src/jalview/gui/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
  22 package jalview.gui;
  23
  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.Color;
  32 import java.awt.Dimension;
  33 import java.awt.event.ActionEvent;
  34 import java.awt.event.ActionListener;
  35 import java.awt.event.ItemEvent;
  36 import java.awt.event.ItemListener;
  37 import java.util.Iterator;
  38
  39 import javax.swing.ButtonGroup;
  40 import javax.swing.JCheckBox;
  41 import javax.swing.JComboBox;
  42 import javax.swing.JInternalFrame;
  43 import javax.swing.JLayeredPane;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButton;
  46 import javax.swing.JTextField;
  47 import javax.swing.border.TitledBorder;
  48 import javax.swing.event.DocumentEvent;
  49 import javax.swing.event.DocumentListener;
  50
  51 import net.miginfocom.swing.MigLayout;
  52
  53 @SuppressWarnings("serial")
  54 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  55         ItemListener
  56 {
  57   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  58
  59   private JPanel annotationComboBoxPanel = new JPanel();
  60
  61   private StructureFilterPanel gStructureFilterPanel;
  62
  63   private StructureFilterPanel ngStructureFilterPanel;
  64
  65   private StructureFilterPanel currentStructureFilterPanel;
  66
  67   private SearchPanel currentSearchPanel;
  68
  69   private SearchPanel gSearchPanel;
  70
  71   private SearchPanel ngSearchPanel;
  72
  73   private FurtherActionPanel currentFurtherActionPanel;
  74
  75   private FurtherActionPanel gFurtherActionPanel;
  76
  77   private FurtherActionPanel ngFurtherActionPanel;
  78
  79   public static final int ACTION_OPTION_SELECT = 1;
  80
  81   public static int ACTION_OPTION_HIDE = 2;
  82
  83   public static String NO_GRAPH_VIEW = "0";
  84
  85   public static String GRAPH_VIEW = "1";
  86
  87   private int actionOption = ACTION_OPTION_SELECT;
  88
  89   private HiddenColumns oldHiddenColumns;
  90
  91   protected int MIN_WIDTH = 420;
  92
  93   protected int MIN_HEIGHT = 430;
  94
  95   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  96   {
  97     super(av, ap);
  98     frame = new JInternalFrame();
  99     frame.setContentPane(this);
 100     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 101     Desktop.addInternalFrame(frame,
 102             MessageManager.getString("label.select_by_annotation"), 520,
 103             215);
 104     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 105
 106     addSliderChangeListener();
 107     addSliderMouseListeners();
 108
 109     if (av.getAlignment().getAlignmentAnnotation() == null)
 110     {
 111       return;
 112     }
 113     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 114     adjusting = true;
 115
 116     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 117     populateThresholdComboBox(threshold);
 118     AnnotationColumnChooser lastChooser = av
 119             .getAnnotationColumnSelectionState();
 120     // restore Object state from the previous session if one exists
 121     if (lastChooser != null)
 122     {
 123       currentSearchPanel = lastChooser
 124               .getCurrentSearchPanel();
 125       currentStructureFilterPanel = lastChooser
 126               .getCurrentStructureFilterPanel();
 127       annotations.setSelectedIndex(lastChooser
 128               .getAnnotations().getSelectedIndex());
 129       threshold.setSelectedIndex(lastChooser
 130               .getThreshold().getSelectedIndex());
 131       actionOption = lastChooser
 132               .getActionOption();
 133       percentThreshold.setSelected(lastChooser.percentThreshold
 134               .isSelected());
 135     }
 136
 137     try
 138     {
 139       jbInit();
 140     } catch (Exception ex)
 141     {
 142     }
 143     adjusting = false;
 144
 145     updateView();
 146     frame.invalidate();
 147     frame.pack();
 148   }
 149
 150   @Override
 151   protected void jbInit()
 152   {
 153     super.jbInit();
 154
 155     JPanel thresholdPanel = new JPanel();
 156     thresholdPanel.setBorder(new TitledBorder(MessageManager
 157             .getString("label.threshold_filter")));
 158     thresholdPanel.setBackground(Color.white);
 159     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 160     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 161
 162     percentThreshold.setBackground(Color.white);
 163     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 164
 165     JPanel actionPanel = new JPanel();
 166     actionPanel.setBackground(Color.white);
 167     actionPanel.setFont(JvSwingUtils.getLabelFont());
 168
 169     JPanel graphFilterView = new JPanel();
 170     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 171     graphFilterView.setBackground(Color.white);
 172
 173     JPanel noGraphFilterView = new JPanel();
 174     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 175     noGraphFilterView.setBackground(Color.white);
 176
 177     annotationComboBoxPanel.setBackground(Color.white);
 178     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 179
 180     gSearchPanel = new SearchPanel(this);
 181     ngSearchPanel = new SearchPanel(this);
 182     gFurtherActionPanel = new FurtherActionPanel(this);
 183     ngFurtherActionPanel = new FurtherActionPanel(this);
 184     gStructureFilterPanel = new StructureFilterPanel(this);
 185     ngStructureFilterPanel = new StructureFilterPanel(this);
 186
 187     thresholdPanel.add(getThreshold());
 188     thresholdPanel.add(percentThreshold, "wrap");
 189     thresholdPanel.add(slider, "grow");
 190     thresholdPanel.add(thresholdValue, "span, wrap");
 191
 192     actionPanel.add(ok);
 193     actionPanel.add(cancel);
 194
 195     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 196     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 197     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 198     graphFilterView.add(gFurtherActionPanel);
 199
 200     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 201     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 202     noGraphFilterView.add(ngFurtherActionPanel);
 203
 204     annotationComboBoxPanel.add(getAnnotations());
 205     switchableViewsPanel.add(noGraphFilterView,
 206             AnnotationColumnChooser.NO_GRAPH_VIEW);
 207     switchableViewsPanel.add(graphFilterView,
 208             AnnotationColumnChooser.GRAPH_VIEW);
 209
 210     this.setLayout(new BorderLayout());
 211     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 212     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 213     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 214
 215     selectedAnnotationChanged();
 216     updateThresholdPanelToolTip();
 217     this.validate();
 218   }
 219
 220   protected void updateThresholdPanelToolTip()
 221   {
 222     thresholdValue.setToolTipText("");
 223     slider.setToolTipText("");
 224
 225     String defaultTtip = MessageManager
 226             .getString("info.change_threshold_mode_to_enable");
 227
 228     String thresh = getThreshold().getSelectedItem().toString();
 229     if (thresh.equalsIgnoreCase("No Threshold"))
 230     {
 231       thresholdValue.setToolTipText(defaultTtip);
 232       slider.setToolTipText(defaultTtip);
 233     }
 234   }
 235
 236   @Override
 237   protected void reset()
 238   {
 239     if (this.getOldHiddenColumns() != null)
 240     {
 241       av.getColumnSelection().clear();
 242
 243       if (av.getAnnotationColumnSelectionState() != null)
 244       {
 245         HiddenColumns oldHidden = av
 246                 .getAnnotationColumnSelectionState()
 247                 .getOldHiddenColumns();
 248         if (oldHidden != null && oldHidden.getHiddenRegions() != null
 249                 && !oldHidden.getHiddenRegions().isEmpty())
 250         {
 251           for (Iterator<int[]> itr = oldHidden.getHiddenRegions()
 252                   .iterator(); itr.hasNext();)
 253           {
 254             int positions[] = itr.next();
 255             av.hideColumns(positions[0], positions[1]);
 256           }
 257         }
 258         av.getAlignment().setHiddenColumns(oldHidden);
 259       }
 260       ap.paintAlignment(true);
 261     }
 262
 263   }
 264
 265   @Override
 266   public void valueChanged(boolean updateAllAnnotation)
 267   {
 268     if (slider.isEnabled())
 269     {
 270       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 271       updateView();
 272       propagateSeqAssociatedThreshold(updateAllAnnotation,
 273               getCurrentAnnotation());
 274       ap.paintAlignment(false);
 275     }
 276   }
 277
 278   @Override
 279   public void updateView()
 280   {
 281     // Check if combobox is still adjusting
 282     if (adjusting)
 283     {
 284       return;
 285     }
 286
 287     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 288
 289     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 290             .getSelectedIndex()]]);
 291
 292     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 293             .getSelectedIndex());
 294
 295     slider.setEnabled(true);
 296     thresholdValue.setEnabled(true);
 297     percentThreshold.setEnabled(true);
 298
 299     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 300     {
 301       slider.setEnabled(false);
 302       thresholdValue.setEnabled(false);
 303       thresholdValue.setText("");
 304       percentThreshold.setEnabled(false);
 305       // build filter params
 306     }
 307     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 308     {
 309       if (getCurrentAnnotation().threshold == null)
 310       {
 311         getCurrentAnnotation()
 312                 .setThreshold(
 313                         new jalview.datamodel.GraphLine(
 314                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 315                                 "Threshold", Color.black));
 316       }
 317
 318       adjusting = true;
 319       float range = getCurrentAnnotation().graphMax * 1000
 320               - getCurrentAnnotation().graphMin * 1000;
 321
 322       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 323       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 324       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 325
 326       setThresholdValueText();
 327
 328       slider.setMajorTickSpacing((int) (range / 10f));
 329       slider.setEnabled(true);
 330       thresholdValue.setEnabled(true);
 331       adjusting = false;
 332
 333       // build filter params
 334       filterParams
 335               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 336       if (getCurrentAnnotation().isQuantitative())
 337       {
 338         filterParams
 339                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 340
 341         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 342         {
 343           filterParams
 344                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 345         }
 346         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 347         {
 348           filterParams
 349                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 350         }
 351       }
 352     }
 353
 354     updateThresholdPanelToolTip();
 355     if (currentStructureFilterPanel != null)
 356     {
 357       if (currentStructureFilterPanel.alphaHelix.isSelected())
 358       {
 359         filterParams.setFilterAlphaHelix(true);
 360       }
 361       if (currentStructureFilterPanel.betaStrand.isSelected())
 362       {
 363         filterParams.setFilterBetaSheet(true);
 364       }
 365       if (currentStructureFilterPanel.turn.isSelected())
 366       {
 367         filterParams.setFilterTurn(true);
 368       }
 369     }
 370
 371     if (currentSearchPanel != null)
 372     {
 373
 374       if (!currentSearchPanel.searchBox.getText().isEmpty())
 375       {
 376         currentSearchPanel.description.setEnabled(true);
 377         currentSearchPanel.displayName.setEnabled(true);
 378         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 379         if (currentSearchPanel.displayName.isSelected())
 380         {
 381           filterParams
 382                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 383         }
 384         if (currentSearchPanel.description.isSelected())
 385         {
 386           filterParams
 387                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 388         }
 389       }
 390       else
 391       {
 392         currentSearchPanel.description.setEnabled(false);
 393         currentSearchPanel.displayName.setEnabled(false);
 394       }
 395     }
 396
 397     av.getColumnSelection().filterAnnotations(
 398             getCurrentAnnotation().annotations, filterParams);
 399
 400     av.showAllHiddenColumns();
 401     if (getActionOption() == ACTION_OPTION_HIDE)
 402     {
 403       av.hideSelectedColumns();
 404     }
 405
 406     filterParams = null;
 407     av.setAnnotationColumnSelectionState(this);
 408     ap.paintAlignment(true);
 409   }
 410
 411   public HiddenColumns getOldHiddenColumns()
 412   {
 413     return oldHiddenColumns;
 414   }
 415
 416   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 417   {
 418     if (currentHiddenColumns != null)
 419     {
 420       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 421     }
 422   }
 423
 424   public FurtherActionPanel getCurrentFutherActionPanel()
 425   {
 426     return currentFurtherActionPanel;
 427   }
 428
 429   public void setCurrentFutherActionPanel(
 430           FurtherActionPanel currentFutherActionPanel)
 431   {
 432     this.currentFurtherActionPanel = currentFutherActionPanel;
 433   }
 434
 435   public SearchPanel getCurrentSearchPanel()
 436   {
 437     return currentSearchPanel;
 438   }
 439
 440   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 441   {
 442     this.currentSearchPanel = currentSearchPanel;
 443   }
 444
 445   public int getActionOption()
 446   {
 447     return actionOption;
 448   }
 449
 450   public void setActionOption(int actionOption)
 451   {
 452     this.actionOption = actionOption;
 453   }
 454
 455   public StructureFilterPanel getCurrentStructureFilterPanel()
 456   {
 457     return currentStructureFilterPanel;
 458   }
 459
 460   public void setCurrentStructureFilterPanel(
 461           StructureFilterPanel currentStructureFilterPanel)
 462   {
 463     this.currentStructureFilterPanel = currentStructureFilterPanel;
 464   }
 465
 466   public void select_action(ActionEvent actionEvent)
 467   {
 468     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 469     if (radioButton.isSelected())
 470     {
 471       setActionOption(ACTION_OPTION_SELECT);
 472       updateView();
 473     }
 474   }
 475
 476   public void hide_action(ActionEvent actionEvent)
 477   {
 478     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 479     if (radioButton.isSelected())
 480     {
 481       setActionOption(ACTION_OPTION_HIDE);
 482       updateView();
 483     }
 484   }
 485
 486   @Override
 487   public void itemStateChanged(ItemEvent e)
 488   {
 489     selectedAnnotationChanged();
 490   }
 491
 492   @Override
 493   public void selectedAnnotationChanged()
 494   {
 495     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 496     if (av.getAlignment()
 497             .getAlignmentAnnotation()[annmap[getAnnotations()
 498             .getSelectedIndex()]].isQuantitative())
 499     {
 500       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 501     }
 502
 503     gSearchPanel.syncState();
 504     gFurtherActionPanel.syncState();
 505     gStructureFilterPanel.syncState();
 506
 507     ngSearchPanel.syncState();
 508     ngFurtherActionPanel.syncState();
 509     ngStructureFilterPanel.syncState();
 510
 511     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 512             .getLayout();
 513     switchableViewsLayout.show(switchableViewsPanel, currentView);
 514     updateView();
 515   }
 516
 517   public class FurtherActionPanel extends JPanel
 518   {
 519     private AnnotationColumnChooser aColChooser;
 520
 521     private JRadioButton hideOption = new JRadioButton();
 522
 523     private JRadioButton selectOption = new JRadioButton();
 524
 525     private ButtonGroup optionsGroup = new ButtonGroup();
 526
 527     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 528     {
 529       this.aColChooser = aColChooser;
 530       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 531       selectOption.addActionListener(new ActionListener()
 532       {
 533         @Override
 534         public void actionPerformed(ActionEvent actionEvent)
 535         {
 536           selectRadioAction(actionEvent);
 537         }
 538       });
 539
 540       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 541       hideOption.addActionListener(new ActionListener()
 542       {
 543         @Override
 544         public void actionPerformed(ActionEvent actionEvent)
 545         {
 546           hideRadioAction(actionEvent);
 547         }
 548       });
 549
 550       optionsGroup.add(selectOption);
 551       optionsGroup.add(hideOption);
 552       optionsGroup.setSelected(selectOption.getModel(), true);
 553
 554       JvSwingUtils.jvInitComponent(this);
 555       syncState();
 556
 557       this.add(selectOption);
 558       this.add(hideOption);
 559     }
 560
 561     public void selectRadioAction(ActionEvent actionEvent)
 562     {
 563       aColChooser.setCurrentFutherActionPanel(this);
 564       aColChooser.select_action(actionEvent);
 565     }
 566
 567     public void hideRadioAction(ActionEvent actionEvent)
 568     {
 569       aColChooser.setCurrentFutherActionPanel(this);
 570       aColChooser.hide_action(actionEvent);
 571     }
 572
 573     public void syncState()
 574     {
 575       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 576       {
 577         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 578       }
 579       else
 580       {
 581         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 582       }
 583     }
 584   }
 585
 586   public class StructureFilterPanel extends JPanel
 587   {
 588     private AnnotationColumnChooser aColChooser;
 589
 590     private JCheckBox alphaHelix = new JCheckBox();
 591
 592     private JCheckBox betaStrand = new JCheckBox();
 593
 594     private JCheckBox turn = new JCheckBox();
 595
 596     private JCheckBox all = new JCheckBox();
 597
 598     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 599     {
 600       this.aColChooser = aColChooser;
 601
 602       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 603       alphaHelix.addActionListener(new ActionListener()
 604       {
 605         @Override
 606         public void actionPerformed(ActionEvent actionEvent)
 607         {
 608           alphaHelix_actionPerformed();
 609         }
 610       });
 611
 612       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 613       betaStrand.addActionListener(new ActionListener()
 614       {
 615         @Override
 616         public void actionPerformed(ActionEvent actionEvent)
 617         {
 618           betaStrand_actionPerformed();
 619         }
 620       });
 621
 622       JvSwingUtils.jvInitComponent(turn, "label.turn");
 623       turn.addActionListener(new ActionListener()
 624       {
 625         @Override
 626         public void actionPerformed(ActionEvent actionEvent)
 627         {
 628           turn_actionPerformed();
 629         }
 630       });
 631
 632       JvSwingUtils.jvInitComponent(all, "label.select_all");
 633       all.addActionListener(new ActionListener()
 634       {
 635         @Override
 636         public void actionPerformed(ActionEvent actionEvent)
 637         {
 638           all_actionPerformed();
 639         }
 640       });
 641
 642       this.setBorder(new TitledBorder(MessageManager
 643               .getString("label.structures_filter")));
 644       JvSwingUtils.jvInitComponent(this);
 645
 646       this.add(all);
 647       this.add(alphaHelix);
 648       this.add(betaStrand);
 649       this.add(turn);
 650     }
 651
 652     public void alphaHelix_actionPerformed()
 653     {
 654       updateSelectAllState();
 655       aColChooser.setCurrentStructureFilterPanel(this);
 656       aColChooser.updateView();
 657     }
 658
 659     public void betaStrand_actionPerformed()
 660     {
 661       updateSelectAllState();
 662       aColChooser.setCurrentStructureFilterPanel(this);
 663       aColChooser.updateView();
 664     }
 665
 666     public void turn_actionPerformed()
 667     {
 668       updateSelectAllState();
 669       aColChooser.setCurrentStructureFilterPanel(this);
 670       aColChooser.updateView();
 671     }
 672
 673     public void all_actionPerformed()
 674     {
 675       if (all.isSelected())
 676       {
 677         alphaHelix.setSelected(true);
 678         betaStrand.setSelected(true);
 679         turn.setSelected(true);
 680       }
 681       else
 682       {
 683         alphaHelix.setSelected(false);
 684         betaStrand.setSelected(false);
 685         turn.setSelected(false);
 686       }
 687       aColChooser.setCurrentStructureFilterPanel(this);
 688       aColChooser.updateView();
 689     }
 690
 691     public void updateSelectAllState()
 692     {
 693       if (alphaHelix.isSelected() && betaStrand.isSelected()
 694               && turn.isSelected())
 695       {
 696         all.setSelected(true);
 697       }
 698       else
 699       {
 700         all.setSelected(false);
 701       }
 702     }
 703
 704     public void syncState()
 705     {
 706       StructureFilterPanel sfp = aColChooser
 707               .getCurrentStructureFilterPanel();
 708       if (sfp != null)
 709       {
 710         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 711         betaStrand.setSelected(sfp.betaStrand.isSelected());
 712         turn.setSelected(sfp.turn.isSelected());
 713         if (sfp.all.isSelected())
 714         {
 715           all.setSelected(true);
 716           alphaHelix.setSelected(true);
 717           betaStrand.setSelected(true);
 718           turn.setSelected(true);
 719         }
 720       }
 721
 722     }
 723   }
 724
 725   public class SearchPanel extends JPanel
 726   {
 727     private AnnotationColumnChooser aColChooser;
 728
 729     private JCheckBox displayName = new JCheckBox();
 730
 731     private JCheckBox description = new JCheckBox();
 732
 733     private JTextField searchBox = new JTextField(10);
 734
 735     public SearchPanel(AnnotationColumnChooser aColChooser)
 736     {
 737
 738       this.aColChooser = aColChooser;
 739       JvSwingUtils.jvInitComponent(this);
 740       this.setBorder(new TitledBorder(MessageManager
 741               .getString("label.search_filter")));
 742
 743       JvSwingUtils.jvInitComponent(searchBox);
 744       searchBox.setToolTipText(MessageManager
 745               .getString("info.enter_search_text_here"));
 746       searchBox.getDocument().addDocumentListener(new DocumentListener()
 747       {
 748         @Override
 749         public void insertUpdate(DocumentEvent e)
 750         {
 751           searchStringAction();
 752         }
 753
 754         @Override
 755         public void removeUpdate(DocumentEvent e)
 756         {
 757           searchStringAction();
 758         }
 759
 760         @Override
 761         public void changedUpdate(DocumentEvent e)
 762         {
 763           searchStringAction();
 764         }
 765       });
 766
 767       JvSwingUtils.jvInitComponent(displayName, "label.label");
 768       displayName.setEnabled(false);
 769       displayName.addActionListener(new ActionListener()
 770       {
 771         @Override
 772         public void actionPerformed(ActionEvent actionEvent)
 773         {
 774           displayNameCheckboxAction();
 775         }
 776       });
 777
 778       JvSwingUtils.jvInitComponent(description, "label.description");
 779       description.setEnabled(false);
 780       description.addActionListener(new ActionListener()
 781       {
 782         @Override
 783         public void actionPerformed(ActionEvent actionEvent)
 784         {
 785           discriptionCheckboxAction();
 786         }
 787       });
 788
 789       syncState();
 790       this.add(searchBox);
 791       this.add(displayName);
 792       this.add(description);
 793     }
 794
 795     public void displayNameCheckboxAction()
 796     {
 797       aColChooser.setCurrentSearchPanel(this);
 798       aColChooser.updateView();
 799     }
 800
 801     public void discriptionCheckboxAction()
 802     {
 803       aColChooser.setCurrentSearchPanel(this);
 804       aColChooser.updateView();
 805     }
 806
 807     public void searchStringAction()
 808     {
 809       aColChooser.setCurrentSearchPanel(this);
 810       aColChooser.updateView();
 811       updateSearchPanelToolTips();
 812     }
 813
 814     public void syncState()
 815     {
 816       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 817       if (sp != null)
 818       {
 819         description.setEnabled(sp.description.isEnabled());
 820         description.setSelected(sp.description.isSelected());
 821
 822         displayName.setEnabled(sp.displayName.isEnabled());
 823         displayName.setSelected(sp.displayName.isSelected());
 824
 825         searchBox.setText(sp.searchBox.getText());
 826       }
 827       updateSearchPanelToolTips();
 828     }
 829
 830     public void updateSearchPanelToolTips()
 831     {
 832       String defaultTtip = MessageManager
 833               .getString("info.enter_search_text_to_enable");
 834       String labelTtip = MessageManager.formatMessage(
 835               "info.search_in_annotation_label", annotations
 836                       .getSelectedItem().toString());
 837       String descTtip = MessageManager.formatMessage(
 838               "info.search_in_annotation_description", annotations
 839                       .getSelectedItem().toString());
 840       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 841               : defaultTtip);
 842       description.setToolTipText(description.isEnabled() ? descTtip
 843               : defaultTtip);
 844     }
 845   }
 846
 847 }