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.AlignmentAnnotation;
  25 import jalview.datamodel.HiddenColumns;
  26 import jalview.schemes.AnnotationColourGradient;
  27 import jalview.util.MessageManager;
  28 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.CardLayout;
  32 import java.awt.Color;
  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   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  92   {
  93     super(av, ap);
  94     frame = new JInternalFrame();
  95     frame.setContentPane(this);
  96     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  97     Desktop.addInternalFrame(frame,
  98             MessageManager.getString("label.select_by_annotation"), 520,
  99             215);
 100
 101     addSliderChangeListener();
 102     addSliderMouseListeners();
 103
 104     if (av.getAlignment().getAlignmentAnnotation() == null)
 105     {
 106       return;
 107     }
 108     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 109     adjusting = true;
 110
 111     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 112     populateThresholdComboBox(threshold);
 113     AnnotationColumnChooser lastChooser = av
 114             .getAnnotationColumnSelectionState();
 115     // restore Object state from the previous session if one exists
 116     if (lastChooser != null)
 117     {
 118       currentSearchPanel = lastChooser
 119               .getCurrentSearchPanel();
 120       currentStructureFilterPanel = lastChooser
 121               .getCurrentStructureFilterPanel();
 122       annotations.setSelectedIndex(lastChooser
 123               .getAnnotations().getSelectedIndex());
 124       threshold.setSelectedIndex(lastChooser
 125               .getThreshold().getSelectedIndex());
 126       actionOption = lastChooser
 127               .getActionOption();
 128       percentThreshold.setSelected(lastChooser.percentThreshold
 129               .isSelected());
 130     }
 131
 132     try
 133     {
 134       jbInit();
 135     } catch (Exception ex)
 136     {
 137     }
 138     adjusting = false;
 139
 140     updateView();
 141     frame.invalidate();
 142     frame.pack();
 143   }
 144
 145   @Override
 146   protected void jbInit()
 147   {
 148     super.jbInit();
 149
 150     JPanel thresholdPanel = new JPanel();
 151     thresholdPanel.setBorder(new TitledBorder(MessageManager
 152             .getString("label.threshold_filter")));
 153     thresholdPanel.setBackground(Color.white);
 154     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 155     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 156
 157     percentThreshold.setBackground(Color.white);
 158     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 159
 160     JPanel actionPanel = new JPanel();
 161     actionPanel.setBackground(Color.white);
 162     actionPanel.setFont(JvSwingUtils.getLabelFont());
 163
 164     JPanel graphFilterView = new JPanel();
 165     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 166     graphFilterView.setBackground(Color.white);
 167
 168     JPanel noGraphFilterView = new JPanel();
 169     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 170     noGraphFilterView.setBackground(Color.white);
 171
 172     annotationComboBoxPanel.setBackground(Color.white);
 173     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 174
 175     gSearchPanel = new SearchPanel(this);
 176     ngSearchPanel = new SearchPanel(this);
 177     gFurtherActionPanel = new FurtherActionPanel(this);
 178     ngFurtherActionPanel = new FurtherActionPanel(this);
 179     gStructureFilterPanel = new StructureFilterPanel(this);
 180     ngStructureFilterPanel = new StructureFilterPanel(this);
 181
 182     thresholdPanel.add(getThreshold());
 183     thresholdPanel.add(percentThreshold, "wrap");
 184     thresholdPanel.add(slider, "grow");
 185     thresholdPanel.add(thresholdValue, "span, wrap");
 186
 187     actionPanel.add(ok);
 188     actionPanel.add(cancel);
 189
 190     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 191     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 192     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 193     graphFilterView.add(gFurtherActionPanel);
 194
 195     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 196     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 197     noGraphFilterView.add(ngFurtherActionPanel);
 198
 199     annotationComboBoxPanel.add(getAnnotations());
 200     switchableViewsPanel.add(noGraphFilterView,
 201             AnnotationColumnChooser.NO_GRAPH_VIEW);
 202     switchableViewsPanel.add(graphFilterView,
 203             AnnotationColumnChooser.GRAPH_VIEW);
 204
 205     this.setLayout(new BorderLayout());
 206     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 207     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 208     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 209
 210     selectedAnnotationChanged();
 211     updateThresholdPanelToolTip();
 212     this.validate();
 213   }
 214
 215   protected void updateThresholdPanelToolTip()
 216   {
 217     thresholdValue.setToolTipText("");
 218     slider.setToolTipText("");
 219
 220     String defaultTtip = MessageManager
 221             .getString("info.change_threshold_mode_to_enable");
 222
 223     String thresh = getThreshold().getSelectedItem().toString();
 224     if (thresh.equalsIgnoreCase("No Threshold"))
 225     {
 226       thresholdValue.setToolTipText(defaultTtip);
 227       slider.setToolTipText(defaultTtip);
 228     }
 229   }
 230
 231   @Override
 232   protected void reset()
 233   {
 234     if (this.getOldHiddenColumns() != null)
 235     {
 236       av.getColumnSelection().clear();
 237
 238       if (av.getAnnotationColumnSelectionState() != null)
 239       {
 240         HiddenColumns oldHidden = av
 241                 .getAnnotationColumnSelectionState()
 242                 .getOldHiddenColumns();
 243         if (oldHidden != null && oldHidden.getListOfCols() != null
 244                 && !oldHidden.getListOfCols().isEmpty())
 245         {
 246           for (Iterator<int[]> itr = oldHidden.getListOfCols()
 247                   .iterator(); itr.hasNext();)
 248           {
 249             int positions[] = itr.next();
 250             av.hideColumns(positions[0], positions[1]);
 251           }
 252         }
 253         av.getAlignment().setHiddenColumns(oldHidden);
 254       }
 255       ap.paintAlignment(true);
 256     }
 257
 258   }
 259
 260   @Override
 261   public void valueChanged(boolean updateAllAnnotation)
 262   {
 263     if (slider.isEnabled())
 264     {
 265       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 266       updateView();
 267       propagateSeqAssociatedThreshold(updateAllAnnotation,
 268               getCurrentAnnotation());
 269       ap.paintAlignment(false);
 270     }
 271   }
 272
 273   @Override
 274   public void updateView()
 275   {
 276     // Check if combobox is still adjusting
 277     if (adjusting)
 278     {
 279       return;
 280     }
 281
 282     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 283
 284     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 285             .getSelectedIndex()]]);
 286
 287     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 288             .getSelectedIndex());
 289
 290     slider.setEnabled(true);
 291     thresholdValue.setEnabled(true);
 292     percentThreshold.setEnabled(true);
 293
 294     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 295     {
 296       slider.setEnabled(false);
 297       thresholdValue.setEnabled(false);
 298       thresholdValue.setText("");
 299       percentThreshold.setEnabled(false);
 300       // build filter params
 301     }
 302     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 303     {
 304       if (getCurrentAnnotation().threshold == null)
 305       {
 306         getCurrentAnnotation()
 307                 .setThreshold(
 308                         new jalview.datamodel.GraphLine(
 309                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 310                                 "Threshold", Color.black));
 311       }
 312
 313       adjusting = true;
 314       float range = getCurrentAnnotation().graphMax * 1000
 315               - getCurrentAnnotation().graphMin * 1000;
 316
 317       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 318       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 319       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 320
 321       setThresholdValueText();
 322
 323       slider.setMajorTickSpacing((int) (range / 10f));
 324       slider.setEnabled(true);
 325       thresholdValue.setEnabled(true);
 326       adjusting = false;
 327
 328       // build filter params
 329       filterParams
 330               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 331       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 332       {
 333         filterParams
 334                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 335
 336         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 337         {
 338           filterParams
 339                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 340         }
 341         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 342         {
 343           filterParams
 344                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 345         }
 346       }
 347     }
 348
 349     updateThresholdPanelToolTip();
 350     if (currentStructureFilterPanel != null)
 351     {
 352       if (currentStructureFilterPanel.alphaHelix.isSelected())
 353       {
 354         filterParams.setFilterAlphaHelix(true);
 355       }
 356       if (currentStructureFilterPanel.betaStrand.isSelected())
 357       {
 358         filterParams.setFilterBetaSheet(true);
 359       }
 360       if (currentStructureFilterPanel.turn.isSelected())
 361       {
 362         filterParams.setFilterTurn(true);
 363       }
 364     }
 365
 366     if (currentSearchPanel != null)
 367     {
 368
 369       if (!currentSearchPanel.searchBox.getText().isEmpty())
 370       {
 371         currentSearchPanel.description.setEnabled(true);
 372         currentSearchPanel.displayName.setEnabled(true);
 373         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 374         if (currentSearchPanel.displayName.isSelected())
 375         {
 376           filterParams
 377                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 378         }
 379         if (currentSearchPanel.description.isSelected())
 380         {
 381           filterParams
 382                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 383         }
 384       }
 385       else
 386       {
 387         currentSearchPanel.description.setEnabled(false);
 388         currentSearchPanel.displayName.setEnabled(false);
 389       }
 390     }
 391
 392     av.getColumnSelection().filterAnnotations(
 393             getCurrentAnnotation().annotations, filterParams);
 394
 395     av.showAllHiddenColumns();
 396     if (getActionOption() == ACTION_OPTION_HIDE)
 397     {
 398       av.hideSelectedColumns();
 399     }
 400
 401     filterParams = null;
 402     av.setAnnotationColumnSelectionState(this);
 403     ap.paintAlignment(true);
 404   }
 405
 406   public HiddenColumns getOldHiddenColumns()
 407   {
 408     return oldHiddenColumns;
 409   }
 410
 411   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 412   {
 413     if (currentHiddenColumns != null)
 414     {
 415       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 416     }
 417   }
 418
 419   public FurtherActionPanel getCurrentFutherActionPanel()
 420   {
 421     return currentFurtherActionPanel;
 422   }
 423
 424   public void setCurrentFutherActionPanel(
 425           FurtherActionPanel currentFutherActionPanel)
 426   {
 427     this.currentFurtherActionPanel = currentFutherActionPanel;
 428   }
 429
 430   public SearchPanel getCurrentSearchPanel()
 431   {
 432     return currentSearchPanel;
 433   }
 434
 435   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 436   {
 437     this.currentSearchPanel = currentSearchPanel;
 438   }
 439
 440   public int getActionOption()
 441   {
 442     return actionOption;
 443   }
 444
 445   public void setActionOption(int actionOption)
 446   {
 447     this.actionOption = actionOption;
 448   }
 449
 450   public StructureFilterPanel getCurrentStructureFilterPanel()
 451   {
 452     return currentStructureFilterPanel;
 453   }
 454
 455   public void setCurrentStructureFilterPanel(
 456           StructureFilterPanel currentStructureFilterPanel)
 457   {
 458     this.currentStructureFilterPanel = currentStructureFilterPanel;
 459   }
 460
 461   public void select_action(ActionEvent actionEvent)
 462   {
 463     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 464     if (radioButton.isSelected())
 465     {
 466       setActionOption(ACTION_OPTION_SELECT);
 467       updateView();
 468     }
 469   }
 470
 471   public void hide_action(ActionEvent actionEvent)
 472   {
 473     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 474     if (radioButton.isSelected())
 475     {
 476       setActionOption(ACTION_OPTION_HIDE);
 477       updateView();
 478     }
 479   }
 480
 481   @Override
 482   public void itemStateChanged(ItemEvent e)
 483   {
 484     selectedAnnotationChanged();
 485   }
 486
 487   @Override
 488   public void selectedAnnotationChanged()
 489   {
 490     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 491     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 492             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 493     {
 494       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 495     }
 496
 497     gSearchPanel.syncState();
 498     gFurtherActionPanel.syncState();
 499     gStructureFilterPanel.syncState();
 500
 501     ngSearchPanel.syncState();
 502     ngFurtherActionPanel.syncState();
 503     ngStructureFilterPanel.syncState();
 504
 505     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 506             .getLayout();
 507     switchableViewsLayout.show(switchableViewsPanel, currentView);
 508     updateView();
 509   }
 510
 511   public class FurtherActionPanel extends JPanel
 512   {
 513     private AnnotationColumnChooser aColChooser;
 514
 515     private JRadioButton hideOption = new JRadioButton();
 516
 517     private JRadioButton selectOption = new JRadioButton();
 518
 519     private ButtonGroup optionsGroup = new ButtonGroup();
 520
 521     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 522     {
 523       this.aColChooser = aColChooser;
 524       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 525       selectOption.addActionListener(new ActionListener()
 526       {
 527         @Override
 528         public void actionPerformed(ActionEvent actionEvent)
 529         {
 530           selectRadioAction(actionEvent);
 531         }
 532       });
 533
 534       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 535       hideOption.addActionListener(new ActionListener()
 536       {
 537         @Override
 538         public void actionPerformed(ActionEvent actionEvent)
 539         {
 540           hideRadioAction(actionEvent);
 541         }
 542       });
 543
 544       optionsGroup.add(selectOption);
 545       optionsGroup.add(hideOption);
 546       optionsGroup.setSelected(selectOption.getModel(), true);
 547
 548       JvSwingUtils.jvInitComponent(this);
 549       syncState();
 550
 551       this.add(selectOption);
 552       this.add(hideOption);
 553     }
 554
 555     public void selectRadioAction(ActionEvent actionEvent)
 556     {
 557       aColChooser.setCurrentFutherActionPanel(this);
 558       aColChooser.select_action(actionEvent);
 559     }
 560
 561     public void hideRadioAction(ActionEvent actionEvent)
 562     {
 563       aColChooser.setCurrentFutherActionPanel(this);
 564       aColChooser.hide_action(actionEvent);
 565     }
 566
 567     public void syncState()
 568     {
 569       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 570       {
 571         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 572       }
 573       else
 574       {
 575         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 576       }
 577     }
 578   }
 579
 580   public class StructureFilterPanel extends JPanel
 581   {
 582     private AnnotationColumnChooser aColChooser;
 583
 584     private JCheckBox alphaHelix = new JCheckBox();
 585
 586     private JCheckBox betaStrand = new JCheckBox();
 587
 588     private JCheckBox turn = new JCheckBox();
 589
 590     private JCheckBox all = new JCheckBox();
 591
 592     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 593     {
 594       this.aColChooser = aColChooser;
 595
 596       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 597       alphaHelix.addActionListener(new ActionListener()
 598       {
 599         @Override
 600         public void actionPerformed(ActionEvent actionEvent)
 601         {
 602           alphaHelix_actionPerformed();
 603         }
 604       });
 605
 606       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 607       betaStrand.addActionListener(new ActionListener()
 608       {
 609         @Override
 610         public void actionPerformed(ActionEvent actionEvent)
 611         {
 612           betaStrand_actionPerformed();
 613         }
 614       });
 615
 616       JvSwingUtils.jvInitComponent(turn, "label.turn");
 617       turn.addActionListener(new ActionListener()
 618       {
 619         @Override
 620         public void actionPerformed(ActionEvent actionEvent)
 621         {
 622           turn_actionPerformed();
 623         }
 624       });
 625
 626       JvSwingUtils.jvInitComponent(all, "label.select_all");
 627       all.addActionListener(new ActionListener()
 628       {
 629         @Override
 630         public void actionPerformed(ActionEvent actionEvent)
 631         {
 632           all_actionPerformed();
 633         }
 634       });
 635
 636       this.setBorder(new TitledBorder(MessageManager
 637               .getString("label.structures_filter")));
 638       JvSwingUtils.jvInitComponent(this);
 639
 640       this.add(all);
 641       this.add(alphaHelix);
 642       this.add(betaStrand);
 643       this.add(turn);
 644     }
 645
 646     public void alphaHelix_actionPerformed()
 647     {
 648       updateSelectAllState();
 649       aColChooser.setCurrentStructureFilterPanel(this);
 650       aColChooser.updateView();
 651     }
 652
 653     public void betaStrand_actionPerformed()
 654     {
 655       updateSelectAllState();
 656       aColChooser.setCurrentStructureFilterPanel(this);
 657       aColChooser.updateView();
 658     }
 659
 660     public void turn_actionPerformed()
 661     {
 662       updateSelectAllState();
 663       aColChooser.setCurrentStructureFilterPanel(this);
 664       aColChooser.updateView();
 665     }
 666
 667     public void all_actionPerformed()
 668     {
 669       if (all.isSelected())
 670       {
 671         alphaHelix.setSelected(true);
 672         betaStrand.setSelected(true);
 673         turn.setSelected(true);
 674       }
 675       else
 676       {
 677         alphaHelix.setSelected(false);
 678         betaStrand.setSelected(false);
 679         turn.setSelected(false);
 680       }
 681       aColChooser.setCurrentStructureFilterPanel(this);
 682       aColChooser.updateView();
 683     }
 684
 685     public void updateSelectAllState()
 686     {
 687       if (alphaHelix.isSelected() && betaStrand.isSelected()
 688               && turn.isSelected())
 689       {
 690         all.setSelected(true);
 691       }
 692       else
 693       {
 694         all.setSelected(false);
 695       }
 696     }
 697
 698     public void syncState()
 699     {
 700       StructureFilterPanel sfp = aColChooser
 701               .getCurrentStructureFilterPanel();
 702       if (sfp != null)
 703       {
 704         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 705         betaStrand.setSelected(sfp.betaStrand.isSelected());
 706         turn.setSelected(sfp.turn.isSelected());
 707         if (sfp.all.isSelected())
 708         {
 709           all.setSelected(true);
 710           alphaHelix.setSelected(true);
 711           betaStrand.setSelected(true);
 712           turn.setSelected(true);
 713         }
 714       }
 715
 716     }
 717   }
 718
 719   public class SearchPanel extends JPanel
 720   {
 721     private AnnotationColumnChooser aColChooser;
 722
 723     private JCheckBox displayName = new JCheckBox();
 724
 725     private JCheckBox description = new JCheckBox();
 726
 727     private JTextField searchBox = new JTextField(10);
 728
 729     public SearchPanel(AnnotationColumnChooser aColChooser)
 730     {
 731
 732       this.aColChooser = aColChooser;
 733       JvSwingUtils.jvInitComponent(this);
 734       this.setBorder(new TitledBorder(MessageManager
 735               .getString("label.search_filter")));
 736
 737       JvSwingUtils.jvInitComponent(searchBox);
 738       searchBox.setToolTipText(MessageManager
 739               .getString("info.enter_search_text_here"));
 740       searchBox.getDocument().addDocumentListener(new DocumentListener()
 741       {
 742         @Override
 743         public void insertUpdate(DocumentEvent e)
 744         {
 745           searchStringAction();
 746         }
 747
 748         @Override
 749         public void removeUpdate(DocumentEvent e)
 750         {
 751           searchStringAction();
 752         }
 753
 754         @Override
 755         public void changedUpdate(DocumentEvent e)
 756         {
 757           searchStringAction();
 758         }
 759       });
 760
 761       JvSwingUtils.jvInitComponent(displayName, "label.label");
 762       displayName.setEnabled(false);
 763       displayName.addActionListener(new ActionListener()
 764       {
 765         @Override
 766         public void actionPerformed(ActionEvent actionEvent)
 767         {
 768           displayNameCheckboxAction();
 769         }
 770       });
 771
 772       JvSwingUtils.jvInitComponent(description, "label.description");
 773       description.setEnabled(false);
 774       description.addActionListener(new ActionListener()
 775       {
 776         @Override
 777         public void actionPerformed(ActionEvent actionEvent)
 778         {
 779           discriptionCheckboxAction();
 780         }
 781       });
 782
 783       syncState();
 784       this.add(searchBox);
 785       this.add(displayName);
 786       this.add(description);
 787     }
 788
 789     public void displayNameCheckboxAction()
 790     {
 791       aColChooser.setCurrentSearchPanel(this);
 792       aColChooser.updateView();
 793     }
 794
 795     public void discriptionCheckboxAction()
 796     {
 797       aColChooser.setCurrentSearchPanel(this);
 798       aColChooser.updateView();
 799     }
 800
 801     public void searchStringAction()
 802     {
 803       aColChooser.setCurrentSearchPanel(this);
 804       aColChooser.updateView();
 805       updateSearchPanelToolTips();
 806     }
 807
 808     public void syncState()
 809     {
 810       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 811       if (sp != null)
 812       {
 813         description.setEnabled(sp.description.isEnabled());
 814         description.setSelected(sp.description.isSelected());
 815
 816         displayName.setEnabled(sp.displayName.isEnabled());
 817         displayName.setSelected(sp.displayName.isSelected());
 818
 819         searchBox.setText(sp.searchBox.getText());
 820       }
 821       updateSearchPanelToolTips();
 822     }
 823
 824     public void updateSearchPanelToolTips()
 825     {
 826       String defaultTtip = MessageManager
 827               .getString("info.enter_search_text_to_enable");
 828       String labelTtip = MessageManager.formatMessage(
 829               "info.search_in_annotation_label", annotations
 830                       .getSelectedItem().toString());
 831       String descTtip = MessageManager.formatMessage(
 832               "info.search_in_annotation_description", annotations
 833                       .getSelectedItem().toString());
 834       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 835               : defaultTtip);
 836       description.setToolTipText(description.isEnabled() ? descTtip
 837               : defaultTtip);
 838     }
 839   }
 840
 841 }