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