src/jalview/appletgui/AnnotationColumnChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.appletgui;
  22
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.ColumnSelection;
  25 import jalview.schemes.AnnotationColourGradient;
  26 import jalview.util.MessageManager;
  27 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.CardLayout;
  31 import java.awt.Checkbox;
  32 import java.awt.Choice;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.Frame;
  36 import java.awt.Panel;
  37 import java.awt.TextField;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.AdjustmentEvent;
  41 import java.awt.event.AdjustmentListener;
  42 import java.awt.event.ItemEvent;
  43 import java.awt.event.ItemListener;
  44 import java.awt.event.MouseAdapter;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.event.MouseListener;
  47 import java.awt.event.TextEvent;
  48 import java.awt.event.TextListener;
  49 import java.util.Iterator;
  50 import java.util.Vector;
  51
  52 //import javax.swing.JPanel;
  53
  54 //import net.miginfocom.swing.MigLayout;
  55
  56 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  57         ActionListener, AdjustmentListener, ItemListener, MouseListener
  58 {
  59
  60   private Choice annotations = new Choice();
  61
  62   private Panel actionPanel = new Panel();
  63
  64   private TitledPanel thresholdPanel = new TitledPanel();
  65
  66   private Panel switchableViewsPanel = new Panel(new CardLayout());
  67
  68   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  69           .getLayout());
  70
  71   private Panel noGraphFilterView = new Panel();
  72
  73   private Panel graphFilterView = new Panel();
  74
  75   private Panel annotationComboBoxPanel = new Panel();
  76
  77   private BorderLayout borderLayout1 = new BorderLayout();
  78
  79   private BorderLayout gBorderLayout = new BorderLayout();
  80
  81   private BorderLayout ngBorderLayout = new BorderLayout();
  82
  83   private Choice threshold = new Choice();
  84
  85   private StructureFilterPanel gStructureFilterPanel;
  86
  87   private StructureFilterPanel ngStructureFilterPanel;
  88
  89   private StructureFilterPanel currentStructureFilterPanel;
  90
  91   private SearchPanel currentSearchPanel;
  92
  93   private SearchPanel gSearchPanel;
  94
  95   private SearchPanel ngSearchPanel;
  96
  97   private FurtherActionPanel currentFurtherActionPanel;
  98
  99   private FurtherActionPanel gFurtherActionPanel;
 100
 101   private FurtherActionPanel ngFurtherActionPanel;
 102
 103   public static final int ACTION_OPTION_SELECT = 1;
 104
 105   public static int ACTION_OPTION_HIDE = 2;
 106
 107   public static String NO_GRAPH_VIEW = "0";
 108
 109   public static String GRAPH_VIEW = "1";
 110
 111   private int actionOption = ACTION_OPTION_SELECT;
 112
 113   private ColumnSelection oldColumnSelection;
 114
 115   public AnnotationColumnChooser()
 116   {
 117     try
 118     {
 119       jbInit();
 120     } catch (Exception ex)
 121     {
 122       ex.printStackTrace();
 123     }
 124   }
 125
 126   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 127   {
 128     super(av, ap);
 129     frame = new Frame();
 130     frame.add(this);
 131     jalview.bin.JalviewLite.addFrame(frame,
 132             MessageManager.getString("label.select_by_annotation"), 520,
 133             215);
 134
 135     slider.addAdjustmentListener(this);
 136     slider.addMouseListener(this);
 137
 138     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 139     if (anns == null)
 140     {
 141       return;
 142     }
 143     setOldColumnSelection(av.getColumnSelection());
 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
 171     // restore Object state from the previous session if one exists
 172     if (av.getAnnotationColumnSelectionState() != null)
 173     {
 174       currentSearchPanel = av.getAnnotationColumnSelectionState()
 175               .getCurrentSearchPanel();
 176       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 177               .getCurrentStructureFilterPanel();
 178       annotations.select(av.getAnnotationColumnSelectionState()
 179               .getAnnotations().getSelectedIndex());
 180       threshold.select(av.getAnnotationColumnSelectionState()
 181               .getThreshold().getSelectedIndex());
 182       actionOption = av.getAnnotationColumnSelectionState()
 183               .getActionOption();
 184     }
 185
 186     try
 187     {
 188       jbInit();
 189     } catch (Exception ex)
 190     {
 191     }
 192     adjusting = false;
 193
 194     updateView();
 195     frame.invalidate();
 196     frame.pack();
 197   }
 198
 199   private void jbInit() throws Exception
 200   {
 201     ok.setLabel(MessageManager.getString("action.ok"));
 202
 203     cancel.setLabel(MessageManager.getString("action.cancel"));
 204
 205     thresholdValue.setEnabled(false);
 206     thresholdValue.setColumns(7);
 207     thresholdValue.setCaretPosition(0);
 208
 209     ok.addActionListener(this);
 210     cancel.addActionListener(this);
 211     annotations.addItemListener(this);
 212     thresholdValue.addActionListener(this);
 213     threshold.addItemListener(this);
 214
 215     slider.setBackground(Color.white);
 216     slider.setEnabled(false);
 217     slider.setPreferredSize(new Dimension(100, 32));
 218
 219     thresholdPanel.setBackground(Color.white);
 220     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 221     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 222
 223     percentThreshold.setLabel("As percentage");
 224     percentThreshold.addItemListener(this);
 225
 226     actionPanel.setBackground(Color.white);
 227     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 228
 229     graphFilterView.setLayout(gBorderLayout);
 230     graphFilterView.setBackground(Color.white);
 231
 232     noGraphFilterView.setLayout(ngBorderLayout);
 233     noGraphFilterView.setBackground(Color.white);
 234
 235     annotationComboBoxPanel.setBackground(Color.white);
 236     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 237
 238     gSearchPanel = new SearchPanel(this);
 239     ngSearchPanel = new SearchPanel(this);
 240     gFurtherActionPanel = new FurtherActionPanel(this);
 241     ngFurtherActionPanel = new FurtherActionPanel(this);
 242     gStructureFilterPanel = new StructureFilterPanel(this);
 243     ngStructureFilterPanel = new StructureFilterPanel(this);
 244
 245     thresholdPanel.setTitle("Threshold Filter");
 246     thresholdPanel.add(percentThreshold);
 247     thresholdPanel.add(getThreshold());
 248     thresholdPanel.add(slider);
 249     thresholdPanel.add(thresholdValue);
 250
 251     actionPanel.add(ok);
 252     actionPanel.add(cancel);
 253
 254     Panel staticPanel = new Panel();
 255     staticPanel.setLayout(new BorderLayout());
 256     staticPanel.setBackground(Color.white);
 257
 258     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 259     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 260
 261     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 262     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 263     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 264
 265     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 266     noGraphFilterView.add(ngStructureFilterPanel,
 267             java.awt.BorderLayout.CENTER);
 268     noGraphFilterView.add(ngFurtherActionPanel,
 269             java.awt.BorderLayout.CENTER);
 270
 271     annotationComboBoxPanel.add(getAnnotations());
 272     switchableViewsPanel.add(noGraphFilterView,
 273             AnnotationColumnChooser.NO_GRAPH_VIEW);
 274     switchableViewsPanel.add(graphFilterView,
 275             AnnotationColumnChooser.GRAPH_VIEW);
 276
 277     this.setLayout(borderLayout1);
 278     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 279     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 280     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 281
 282     selectedAnnotationChanged();
 283     this.validate();
 284   }
 285
 286   @Override
 287   @SuppressWarnings("unchecked")
 288   public void reset()
 289   {
 290     if (this.getOldColumnSelection() != null)
 291     {
 292       av.getColumnSelection().clear();
 293
 294       if (av.getAnnotationColumnSelectionState() != null)
 295       {
 296         ColumnSelection oldSelection = av
 297                 .getAnnotationColumnSelectionState()
 298                 .getOldColumnSelection();
 299         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 300                 && !oldSelection.getHiddenColumns().isEmpty())
 301         {
 302           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 303                   .iterator(); itr.hasNext();)
 304           {
 305             int positions[] = itr.next();
 306             av.hideColumns(positions[0], positions[1]);
 307           }
 308         }
 309         av.setColumnSelection(oldSelection);
 310       }
 311       ap.paintAlignment(true);
 312     }
 313
 314   }
 315
 316   @Override
 317   public void adjustmentValueChanged(AdjustmentEvent evt)
 318   {
 319     if (!adjusting)
 320     {
 321       thresholdValue.setText((slider.getValue() / 1000f) + "");
 322       valueChanged(!sliderDragging);
 323     }
 324   }
 325
 326   protected void addSliderMouseListeners()
 327   {
 328
 329     slider.addMouseListener(new MouseAdapter()
 330     {
 331       @Override
 332       public void mousePressed(MouseEvent e)
 333       {
 334         sliderDragging = true;
 335         super.mousePressed(e);
 336       }
 337
 338       @Override
 339       public void mouseDragged(MouseEvent e)
 340       {
 341         sliderDragging = true;
 342         super.mouseDragged(e);
 343       }
 344
 345       @Override
 346       public void mouseReleased(MouseEvent evt)
 347       {
 348         if (sliderDragging)
 349         {
 350           sliderDragging = false;
 351           valueChanged(true);
 352         }
 353         ap.paintAlignment(true);
 354       }
 355     });
 356   }
 357
 358   @Override
 359   public void valueChanged(boolean updateAllAnnotation)
 360   {
 361     if (slider.isEnabled())
 362     {
 363       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 364       updateView();
 365       ap.paintAlignment(false);
 366     }
 367   }
 368
 369   public Choice getThreshold()
 370   {
 371     return threshold;
 372   }
 373
 374   public void setThreshold(Choice threshold)
 375   {
 376     this.threshold = threshold;
 377   }
 378
 379   public Choice getAnnotations()
 380   {
 381     return annotations;
 382   }
 383
 384   public void setAnnotations(Choice annotations)
 385   {
 386     this.annotations = annotations;
 387   }
 388
 389   @Override
 390   public void updateView()
 391   {
 392     // Check if combobox is still adjusting
 393     if (adjusting)
 394     {
 395       return;
 396     }
 397
 398     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 399     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 400             .getSelectedIndex()]);
 401
 402     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 403             .getSelectedIndex());
 404
 405     slider.setEnabled(true);
 406     thresholdValue.setEnabled(true);
 407
 408     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 409     {
 410       slider.setEnabled(false);
 411       thresholdValue.setEnabled(false);
 412       thresholdValue.setText("");
 413       // build filter params
 414     }
 415     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 416     {
 417       if (getCurrentAnnotation().threshold == null)
 418       {
 419         getCurrentAnnotation()
 420                 .setThreshold(
 421                         new jalview.datamodel.GraphLine(
 422                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 423                                 "Threshold", Color.black));
 424       }
 425
 426       adjusting = true;
 427       float range = getCurrentAnnotation().graphMax * 1000
 428               - getCurrentAnnotation().graphMin * 1000;
 429
 430       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 431       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 432       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 433       setThresholdValueText();
 434       // slider.setMajorTickSpacing((int) (range / 10f));
 435       slider.setEnabled(true);
 436       thresholdValue.setEnabled(true);
 437       adjusting = false;
 438
 439       // build filter params
 440       filterParams
 441               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 442       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 443       {
 444         filterParams
 445                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 446
 447         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 448         {
 449           filterParams
 450                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 451         }
 452         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 453         {
 454           filterParams
 455                   .setThresholdType(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
 487                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 488         }
 489         if (currentSearchPanel.description.getState())
 490         {
 491           filterParams
 492                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 493         }
 494       }
 495       else
 496       {
 497         currentSearchPanel.description.setEnabled(false);
 498         currentSearchPanel.displayName.setEnabled(false);
 499       }
 500     }
 501
 502     av.getColumnSelection().filterAnnotations(
 503             getCurrentAnnotation().annotations, filterParams);
 504
 505     av.showAllHiddenColumns();
 506     if (getActionOption() == ACTION_OPTION_HIDE)
 507     {
 508       av.hideSelectedColumns();
 509     }
 510
 511     filterParams = null;
 512     av.setAnnotationColumnSelectionState(this);
 513     ap.paintAlignment(true);
 514   }
 515
 516   public ColumnSelection getOldColumnSelection()
 517   {
 518     return oldColumnSelection;
 519   }
 520
 521   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 522   {
 523     if (currentColumnSelection != null)
 524     {
 525       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 526     }
 527   }
 528
 529   public FurtherActionPanel getCurrentFutherActionPanel()
 530   {
 531     return currentFurtherActionPanel;
 532   }
 533
 534   public void setCurrentFutherActionPanel(
 535           FurtherActionPanel currentFutherActionPanel)
 536   {
 537     this.currentFurtherActionPanel = currentFutherActionPanel;
 538   }
 539
 540   public SearchPanel getCurrentSearchPanel()
 541   {
 542     return currentSearchPanel;
 543   }
 544
 545   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 546   {
 547     this.currentSearchPanel = currentSearchPanel;
 548   }
 549
 550   public int getActionOption()
 551   {
 552     return actionOption;
 553   }
 554
 555   public void setActionOption(int actionOption)
 556   {
 557     this.actionOption = actionOption;
 558   }
 559
 560   public StructureFilterPanel getCurrentStructureFilterPanel()
 561   {
 562     return currentStructureFilterPanel;
 563   }
 564
 565   public void setCurrentStructureFilterPanel(
 566           StructureFilterPanel currentStructureFilterPanel)
 567   {
 568     this.currentStructureFilterPanel = currentStructureFilterPanel;
 569   }
 570
 571   @Override
 572   public void itemStateChanged(ItemEvent e)
 573   {
 574     if (e.getSource() == annotations)
 575     {
 576       selectedAnnotationChanged();
 577     }
 578     else if (e.getSource() == threshold)
 579     {
 580       threshold_actionPerformed(null);
 581     }
 582     else if (e.getSource() == percentThreshold)
 583     {
 584       if (!adjusting)
 585       {
 586         percentageValue_actionPerformed();
 587       }
 588
 589     }
 590   }
 591
 592   public void selectedAnnotationChanged()
 593   {
 594     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 595     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 596             .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
 597     {
 598       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 599     }
 600
 601     gSearchPanel.syncState();
 602     gFurtherActionPanel.syncState();
 603     gStructureFilterPanel.syncState();
 604
 605     ngSearchPanel.syncState();
 606     ngFurtherActionPanel.syncState();
 607     ngStructureFilterPanel.syncState();
 608
 609     switchableViewsLayout.show(switchableViewsPanel, currentView);
 610     updateView();
 611   }
 612
 613   public class FurtherActionPanel extends Panel implements ItemListener
 614   {
 615     private AnnotationColumnChooser aColChooser;
 616
 617     private Choice furtherAction = new Choice();
 618
 619     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 620     {
 621       this.aColChooser = aColChooser;
 622       furtherAction.addItem("Select");
 623       furtherAction.addItem("Hide");
 624       furtherAction.addItemListener(this);
 625       syncState();
 626
 627       // this.setTitle("Filter Actions");
 628       // this.setFont(JvSwingUtils.getLabelFont());
 629
 630       this.add(furtherAction);
 631     }
 632
 633     public void syncState()
 634     {
 635       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 636       {
 637         furtherAction.select("Hide");
 638       }
 639       else
 640       {
 641         furtherAction.select("Select");
 642       }
 643     }
 644
 645     @Override
 646     public void itemStateChanged(ItemEvent e)
 647     {
 648       aColChooser.setCurrentFutherActionPanel(this);
 649       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 650       {
 651         setActionOption(ACTION_OPTION_SELECT);
 652         updateView();
 653       }
 654       else
 655       {
 656         setActionOption(ACTION_OPTION_HIDE);
 657         updateView();
 658       }
 659
 660     }
 661   }
 662
 663   public class StructureFilterPanel extends TitledPanel implements
 664           ItemListener
 665   {
 666     private AnnotationColumnChooser aColChooser;
 667
 668     private Checkbox alphaHelix = new Checkbox();
 669
 670     private Checkbox betaStrand = new Checkbox();
 671
 672     private Checkbox turn = new Checkbox();
 673
 674     private Checkbox all = new Checkbox();
 675
 676     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 677     {
 678       this.aColChooser = aColChooser;
 679
 680       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 681       alphaHelix.setBackground(Color.white);
 682
 683       alphaHelix.addItemListener(this);
 684
 685       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 686       betaStrand.setBackground(Color.white);
 687       betaStrand.addItemListener(this);
 688
 689       turn.setLabel(MessageManager.getString("label.turn"));
 690       turn.setBackground(Color.white);
 691       turn.addItemListener(this);
 692
 693       all.setLabel(MessageManager.getString("label.select_all"));
 694       all.setBackground(Color.white);
 695       all.addItemListener(this);
 696
 697       this.setBackground(Color.white);
 698       this.setTitle("Structure Filter");
 699       // this.setFont(JvSwingUtils.getLabelFont());
 700
 701       this.add(all);
 702       this.add(alphaHelix);
 703       this.add(betaStrand);
 704       this.add(turn);
 705     }
 706
 707     public void alphaHelix_actionPerformed()
 708     {
 709       updateSelectAllState();
 710       aColChooser.setCurrentStructureFilterPanel(this);
 711       aColChooser.updateView();
 712     }
 713
 714     public void betaStrand_actionPerformed()
 715     {
 716       updateSelectAllState();
 717       aColChooser.setCurrentStructureFilterPanel(this);
 718       aColChooser.updateView();
 719     }
 720
 721     public void turn_actionPerformed()
 722     {
 723       updateSelectAllState();
 724       aColChooser.setCurrentStructureFilterPanel(this);
 725       aColChooser.updateView();
 726     }
 727
 728     public void all_actionPerformed()
 729     {
 730       if (all.getState())
 731       {
 732         alphaHelix.setState(true);
 733         betaStrand.setState(true);
 734         turn.setState(true);
 735       }
 736       else
 737       {
 738         alphaHelix.setState(false);
 739         betaStrand.setState(false);
 740         turn.setState(false);
 741       }
 742       aColChooser.setCurrentStructureFilterPanel(this);
 743       aColChooser.updateView();
 744     }
 745
 746     public void updateSelectAllState()
 747     {
 748       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 749       {
 750         all.setState(true);
 751       }
 752       else
 753       {
 754         all.setState(false);
 755       }
 756     }
 757
 758     public void syncState()
 759     {
 760       StructureFilterPanel sfp = aColChooser
 761               .getCurrentStructureFilterPanel();
 762       if (sfp != null)
 763       {
 764         alphaHelix.setState(sfp.alphaHelix.getState());
 765         betaStrand.setState(sfp.betaStrand.getState());
 766         turn.setState(sfp.turn.getState());
 767         if (sfp.all.getState())
 768         {
 769           all.setState(true);
 770           alphaHelix.setState(true);
 771           betaStrand.setState(true);
 772           turn.setState(true);
 773         }
 774       }
 775
 776     }
 777
 778     @Override
 779     public void itemStateChanged(ItemEvent e)
 780     {
 781       if (e.getSource() == alphaHelix)
 782       {
 783         alphaHelix_actionPerformed();
 784       }
 785       else if (e.getSource() == betaStrand)
 786       {
 787         betaStrand_actionPerformed();
 788       }
 789       else if (e.getSource() == turn)
 790       {
 791         turn_actionPerformed();
 792       }
 793       else if (e.getSource() == all)
 794       {
 795         all_actionPerformed();
 796       }
 797     }
 798   }
 799
 800   public class SearchPanel extends TitledPanel implements ItemListener
 801   {
 802     private AnnotationColumnChooser aColChooser;
 803
 804     private Checkbox displayName = new Checkbox();
 805
 806     private Checkbox description = new Checkbox();
 807
 808     private TextField searchBox = new TextField(10);
 809
 810     public SearchPanel(AnnotationColumnChooser aColChooser)
 811     {
 812
 813       this.aColChooser = aColChooser;
 814       searchBox.addTextListener(new TextListener()
 815       {
 816
 817         @Override
 818         public void textValueChanged(TextEvent e)
 819         {
 820           searchStringAction();
 821
 822         }
 823
 824       });
 825
 826       displayName.setLabel(MessageManager.getString("label.label"));
 827       displayName.setEnabled(false);
 828       displayName.addItemListener(this);
 829
 830       description.setLabel(MessageManager.getString("label.description"));
 831       description.setEnabled(false);
 832       description.addItemListener(this);
 833       this.setTitle("Search Filter");
 834       // this.setFont(JvSwingUtils.getLabelFont());
 835
 836       syncState();
 837       this.add(searchBox);
 838       this.add(displayName);
 839       this.add(description);
 840     }
 841
 842     public void displayNameCheckboxAction()
 843     {
 844       aColChooser.setCurrentSearchPanel(this);
 845       aColChooser.updateView();
 846     }
 847
 848     public void discriptionCheckboxAction()
 849     {
 850       aColChooser.setCurrentSearchPanel(this);
 851       aColChooser.updateView();
 852     }
 853
 854     public void searchStringAction()
 855     {
 856       aColChooser.setCurrentSearchPanel(this);
 857       aColChooser.updateView();
 858     }
 859
 860     public void syncState()
 861     {
 862       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 863       if (sp != null)
 864       {
 865         description.setEnabled(sp.description.isEnabled());
 866         description.setState(sp.description.getState());
 867
 868         displayName.setEnabled(sp.displayName.isEnabled());
 869         displayName.setState(sp.displayName.getState());
 870
 871         searchBox.setText(sp.searchBox.getText());
 872       }
 873     }
 874
 875     @Override
 876     public void itemStateChanged(ItemEvent e)
 877     {
 878       if (e.getSource() == displayName)
 879       {
 880         displayNameCheckboxAction();
 881       }
 882       else if (e.getSource() == description)
 883       {
 884         discriptionCheckboxAction();
 885       }
 886
 887     }
 888   }
 889
 890   @Override
 891   public void actionPerformed(ActionEvent evt)
 892   {
 893     if (evt.getSource() == thresholdValue)
 894     {
 895       try
 896       {
 897         float f = new Float(thresholdValue.getText()).floatValue();
 898         slider.setValue((int) (f * 1000));
 899         adjustmentValueChanged(null);
 900       } catch (NumberFormatException ex)
 901       {
 902       }
 903     }
 904
 905     else if (evt.getSource() == ok)
 906     {
 907       ok_actionPerformed(null);
 908     }
 909     else if (evt.getSource() == cancel)
 910     {
 911       cancel_actionPerformed(null);
 912     }
 913     else if (evt.getSource() == thresholdValue)
 914     {
 915       thresholdValue_actionPerformed(null);
 916     }
 917     else
 918     {
 919       updateView();
 920     }
 921   }
 922
 923   @Override
 924   public void mouseClicked(MouseEvent e)
 925   {
 926     // TODO Auto-generated method stub
 927
 928   }
 929
 930   @Override
 931   public void mousePressed(MouseEvent e)
 932   {
 933     if (e.getSource() == slider)
 934     {
 935       updateView();
 936     }
 937
 938   }
 939
 940   @Override
 941   public void mouseReleased(MouseEvent e)
 942   {
 943     if (e.getSource() == slider)
 944     {
 945       updateView();
 946     }
 947   }
 948
 949   @Override
 950   public void mouseEntered(MouseEvent e)
 951   {
 952     if (e.getSource() == slider)
 953     {
 954       updateView();
 955     }
 956   }
 957
 958   @Override
 959   public void mouseExited(MouseEvent e)
 960   {
 961     if (e.getSource() == slider)
 962     {
 963       updateView();
 964     }
 965   }
 966
 967 }