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.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.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 ColumnSelection oldColumnSelection;
  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     setOldColumnSelection(av.getColumnSelection());
 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.getOldColumnSelection() != null)
 240     {
 241       av.getColumnSelection().clear();
 242
 243       if (av.getAnnotationColumnSelectionState() != null)
 244       {
 245         ColumnSelection oldSelection = av
 246                 .getAnnotationColumnSelectionState()
 247                 .getOldColumnSelection();
 248         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 249                 && !oldSelection.getHiddenColumns().isEmpty())
 250         {
 251           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 252                   .iterator(); itr.hasNext();)
 253           {
 254             int positions[] = itr.next();
 255             av.hideColumns(positions[0], positions[1]);
 256           }
 257         }
 258         av.setColumnSelection(oldSelection);
 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
 412   public ColumnSelection getOldColumnSelection()
 413   {
 414     return oldColumnSelection;
 415   }
 416
 417   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 418   {
 419     if (currentColumnSelection != null)
 420     {
 421       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 422     }
 423   }
 424
 425   public FurtherActionPanel getCurrentFutherActionPanel()
 426   {
 427     return currentFurtherActionPanel;
 428   }
 429
 430   public void setCurrentFutherActionPanel(
 431           FurtherActionPanel currentFutherActionPanel)
 432   {
 433     this.currentFurtherActionPanel = currentFutherActionPanel;
 434   }
 435
 436   public SearchPanel getCurrentSearchPanel()
 437   {
 438     return currentSearchPanel;
 439   }
 440
 441   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 442   {
 443     this.currentSearchPanel = currentSearchPanel;
 444   }
 445
 446   public int getActionOption()
 447   {
 448     return actionOption;
 449   }
 450
 451   public void setActionOption(int actionOption)
 452   {
 453     this.actionOption = actionOption;
 454   }
 455
 456   public StructureFilterPanel getCurrentStructureFilterPanel()
 457   {
 458     return currentStructureFilterPanel;
 459   }
 460
 461   public void setCurrentStructureFilterPanel(
 462           StructureFilterPanel currentStructureFilterPanel)
 463   {
 464     this.currentStructureFilterPanel = currentStructureFilterPanel;
 465   }
 466
 467   public void select_action(ActionEvent actionEvent)
 468   {
 469     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 470     if (radioButton.isSelected())
 471     {
 472       setActionOption(ACTION_OPTION_SELECT);
 473       updateView();
 474     }
 475   }
 476
 477   public void hide_action(ActionEvent actionEvent)
 478   {
 479     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 480     if (radioButton.isSelected())
 481     {
 482       setActionOption(ACTION_OPTION_HIDE);
 483       updateView();
 484     }
 485   }
 486
 487   @Override
 488   public void itemStateChanged(ItemEvent e)
 489   {
 490     selectedAnnotationChanged();
 491   }
 492
 493   @Override
 494   public void selectedAnnotationChanged()
 495   {
 496     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 497     if (av.getAlignment()
 498             .getAlignmentAnnotation()[annmap[getAnnotations()
 499             .getSelectedIndex()]].isQuantitative())
 500     {
 501       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 502     }
 503
 504     gSearchPanel.syncState();
 505     gFurtherActionPanel.syncState();
 506     gStructureFilterPanel.syncState();
 507
 508     ngSearchPanel.syncState();
 509     ngFurtherActionPanel.syncState();
 510     ngStructureFilterPanel.syncState();
 511
 512     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 513             .getLayout();
 514     switchableViewsLayout.show(switchableViewsPanel, currentView);
 515     updateView();
 516   }
 517
 518   public class FurtherActionPanel extends JPanel
 519   {
 520     private AnnotationColumnChooser aColChooser;
 521
 522     private JRadioButton hideOption = new JRadioButton();
 523
 524     private JRadioButton selectOption = new JRadioButton();
 525
 526     private ButtonGroup optionsGroup = new ButtonGroup();
 527
 528     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 529     {
 530       this.aColChooser = aColChooser;
 531       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 532       selectOption.addActionListener(new ActionListener()
 533       {
 534         @Override
 535         public void actionPerformed(ActionEvent actionEvent)
 536         {
 537           selectRadioAction(actionEvent);
 538         }
 539       });
 540
 541       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 542       hideOption.addActionListener(new ActionListener()
 543       {
 544         @Override
 545         public void actionPerformed(ActionEvent actionEvent)
 546         {
 547           hideRadioAction(actionEvent);
 548         }
 549       });
 550
 551       optionsGroup.add(selectOption);
 552       optionsGroup.add(hideOption);
 553       optionsGroup.setSelected(selectOption.getModel(), true);
 554
 555       JvSwingUtils.jvInitComponent(this);
 556       syncState();
 557
 558       this.add(selectOption);
 559       this.add(hideOption);
 560     }
 561
 562     public void selectRadioAction(ActionEvent actionEvent)
 563     {
 564       aColChooser.setCurrentFutherActionPanel(this);
 565       aColChooser.select_action(actionEvent);
 566     }
 567
 568     public void hideRadioAction(ActionEvent actionEvent)
 569     {
 570       aColChooser.setCurrentFutherActionPanel(this);
 571       aColChooser.hide_action(actionEvent);
 572     }
 573
 574     public void syncState()
 575     {
 576       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 577       {
 578         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 579       }
 580       else
 581       {
 582         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 583       }
 584     }
 585   }
 586
 587   public class StructureFilterPanel extends JPanel
 588   {
 589     private AnnotationColumnChooser aColChooser;
 590
 591     private JCheckBox alphaHelix = new JCheckBox();
 592
 593     private JCheckBox betaStrand = new JCheckBox();
 594
 595     private JCheckBox turn = new JCheckBox();
 596
 597     private JCheckBox all = new JCheckBox();
 598
 599     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 600     {
 601       this.aColChooser = aColChooser;
 602
 603       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 604       alphaHelix.addActionListener(new ActionListener()
 605       {
 606         @Override
 607         public void actionPerformed(ActionEvent actionEvent)
 608         {
 609           alphaHelix_actionPerformed();
 610         }
 611       });
 612
 613       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 614       betaStrand.addActionListener(new ActionListener()
 615       {
 616         @Override
 617         public void actionPerformed(ActionEvent actionEvent)
 618         {
 619           betaStrand_actionPerformed();
 620         }
 621       });
 622
 623       JvSwingUtils.jvInitComponent(turn, "label.turn");
 624       turn.addActionListener(new ActionListener()
 625       {
 626         @Override
 627         public void actionPerformed(ActionEvent actionEvent)
 628         {
 629           turn_actionPerformed();
 630         }
 631       });
 632
 633       JvSwingUtils.jvInitComponent(all, "label.select_all");
 634       all.addActionListener(new ActionListener()
 635       {
 636         @Override
 637         public void actionPerformed(ActionEvent actionEvent)
 638         {
 639           all_actionPerformed();
 640         }
 641       });
 642
 643       this.setBorder(new TitledBorder(MessageManager
 644               .getString("label.structures_filter")));
 645       JvSwingUtils.jvInitComponent(this);
 646
 647       this.add(all);
 648       this.add(alphaHelix);
 649       this.add(betaStrand);
 650       this.add(turn);
 651     }
 652
 653     public void alphaHelix_actionPerformed()
 654     {
 655       updateSelectAllState();
 656       aColChooser.setCurrentStructureFilterPanel(this);
 657       aColChooser.updateView();
 658     }
 659
 660     public void betaStrand_actionPerformed()
 661     {
 662       updateSelectAllState();
 663       aColChooser.setCurrentStructureFilterPanel(this);
 664       aColChooser.updateView();
 665     }
 666
 667     public void turn_actionPerformed()
 668     {
 669       updateSelectAllState();
 670       aColChooser.setCurrentStructureFilterPanel(this);
 671       aColChooser.updateView();
 672     }
 673
 674     public void all_actionPerformed()
 675     {
 676       if (all.isSelected())
 677       {
 678         alphaHelix.setSelected(true);
 679         betaStrand.setSelected(true);
 680         turn.setSelected(true);
 681       }
 682       else
 683       {
 684         alphaHelix.setSelected(false);
 685         betaStrand.setSelected(false);
 686         turn.setSelected(false);
 687       }
 688       aColChooser.setCurrentStructureFilterPanel(this);
 689       aColChooser.updateView();
 690     }
 691
 692     public void updateSelectAllState()
 693     {
 694       if (alphaHelix.isSelected() && betaStrand.isSelected()
 695               && turn.isSelected())
 696       {
 697         all.setSelected(true);
 698       }
 699       else
 700       {
 701         all.setSelected(false);
 702       }
 703     }
 704
 705     public void syncState()
 706     {
 707       StructureFilterPanel sfp = aColChooser
 708               .getCurrentStructureFilterPanel();
 709       if (sfp != null)
 710       {
 711         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 712         betaStrand.setSelected(sfp.betaStrand.isSelected());
 713         turn.setSelected(sfp.turn.isSelected());
 714         if (sfp.all.isSelected())
 715         {
 716           all.setSelected(true);
 717           alphaHelix.setSelected(true);
 718           betaStrand.setSelected(true);
 719           turn.setSelected(true);
 720         }
 721       }
 722
 723     }
 724   }
 725
 726   public class SearchPanel extends JPanel
 727   {
 728     private AnnotationColumnChooser aColChooser;
 729
 730     private JCheckBox displayName = new JCheckBox();
 731
 732     private JCheckBox description = new JCheckBox();
 733
 734     private JTextField searchBox = new JTextField(10);
 735
 736     public SearchPanel(AnnotationColumnChooser aColChooser)
 737     {
 738
 739       this.aColChooser = aColChooser;
 740       JvSwingUtils.jvInitComponent(this);
 741       this.setBorder(new TitledBorder(MessageManager
 742               .getString("label.search_filter")));
 743
 744       JvSwingUtils.jvInitComponent(searchBox);
 745       searchBox.setToolTipText(MessageManager
 746               .getString("info.enter_search_text_here"));
 747       searchBox.getDocument().addDocumentListener(new DocumentListener()
 748       {
 749         @Override
 750         public void insertUpdate(DocumentEvent e)
 751         {
 752           searchStringAction();
 753         }
 754
 755         @Override
 756         public void removeUpdate(DocumentEvent e)
 757         {
 758           searchStringAction();
 759         }
 760
 761         @Override
 762         public void changedUpdate(DocumentEvent e)
 763         {
 764           searchStringAction();
 765         }
 766       });
 767
 768       JvSwingUtils.jvInitComponent(displayName, "label.label");
 769       displayName.setEnabled(false);
 770       displayName.addActionListener(new ActionListener()
 771       {
 772         @Override
 773         public void actionPerformed(ActionEvent actionEvent)
 774         {
 775           displayNameCheckboxAction();
 776         }
 777       });
 778
 779       JvSwingUtils.jvInitComponent(description, "label.description");
 780       description.setEnabled(false);
 781       description.addActionListener(new ActionListener()
 782       {
 783         @Override
 784         public void actionPerformed(ActionEvent actionEvent)
 785         {
 786           discriptionCheckboxAction();
 787         }
 788       });
 789
 790       syncState();
 791       this.add(searchBox);
 792       this.add(displayName);
 793       this.add(description);
 794     }
 795
 796     public void displayNameCheckboxAction()
 797     {
 798       aColChooser.setCurrentSearchPanel(this);
 799       aColChooser.updateView();
 800     }
 801
 802     public void discriptionCheckboxAction()
 803     {
 804       aColChooser.setCurrentSearchPanel(this);
 805       aColChooser.updateView();
 806     }
 807
 808     public void searchStringAction()
 809     {
 810       aColChooser.setCurrentSearchPanel(this);
 811       aColChooser.updateView();
 812       updateSearchPanelToolTips();
 813     }
 814
 815     public void syncState()
 816     {
 817       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 818       if (sp != null)
 819       {
 820         description.setEnabled(sp.description.isEnabled());
 821         description.setSelected(sp.description.isSelected());
 822
 823         displayName.setEnabled(sp.displayName.isEnabled());
 824         displayName.setSelected(sp.displayName.isSelected());
 825
 826         searchBox.setText(sp.searchBox.getText());
 827       }
 828       updateSearchPanelToolTips();
 829     }
 830
 831     public void updateSearchPanelToolTips()
 832     {
 833       String defaultTtip = MessageManager
 834               .getString("info.enter_search_text_to_enable");
 835       String labelTtip = MessageManager.formatMessage(
 836               "info.search_in_annotation_label", annotations
 837                       .getSelectedItem().toString());
 838       String descTtip = MessageManager.formatMessage(
 839               "info.search_in_annotation_description", annotations
 840                       .getSelectedItem().toString());
 841       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 842               : defaultTtip);
 843       description.setToolTipText(description.isEnabled() ? descTtip
 844               : defaultTtip);
 845     }
 846   }
 847
 848 }