506     ap.paintAlignment(true, true);
 507   }
 508
 509   public HiddenColumns getOldHiddenColumns()
 510   {
 511     return oldHiddenColumns;
 512   }
 513
 514   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 515   {
 516     if (currentHiddenColumns != null)
 517     {
 518       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 519     }
 520   }
 521
 522   public FurtherActionPanel getCurrentFutherActionPanel()
 523   {
 524     return currentFurtherActionPanel;
 525   }
 526
 527   public void setCurrentFutherActionPanel(
 528           FurtherActionPanel currentFutherActionPanel)
 529   {
 530     this.currentFurtherActionPanel = currentFutherActionPanel;
 531   }
 532
 533   public SearchPanel getCurrentSearchPanel()
 534   {
 535     return currentSearchPanel;
 536   }
 537
 538   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 539   {
 540     this.currentSearchPanel = currentSearchPanel;
 541   }
 542
 543   public int getActionOption()
 544   {
 545     return actionOption;
 546   }
 547
 548   public void setActionOption(int actionOption)
 549   {
 550     this.actionOption = actionOption;
 551   }
 552
 553   public StructureFilterPanel getCurrentStructureFilterPanel()
 554   {
 555     return currentStructureFilterPanel;
 556   }
 557
 558   public void setCurrentStructureFilterPanel(
 559           StructureFilterPanel currentStructureFilterPanel)
 560   {
 561     this.currentStructureFilterPanel = currentStructureFilterPanel;
 562   }
 563
 564   @Override
 565   public void itemStateChanged(ItemEvent e)
 566   {
 567     if (e.getSource() == annotations)
 568     {
 569       selectedAnnotationChanged();
 570     }
 571     else if (e.getSource() == threshold)
 572     {
 573       threshold_actionPerformed(null);
 574     }
 575     else if (e.getSource() == percentThreshold)
 576     {
 577       if (!adjusting)
 578       {
 579         percentageValue_actionPerformed();
 580       }
 581
 582     }
 583   }
 584
 585   public void selectedAnnotationChanged()
 586   {
 587     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 588     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 589             .getSelectedIndex()].isQuantitative())
 590     {
 591       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 592     }
 593
 594     gSearchPanel.syncState();
 595     gFurtherActionPanel.syncState();
 596     gStructureFilterPanel.syncState();
 597
 598     ngSearchPanel.syncState();
 599     ngFurtherActionPanel.syncState();
 600     ngStructureFilterPanel.syncState();
 601
 602     switchableViewsLayout.show(switchableViewsPanel, currentView);
 603     updateView();
 604   }
 605
 606   public class FurtherActionPanel extends Panel implements ItemListener
 607   {
 608     private AnnotationColumnChooser aColChooser;
 609
 610     private Choice furtherAction = new Choice();
 611
 612     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 613     {
 614       this.aColChooser = aColChooser;
 615       furtherAction.addItem("Select");
 616       furtherAction.addItem("Hide");
 617       furtherAction.addItemListener(this);
 618       syncState();
 619
 620       // this.setTitle("Filter Actions");
 621       // this.setFont(JvSwingUtils.getLabelFont());
 622
 623       this.add(furtherAction);
 624     }
 625
 626     public void syncState()
 627     {
 628       if (aColChooser
 629               .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 630       {
 631         furtherAction.select("Hide");
 632       }
 633       else
 634       {
 635         furtherAction.select("Select");
 636       }
 637     }
 638
 639     @Override
 640     public void itemStateChanged(ItemEvent e)
 641     {
 642       aColChooser.setCurrentFutherActionPanel(this);
 643       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 644       {
 645         setActionOption(ACTION_OPTION_SELECT);
 646         updateView();
 647       }
 648       else
 649       {
 650         setActionOption(ACTION_OPTION_HIDE);
 651         updateView();
 652       }
 653
 654     }
 655   }
 656
 657   public class StructureFilterPanel extends TitledPanel
 658           implements ItemListener
 659   {
 660     private AnnotationColumnChooser aColChooser;
 661
 662     private Checkbox alphaHelix = new Checkbox();
 663
 664     private Checkbox betaStrand = new Checkbox();
 665
 666     private Checkbox turn = new Checkbox();
 667
 668     private Checkbox all = new Checkbox();
 669
 670     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 671     {
 672       this.aColChooser = aColChooser;
 673
 674       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 675       alphaHelix.setBackground(Color.white);
 676
 677       alphaHelix.addItemListener(this);
 678
 679       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 680       betaStrand.setBackground(Color.white);
 681       betaStrand.addItemListener(this);
 682
 683       turn.setLabel(MessageManager.getString("label.turn"));
 684       turn.setBackground(Color.white);
 685       turn.addItemListener(this);
 686
 687       all.setLabel(MessageManager.getString("label.select_all"));
 688       all.setBackground(Color.white);
 689       all.addItemListener(this);
 690
 691       this.setBackground(Color.white);
 692       this.setTitle("Structure Filter");
 693       // this.setFont(JvSwingUtils.getLabelFont());
 694
 695       this.add(all);
 696       this.add(alphaHelix);
 697       this.add(betaStrand);
 698       this.add(turn);
 699     }
 700
 701     public void alphaHelix_actionPerformed()
 702     {
 703       updateSelectAllState();
 704       aColChooser.setCurrentStructureFilterPanel(this);
 705       aColChooser.updateView();
 706     }
 707
 708     public void betaStrand_actionPerformed()
 709     {
 710       updateSelectAllState();
 711       aColChooser.setCurrentStructureFilterPanel(this);
 712       aColChooser.updateView();
 713     }
 714
 715     public void turn_actionPerformed()
 716     {
 717       updateSelectAllState();
 718       aColChooser.setCurrentStructureFilterPanel(this);
 719       aColChooser.updateView();
 720     }
 721
 722     public void all_actionPerformed()
 723     {
 724       if (all.getState())
 725       {
 726         alphaHelix.setState(true);
 727         betaStrand.setState(true);
 728         turn.setState(true);
 729       }
 730       else
 731       {
 732         alphaHelix.setState(false);
 733         betaStrand.setState(false);
 734         turn.setState(false);
 735       }
 736       aColChooser.setCurrentStructureFilterPanel(this);
 737       aColChooser.updateView();
 738     }
 739
 740     public void updateSelectAllState()
 741     {
 742       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 743       {
 744         all.setState(true);
 745       }
 746       else
 747       {
 748         all.setState(false);
 749       }
 750     }
 751
 752     public void syncState()
 753     {
 754       StructureFilterPanel sfp = aColChooser
 755               .getCurrentStructureFilterPanel();
 756       if (sfp != null)
 757       {
 758         alphaHelix.setState(sfp.alphaHelix.getState());
 759         betaStrand.setState(sfp.betaStrand.getState());
 760         turn.setState(sfp.turn.getState());
 761         if (sfp.all.getState())
 762         {
 763           all.setState(true);
 764           alphaHelix.setState(true);
 765           betaStrand.setState(true);
 766           turn.setState(true);
 767         }
 768       }
 769
 770     }
 771
 772     @Override
 773     public void itemStateChanged(ItemEvent e)
 774     {
 775       if (e.getSource() == alphaHelix)
 776       {
 777         alphaHelix_actionPerformed();
 778       }
 779       else if (e.getSource() == betaStrand)
 780       {
 781         betaStrand_actionPerformed();
 782       }
 783       else if (e.getSource() == turn)
 784       {
 785         turn_actionPerformed();
 786       }
 787       else if (e.getSource() == all)
 788       {
 789         all_actionPerformed();
 790       }
 791     }
 792   }
 793
 794   public class SearchPanel extends TitledPanel implements ItemListener
 795   {
 796     private AnnotationColumnChooser aColChooser;
 797
 798     private Checkbox displayName = new Checkbox();
 799
 800     private Checkbox description = new Checkbox();
 801
 802     private TextField searchBox = new TextField(10);
 803
 804     public SearchPanel(AnnotationColumnChooser aColChooser)
 805     {
 806
 807       this.aColChooser = aColChooser;
 808       searchBox.addTextListener(new TextListener()
 809       {
 810
 811         @Override
 812         public void textValueChanged(TextEvent e)
 813         {
 814           searchStringAction();
 815
 816         }
 817
 818       });
 819
 820       displayName.setLabel(MessageManager.getString("label.label"));
 821       displayName.setEnabled(false);
 822       displayName.addItemListener(this);
 823
 824       description.setLabel(MessageManager.getString("label.description"));
 825       description.setEnabled(false);
 826       description.addItemListener(this);
 827       this.setTitle("Search Filter");
 828       // this.setFont(JvSwingUtils.getLabelFont());
 829
 830       syncState();
 831       this.add(searchBox);
 832       this.add(displayName);
 833       this.add(description);
 834     }
 835
 836     public void displayNameCheckboxAction()
 837     {
 838       aColChooser.setCurrentSearchPanel(this);
 839       aColChooser.updateView();
 840     }
 841
 842     public void discriptionCheckboxAction()
 843     {
 844       aColChooser.setCurrentSearchPanel(this);
 845       aColChooser.updateView();
 846     }
 847
 848     public void searchStringAction()
 849     {
 850       aColChooser.setCurrentSearchPanel(this);
 851       aColChooser.updateView();
 852     }
 853
 854     public void syncState()
 855     {
 856       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 857       if (sp != null)
 858       {
 859         description.setEnabled(sp.description.isEnabled());
 860         description.setState(sp.description.getState());
 861
 862         displayName.setEnabled(sp.displayName.isEnabled());
 863         displayName.setState(sp.displayName.getState());
 864
 865         searchBox.setText(sp.searchBox.getText());
 866       }
 867     }
 868
 869     @Override
 870     public void itemStateChanged(ItemEvent e)
 871     {
 872       if (e.getSource() == displayName)
 873       {
 874         displayNameCheckboxAction();
 875       }
 876       else if (e.getSource() == description)
 877       {
 878         discriptionCheckboxAction();
 879       }
 880
 881     }
 882   }
 883
 884   @Override
 885   public void actionPerformed(ActionEvent evt)
 886   {
 887
 888     if (evt.getSource() == ok)
 889     {
 890       ok_actionPerformed(null);
 891     }
 892     else if (evt.getSource() == cancel)
 893     {
 894       cancel_actionPerformed(null);
 895     }
 896     else if (evt.getSource() == thresholdValue)
 897     {
 898       thresholdValue_actionPerformed(null);
 899     }
 900     else
 901     {
 902       updateView();
 903     }
 904   }
 905
 906   @Override
 907   public void mouseClicked(MouseEvent e)
 908   {
 909     // TODO Auto-generated method stub
 910
 911   }
 912
 913   @Override
 914   public void mousePressed(MouseEvent e)
 915   {
 916     if (e.getSource() == slider)
 917     {
 918       updateView();
 919     }
 920
 921   }
 922
 923   @Override
 924   public void mouseReleased(MouseEvent e)
 925   {
 926     if (e.getSource() == slider)
 927     {
 928       updateView();
 929     }
 930   }
 931
 932   @Override
 933   public void mouseEntered(MouseEvent e)
 934   {
 935     if (e.getSource() == slider)
 936     {
 937       updateView();
 938     }
 939   }
 940
 941   @Override
 942   public void mouseExited(MouseEvent e)
 943   {
 944     if (e.getSource() == slider)
 945     {
 946       updateView();
 947     }
 948   }
 949
 950 }