src/jalview/gui/AnnotationColumnChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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.Dimension;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.ItemEvent;
  37 import java.awt.event.ItemListener;
  38 import java.util.Iterator;
  39
  40 import javax.swing.ButtonGroup;
  41 import javax.swing.JCheckBox;
  42 import javax.swing.JComboBox;
  43 import javax.swing.JInternalFrame;
  44 import javax.swing.JLayeredPane;
  45 import javax.swing.JPanel;
  46 import javax.swing.JRadioButton;
  47 import javax.swing.JTextField;
  48 import javax.swing.border.TitledBorder;
  49 import javax.swing.event.DocumentEvent;
  50 import javax.swing.event.DocumentListener;
  51
  52 import net.miginfocom.swing.MigLayout;
  53
  54 @SuppressWarnings("serial")
  55 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  56         ItemListener
  57 {
  58
  59   private JComboBox<String> annotations;
  60
  61   private JPanel actionPanel = new JPanel();
  62
  63   private JPanel thresholdPanel = new JPanel();
  64
  65   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  66
  67   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  68           .getLayout());
  69
  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
 299   public void reset()
 300   {
 301     if (this.getOldColumnSelection() != null)
 302     {
 303       av.getColumnSelection().clear();
 304
 305       if (av.getAnnotationColumnSelectionState() != null)
 306       {
 307         ColumnSelection oldSelection = av
 308                 .getAnnotationColumnSelectionState()
 309                 .getOldColumnSelection();
 310         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 311                 && !oldSelection.getHiddenColumns().isEmpty())
 312         {
 313           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 314                   .iterator(); itr.hasNext();)
 315           {
 316             int positions[] = itr.next();
 317             av.hideColumns(positions[0], positions[1]);
 318           }
 319         }
 320         av.setColumnSelection(oldSelection);
 321       }
 322       ap.paintAlignment(true);
 323     }
 324
 325   }
 326
 327   public void valueChanged(boolean updateAllAnnotation)
 328   {
 329     if (slider.isEnabled())
 330     {
 331       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 332       updateView();
 333       propagateSeqAssociatedThreshold(updateAllAnnotation,
 334               getCurrentAnnotation());
 335       ap.paintAlignment(false);
 336     }
 337   }
 338
 339   public JComboBox<String> getThreshold()
 340   {
 341     return threshold;
 342   }
 343
 344   public void setThreshold(JComboBox<String> threshold)
 345   {
 346     this.threshold = threshold;
 347   }
 348
 349   public JComboBox<String> getAnnotations()
 350   {
 351     return annotations;
 352   }
 353
 354   public void setAnnotations(JComboBox<String> annotations)
 355   {
 356     this.annotations = annotations;
 357   }
 358
 359   @Override
 360   public void updateView()
 361   {
 362     // Check if combobox is still adjusting
 363     if (adjusting)
 364     {
 365       return;
 366     }
 367
 368     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 369
 370     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 371             .getSelectedIndex()]]);
 372
 373     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 374             .getSelectedIndex());
 375
 376     slider.setEnabled(true);
 377     thresholdValue.setEnabled(true);
 378
 379     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 380     {
 381       slider.setEnabled(false);
 382       thresholdValue.setEnabled(false);
 383       thresholdValue.setText("");
 384       // build filter params
 385     }
 386     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 387     {
 388       if (getCurrentAnnotation().threshold == null)
 389       {
 390         getCurrentAnnotation()
 391                 .setThreshold(
 392                         new jalview.datamodel.GraphLine(
 393                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 394                                 "Threshold", Color.black));
 395       }
 396
 397       adjusting = true;
 398       float range = getCurrentAnnotation().graphMax * 1000
 399               - getCurrentAnnotation().graphMin * 1000;
 400
 401       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 402       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 403       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 404       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 405       slider.setMajorTickSpacing((int) (range / 10f));
 406       slider.setEnabled(true);
 407       thresholdValue.setEnabled(true);
 408       adjusting = false;
 409
 410       // build filter params
 411       filterParams
 412               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 413       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 414       {
 415         filterParams
 416                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 417
 418         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 419         {
 420           filterParams
 421                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 422         }
 423         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 424         {
 425           filterParams
 426                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 427         }
 428       }
 429     }
 430
 431     updateThresholdPanelToolTip();
 432     if (currentStructureFilterPanel != null)
 433     {
 434       if (currentStructureFilterPanel.alphaHelix.isSelected())
 435       {
 436         filterParams.setFilterAlphaHelix(true);
 437       }
 438       if (currentStructureFilterPanel.betaStrand.isSelected())
 439       {
 440         filterParams.setFilterBetaSheet(true);
 441       }
 442       if (currentStructureFilterPanel.turn.isSelected())
 443       {
 444         filterParams.setFilterTurn(true);
 445       }
 446     }
 447
 448     if (currentSearchPanel != null)
 449     {
 450
 451       if (!currentSearchPanel.searchBox.getText().isEmpty())
 452       {
 453         currentSearchPanel.description.setEnabled(true);
 454         currentSearchPanel.displayName.setEnabled(true);
 455         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 456         if (currentSearchPanel.displayName.isSelected())
 457         {
 458           filterParams
 459                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 460         }
 461         if (currentSearchPanel.description.isSelected())
 462         {
 463           filterParams
 464                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 465         }
 466       }
 467       else
 468       {
 469         currentSearchPanel.description.setEnabled(false);
 470         currentSearchPanel.displayName.setEnabled(false);
 471       }
 472     }
 473
 474     av.getColumnSelection().filterAnnotations(
 475             getCurrentAnnotation().annotations, filterParams);
 476
 477     av.showAllHiddenColumns();
 478     if (getActionOption() == ACTION_OPTION_HIDE)
 479     {
 480       av.hideSelectedColumns();
 481     }
 482
 483     filterParams = null;
 484     av.setAnnotationColumnSelectionState(this);
 485     ap.paintAlignment(true);
 486   }
 487
 488   public ColumnSelection getOldColumnSelection()
 489   {
 490     return oldColumnSelection;
 491   }
 492
 493   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 494   {
 495     if (currentColumnSelection != null)
 496     {
 497       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 498     }
 499   }
 500
 501   public FurtherActionPanel getCurrentFutherActionPanel()
 502   {
 503     return currentFurtherActionPanel;
 504   }
 505
 506   public void setCurrentFutherActionPanel(
 507           FurtherActionPanel currentFutherActionPanel)
 508   {
 509     this.currentFurtherActionPanel = currentFutherActionPanel;
 510   }
 511
 512   public SearchPanel getCurrentSearchPanel()
 513   {
 514     return currentSearchPanel;
 515   }
 516
 517   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 518   {
 519     this.currentSearchPanel = currentSearchPanel;
 520   }
 521
 522   public int getActionOption()
 523   {
 524     return actionOption;
 525   }
 526
 527   public void setActionOption(int actionOption)
 528   {
 529     this.actionOption = actionOption;
 530   }
 531
 532   public StructureFilterPanel getCurrentStructureFilterPanel()
 533   {
 534     return currentStructureFilterPanel;
 535   }
 536
 537   public void setCurrentStructureFilterPanel(
 538           StructureFilterPanel currentStructureFilterPanel)
 539   {
 540     this.currentStructureFilterPanel = currentStructureFilterPanel;
 541   }
 542
 543   public void select_action(ActionEvent actionEvent)
 544   {
 545     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 546     if (radioButton.isSelected())
 547     {
 548       setActionOption(ACTION_OPTION_SELECT);
 549       updateView();
 550     }
 551   }
 552
 553   public void hide_action(ActionEvent actionEvent)
 554   {
 555     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 556     if (radioButton.isSelected())
 557     {
 558       setActionOption(ACTION_OPTION_HIDE);
 559       updateView();
 560     }
 561   }
 562
 563   @Override
 564   public void itemStateChanged(ItemEvent e)
 565   {
 566     selectedAnnotationChanged();
 567   }
 568
 569   public void selectedAnnotationChanged()
 570   {
 571     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 572     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 573             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 574     {
 575       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 576     }
 577
 578     gSearchPanel.syncState();
 579     gFurtherActionPanel.syncState();
 580     gStructureFilterPanel.syncState();
 581
 582     ngSearchPanel.syncState();
 583     ngFurtherActionPanel.syncState();
 584     ngStructureFilterPanel.syncState();
 585
 586     switchableViewsLayout.show(switchableViewsPanel, currentView);
 587     updateView();
 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(), true);
 651       }
 652       else
 653       {
 654         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 655       }
 656     }
 657   }
 658
 659   public class StructureFilterPanel extends JPanel
 660   {
 661     private AnnotationColumnChooser aColChooser;
 662
 663     private JCheckBox alphaHelix = new JCheckBox();
 664
 665     private JCheckBox betaStrand = new JCheckBox();
 666
 667     private JCheckBox turn = new JCheckBox();
 668
 669     private JCheckBox all = new JCheckBox();
 670
 671     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 672     {
 673       this.aColChooser = aColChooser;
 674
 675       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 676       alphaHelix.addActionListener(new ActionListener()
 677       {
 678         @Override
 679         public void actionPerformed(ActionEvent actionEvent)
 680         {
 681           alphaHelix_actionPerformed();
 682         }
 683       });
 684
 685       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 686       betaStrand.addActionListener(new ActionListener()
 687       {
 688         @Override
 689         public void actionPerformed(ActionEvent actionEvent)
 690         {
 691           betaStrand_actionPerformed();
 692         }
 693       });
 694
 695       JvSwingUtils.jvInitComponent(turn, "label.turn");
 696       turn.addActionListener(new ActionListener()
 697       {
 698         @Override
 699         public void actionPerformed(ActionEvent actionEvent)
 700         {
 701           turn_actionPerformed();
 702         }
 703       });
 704
 705       JvSwingUtils.jvInitComponent(all, "label.select_all");
 706       all.addActionListener(new ActionListener()
 707       {
 708         @Override
 709         public void actionPerformed(ActionEvent actionEvent)
 710         {
 711           all_actionPerformed();
 712         }
 713       });
 714
 715       this.setBorder(new TitledBorder(MessageManager
 716               .getString("label.structures_filter")));
 717       JvSwingUtils.jvInitComponent(this);
 718
 719       this.add(all);
 720       this.add(alphaHelix);
 721       this.add(betaStrand);
 722       this.add(turn);
 723     }
 724
 725     public void alphaHelix_actionPerformed()
 726     {
 727       updateSelectAllState();
 728       aColChooser.setCurrentStructureFilterPanel(this);
 729       aColChooser.updateView();
 730     }
 731
 732     public void betaStrand_actionPerformed()
 733     {
 734       updateSelectAllState();
 735       aColChooser.setCurrentStructureFilterPanel(this);
 736       aColChooser.updateView();
 737     }
 738
 739     public void turn_actionPerformed()
 740     {
 741       updateSelectAllState();
 742       aColChooser.setCurrentStructureFilterPanel(this);
 743       aColChooser.updateView();
 744     }
 745
 746     public void all_actionPerformed()
 747     {
 748       if (all.isSelected())
 749       {
 750         alphaHelix.setSelected(true);
 751         betaStrand.setSelected(true);
 752         turn.setSelected(true);
 753       }
 754       else
 755       {
 756         alphaHelix.setSelected(false);
 757         betaStrand.setSelected(false);
 758         turn.setSelected(false);
 759       }
 760       aColChooser.setCurrentStructureFilterPanel(this);
 761       aColChooser.updateView();
 762     }
 763
 764     public void updateSelectAllState()
 765     {
 766       if (alphaHelix.isSelected() && betaStrand.isSelected()
 767               && turn.isSelected())
 768       {
 769         all.setSelected(true);
 770       }
 771       else
 772       {
 773         all.setSelected(false);
 774       }
 775     }
 776
 777     public void syncState()
 778     {
 779       StructureFilterPanel sfp = aColChooser
 780               .getCurrentStructureFilterPanel();
 781       if (sfp != null)
 782       {
 783         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 784         betaStrand.setSelected(sfp.betaStrand.isSelected());
 785         turn.setSelected(sfp.turn.isSelected());
 786         if (sfp.all.isSelected())
 787         {
 788           all.setSelected(true);
 789           alphaHelix.setSelected(true);
 790           betaStrand.setSelected(true);
 791           turn.setSelected(true);
 792         }
 793       }
 794
 795     }
 796   }
 797
 798   public class SearchPanel extends JPanel
 799   {
 800     private AnnotationColumnChooser aColChooser;
 801
 802     private JCheckBox displayName = new JCheckBox();
 803
 804     private JCheckBox description = new JCheckBox();
 805
 806     private JTextField searchBox = new JTextField(10);
 807
 808     public SearchPanel(AnnotationColumnChooser aColChooser)
 809     {
 810
 811       this.aColChooser = aColChooser;
 812       JvSwingUtils.jvInitComponent(this);
 813       this.setBorder(new TitledBorder(MessageManager
 814               .getString("label.search_filter")));
 815
 816       JvSwingUtils.jvInitComponent(searchBox);
 817       searchBox.setToolTipText(MessageManager
 818               .getString("info.enter_search_text_here"));
 819       searchBox.getDocument().addDocumentListener(new DocumentListener()
 820       {
 821         @Override
 822         public void insertUpdate(DocumentEvent e)
 823         {
 824           searchStringAction();
 825         }
 826
 827         @Override
 828         public void removeUpdate(DocumentEvent e)
 829         {
 830           searchStringAction();
 831         }
 832
 833         @Override
 834         public void changedUpdate(DocumentEvent e)
 835         {
 836           searchStringAction();
 837         }
 838       });
 839
 840       JvSwingUtils.jvInitComponent(displayName, "label.label");
 841       displayName.setEnabled(false);
 842       displayName.addActionListener(new ActionListener()
 843       {
 844         @Override
 845         public void actionPerformed(ActionEvent actionEvent)
 846         {
 847           displayNameCheckboxAction();
 848         }
 849       });
 850
 851       JvSwingUtils.jvInitComponent(description, "label.description");
 852       description.setEnabled(false);
 853       description.addActionListener(new ActionListener()
 854       {
 855         @Override
 856         public void actionPerformed(ActionEvent actionEvent)
 857         {
 858           discriptionCheckboxAction();
 859         }
 860       });
 861
 862       syncState();
 863       this.add(searchBox);
 864       this.add(displayName);
 865       this.add(description);
 866     }
 867
 868     public void displayNameCheckboxAction()
 869     {
 870       aColChooser.setCurrentSearchPanel(this);
 871       aColChooser.updateView();
 872     }
 873
 874     public void discriptionCheckboxAction()
 875     {
 876       aColChooser.setCurrentSearchPanel(this);
 877       aColChooser.updateView();
 878     }
 879
 880     public void searchStringAction()
 881     {
 882       aColChooser.setCurrentSearchPanel(this);
 883       aColChooser.updateView();
 884       updateSearchPanelToolTips();
 885     }
 886
 887     public void syncState()
 888     {
 889       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 890       if (sp != null)
 891       {
 892         description.setEnabled(sp.description.isEnabled());
 893         description.setSelected(sp.description.isSelected());
 894
 895         displayName.setEnabled(sp.displayName.isEnabled());
 896         displayName.setSelected(sp.displayName.isSelected());
 897
 898         searchBox.setText(sp.searchBox.getText());
 899       }
 900       updateSearchPanelToolTips();
 901     }
 902
 903     public void updateSearchPanelToolTips()
 904     {
 905       String defaultTtip = MessageManager
 906               .getString("info.enter_search_text_to_enable");
 907       String labelTtip = MessageManager.formatMessage(
 908               "info.search_in_annotation_label", annotations
 909                       .getSelectedItem().toString());
 910       String descTtip = MessageManager.formatMessage(
 911               "info.search_in_annotation_description", annotations
 912                       .getSelectedItem().toString());
 913       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 914               : defaultTtip);
 915       description.setToolTipText(description.isEnabled() ? descTtip
 916               : defaultTtip);
 917     }
 918   }
 919
 920 }