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.ArrayList;
  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<>();
 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.getCurrentSearchPanel();
 176       currentStructureFilterPanel = lastChooser
 177               .getCurrentStructureFilterPanel();
 178       annotations.select(lastChooser.getAnnotations().getSelectedIndex());
 179       threshold.select(lastChooser.getThreshold().getSelectedIndex());
 180       actionOption = lastChooser.getActionOption();
 181       percentThreshold.setState(lastChooser.percentThreshold.getState());
 182     }
 183
 184     try
 185     {
 186       jbInit();
 187     } catch (Exception ex)
 188     {
 189     }
 190     adjusting = false;
 191
 192     updateView();
 193     frame.invalidate();
 194     frame.pack();
 195   }
 196
 197   private void jbInit() throws Exception
 198   {
 199     ok.setLabel(MessageManager.getString("action.ok"));
 200
 201     cancel.setLabel(MessageManager.getString("action.cancel"));
 202
 203     thresholdValue.setEnabled(false);
 204     thresholdValue.setColumns(7);
 205     thresholdValue.setCaretPosition(0);
 206
 207     ok.addActionListener(this);
 208     cancel.addActionListener(this);
 209     annotations.addItemListener(this);
 210     thresholdValue.addActionListener(this);
 211     threshold.addItemListener(this);
 212
 213     slider.setBackground(Color.white);
 214     slider.setEnabled(false);
 215     slider.setPreferredSize(new Dimension(100, 32));
 216
 217     thresholdPanel.setBackground(Color.white);
 218     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 219     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 220
 221     percentThreshold.setLabel("As percentage");
 222     percentThreshold.addItemListener(this);
 223
 224     actionPanel.setBackground(Color.white);
 225     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 226
 227     graphFilterView.setLayout(gBorderLayout);
 228     graphFilterView.setBackground(Color.white);
 229
 230     noGraphFilterView.setLayout(ngBorderLayout);
 231     noGraphFilterView.setBackground(Color.white);
 232
 233     annotationComboBoxPanel.setBackground(Color.white);
 234     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 235
 236     gSearchPanel = new SearchPanel(this);
 237     ngSearchPanel = new SearchPanel(this);
 238     gFurtherActionPanel = new FurtherActionPanel(this);
 239     ngFurtherActionPanel = new FurtherActionPanel(this);
 240     gStructureFilterPanel = new StructureFilterPanel(this);
 241     ngStructureFilterPanel = new StructureFilterPanel(this);
 242
 243     thresholdPanel.setTitle("Threshold Filter");
 244     thresholdPanel.add(getThreshold());
 245     thresholdPanel.add(slider);
 246     thresholdPanel.add(thresholdValue);
 247     thresholdPanel.add(percentThreshold);
 248
 249     actionPanel.add(ok);
 250     actionPanel.add(cancel);
 251
 252     Panel staticPanel = new Panel();
 253     staticPanel.setLayout(new BorderLayout());
 254     staticPanel.setBackground(Color.white);
 255
 256     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 257     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 258
 259     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 260     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 261     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 262
 263     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 264     noGraphFilterView.add(ngStructureFilterPanel,
 265             java.awt.BorderLayout.CENTER);
 266     noGraphFilterView.add(ngFurtherActionPanel,
 267             java.awt.BorderLayout.CENTER);
 268
 269     annotationComboBoxPanel.add(getAnnotations());
 270     switchableViewsPanel.add(noGraphFilterView,
 271             AnnotationColumnChooser.NO_GRAPH_VIEW);
 272     switchableViewsPanel.add(graphFilterView,
 273             AnnotationColumnChooser.GRAPH_VIEW);
 274
 275     this.setLayout(borderLayout1);
 276     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 277     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 278     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 279
 280     selectedAnnotationChanged();
 281     this.validate();
 282   }
 283
 284   @Override
 285   @SuppressWarnings("unchecked")
 286   public void reset()
 287   {
 288     if (this.getOldHiddenColumns() != null)
 289     {
 290       av.getColumnSelection().clear();
 291
 292       if (av.getAnnotationColumnSelectionState() != null)
 293       {
 294         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
 295                 .getOldHiddenColumns();
 296         if (oldHidden != null)
 297         {
 298           ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
 299           for (int[] positions : regions)
 300           {
 301             av.hideColumns(positions[0], positions[1]);
 302           }
 303         }
 304         // TODO not clear why we need to hide all the columns (above) if we are
 305         // going to copy the hidden columns over wholesale anyway
 306         av.getAlignment().setHiddenColumns(oldHidden);
 307       }
 308       av.sendSelection();
 309       ap.paintAlignment(true, true);
 310     }
 311
 312   }
 313
 314   @Override
 315   public void adjustmentValueChanged(AdjustmentEvent evt)
 316   {
 317     if (!adjusting)
 318     {
 319       setThresholdValueText();
 320       valueChanged(!sliderDragging);
 321     }
 322   }
 323
 324   protected void addSliderMouseListeners()
 325   {
 326
 327     slider.addMouseListener(new MouseAdapter()
 328     {
 329       @Override
 330       public void mousePressed(MouseEvent e)
 331       {
 332         sliderDragging = true;
 333         super.mousePressed(e);
 334       }
 335
 336       @Override
 337       public void mouseDragged(MouseEvent e)
 338       {
 339         sliderDragging = true;
 340         super.mouseDragged(e);
 341       }
 342
 343       @Override
 344       public void mouseReleased(MouseEvent evt)
 345       {
 346         if (sliderDragging)
 347         {
 348           sliderDragging = false;
 349           valueChanged(true);
 350         }
 351         ap.paintAlignment(true, true);
 352       }
 353     });
 354   }
 355
 356   @Override
 357   public void valueChanged(boolean updateAllAnnotation)
 358   {
 359     if (slider.isEnabled())
 360     {
 361       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 362       updateView(); // this also calls paintAlignment(true,true)
 363     }
 364   }
 365
 366   public Choice getThreshold()
 367   {
 368     return threshold;
 369   }
 370
 371   public void setThreshold(Choice threshold)
 372   {
 373     this.threshold = threshold;
 374   }
 375
 376   public Choice getAnnotations()
 377   {
 378     return annotations;
 379   }
 380
 381   public void setAnnotations(Choice annotations)
 382   {
 383     this.annotations = annotations;
 384   }
 385
 386   @Override
 387   public void updateView()
 388   {
 389     // Check if combobox is still adjusting
 390     if (adjusting)
 391     {
 392       return;
 393     }
 394
 395     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 396     setCurrentAnnotation(av.getAlignment()
 397             .getAlignmentAnnotation()[getAnnotations().getSelectedIndex()]);
 398
 399     int selectedThresholdItem = getSelectedThresholdItem(
 400             getThreshold().getSelectedIndex());
 401
 402     slider.setEnabled(true);
 403     thresholdValue.setEnabled(true);
 404     percentThreshold.setEnabled(true);
 405
 406     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 407     {
 408       slider.setEnabled(false);
 409       thresholdValue.setEnabled(false);
 410       thresholdValue.setText("");
 411       percentThreshold.setEnabled(false);
 412       // build filter params
 413     }
 414     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 415     {
 416       if (getCurrentAnnotation().threshold == null)
 417       {
 418         getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
 419                 (getCurrentAnnotation().graphMax
 420                         - getCurrentAnnotation().graphMin) / 2f,
 421                 "Threshold", Color.black));
 422       }
 423
 424       adjusting = true;
 425       // float range = getCurrentAnnotation().graphMax * 1000
 426       // - getCurrentAnnotation().graphMin * 1000;
 427
 428       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 429       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 430       slider.setValue(
 431               (int) (getCurrentAnnotation().threshold.value * 1000));
 432       setThresholdValueText();
 433       // slider.setMajorTickSpacing((int) (range / 10f));
 434       slider.setEnabled(true);
 435       thresholdValue.setEnabled(true);
 436       percentThreshold.setEnabled(true);
 437       adjusting = false;
 438
 439       // build filter params
 440       filterParams.setThresholdType(
 441               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 442       if (getCurrentAnnotation().isQuantitative())
 443       {
 444         filterParams
 445                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 446
 447         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 448         {
 449           filterParams.setThresholdType(
 450                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 451         }
 452         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 453         {
 454           filterParams.setThresholdType(
 455                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 456         }
 457       }
 458     }
 459
 460     if (currentStructureFilterPanel != null)
 461     {
 462       if (currentStructureFilterPanel.alphaHelix.getState())
 463       {
 464         filterParams.setFilterAlphaHelix(true);
 465       }
 466       if (currentStructureFilterPanel.betaStrand.getState())
 467       {
 468         filterParams.setFilterBetaSheet(true);
 469       }
 470       if (currentStructureFilterPanel.turn.getState())
 471       {
 472         filterParams.setFilterTurn(true);
 473       }
 474     }
 475
 476     if (currentSearchPanel != null)
 477     {
 478
 479       if (!currentSearchPanel.searchBox.getText().isEmpty())
 480       {
 481         currentSearchPanel.description.setEnabled(true);
 482         currentSearchPanel.displayName.setEnabled(true);
 483         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 484         if (currentSearchPanel.displayName.getState())
 485         {
 486           filterParams.addRegexSearchField(
 487                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 488         }
 489         if (currentSearchPanel.description.getState())
 490         {
 491           filterParams.addRegexSearchField(
 492                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 493         }
 494       }
 495       else
 496       {
 497         currentSearchPanel.description.setEnabled(false);
 498         currentSearchPanel.displayName.setEnabled(false);
 499       }
 500     }
 501
 502     // show hidden columns here, before changing the column selection in
 503     // filterAnnotations, because showing hidden columns has the side effect of
 504     // adding them to the selection
 505     av.showAllHiddenColumns();
 506     av.getColumnSelection().filterAnnotations(
 507             getCurrentAnnotation().annotations, filterParams);
 508
 509     if (getActionOption() == ACTION_OPTION_HIDE)
 510     {
 511       av.hideSelectedColumns();
 512     }
 513
 514     filterParams = null;
 515     av.setAnnotationColumnSelectionState(this);
 516     av.sendSelection();
 517     ap.paintAlignment(true, true);
 518   }
 519
 520   public HiddenColumns getOldHiddenColumns()
 521   {
 522     return oldHiddenColumns;
 523   }
 524
 525   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 526   {
 527     if (currentHiddenColumns != null)
 528     {
 529       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 530     }
 531   }
 532
 533   public FurtherActionPanel getCurrentFutherActionPanel()
 534   {
 535     return currentFurtherActionPanel;
 536   }
 537
 538   public void setCurrentFutherActionPanel(
 539           FurtherActionPanel currentFutherActionPanel)
 540   {
 541     this.currentFurtherActionPanel = currentFutherActionPanel;
 542   }
 543
 544   public SearchPanel getCurrentSearchPanel()
 545   {
 546     return currentSearchPanel;
 547   }
 548
 549   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 550   {
 551     this.currentSearchPanel = currentSearchPanel;
 552   }
 553
 554   public int getActionOption()
 555   {
 556     return actionOption;
 557   }
 558
 559   public void setActionOption(int actionOption)
 560   {
 561     this.actionOption = actionOption;
 562   }
 563
 564   public StructureFilterPanel getCurrentStructureFilterPanel()
 565   {
 566     return currentStructureFilterPanel;
 567   }
 568
 569   public void setCurrentStructureFilterPanel(
 570           StructureFilterPanel currentStructureFilterPanel)
 571   {
 572     this.currentStructureFilterPanel = currentStructureFilterPanel;
 573   }
 574
 575   @Override
 576   public void itemStateChanged(ItemEvent e)
 577   {
 578     if (e.getSource() == annotations)
 579     {
 580       selectedAnnotationChanged();
 581     }
 582     else if (e.getSource() == threshold)
 583     {
 584       threshold_actionPerformed(null);
 585     }
 586     else if (e.getSource() == percentThreshold)
 587     {
 588       if (!adjusting)
 589       {
 590         percentageValue_actionPerformed();
 591       }
 592
 593     }
 594   }
 595
 596   public void selectedAnnotationChanged()
 597   {
 598     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 599     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 600             .getSelectedIndex()].isQuantitative())
 601     {
 602       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 603     }
 604
 605     gSearchPanel.syncState();
 606     gFurtherActionPanel.syncState();
 607     gStructureFilterPanel.syncState();
 608
 609     ngSearchPanel.syncState();
 610     ngFurtherActionPanel.syncState();
 611     ngStructureFilterPanel.syncState();
 612
 613     switchableViewsLayout.show(switchableViewsPanel, currentView);
 614     updateView();
 615   }
 616
 617   public class FurtherActionPanel extends Panel implements ItemListener
 618   {
 619     private AnnotationColumnChooser aColChooser;
 620
 621     private Choice furtherAction = new Choice();
 622
 623     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 624     {
 625       this.aColChooser = aColChooser;
 626       furtherAction.addItem("Select");
 627       furtherAction.addItem("Hide");
 628       furtherAction.addItemListener(this);
 629       syncState();
 630
 631       // this.setTitle("Filter Actions");
 632       // this.setFont(JvSwingUtils.getLabelFont());
 633
 634       this.add(furtherAction);
 635     }
 636
 637     public void syncState()
 638     {
 639       if (aColChooser
 640               .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
 669           implements 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 }