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.datamodel.GraphLine;
  27 import jalview.schemes.AnnotationColourGradient;
  28 import jalview.util.MessageManager;
  29 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.CardLayout;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.awt.event.ItemEvent;
  38 import java.awt.event.ItemListener;
  39 import java.util.Iterator;
  40
  41 import javax.swing.ButtonGroup;
  42 import javax.swing.JCheckBox;
  43 import javax.swing.JComboBox;
  44 import javax.swing.JInternalFrame;
  45 import javax.swing.JLayeredPane;
  46 import javax.swing.JPanel;
  47 import javax.swing.JRadioButton;
  48 import javax.swing.JTextField;
  49 import javax.swing.border.TitledBorder;
  50 import javax.swing.event.DocumentEvent;
  51 import javax.swing.event.DocumentListener;
  52
  53 import net.miginfocom.swing.MigLayout;
  54
  55 @SuppressWarnings("serial")
  56 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  57         ItemListener
  58 {
  59
  60   private JComboBox<String> annotations;
  61
  62   private JPanel actionPanel = new JPanel();
  63
  64   private JPanel thresholdPanel = new JPanel();
  65
  66   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  67
  68   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  69           .getLayout());
  70   private JPanel noGraphFilterView = new JPanel();
  71
  72   private JPanel graphFilterView = new JPanel();
  73
  74   private JPanel annotationComboBoxPanel = new JPanel();
  75
  76   private BorderLayout borderLayout1 = new BorderLayout();
  77
  78   private JComboBox<String> threshold = new JComboBox<String>();
  79
  80   private StructureFilterPanel gStructureFilterPanel;
  81
  82   private StructureFilterPanel ngStructureFilterPanel;
  83
  84   private StructureFilterPanel currentStructureFilterPanel;
  85
  86   private SearchPanel currentSearchPanel;
  87
  88   private SearchPanel gSearchPanel;
  89
  90   private SearchPanel ngSearchPanel;
  91
  92   private FurtherActionPanel currentFurtherActionPanel;
  93
  94   private FurtherActionPanel gFurtherActionPanel;
  95
  96   private FurtherActionPanel ngFurtherActionPanel;
  97
  98   public static final int ACTION_OPTION_SELECT = 1;
  99
 100   public static int ACTION_OPTION_HIDE = 2;
 101
 102   public static String NO_GRAPH_VIEW = "0";
 103
 104   public static String GRAPH_VIEW = "1";
 105
 106   private int actionOption = ACTION_OPTION_SELECT;
 107
 108   private ColumnSelection oldColumnSelection;
 109
 110   public AnnotationColumnChooser()
 111   {
 112     try
 113     {
 114       jbInit();
 115     } catch (Exception ex)
 116     {
 117       ex.printStackTrace();
 118     }
 119   }
 120
 121   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 122   {
 123     super(av, ap);
 124     frame = new JInternalFrame();
 125     frame.setContentPane(this);
 126     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 127     Desktop.addInternalFrame(frame,
 128             MessageManager.getString("label.select_by_annotation"), 520,
 129             215);
 130
 131     addSliderChangeListener();
 132     addSliderMouseListeners();
 133
 134     if (av.getAlignment().getAlignmentAnnotation() == null)
 135     {
 136       return;
 137     }
 138     setOldColumnSelection(av.getColumnSelection());
 139     adjusting = true;
 140
 141     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 142     populateThresholdComboBox(threshold);
 143
 144     // restore Object state from the previous session if one exists
 145     if (av.getAnnotationColumnSelectionState() != null)
 146     {
 147       currentSearchPanel = av.getAnnotationColumnSelectionState()
 148               .getCurrentSearchPanel();
 149       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 150               .getCurrentStructureFilterPanel();
 151       annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
 152               .getAnnotations().getSelectedIndex());
 153       threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
 154               .getThreshold().getSelectedIndex());
 155       actionOption = av.getAnnotationColumnSelectionState()
 156               .getActionOption();
 157     }
 158
 159     try
 160     {
 161       jbInit();
 162     } catch (Exception ex)
 163     {
 164     }
 165     adjusting = false;
 166
 167     updateView();
 168     frame.invalidate();
 169     frame.pack();
 170   }
 171
 172   private void jbInit() throws Exception
 173   {
 174     ok.setOpaque(false);
 175     ok.setText(MessageManager.getString("action.ok"));
 176     ok.addActionListener(new ActionListener()
 177     {
 178       @Override
 179       public void actionPerformed(ActionEvent e)
 180       {
 181         ok_actionPerformed(e);
 182       }
 183     });
 184
 185     cancel.setOpaque(false);
 186     cancel.setText(MessageManager.getString("action.cancel"));
 187     cancel.addActionListener(new ActionListener()
 188     {
 189       @Override
 190       public void actionPerformed(ActionEvent e)
 191       {
 192         cancel_actionPerformed(e);
 193       }
 194     });
 195
 196     annotations.addItemListener(this);
 197     annotations.setToolTipText(MessageManager
 198             .getString("info.select_annotation_row"));
 199     threshold.addActionListener(new ActionListener()
 200     {
 201       @Override
 202       public void actionPerformed(ActionEvent e)
 203       {
 204         threshold_actionPerformed(e);
 205       }
 206     });
 207
 208     thresholdValue.setEnabled(false);
 209     thresholdValue.setColumns(7);
 210     thresholdValue.addActionListener(new ActionListener()
 211     {
 212       @Override
 213       public void actionPerformed(ActionEvent e)
 214       {
 215         thresholdValue_actionPerformed(e);
 216       }
 217     });
 218
 219     slider.setPaintLabels(false);
 220     slider.setPaintTicks(true);
 221     slider.setBackground(Color.white);
 222     slider.setEnabled(false);
 223     slider.setOpaque(false);
 224     slider.setPreferredSize(new Dimension(100, 32));
 225
 226     thresholdPanel.setBorder(new TitledBorder(MessageManager
 227             .getString("label.threshold_filter")));
 228     thresholdPanel.setBackground(Color.white);
 229     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 230     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 231
 232     actionPanel.setBackground(Color.white);
 233     actionPanel.setFont(JvSwingUtils.getLabelFont());
 234
 235     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 236     graphFilterView.setBackground(Color.white);
 237
 238     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 239     noGraphFilterView.setBackground(Color.white);
 240
 241     annotationComboBoxPanel.setBackground(Color.white);
 242     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 243
 244     gSearchPanel = new SearchPanel(this);
 245     ngSearchPanel = new SearchPanel(this);
 246     gFurtherActionPanel = new FurtherActionPanel(this);
 247     ngFurtherActionPanel = new FurtherActionPanel(this);
 248     gStructureFilterPanel = new StructureFilterPanel(this);
 249     ngStructureFilterPanel = new StructureFilterPanel(this);
 250
 251     thresholdPanel.add(getThreshold());
 252     thresholdPanel.add(thresholdValue, "wrap");
 253     thresholdPanel.add(slider, "grow, span, wrap");
 254
 255     actionPanel.add(ok);
 256     actionPanel.add(cancel);
 257
 258     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 259     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 260     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 261     graphFilterView.add(gFurtherActionPanel);
 262
 263     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 264     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 265     noGraphFilterView.add(ngFurtherActionPanel);
 266
 267     annotationComboBoxPanel.add(getAnnotations());
 268     switchableViewsPanel.add(noGraphFilterView,
 269             AnnotationColumnChooser.NO_GRAPH_VIEW);
 270     switchableViewsPanel.add(graphFilterView,
 271             AnnotationColumnChooser.GRAPH_VIEW);
 272
 273     this.setLayout(borderLayout1);
 274     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 275     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 276     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 277
 278     selectedAnnotationChanged();
 279     updateThresholdPanelToolTip();
 280     this.validate();
 281   }
 282
 283   public void updateThresholdPanelToolTip()
 284   {
 285     thresholdValue.setToolTipText("");
 286     slider.setToolTipText("");
 287
 288     String defaultTtip = MessageManager
 289             .getString("info.change_threshold_mode_to_enable");
 290
 291     String threshold = getThreshold().getSelectedItem().toString();
 292     if (threshold.equalsIgnoreCase("No Threshold"))
 293     {
 294       thresholdValue.setToolTipText(defaultTtip);
 295       slider.setToolTipText(defaultTtip);
 296     }
 297   }
 298   public void reset()
 299   {
 300     if (this.getOldColumnSelection() != null)
 301     {
 302       av.getColumnSelection().clear();
 303
 304       if (av.getAnnotationColumnSelectionState() != null)
 305       {
 306         ColumnSelection oldSelection = av
 307                 .getAnnotationColumnSelectionState()
 308                 .getOldColumnSelection();
 309         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 310                 && !oldSelection.getHiddenColumns().isEmpty())
 311         {
 312           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 313                   .iterator(); itr.hasNext();)
 314           {
 315             int positions[] = itr.next();
 316             av.hideColumns(positions[0], positions[1]);
 317           }
 318         }
 319         av.setColumnSelection(oldSelection);
 320       }
 321       ap.paintAlignment(true);
 322     }
 323
 324   }
 325
 326   public void valueChanged(boolean updateAllAnnotation)
 327   {
 328     if (slider.isEnabled())
 329     {
 330       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 331       updateView();
 332       propagateSeqAssociatedThreshold(updateAllAnnotation,
 333               getCurrentAnnotation());
 334       ap.paintAlignment(false);
 335     }
 336   }
 337
 338   public JComboBox<String> getThreshold()
 339   {
 340     return threshold;
 341   }
 342
 343   public void setThreshold(JComboBox<String> threshold)
 344   {
 345     this.threshold = threshold;
 346   }
 347
 348   public JComboBox<String> getAnnotations()
 349   {
 350     return annotations;
 351   }
 352
 353   public void setAnnotations(JComboBox<String> annotations)
 354   {
 355     this.annotations = annotations;
 356   }
 357
 358   @Override
 359   public void updateView()
 360   {
 361     // Check if combobox is still adjusting
 362     if (adjusting)
 363     {
 364       return;
 365     }
 366
 367     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 368
 369     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 370             .getSelectedIndex()]]);
 371
 372     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 373             .getSelectedIndex());
 374
 375     slider.setEnabled(true);
 376     thresholdValue.setEnabled(true);
 377
 378     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 379     {
 380       slider.setEnabled(false);
 381       thresholdValue.setEnabled(false);
 382       thresholdValue.setText("");
 383       // build filter params
 384     }
 385     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 386     {
 387       if (getCurrentAnnotation().threshold == null)
 388       {
 389         getCurrentAnnotation()
 390                 .setThreshold(
 391                         new GraphLine(
 392                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 393                                 "Threshold", Color.black));
 394       }
 395
 396       adjusting = true;
 397       float range = getCurrentAnnotation().graphMax * 1000
 398               - getCurrentAnnotation().graphMin * 1000;
 399
 400       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 401       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 402       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 403       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 404       slider.setMajorTickSpacing((int) (range / 10f));
 405       slider.setEnabled(true);
 406       thresholdValue.setEnabled(true);
 407       adjusting = false;
 408
 409       // build filter params
 410       filterParams
 411               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 412       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 413       {
 414         filterParams
 415                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 416
 417         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 418         {
 419           filterParams
 420                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 421         }
 422         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 423         {
 424           filterParams
 425                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 426         }
 427       }
 428     }
 429
 430     updateThresholdPanelToolTip();
 431     if (currentStructureFilterPanel != null)
 432     {
 433       if (currentStructureFilterPanel.alphaHelix.isSelected())
 434       {
 435         filterParams.setFilterAlphaHelix(true);
 436       }
 437       if (currentStructureFilterPanel.betaStrand.isSelected())
 438       {
 439         filterParams.setFilterBetaSheet(true);
 440       }
 441       if (currentStructureFilterPanel.turn.isSelected())
 442       {
 443         filterParams.setFilterTurn(true);
 444       }
 445     }
 446
 447     if (currentSearchPanel != null)
 448     {
 449
 450       if (!currentSearchPanel.searchBox.getText().isEmpty())
 451       {
 452         currentSearchPanel.description.setEnabled(true);
 453         currentSearchPanel.displayName.setEnabled(true);
 454         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 455         if (currentSearchPanel.displayName.isSelected())
 456         {
 457           filterParams
 458                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 459         }
 460         if (currentSearchPanel.description.isSelected())
 461         {
 462           filterParams
 463                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 464         }
 465       }
 466       else
 467       {
 468         currentSearchPanel.description.setEnabled(false);
 469         currentSearchPanel.displayName.setEnabled(false);
 470       }
 471     }
 472
 473     av.getColumnSelection().filterAnnotations(
 474             getCurrentAnnotation().annotations, filterParams);
 475
 476     av.showAllHiddenColumns();
 477     if (getActionOption() == ACTION_OPTION_HIDE)
 478     {
 479       av.hideSelectedColumns();
 480     }
 481
 482     filterParams = null;
 483     av.setAnnotationColumnSelectionState(this);
 484     ap.paintAlignment(true);
 485   }
 486
 487   public ColumnSelection getOldColumnSelection()
 488   {
 489     return oldColumnSelection;
 490   }
 491
 492   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 493   {
 494     if (currentColumnSelection != null)
 495     {
 496       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 497     }
 498   }
 499
 500   public FurtherActionPanel getCurrentFutherActionPanel()
 501   {
 502     return currentFurtherActionPanel;
 503   }
 504
 505   public void setCurrentFutherActionPanel(
 506           FurtherActionPanel currentFutherActionPanel)
 507   {
 508     this.currentFurtherActionPanel = currentFutherActionPanel;
 509   }
 510
 511   public SearchPanel getCurrentSearchPanel()
 512   {
 513     return currentSearchPanel;
 514   }
 515
 516   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 517   {
 518     this.currentSearchPanel = currentSearchPanel;
 519   }
 520
 521   public int getActionOption()
 522   {
 523     return actionOption;
 524   }
 525
 526   public void setActionOption(int actionOption)
 527   {
 528     this.actionOption = actionOption;
 529   }
 530
 531   public StructureFilterPanel getCurrentStructureFilterPanel()
 532   {
 533     return currentStructureFilterPanel;
 534   }
 535
 536   public void setCurrentStructureFilterPanel(
 537           StructureFilterPanel currentStructureFilterPanel)
 538   {
 539     this.currentStructureFilterPanel = currentStructureFilterPanel;
 540   }
 541
 542   public void select_action(ActionEvent actionEvent)
 543   {
 544     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 545     if (radioButton.isSelected())
 546     {
 547       setActionOption(ACTION_OPTION_SELECT);
 548       updateView();
 549     }
 550   }
 551
 552   public void hide_action(ActionEvent actionEvent)
 553   {
 554     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 555     if (radioButton.isSelected())
 556     {
 557       setActionOption(ACTION_OPTION_HIDE);
 558       updateView();
 559     }
 560   }
 561
 562   @Override
 563   public void itemStateChanged(ItemEvent e)
 564   {
 565     selectedAnnotationChanged();
 566   }
 567
 568   public void selectedAnnotationChanged()
 569   {
 570     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 571     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 572             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 573     {
 574       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 575     }
 576
 577     gSearchPanel.syncState();
 578     gFurtherActionPanel.syncState();
 579     gStructureFilterPanel.syncState();
 580
 581     ngSearchPanel.syncState();
 582     ngFurtherActionPanel.syncState();
 583     ngStructureFilterPanel.syncState();
 584
 585     switchableViewsLayout.show(switchableViewsPanel, currentView);
 586     updateView();
 587   }
 588
 589
 590   public class FurtherActionPanel extends JPanel
 591   {
 592     private AnnotationColumnChooser aColChooser;
 593
 594     private JRadioButton hideOption = new JRadioButton();
 595
 596     private JRadioButton selectOption = new JRadioButton();
 597
 598     private ButtonGroup optionsGroup = new ButtonGroup();
 599
 600     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 601     {
 602       this.aColChooser = aColChooser;
 603       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 604       selectOption.addActionListener(new ActionListener()
 605       {
 606         @Override
 607         public void actionPerformed(ActionEvent actionEvent)
 608         {
 609           selectRadioAction(actionEvent);
 610         }
 611       });
 612
 613       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 614       hideOption.addActionListener(new ActionListener()
 615       {
 616         @Override
 617         public void actionPerformed(ActionEvent actionEvent)
 618         {
 619           hideRadioAction(actionEvent);
 620         }
 621       });
 622
 623       optionsGroup.add(selectOption);
 624       optionsGroup.add(hideOption);
 625       optionsGroup.setSelected(selectOption.getModel(), true);
 626
 627       JvSwingUtils.jvInitComponent(this);
 628       syncState();
 629
 630       this.add(selectOption);
 631       this.add(hideOption);
 632     }
 633
 634     public void selectRadioAction(ActionEvent actionEvent)
 635     {
 636       aColChooser.setCurrentFutherActionPanel(this);
 637       aColChooser.select_action(actionEvent);
 638     }
 639
 640     public void hideRadioAction(ActionEvent actionEvent)
 641     {
 642       aColChooser.setCurrentFutherActionPanel(this);
 643       aColChooser.hide_action(actionEvent);
 644     }
 645
 646     public void syncState()
 647     {
 648       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 649       {
 650         this.optionsGroup.setSelected(this.hideOption.getModel(),
 651                 true);
 652       }
 653       else
 654       {
 655         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 656       }
 657     }
 658   }
 659
 660   public class StructureFilterPanel extends JPanel
 661   {
 662     private AnnotationColumnChooser aColChooser;
 663
 664     private JCheckBox alphaHelix = new JCheckBox();
 665
 666     private JCheckBox betaStrand = new JCheckBox();
 667
 668     private JCheckBox turn = new JCheckBox();
 669
 670     private JCheckBox all = new JCheckBox();
 671
 672     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 673     {
 674       this.aColChooser = aColChooser;
 675
 676       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 677       alphaHelix.addActionListener(new ActionListener()
 678       {
 679         @Override
 680         public void actionPerformed(ActionEvent actionEvent)
 681         {
 682           alphaHelix_actionPerformed();
 683         }
 684       });
 685
 686       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 687       betaStrand.addActionListener(new ActionListener()
 688       {
 689         @Override
 690         public void actionPerformed(ActionEvent actionEvent)
 691         {
 692           betaStrand_actionPerformed();
 693         }
 694       });
 695
 696       JvSwingUtils.jvInitComponent(turn, "label.turn");
 697       turn.addActionListener(new ActionListener()
 698       {
 699         @Override
 700         public void actionPerformed(ActionEvent actionEvent)
 701         {
 702           turn_actionPerformed();
 703         }
 704       });
 705
 706       JvSwingUtils.jvInitComponent(all, "label.select_all");
 707       all.addActionListener(new ActionListener()
 708       {
 709         @Override
 710         public void actionPerformed(ActionEvent actionEvent)
 711         {
 712           all_actionPerformed();
 713         }
 714       });
 715
 716       this.setBorder(new TitledBorder(MessageManager
 717               .getString("label.structures_filter")));
 718       JvSwingUtils.jvInitComponent(this);
 719
 720       this.add(all);
 721       this.add(alphaHelix);
 722       this.add(betaStrand);
 723       this.add(turn);
 724     }
 725
 726     public void alphaHelix_actionPerformed()
 727     {
 728       updateSelectAllState();
 729       aColChooser.setCurrentStructureFilterPanel(this);
 730       aColChooser.updateView();
 731     }
 732
 733     public void betaStrand_actionPerformed()
 734     {
 735       updateSelectAllState();
 736       aColChooser.setCurrentStructureFilterPanel(this);
 737       aColChooser.updateView();
 738     }
 739
 740     public void turn_actionPerformed()
 741     {
 742       updateSelectAllState();
 743       aColChooser.setCurrentStructureFilterPanel(this);
 744       aColChooser.updateView();
 745     }
 746
 747     public void all_actionPerformed()
 748     {
 749       if (all.isSelected())
 750       {
 751         alphaHelix.setSelected(true);
 752         betaStrand.setSelected(true);
 753         turn.setSelected(true);
 754       }
 755       else
 756       {
 757         alphaHelix.setSelected(false);
 758         betaStrand.setSelected(false);
 759         turn.setSelected(false);
 760       }
 761       aColChooser.setCurrentStructureFilterPanel(this);
 762       aColChooser.updateView();
 763     }
 764
 765     public void updateSelectAllState()
 766     {
 767       if (alphaHelix.isSelected() && betaStrand.isSelected()
 768               && turn.isSelected())
 769       {
 770         all.setSelected(true);
 771       }
 772       else
 773       {
 774         all.setSelected(false);
 775       }
 776     }
 777
 778     public void syncState()
 779     {
 780       StructureFilterPanel sfp = aColChooser
 781               .getCurrentStructureFilterPanel();
 782       if (sfp != null)
 783       {
 784         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 785         betaStrand.setSelected(sfp.betaStrand.isSelected());
 786         turn.setSelected(sfp.turn.isSelected());
 787         if (sfp.all.isSelected())
 788         {
 789           all.setSelected(true);
 790           alphaHelix.setSelected(true);
 791           betaStrand.setSelected(true);
 792           turn.setSelected(true);
 793         }
 794       }
 795
 796     }
 797   }
 798
 799   public class SearchPanel extends JPanel
 800   {
 801     private AnnotationColumnChooser aColChooser;
 802
 803     private JCheckBox displayName = new JCheckBox();
 804
 805     private JCheckBox description = new JCheckBox();
 806
 807     private JTextField searchBox = new JTextField(10);
 808
 809     public SearchPanel(AnnotationColumnChooser aColChooser)
 810     {
 811
 812       this.aColChooser = aColChooser;
 813       JvSwingUtils.jvInitComponent(this);
 814       this.setBorder(new TitledBorder(MessageManager
 815               .getString("label.search_filter")));
 816
 817       JvSwingUtils.jvInitComponent(searchBox);
 818       searchBox.setToolTipText(MessageManager
 819               .getString("info.enter_search_text_here"));
 820       searchBox.getDocument().addDocumentListener(
 821               new DocumentListener()
 822               {
 823                 @Override
 824                 public void insertUpdate(DocumentEvent e)
 825                 {
 826                   searchStringAction();
 827                 }
 828
 829                 @Override
 830                 public void removeUpdate(DocumentEvent e)
 831                 {
 832                   searchStringAction();
 833                 }
 834
 835                 @Override
 836                 public void changedUpdate(DocumentEvent e)
 837                 {
 838                   searchStringAction();
 839                 }
 840               });
 841
 842       JvSwingUtils.jvInitComponent(displayName, "label.label");
 843       displayName.setEnabled(false);
 844       displayName.addActionListener(new ActionListener()
 845       {
 846         @Override
 847         public void actionPerformed(ActionEvent actionEvent)
 848         {
 849           displayNameCheckboxAction();
 850         }
 851       });
 852
 853       JvSwingUtils.jvInitComponent(description, "label.description");
 854       description.setEnabled(false);
 855       description.addActionListener(new ActionListener()
 856       {
 857         @Override
 858         public void actionPerformed(ActionEvent actionEvent)
 859         {
 860           discriptionCheckboxAction();
 861         }
 862       });
 863
 864       syncState();
 865       this.add(searchBox);
 866       this.add(displayName);
 867       this.add(description);
 868     }
 869
 870     public void displayNameCheckboxAction()
 871     {
 872       aColChooser.setCurrentSearchPanel(this);
 873       aColChooser.updateView();
 874     }
 875
 876     public void discriptionCheckboxAction()
 877     {
 878       aColChooser.setCurrentSearchPanel(this);
 879       aColChooser.updateView();
 880     }
 881
 882     public void searchStringAction()
 883     {
 884       aColChooser.setCurrentSearchPanel(this);
 885       aColChooser.updateView();
 886       updateSearchPanelToolTips();
 887     }
 888
 889     public void syncState()
 890     {
 891       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 892       if (sp != null)
 893       {
 894         description.setEnabled(sp.description.isEnabled());
 895         description.setSelected(sp.description.isSelected());
 896
 897         displayName.setEnabled(sp.displayName.isEnabled());
 898         displayName.setSelected(sp.displayName.isSelected());
 899
 900         searchBox.setText(sp.searchBox.getText());
 901       }
 902       updateSearchPanelToolTips();
 903     }
 904
 905     public void updateSearchPanelToolTips()
 906     {
 907       String defaultTtip = MessageManager
 908               .getString("info.enter_search_text_to_enable");
 909       String labelTtip = MessageManager
 910 .formatMessage(
 911               "info.search_in_annotation_label", annotations
 912                       .getSelectedItem().toString());
 913       String descTtip = MessageManager
 914 .formatMessage(
 915               "info.search_in_annotation_description", annotations
 916                       .getSelectedItem().toString());
 917       displayName.setToolTipText(displayName.isEnabled() ? labelTtip : defaultTtip);
 918       description.setToolTipText(description.isEnabled() ? descTtip
 919               : defaultTtip);
 920     }
 921   }
 922
 923 }