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       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.getOldColumnSelection() != null)
 235     {
 236       av.getColumnSelection().clear();
 237
 238       if (av.getAnnotationColumnSelectionState() != null)
 239       {
 240         ColumnSelection oldSelection = av
 241                 .getAnnotationColumnSelectionState()
 242                 .getOldColumnSelection();
 243         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 244                 && !oldSelection.getHiddenColumns().isEmpty())
 245         {
 246           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 247                   .iterator(); itr.hasNext();)
 248           {
 249             int positions[] = itr.next();
 250             av.hideColumns(positions[0], positions[1]);
 251           }
 252         }
 253         av.setColumnSelection(oldSelection);
 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       if (percentThreshold.isSelected())
 322       {
 323         thresholdValue
 324                 .setText(""
 325                         + ((getCurrentAnnotation().threshold.value - getCurrentAnnotation().graphMin) * 100f / (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin)));
 326       }
 327       else
 328       {
 329         thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 330       }
 331
 332       slider.setMajorTickSpacing((int) (range / 10f));
 333       slider.setEnabled(true);
 334       thresholdValue.setEnabled(true);
 335       adjusting = false;
 336
 337       // build filter params
 338       filterParams
 339               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 340       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 341       {
 342         filterParams
 343                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 344
 345         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 346         {
 347           filterParams
 348                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 349         }
 350         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 351         {
 352           filterParams
 353                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 354         }
 355       }
 356     }
 357
 358     updateThresholdPanelToolTip();
 359     if (currentStructureFilterPanel != null)
 360     {
 361       if (currentStructureFilterPanel.alphaHelix.isSelected())
 362       {
 363         filterParams.setFilterAlphaHelix(true);
 364       }
 365       if (currentStructureFilterPanel.betaStrand.isSelected())
 366       {
 367         filterParams.setFilterBetaSheet(true);
 368       }
 369       if (currentStructureFilterPanel.turn.isSelected())
 370       {
 371         filterParams.setFilterTurn(true);
 372       }
 373     }
 374
 375     if (currentSearchPanel != null)
 376     {
 377
 378       if (!currentSearchPanel.searchBox.getText().isEmpty())
 379       {
 380         currentSearchPanel.description.setEnabled(true);
 381         currentSearchPanel.displayName.setEnabled(true);
 382         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 383         if (currentSearchPanel.displayName.isSelected())
 384         {
 385           filterParams
 386                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 387         }
 388         if (currentSearchPanel.description.isSelected())
 389         {
 390           filterParams
 391                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 392         }
 393       }
 394       else
 395       {
 396         currentSearchPanel.description.setEnabled(false);
 397         currentSearchPanel.displayName.setEnabled(false);
 398       }
 399     }
 400
 401     av.getColumnSelection().filterAnnotations(
 402             getCurrentAnnotation().annotations, filterParams);
 403
 404     av.showAllHiddenColumns();
 405     if (getActionOption() == ACTION_OPTION_HIDE)
 406     {
 407       av.hideSelectedColumns();
 408     }
 409
 410     filterParams = null;
 411     av.setAnnotationColumnSelectionState(this);
 412     ap.paintAlignment(true);
 413   }
 414
 415
 416   public ColumnSelection getOldColumnSelection()
 417   {
 418     return oldColumnSelection;
 419   }
 420
 421   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 422   {
 423     if (currentColumnSelection != null)
 424     {
 425       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 426     }
 427   }
 428
 429   public FurtherActionPanel getCurrentFutherActionPanel()
 430   {
 431     return currentFurtherActionPanel;
 432   }
 433
 434   public void setCurrentFutherActionPanel(
 435           FurtherActionPanel currentFutherActionPanel)
 436   {
 437     this.currentFurtherActionPanel = currentFutherActionPanel;
 438   }
 439
 440   public SearchPanel getCurrentSearchPanel()
 441   {
 442     return currentSearchPanel;
 443   }
 444
 445   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 446   {
 447     this.currentSearchPanel = currentSearchPanel;
 448   }
 449
 450   public int getActionOption()
 451   {
 452     return actionOption;
 453   }
 454
 455   public void setActionOption(int actionOption)
 456   {
 457     this.actionOption = actionOption;
 458   }
 459
 460   public StructureFilterPanel getCurrentStructureFilterPanel()
 461   {
 462     return currentStructureFilterPanel;
 463   }
 464
 465   public void setCurrentStructureFilterPanel(
 466           StructureFilterPanel currentStructureFilterPanel)
 467   {
 468     this.currentStructureFilterPanel = currentStructureFilterPanel;
 469   }
 470
 471   public void select_action(ActionEvent actionEvent)
 472   {
 473     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 474     if (radioButton.isSelected())
 475     {
 476       setActionOption(ACTION_OPTION_SELECT);
 477       updateView();
 478     }
 479   }
 480
 481   public void hide_action(ActionEvent actionEvent)
 482   {
 483     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 484     if (radioButton.isSelected())
 485     {
 486       setActionOption(ACTION_OPTION_HIDE);
 487       updateView();
 488     }
 489   }
 490
 491   @Override
 492   public void itemStateChanged(ItemEvent e)
 493   {
 494     selectedAnnotationChanged();
 495   }
 496
 497   @Override
 498   public void selectedAnnotationChanged()
 499   {
 500     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 501     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 502             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 503     {
 504       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 505     }
 506
 507     gSearchPanel.syncState();
 508     gFurtherActionPanel.syncState();
 509     gStructureFilterPanel.syncState();
 510
 511     ngSearchPanel.syncState();
 512     ngFurtherActionPanel.syncState();
 513     ngStructureFilterPanel.syncState();
 514
 515     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 516             .getLayout();
 517     switchableViewsLayout.show(switchableViewsPanel, currentView);
 518     updateView();
 519   }
 520
 521   public class FurtherActionPanel extends JPanel
 522   {
 523     private AnnotationColumnChooser aColChooser;
 524
 525     private JRadioButton hideOption = new JRadioButton();
 526
 527     private JRadioButton selectOption = new JRadioButton();
 528
 529     private ButtonGroup optionsGroup = new ButtonGroup();
 530
 531     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 532     {
 533       this.aColChooser = aColChooser;
 534       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 535       selectOption.addActionListener(new ActionListener()
 536       {
 537         @Override
 538         public void actionPerformed(ActionEvent actionEvent)
 539         {
 540           selectRadioAction(actionEvent);
 541         }
 542       });
 543
 544       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 545       hideOption.addActionListener(new ActionListener()
 546       {
 547         @Override
 548         public void actionPerformed(ActionEvent actionEvent)
 549         {
 550           hideRadioAction(actionEvent);
 551         }
 552       });
 553
 554       optionsGroup.add(selectOption);
 555       optionsGroup.add(hideOption);
 556       optionsGroup.setSelected(selectOption.getModel(), true);
 557
 558       JvSwingUtils.jvInitComponent(this);
 559       syncState();
 560
 561       this.add(selectOption);
 562       this.add(hideOption);
 563     }
 564
 565     public void selectRadioAction(ActionEvent actionEvent)
 566     {
 567       aColChooser.setCurrentFutherActionPanel(this);
 568       aColChooser.select_action(actionEvent);
 569     }
 570
 571     public void hideRadioAction(ActionEvent actionEvent)
 572     {
 573       aColChooser.setCurrentFutherActionPanel(this);
 574       aColChooser.hide_action(actionEvent);
 575     }
 576
 577     public void syncState()
 578     {
 579       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 580       {
 581         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 582       }
 583       else
 584       {
 585         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 586       }
 587     }
 588   }
 589
 590   public class StructureFilterPanel extends JPanel
 591   {
 592     private AnnotationColumnChooser aColChooser;
 593
 594     private JCheckBox alphaHelix = new JCheckBox();
 595
 596     private JCheckBox betaStrand = new JCheckBox();
 597
 598     private JCheckBox turn = new JCheckBox();
 599
 600     private JCheckBox all = new JCheckBox();
 601
 602     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 603     {
 604       this.aColChooser = aColChooser;
 605
 606       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 607       alphaHelix.addActionListener(new ActionListener()
 608       {
 609         @Override
 610         public void actionPerformed(ActionEvent actionEvent)
 611         {
 612           alphaHelix_actionPerformed();
 613         }
 614       });
 615
 616       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 617       betaStrand.addActionListener(new ActionListener()
 618       {
 619         @Override
 620         public void actionPerformed(ActionEvent actionEvent)
 621         {
 622           betaStrand_actionPerformed();
 623         }
 624       });
 625
 626       JvSwingUtils.jvInitComponent(turn, "label.turn");
 627       turn.addActionListener(new ActionListener()
 628       {
 629         @Override
 630         public void actionPerformed(ActionEvent actionEvent)
 631         {
 632           turn_actionPerformed();
 633         }
 634       });
 635
 636       JvSwingUtils.jvInitComponent(all, "label.select_all");
 637       all.addActionListener(new ActionListener()
 638       {
 639         @Override
 640         public void actionPerformed(ActionEvent actionEvent)
 641         {
 642           all_actionPerformed();
 643         }
 644       });
 645
 646       this.setBorder(new TitledBorder(MessageManager
 647               .getString("label.structures_filter")));
 648       JvSwingUtils.jvInitComponent(this);
 649
 650       this.add(all);
 651       this.add(alphaHelix);
 652       this.add(betaStrand);
 653       this.add(turn);
 654     }
 655
 656     public void alphaHelix_actionPerformed()
 657     {
 658       updateSelectAllState();
 659       aColChooser.setCurrentStructureFilterPanel(this);
 660       aColChooser.updateView();
 661     }
 662
 663     public void betaStrand_actionPerformed()
 664     {
 665       updateSelectAllState();
 666       aColChooser.setCurrentStructureFilterPanel(this);
 667       aColChooser.updateView();
 668     }
 669
 670     public void turn_actionPerformed()
 671     {
 672       updateSelectAllState();
 673       aColChooser.setCurrentStructureFilterPanel(this);
 674       aColChooser.updateView();
 675     }
 676
 677     public void all_actionPerformed()
 678     {
 679       if (all.isSelected())
 680       {
 681         alphaHelix.setSelected(true);
 682         betaStrand.setSelected(true);
 683         turn.setSelected(true);
 684       }
 685       else
 686       {
 687         alphaHelix.setSelected(false);
 688         betaStrand.setSelected(false);
 689         turn.setSelected(false);
 690       }
 691       aColChooser.setCurrentStructureFilterPanel(this);
 692       aColChooser.updateView();
 693     }
 694
 695     public void updateSelectAllState()
 696     {
 697       if (alphaHelix.isSelected() && betaStrand.isSelected()
 698               && turn.isSelected())
 699       {
 700         all.setSelected(true);
 701       }
 702       else
 703       {
 704         all.setSelected(false);
 705       }
 706     }
 707
 708     public void syncState()
 709     {
 710       StructureFilterPanel sfp = aColChooser
 711               .getCurrentStructureFilterPanel();
 712       if (sfp != null)
 713       {
 714         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 715         betaStrand.setSelected(sfp.betaStrand.isSelected());
 716         turn.setSelected(sfp.turn.isSelected());
 717         if (sfp.all.isSelected())
 718         {
 719           all.setSelected(true);
 720           alphaHelix.setSelected(true);
 721           betaStrand.setSelected(true);
 722           turn.setSelected(true);
 723         }
 724       }
 725
 726     }
 727   }
 728
 729   public class SearchPanel extends JPanel
 730   {
 731     private AnnotationColumnChooser aColChooser;
 732
 733     private JCheckBox displayName = new JCheckBox();
 734
 735     private JCheckBox description = new JCheckBox();
 736
 737     private JTextField searchBox = new JTextField(10);
 738
 739     public SearchPanel(AnnotationColumnChooser aColChooser)
 740     {
 741
 742       this.aColChooser = aColChooser;
 743       JvSwingUtils.jvInitComponent(this);
 744       this.setBorder(new TitledBorder(MessageManager
 745               .getString("label.search_filter")));
 746
 747       JvSwingUtils.jvInitComponent(searchBox);
 748       searchBox.setToolTipText(MessageManager
 749               .getString("info.enter_search_text_here"));
 750       searchBox.getDocument().addDocumentListener(new DocumentListener()
 751       {
 752         @Override
 753         public void insertUpdate(DocumentEvent e)
 754         {
 755           searchStringAction();
 756         }
 757
 758         @Override
 759         public void removeUpdate(DocumentEvent e)
 760         {
 761           searchStringAction();
 762         }
 763
 764         @Override
 765         public void changedUpdate(DocumentEvent e)
 766         {
 767           searchStringAction();
 768         }
 769       });
 770
 771       JvSwingUtils.jvInitComponent(displayName, "label.label");
 772       displayName.setEnabled(false);
 773       displayName.addActionListener(new ActionListener()
 774       {
 775         @Override
 776         public void actionPerformed(ActionEvent actionEvent)
 777         {
 778           displayNameCheckboxAction();
 779         }
 780       });
 781
 782       JvSwingUtils.jvInitComponent(description, "label.description");
 783       description.setEnabled(false);
 784       description.addActionListener(new ActionListener()
 785       {
 786         @Override
 787         public void actionPerformed(ActionEvent actionEvent)
 788         {
 789           discriptionCheckboxAction();
 790         }
 791       });
 792
 793       syncState();
 794       this.add(searchBox);
 795       this.add(displayName);
 796       this.add(description);
 797     }
 798
 799     public void displayNameCheckboxAction()
 800     {
 801       aColChooser.setCurrentSearchPanel(this);
 802       aColChooser.updateView();
 803     }
 804
 805     public void discriptionCheckboxAction()
 806     {
 807       aColChooser.setCurrentSearchPanel(this);
 808       aColChooser.updateView();
 809     }
 810
 811     public void searchStringAction()
 812     {
 813       aColChooser.setCurrentSearchPanel(this);
 814       aColChooser.updateView();
 815       updateSearchPanelToolTips();
 816     }
 817
 818     public void syncState()
 819     {
 820       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 821       if (sp != null)
 822       {
 823         description.setEnabled(sp.description.isEnabled());
 824         description.setSelected(sp.description.isSelected());
 825
 826         displayName.setEnabled(sp.displayName.isEnabled());
 827         displayName.setSelected(sp.displayName.isSelected());
 828
 829         searchBox.setText(sp.searchBox.getText());
 830       }
 831       updateSearchPanelToolTips();
 832     }
 833
 834     public void updateSearchPanelToolTips()
 835     {
 836       String defaultTtip = MessageManager
 837               .getString("info.enter_search_text_to_enable");
 838       String labelTtip = MessageManager.formatMessage(
 839               "info.search_in_annotation_label", annotations
 840                       .getSelectedItem().toString());
 841       String descTtip = MessageManager.formatMessage(
 842               "info.search_in_annotation_description", annotations
 843                       .getSelectedItem().toString());
 844       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 845               : defaultTtip);
 846       description.setToolTipText(description.isEnabled() ? descTtip
 847               : defaultTtip);
 848     }
 849   }
 850
 851 }