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
  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();
 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();
 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();
 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();
 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 thresh = getThreshold().getSelectedItem().toString();
 292     if (thresh.equalsIgnoreCase("No Threshold"))
 293     {
 294       thresholdValue.setToolTipText(defaultTtip);
 295       slider.setToolTipText(defaultTtip);
 296     }
 297   }
 298
 299   @Override
 300   public void reset()
 301   {
 302     if (this.getOldColumnSelection() != null)
 303     {
 304       av.getColumnSelection().clear();
 305
 306       if (av.getAnnotationColumnSelectionState() != null)
 307       {
 308         ColumnSelection oldSelection = av
 309                 .getAnnotationColumnSelectionState()
 310                 .getOldColumnSelection();
 311         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 312                 && !oldSelection.getHiddenColumns().isEmpty())
 313         {
 314           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 315                   .iterator(); itr.hasNext();)
 316           {
 317             int positions[] = itr.next();
 318             av.hideColumns(positions[0], positions[1]);
 319           }
 320         }
 321         av.setColumnSelection(oldSelection);
 322       }
 323       ap.paintAlignment(true);
 324     }
 325
 326   }
 327
 328   @Override
 329   public void valueChanged(boolean updateAllAnnotation)
 330   {
 331     if (slider.isEnabled())
 332     {
 333       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 334       updateView();
 335       propagateSeqAssociatedThreshold(updateAllAnnotation,
 336               getCurrentAnnotation());
 337       ap.paintAlignment(false);
 338     }
 339   }
 340
 341   public JComboBox<String> getThreshold()
 342   {
 343     return threshold;
 344   }
 345
 346   public void setThreshold(JComboBox<String> threshold)
 347   {
 348     this.threshold = threshold;
 349   }
 350
 351   public JComboBox<String> getAnnotations()
 352   {
 353     return annotations;
 354   }
 355
 356   public void setAnnotations(JComboBox<String> annotations)
 357   {
 358     this.annotations = annotations;
 359   }
 360
 361   @Override
 362   public void updateView()
 363   {
 364     // Check if combobox is still adjusting
 365     if (adjusting)
 366     {
 367       return;
 368     }
 369
 370     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 371
 372     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 373             .getSelectedIndex()]]);
 374
 375     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 376             .getSelectedIndex());
 377
 378     slider.setEnabled(true);
 379     thresholdValue.setEnabled(true);
 380
 381     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 382     {
 383       slider.setEnabled(false);
 384       thresholdValue.setEnabled(false);
 385       thresholdValue.setText("");
 386       // build filter params
 387     }
 388     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 389     {
 390       if (getCurrentAnnotation().threshold == null)
 391       {
 392         getCurrentAnnotation()
 393                 .setThreshold(
 394                         new jalview.datamodel.GraphLine(
 395                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 396                                 "Threshold", Color.black));
 397       }
 398
 399       adjusting = true;
 400       float range = getCurrentAnnotation().graphMax * 1000
 401               - getCurrentAnnotation().graphMin * 1000;
 402
 403       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 404       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 405       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 406       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 407       slider.setMajorTickSpacing((int) (range / 10f));
 408       slider.setEnabled(true);
 409       thresholdValue.setEnabled(true);
 410       adjusting = false;
 411
 412       // build filter params
 413       filterParams
 414               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 415       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 416       {
 417         filterParams
 418                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 419
 420         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 421         {
 422           filterParams
 423                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 424         }
 425         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 426         {
 427           filterParams
 428                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 429         }
 430       }
 431     }
 432
 433     updateThresholdPanelToolTip();
 434     if (currentStructureFilterPanel != null)
 435     {
 436       if (currentStructureFilterPanel.alphaHelix.isSelected())
 437       {
 438         filterParams.setFilterAlphaHelix(true);
 439       }
 440       if (currentStructureFilterPanel.betaStrand.isSelected())
 441       {
 442         filterParams.setFilterBetaSheet(true);
 443       }
 444       if (currentStructureFilterPanel.turn.isSelected())
 445       {
 446         filterParams.setFilterTurn(true);
 447       }
 448     }
 449
 450     if (currentSearchPanel != null)
 451     {
 452
 453       if (!currentSearchPanel.searchBox.getText().isEmpty())
 454       {
 455         currentSearchPanel.description.setEnabled(true);
 456         currentSearchPanel.displayName.setEnabled(true);
 457         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 458         if (currentSearchPanel.displayName.isSelected())
 459         {
 460           filterParams
 461                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 462         }
 463         if (currentSearchPanel.description.isSelected())
 464         {
 465           filterParams
 466                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 467         }
 468       }
 469       else
 470       {
 471         currentSearchPanel.description.setEnabled(false);
 472         currentSearchPanel.displayName.setEnabled(false);
 473       }
 474     }
 475
 476     av.getColumnSelection().filterAnnotations(
 477             getCurrentAnnotation().annotations, filterParams);
 478
 479     av.showAllHiddenColumns();
 480     if (getActionOption() == ACTION_OPTION_HIDE)
 481     {
 482       av.hideSelectedColumns();
 483     }
 484
 485     filterParams = null;
 486     av.setAnnotationColumnSelectionState(this);
 487     ap.paintAlignment(true);
 488   }
 489
 490   public ColumnSelection getOldColumnSelection()
 491   {
 492     return oldColumnSelection;
 493   }
 494
 495   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 496   {
 497     if (currentColumnSelection != null)
 498     {
 499       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 500     }
 501   }
 502
 503   public FurtherActionPanel getCurrentFutherActionPanel()
 504   {
 505     return currentFurtherActionPanel;
 506   }
 507
 508   public void setCurrentFutherActionPanel(
 509           FurtherActionPanel currentFutherActionPanel)
 510   {
 511     this.currentFurtherActionPanel = currentFutherActionPanel;
 512   }
 513
 514   public SearchPanel getCurrentSearchPanel()
 515   {
 516     return currentSearchPanel;
 517   }
 518
 519   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 520   {
 521     this.currentSearchPanel = currentSearchPanel;
 522   }
 523
 524   public int getActionOption()
 525   {
 526     return actionOption;
 527   }
 528
 529   public void setActionOption(int actionOption)
 530   {
 531     this.actionOption = actionOption;
 532   }
 533
 534   public StructureFilterPanel getCurrentStructureFilterPanel()
 535   {
 536     return currentStructureFilterPanel;
 537   }
 538
 539   public void setCurrentStructureFilterPanel(
 540           StructureFilterPanel currentStructureFilterPanel)
 541   {
 542     this.currentStructureFilterPanel = currentStructureFilterPanel;
 543   }
 544
 545   public void select_action(ActionEvent actionEvent)
 546   {
 547     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 548     if (radioButton.isSelected())
 549     {
 550       setActionOption(ACTION_OPTION_SELECT);
 551       updateView();
 552     }
 553   }
 554
 555   public void hide_action(ActionEvent actionEvent)
 556   {
 557     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 558     if (radioButton.isSelected())
 559     {
 560       setActionOption(ACTION_OPTION_HIDE);
 561       updateView();
 562     }
 563   }
 564
 565   @Override
 566   public void itemStateChanged(ItemEvent e)
 567   {
 568     selectedAnnotationChanged();
 569   }
 570
 571   public void selectedAnnotationChanged()
 572   {
 573     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 574     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 575             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 576     {
 577       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 578     }
 579
 580     gSearchPanel.syncState();
 581     gFurtherActionPanel.syncState();
 582     gStructureFilterPanel.syncState();
 583
 584     ngSearchPanel.syncState();
 585     ngFurtherActionPanel.syncState();
 586     ngStructureFilterPanel.syncState();
 587
 588     switchableViewsLayout.show(switchableViewsPanel, currentView);
 589     updateView();
 590   }
 591
 592   public class FurtherActionPanel extends JPanel
 593   {
 594     private AnnotationColumnChooser aColChooser;
 595
 596     private JRadioButton hideOption = new JRadioButton();
 597
 598     private JRadioButton selectOption = new JRadioButton();
 599
 600     private ButtonGroup optionsGroup = new ButtonGroup();
 601
 602     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 603     {
 604       this.aColChooser = aColChooser;
 605       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 606       selectOption.addActionListener(new ActionListener()
 607       {
 608         @Override
 609         public void actionPerformed(ActionEvent actionEvent)
 610         {
 611           selectRadioAction(actionEvent);
 612         }
 613       });
 614
 615       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 616       hideOption.addActionListener(new ActionListener()
 617       {
 618         @Override
 619         public void actionPerformed(ActionEvent actionEvent)
 620         {
 621           hideRadioAction(actionEvent);
 622         }
 623       });
 624
 625       optionsGroup.add(selectOption);
 626       optionsGroup.add(hideOption);
 627       optionsGroup.setSelected(selectOption.getModel(), true);
 628
 629       JvSwingUtils.jvInitComponent(this);
 630       syncState();
 631
 632       this.add(selectOption);
 633       this.add(hideOption);
 634     }
 635
 636     public void selectRadioAction(ActionEvent actionEvent)
 637     {
 638       aColChooser.setCurrentFutherActionPanel(this);
 639       aColChooser.select_action(actionEvent);
 640     }
 641
 642     public void hideRadioAction(ActionEvent actionEvent)
 643     {
 644       aColChooser.setCurrentFutherActionPanel(this);
 645       aColChooser.hide_action(actionEvent);
 646     }
 647
 648     public void syncState()
 649     {
 650       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 651       {
 652         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 653       }
 654       else
 655       {
 656         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 657       }
 658     }
 659   }
 660
 661   public class StructureFilterPanel extends JPanel
 662   {
 663     private AnnotationColumnChooser aColChooser;
 664
 665     private JCheckBox alphaHelix = new JCheckBox();
 666
 667     private JCheckBox betaStrand = new JCheckBox();
 668
 669     private JCheckBox turn = new JCheckBox();
 670
 671     private JCheckBox all = new JCheckBox();
 672
 673     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 674     {
 675       this.aColChooser = aColChooser;
 676
 677       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 678       alphaHelix.addActionListener(new ActionListener()
 679       {
 680         @Override
 681         public void actionPerformed(ActionEvent actionEvent)
 682         {
 683           alphaHelix_actionPerformed();
 684         }
 685       });
 686
 687       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 688       betaStrand.addActionListener(new ActionListener()
 689       {
 690         @Override
 691         public void actionPerformed(ActionEvent actionEvent)
 692         {
 693           betaStrand_actionPerformed();
 694         }
 695       });
 696
 697       JvSwingUtils.jvInitComponent(turn, "label.turn");
 698       turn.addActionListener(new ActionListener()
 699       {
 700         @Override
 701         public void actionPerformed(ActionEvent actionEvent)
 702         {
 703           turn_actionPerformed();
 704         }
 705       });
 706
 707       JvSwingUtils.jvInitComponent(all, "label.select_all");
 708       all.addActionListener(new ActionListener()
 709       {
 710         @Override
 711         public void actionPerformed(ActionEvent actionEvent)
 712         {
 713           all_actionPerformed();
 714         }
 715       });
 716
 717       this.setBorder(new TitledBorder(MessageManager
 718               .getString("label.structures_filter")));
 719       JvSwingUtils.jvInitComponent(this);
 720
 721       this.add(all);
 722       this.add(alphaHelix);
 723       this.add(betaStrand);
 724       this.add(turn);
 725     }
 726
 727     public void alphaHelix_actionPerformed()
 728     {
 729       updateSelectAllState();
 730       aColChooser.setCurrentStructureFilterPanel(this);
 731       aColChooser.updateView();
 732     }
 733
 734     public void betaStrand_actionPerformed()
 735     {
 736       updateSelectAllState();
 737       aColChooser.setCurrentStructureFilterPanel(this);
 738       aColChooser.updateView();
 739     }
 740
 741     public void turn_actionPerformed()
 742     {
 743       updateSelectAllState();
 744       aColChooser.setCurrentStructureFilterPanel(this);
 745       aColChooser.updateView();
 746     }
 747
 748     public void all_actionPerformed()
 749     {
 750       if (all.isSelected())
 751       {
 752         alphaHelix.setSelected(true);
 753         betaStrand.setSelected(true);
 754         turn.setSelected(true);
 755       }
 756       else
 757       {
 758         alphaHelix.setSelected(false);
 759         betaStrand.setSelected(false);
 760         turn.setSelected(false);
 761       }
 762       aColChooser.setCurrentStructureFilterPanel(this);
 763       aColChooser.updateView();
 764     }
 765
 766     public void updateSelectAllState()
 767     {
 768       if (alphaHelix.isSelected() && betaStrand.isSelected()
 769               && turn.isSelected())
 770       {
 771         all.setSelected(true);
 772       }
 773       else
 774       {
 775         all.setSelected(false);
 776       }
 777     }
 778
 779     public void syncState()
 780     {
 781       StructureFilterPanel sfp = aColChooser
 782               .getCurrentStructureFilterPanel();
 783       if (sfp != null)
 784       {
 785         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 786         betaStrand.setSelected(sfp.betaStrand.isSelected());
 787         turn.setSelected(sfp.turn.isSelected());
 788         if (sfp.all.isSelected())
 789         {
 790           all.setSelected(true);
 791           alphaHelix.setSelected(true);
 792           betaStrand.setSelected(true);
 793           turn.setSelected(true);
 794         }
 795       }
 796
 797     }
 798   }
 799
 800   public class SearchPanel extends JPanel
 801   {
 802     private AnnotationColumnChooser aColChooser;
 803
 804     private JCheckBox displayName = new JCheckBox();
 805
 806     private JCheckBox description = new JCheckBox();
 807
 808     private JTextField searchBox = new JTextField(10);
 809
 810     public SearchPanel(AnnotationColumnChooser aColChooser)
 811     {
 812
 813       this.aColChooser = aColChooser;
 814       JvSwingUtils.jvInitComponent(this);
 815       this.setBorder(new TitledBorder(MessageManager
 816               .getString("label.search_filter")));
 817
 818       JvSwingUtils.jvInitComponent(searchBox);
 819       searchBox.setToolTipText(MessageManager
 820               .getString("info.enter_search_text_here"));
 821       searchBox.getDocument().addDocumentListener(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.formatMessage(
 910               "info.search_in_annotation_label", annotations
 911                       .getSelectedItem().toString());
 912       String descTtip = MessageManager.formatMessage(
 913               "info.search_in_annotation_description", annotations
 914                       .getSelectedItem().toString());
 915       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 916               : defaultTtip);
 917       description.setToolTipText(description.isEnabled() ? descTtip
 918               : defaultTtip);
 919     }
 920   }
 921
 922 }