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.ColumnSelection;
  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 ColumnSelection oldColumnSelection;
  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     setOldColumnSelection(av.getColumnSelection());
 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     }
 129
 130     try
 131     {
 132       jbInit();
 133     } catch (Exception ex)
 134     {
 135     }
 136     adjusting = false;
 137
 138     updateView();
 139     frame.invalidate();
 140     frame.pack();
 141   }
 142
 143   @Override
 144   protected void jbInit()
 145   {
 146     super.jbInit();
 147
 148     JPanel thresholdPanel = new JPanel();
 149     thresholdPanel.setBorder(new TitledBorder(MessageManager
 150             .getString("label.threshold_filter")));
 151     thresholdPanel.setBackground(Color.white);
 152     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 153     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 154
 155     percentThreshold.setBackground(Color.white);
 156     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 157
 158     JPanel actionPanel = new JPanel();
 159     actionPanel.setBackground(Color.white);
 160     actionPanel.setFont(JvSwingUtils.getLabelFont());
 161
 162     JPanel graphFilterView = new JPanel();
 163     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 164     graphFilterView.setBackground(Color.white);
 165
 166     JPanel noGraphFilterView = new JPanel();
 167     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 168     noGraphFilterView.setBackground(Color.white);
 169
 170     annotationComboBoxPanel.setBackground(Color.white);
 171     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 172
 173     gSearchPanel = new SearchPanel(this);
 174     ngSearchPanel = new SearchPanel(this);
 175     gFurtherActionPanel = new FurtherActionPanel(this);
 176     ngFurtherActionPanel = new FurtherActionPanel(this);
 177     gStructureFilterPanel = new StructureFilterPanel(this);
 178     ngStructureFilterPanel = new StructureFilterPanel(this);
 179
 180     thresholdPanel.add(getThreshold());
 181     thresholdPanel.add(percentThreshold, "wrap");
 182     thresholdPanel.add(slider, "grow");
 183     thresholdPanel.add(thresholdValue, "span, wrap");
 184
 185     actionPanel.add(ok);
 186     actionPanel.add(cancel);
 187
 188     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 189     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 190     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 191     graphFilterView.add(gFurtherActionPanel);
 192
 193     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 194     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 195     noGraphFilterView.add(ngFurtherActionPanel);
 196
 197     annotationComboBoxPanel.add(getAnnotations());
 198     switchableViewsPanel.add(noGraphFilterView,
 199             AnnotationColumnChooser.NO_GRAPH_VIEW);
 200     switchableViewsPanel.add(graphFilterView,
 201             AnnotationColumnChooser.GRAPH_VIEW);
 202
 203     this.setLayout(new BorderLayout());
 204     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 205     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 206     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 207
 208     selectedAnnotationChanged();
 209     updateThresholdPanelToolTip();
 210     this.validate();
 211   }
 212
 213   protected void updateThresholdPanelToolTip()
 214   {
 215     thresholdValue.setToolTipText("");
 216     slider.setToolTipText("");
 217
 218     String defaultTtip = MessageManager
 219             .getString("info.change_threshold_mode_to_enable");
 220
 221     String thresh = getThreshold().getSelectedItem().toString();
 222     if (thresh.equalsIgnoreCase("No Threshold"))
 223     {
 224       thresholdValue.setToolTipText(defaultTtip);
 225       slider.setToolTipText(defaultTtip);
 226     }
 227   }
 228
 229   @Override
 230   protected void reset()
 231   {
 232     if (this.getOldColumnSelection() != null)
 233     {
 234       av.getColumnSelection().clear();
 235
 236       if (av.getAnnotationColumnSelectionState() != null)
 237       {
 238         ColumnSelection oldSelection = av
 239                 .getAnnotationColumnSelectionState()
 240                 .getOldColumnSelection();
 241         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 242                 && !oldSelection.getHiddenColumns().isEmpty())
 243         {
 244           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 245                   .iterator(); itr.hasNext();)
 246           {
 247             int positions[] = itr.next();
 248             av.hideColumns(positions[0], positions[1]);
 249           }
 250         }
 251         av.setColumnSelection(oldSelection);
 252       }
 253       ap.paintAlignment(true);
 254     }
 255
 256   }
 257
 258   @Override
 259   public void valueChanged(boolean updateAllAnnotation)
 260   {
 261     if (slider.isEnabled())
 262     {
 263       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 264       updateView();
 265       propagateSeqAssociatedThreshold(updateAllAnnotation,
 266               getCurrentAnnotation());
 267       ap.paintAlignment(false);
 268     }
 269   }
 270
 271   @Override
 272   public void updateView()
 273   {
 274     // Check if combobox is still adjusting
 275     if (adjusting)
 276     {
 277       return;
 278     }
 279
 280     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 281
 282     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 283             .getSelectedIndex()]]);
 284
 285     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 286             .getSelectedIndex());
 287
 288     slider.setEnabled(true);
 289     thresholdValue.setEnabled(true);
 290     percentThreshold.setEnabled(true);
 291
 292     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 293     {
 294       slider.setEnabled(false);
 295       thresholdValue.setEnabled(false);
 296       thresholdValue.setText("");
 297       percentThreshold.setEnabled(false);
 298       // build filter params
 299     }
 300     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 301     {
 302       if (getCurrentAnnotation().threshold == null)
 303       {
 304         getCurrentAnnotation()
 305                 .setThreshold(
 306                         new jalview.datamodel.GraphLine(
 307                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 308                                 "Threshold", Color.black));
 309       }
 310
 311       adjusting = true;
 312       float range = getCurrentAnnotation().graphMax * 1000
 313               - getCurrentAnnotation().graphMin * 1000;
 314
 315       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 316       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 317       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 318
 319       if (percentThreshold.isSelected())
 320       {
 321         thresholdValue
 322                 .setText(""
 323                         + ((getCurrentAnnotation().threshold.value - getCurrentAnnotation().graphMin) * 100f / (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin)));
 324       }
 325       else
 326       {
 327         thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 328       }
 329
 330       slider.setMajorTickSpacing((int) (range / 10f));
 331       slider.setEnabled(true);
 332       thresholdValue.setEnabled(true);
 333       adjusting = false;
 334
 335       // build filter params
 336       filterParams
 337               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 338       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 339       {
 340         filterParams
 341                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 342
 343         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 344         {
 345           filterParams
 346                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 347         }
 348         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 349         {
 350           filterParams
 351                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 352         }
 353       }
 354     }
 355
 356     updateThresholdPanelToolTip();
 357     if (currentStructureFilterPanel != null)
 358     {
 359       if (currentStructureFilterPanel.alphaHelix.isSelected())
 360       {
 361         filterParams.setFilterAlphaHelix(true);
 362       }
 363       if (currentStructureFilterPanel.betaStrand.isSelected())
 364       {
 365         filterParams.setFilterBetaSheet(true);
 366       }
 367       if (currentStructureFilterPanel.turn.isSelected())
 368       {
 369         filterParams.setFilterTurn(true);
 370       }
 371     }
 372
 373     if (currentSearchPanel != null)
 374     {
 375
 376       if (!currentSearchPanel.searchBox.getText().isEmpty())
 377       {
 378         currentSearchPanel.description.setEnabled(true);
 379         currentSearchPanel.displayName.setEnabled(true);
 380         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 381         if (currentSearchPanel.displayName.isSelected())
 382         {
 383           filterParams
 384                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 385         }
 386         if (currentSearchPanel.description.isSelected())
 387         {
 388           filterParams
 389                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 390         }
 391       }
 392       else
 393       {
 394         currentSearchPanel.description.setEnabled(false);
 395         currentSearchPanel.displayName.setEnabled(false);
 396       }
 397     }
 398
 399     av.getColumnSelection().filterAnnotations(
 400             getCurrentAnnotation().annotations, filterParams);
 401
 402     av.showAllHiddenColumns();
 403     if (getActionOption() == ACTION_OPTION_HIDE)
 404     {
 405       av.hideSelectedColumns();
 406     }
 407
 408     filterParams = null;
 409     av.setAnnotationColumnSelectionState(this);
 410     ap.paintAlignment(true);
 411   }
 412
 413
 414   public ColumnSelection getOldColumnSelection()
 415   {
 416     return oldColumnSelection;
 417   }
 418
 419   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 420   {
 421     if (currentColumnSelection != null)
 422     {
 423       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 424     }
 425   }
 426
 427   public FurtherActionPanel getCurrentFutherActionPanel()
 428   {
 429     return currentFurtherActionPanel;
 430   }
 431
 432   public void setCurrentFutherActionPanel(
 433           FurtherActionPanel currentFutherActionPanel)
 434   {
 435     this.currentFurtherActionPanel = currentFutherActionPanel;
 436   }
 437
 438   public SearchPanel getCurrentSearchPanel()
 439   {
 440     return currentSearchPanel;
 441   }
 442
 443   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 444   {
 445     this.currentSearchPanel = currentSearchPanel;
 446   }
 447
 448   public int getActionOption()
 449   {
 450     return actionOption;
 451   }
 452
 453   public void setActionOption(int actionOption)
 454   {
 455     this.actionOption = actionOption;
 456   }
 457
 458   public StructureFilterPanel getCurrentStructureFilterPanel()
 459   {
 460     return currentStructureFilterPanel;
 461   }
 462
 463   public void setCurrentStructureFilterPanel(
 464           StructureFilterPanel currentStructureFilterPanel)
 465   {
 466     this.currentStructureFilterPanel = currentStructureFilterPanel;
 467   }
 468
 469   public void select_action(ActionEvent actionEvent)
 470   {
 471     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 472     if (radioButton.isSelected())
 473     {
 474       setActionOption(ACTION_OPTION_SELECT);
 475       updateView();
 476     }
 477   }
 478
 479   public void hide_action(ActionEvent actionEvent)
 480   {
 481     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 482     if (radioButton.isSelected())
 483     {
 484       setActionOption(ACTION_OPTION_HIDE);
 485       updateView();
 486     }
 487   }
 488
 489   @Override
 490   public void itemStateChanged(ItemEvent e)
 491   {
 492     selectedAnnotationChanged();
 493   }
 494
 495   @Override
 496   public void selectedAnnotationChanged()
 497   {
 498     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 499     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 500             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 501     {
 502       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 503     }
 504
 505     gSearchPanel.syncState();
 506     gFurtherActionPanel.syncState();
 507     gStructureFilterPanel.syncState();
 508
 509     ngSearchPanel.syncState();
 510     ngFurtherActionPanel.syncState();
 511     ngStructureFilterPanel.syncState();
 512
 513     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 514             .getLayout();
 515     switchableViewsLayout.show(switchableViewsPanel, currentView);
 516     updateView();
 517   }
 518
 519   public class FurtherActionPanel extends JPanel
 520   {
 521     private AnnotationColumnChooser aColChooser;
 522
 523     private JRadioButton hideOption = new JRadioButton();
 524
 525     private JRadioButton selectOption = new JRadioButton();
 526
 527     private ButtonGroup optionsGroup = new ButtonGroup();
 528
 529     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 530     {
 531       this.aColChooser = aColChooser;
 532       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 533       selectOption.addActionListener(new ActionListener()
 534       {
 535         @Override
 536         public void actionPerformed(ActionEvent actionEvent)
 537         {
 538           selectRadioAction(actionEvent);
 539         }
 540       });
 541
 542       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 543       hideOption.addActionListener(new ActionListener()
 544       {
 545         @Override
 546         public void actionPerformed(ActionEvent actionEvent)
 547         {
 548           hideRadioAction(actionEvent);
 549         }
 550       });
 551
 552       optionsGroup.add(selectOption);
 553       optionsGroup.add(hideOption);
 554       optionsGroup.setSelected(selectOption.getModel(), true);
 555
 556       JvSwingUtils.jvInitComponent(this);
 557       syncState();
 558
 559       this.add(selectOption);
 560       this.add(hideOption);
 561     }
 562
 563     public void selectRadioAction(ActionEvent actionEvent)
 564     {
 565       aColChooser.setCurrentFutherActionPanel(this);
 566       aColChooser.select_action(actionEvent);
 567     }
 568
 569     public void hideRadioAction(ActionEvent actionEvent)
 570     {
 571       aColChooser.setCurrentFutherActionPanel(this);
 572       aColChooser.hide_action(actionEvent);
 573     }
 574
 575     public void syncState()
 576     {
 577       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 578       {
 579         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 580       }
 581       else
 582       {
 583         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 584       }
 585     }
 586   }
 587
 588   public class StructureFilterPanel extends JPanel
 589   {
 590     private AnnotationColumnChooser aColChooser;
 591
 592     private JCheckBox alphaHelix = new JCheckBox();
 593
 594     private JCheckBox betaStrand = new JCheckBox();
 595
 596     private JCheckBox turn = new JCheckBox();
 597
 598     private JCheckBox all = new JCheckBox();
 599
 600     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 601     {
 602       this.aColChooser = aColChooser;
 603
 604       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 605       alphaHelix.addActionListener(new ActionListener()
 606       {
 607         @Override
 608         public void actionPerformed(ActionEvent actionEvent)
 609         {
 610           alphaHelix_actionPerformed();
 611         }
 612       });
 613
 614       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 615       betaStrand.addActionListener(new ActionListener()
 616       {
 617         @Override
 618         public void actionPerformed(ActionEvent actionEvent)
 619         {
 620           betaStrand_actionPerformed();
 621         }
 622       });
 623
 624       JvSwingUtils.jvInitComponent(turn, "label.turn");
 625       turn.addActionListener(new ActionListener()
 626       {
 627         @Override
 628         public void actionPerformed(ActionEvent actionEvent)
 629         {
 630           turn_actionPerformed();
 631         }
 632       });
 633
 634       JvSwingUtils.jvInitComponent(all, "label.select_all");
 635       all.addActionListener(new ActionListener()
 636       {
 637         @Override
 638         public void actionPerformed(ActionEvent actionEvent)
 639         {
 640           all_actionPerformed();
 641         }
 642       });
 643
 644       this.setBorder(new TitledBorder(MessageManager
 645               .getString("label.structures_filter")));
 646       JvSwingUtils.jvInitComponent(this);
 647
 648       this.add(all);
 649       this.add(alphaHelix);
 650       this.add(betaStrand);
 651       this.add(turn);
 652     }
 653
 654     public void alphaHelix_actionPerformed()
 655     {
 656       updateSelectAllState();
 657       aColChooser.setCurrentStructureFilterPanel(this);
 658       aColChooser.updateView();
 659     }
 660
 661     public void betaStrand_actionPerformed()
 662     {
 663       updateSelectAllState();
 664       aColChooser.setCurrentStructureFilterPanel(this);
 665       aColChooser.updateView();
 666     }
 667
 668     public void turn_actionPerformed()
 669     {
 670       updateSelectAllState();
 671       aColChooser.setCurrentStructureFilterPanel(this);
 672       aColChooser.updateView();
 673     }
 674
 675     public void all_actionPerformed()
 676     {
 677       if (all.isSelected())
 678       {
 679         alphaHelix.setSelected(true);
 680         betaStrand.setSelected(true);
 681         turn.setSelected(true);
 682       }
 683       else
 684       {
 685         alphaHelix.setSelected(false);
 686         betaStrand.setSelected(false);
 687         turn.setSelected(false);
 688       }
 689       aColChooser.setCurrentStructureFilterPanel(this);
 690       aColChooser.updateView();
 691     }
 692
 693     public void updateSelectAllState()
 694     {
 695       if (alphaHelix.isSelected() && betaStrand.isSelected()
 696               && turn.isSelected())
 697       {
 698         all.setSelected(true);
 699       }
 700       else
 701       {
 702         all.setSelected(false);
 703       }
 704     }
 705
 706     public void syncState()
 707     {
 708       StructureFilterPanel sfp = aColChooser
 709               .getCurrentStructureFilterPanel();
 710       if (sfp != null)
 711       {
 712         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 713         betaStrand.setSelected(sfp.betaStrand.isSelected());
 714         turn.setSelected(sfp.turn.isSelected());
 715         if (sfp.all.isSelected())
 716         {
 717           all.setSelected(true);
 718           alphaHelix.setSelected(true);
 719           betaStrand.setSelected(true);
 720           turn.setSelected(true);
 721         }
 722       }
 723
 724     }
 725   }
 726
 727   public class SearchPanel extends JPanel
 728   {
 729     private AnnotationColumnChooser aColChooser;
 730
 731     private JCheckBox displayName = new JCheckBox();
 732
 733     private JCheckBox description = new JCheckBox();
 734
 735     private JTextField searchBox = new JTextField(10);
 736
 737     public SearchPanel(AnnotationColumnChooser aColChooser)
 738     {
 739
 740       this.aColChooser = aColChooser;
 741       JvSwingUtils.jvInitComponent(this);
 742       this.setBorder(new TitledBorder(MessageManager
 743               .getString("label.search_filter")));
 744
 745       JvSwingUtils.jvInitComponent(searchBox);
 746       searchBox.setToolTipText(MessageManager
 747               .getString("info.enter_search_text_here"));
 748       searchBox.getDocument().addDocumentListener(new DocumentListener()
 749       {
 750         @Override
 751         public void insertUpdate(DocumentEvent e)
 752         {
 753           searchStringAction();
 754         }
 755
 756         @Override
 757         public void removeUpdate(DocumentEvent e)
 758         {
 759           searchStringAction();
 760         }
 761
 762         @Override
 763         public void changedUpdate(DocumentEvent e)
 764         {
 765           searchStringAction();
 766         }
 767       });
 768
 769       JvSwingUtils.jvInitComponent(displayName, "label.label");
 770       displayName.setEnabled(false);
 771       displayName.addActionListener(new ActionListener()
 772       {
 773         @Override
 774         public void actionPerformed(ActionEvent actionEvent)
 775         {
 776           displayNameCheckboxAction();
 777         }
 778       });
 779
 780       JvSwingUtils.jvInitComponent(description, "label.description");
 781       description.setEnabled(false);
 782       description.addActionListener(new ActionListener()
 783       {
 784         @Override
 785         public void actionPerformed(ActionEvent actionEvent)
 786         {
 787           discriptionCheckboxAction();
 788         }
 789       });
 790
 791       syncState();
 792       this.add(searchBox);
 793       this.add(displayName);
 794       this.add(description);
 795     }
 796
 797     public void displayNameCheckboxAction()
 798     {
 799       aColChooser.setCurrentSearchPanel(this);
 800       aColChooser.updateView();
 801     }
 802
 803     public void discriptionCheckboxAction()
 804     {
 805       aColChooser.setCurrentSearchPanel(this);
 806       aColChooser.updateView();
 807     }
 808
 809     public void searchStringAction()
 810     {
 811       aColChooser.setCurrentSearchPanel(this);
 812       aColChooser.updateView();
 813       updateSearchPanelToolTips();
 814     }
 815
 816     public void syncState()
 817     {
 818       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 819       if (sp != null)
 820       {
 821         description.setEnabled(sp.description.isEnabled());
 822         description.setSelected(sp.description.isSelected());
 823
 824         displayName.setEnabled(sp.displayName.isEnabled());
 825         displayName.setSelected(sp.displayName.isSelected());
 826
 827         searchBox.setText(sp.searchBox.getText());
 828       }
 829       updateSearchPanelToolTips();
 830     }
 831
 832     public void updateSearchPanelToolTips()
 833     {
 834       String defaultTtip = MessageManager
 835               .getString("info.enter_search_text_to_enable");
 836       String labelTtip = MessageManager.formatMessage(
 837               "info.search_in_annotation_label", annotations
 838                       .getSelectedItem().toString());
 839       String descTtip = MessageManager.formatMessage(
 840               "info.search_in_annotation_description", annotations
 841                       .getSelectedItem().toString());
 842       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 843               : defaultTtip);
 844       description.setToolTipText(description.isEnabled() ? descTtip
 845               : defaultTtip);
 846     }
 847   }
 848
 849 }