src/jalview/gui/AnnotationColumnChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21
  22 package jalview.gui;
  23
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.datamodel.ColumnSelection;
  26 import jalview.schemes.AnnotationColourGradient;
  27 import jalview.util.MessageManager;
  28 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.CardLayout;
  32 import java.awt.Color;
  33 import java.awt.event.ActionEvent;
  34 import java.awt.event.ActionListener;
  35 import java.awt.event.ItemEvent;
  36 import java.awt.event.ItemListener;
  37 import java.util.Iterator;
  38
  39 import javax.swing.ButtonGroup;
  40 import javax.swing.JCheckBox;
  41 import javax.swing.JComboBox;
  42 import javax.swing.JInternalFrame;
  43 import javax.swing.JLayeredPane;
  44 import javax.swing.JPanel;
  45 import javax.swing.JRadioButton;
  46 import javax.swing.JTextField;
  47 import javax.swing.border.TitledBorder;
  48 import javax.swing.event.DocumentEvent;
  49 import javax.swing.event.DocumentListener;
  50
  51 import net.miginfocom.swing.MigLayout;
  52
  53 @SuppressWarnings("serial")
  54 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  55         ItemListener
  56 {
  57   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  58
  59   private JPanel annotationComboBoxPanel = new JPanel();
  60
  61   private StructureFilterPanel gStructureFilterPanel;
  62
  63   private StructureFilterPanel ngStructureFilterPanel;
  64
  65   private StructureFilterPanel currentStructureFilterPanel;
  66
  67   private SearchPanel currentSearchPanel;
  68
  69   private SearchPanel gSearchPanel;
  70
  71   private SearchPanel ngSearchPanel;
  72
  73   private FurtherActionPanel currentFurtherActionPanel;
  74
  75   private FurtherActionPanel gFurtherActionPanel;
  76
  77   private FurtherActionPanel ngFurtherActionPanel;
  78
  79   public static final int ACTION_OPTION_SELECT = 1;
  80
  81   public static int ACTION_OPTION_HIDE = 2;
  82
  83   public static String NO_GRAPH_VIEW = "0";
  84
  85   public static String GRAPH_VIEW = "1";
  86
  87   private int actionOption = ACTION_OPTION_SELECT;
  88
  89   private ColumnSelection oldColumnSelection;
  90
  91   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  92   {
  93     super(av, ap);
  94     frame = new JInternalFrame();
  95     frame.setContentPane(this);
  96     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  97     Desktop.addInternalFrame(frame,
  98             MessageManager.getString("label.select_by_annotation"), 520,
  99             215);
 100
 101     addSliderChangeListener();
 102     addSliderMouseListeners();
 103
 104     if (av.getAlignment().getAlignmentAnnotation() == null)
 105     {
 106       return;
 107     }
 108     setOldColumnSelection(av.getColumnSelection());
 109     adjusting = true;
 110
 111     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 112     populateThresholdComboBox(threshold);
 113
 114     // restore Object state from the previous session if one exists
 115     if (av.getAnnotationColumnSelectionState() != null)
 116     {
 117       currentSearchPanel = av.getAnnotationColumnSelectionState()
 118               .getCurrentSearchPanel();
 119       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 120               .getCurrentStructureFilterPanel();
 121       annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
 122               .getAnnotations().getSelectedIndex());
 123       threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
 124               .getThreshold().getSelectedIndex());
 125       actionOption = av.getAnnotationColumnSelectionState()
 126               .getActionOption();
 127     }
 128
 129     try
 130     {
 131       jbInit();
 132     } catch (Exception ex)
 133     {
 134     }
 135     adjusting = false;
 136
 137     updateView();
 138     frame.invalidate();
 139     frame.pack();
 140   }
 141
 142   @Override
 143   protected void jbInit()
 144   {
 145     super.jbInit();
 146
 147     JPanel thresholdPanel = new JPanel();
 148     thresholdPanel.setBorder(new TitledBorder(MessageManager
 149             .getString("label.threshold_filter")));
 150     thresholdPanel.setBackground(Color.white);
 151     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 152     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 153
 154     percentThreshold.setBackground(Color.white);
 155     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 156
 157     JPanel actionPanel = new JPanel();
 158     actionPanel.setBackground(Color.white);
 159     actionPanel.setFont(JvSwingUtils.getLabelFont());
 160
 161     JPanel graphFilterView = new JPanel();
 162     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 163     graphFilterView.setBackground(Color.white);
 164
 165     JPanel noGraphFilterView = new JPanel();
 166     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 167     noGraphFilterView.setBackground(Color.white);
 168
 169     annotationComboBoxPanel.setBackground(Color.white);
 170     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 171
 172     gSearchPanel = new SearchPanel(this);
 173     ngSearchPanel = new SearchPanel(this);
 174     gFurtherActionPanel = new FurtherActionPanel(this);
 175     ngFurtherActionPanel = new FurtherActionPanel(this);
 176     gStructureFilterPanel = new StructureFilterPanel(this);
 177     ngStructureFilterPanel = new StructureFilterPanel(this);
 178
 179     thresholdPanel.add(getThreshold());
 180     thresholdPanel.add(percentThreshold, "wrap");
 181     thresholdPanel.add(slider, "grow");
 182     thresholdPanel.add(thresholdValue, "span, wrap");
 183
 184     actionPanel.add(ok);
 185     actionPanel.add(cancel);
 186
 187     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 188     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 189     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 190     graphFilterView.add(gFurtherActionPanel);
 191
 192     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 193     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 194     noGraphFilterView.add(ngFurtherActionPanel);
 195
 196     annotationComboBoxPanel.add(getAnnotations());
 197     switchableViewsPanel.add(noGraphFilterView,
 198             AnnotationColumnChooser.NO_GRAPH_VIEW);
 199     switchableViewsPanel.add(graphFilterView,
 200             AnnotationColumnChooser.GRAPH_VIEW);
 201
 202     this.setLayout(new BorderLayout());
 203     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 204     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 205     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 206
 207     selectedAnnotationChanged();
 208     updateThresholdPanelToolTip();
 209     this.validate();
 210   }
 211
 212   protected void updateThresholdPanelToolTip()
 213   {
 214     thresholdValue.setToolTipText("");
 215     slider.setToolTipText("");
 216
 217     String defaultTtip = MessageManager
 218             .getString("info.change_threshold_mode_to_enable");
 219
 220     String thresh = getThreshold().getSelectedItem().toString();
 221     if (thresh.equalsIgnoreCase("No Threshold"))
 222     {
 223       thresholdValue.setToolTipText(defaultTtip);
 224       slider.setToolTipText(defaultTtip);
 225     }
 226   }
 227
 228   @Override
 229   protected void reset()
 230   {
 231     if (this.getOldColumnSelection() != null)
 232     {
 233       av.getColumnSelection().clear();
 234
 235       if (av.getAnnotationColumnSelectionState() != null)
 236       {
 237         ColumnSelection oldSelection = av
 238                 .getAnnotationColumnSelectionState()
 239                 .getOldColumnSelection();
 240         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 241                 && !oldSelection.getHiddenColumns().isEmpty())
 242         {
 243           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 244                   .iterator(); itr.hasNext();)
 245           {
 246             int positions[] = itr.next();
 247             av.hideColumns(positions[0], positions[1]);
 248           }
 249         }
 250         av.setColumnSelection(oldSelection);
 251       }
 252       ap.paintAlignment(true);
 253     }
 254
 255   }
 256
 257   @Override
 258   public void valueChanged(boolean updateAllAnnotation)
 259   {
 260     if (slider.isEnabled())
 261     {
 262       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 263       updateView();
 264       propagateSeqAssociatedThreshold(updateAllAnnotation,
 265               getCurrentAnnotation());
 266       ap.paintAlignment(false);
 267     }
 268   }
 269
 270   @Override
 271   public void updateView()
 272   {
 273     // Check if combobox is still adjusting
 274     if (adjusting)
 275     {
 276       return;
 277     }
 278
 279     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 280
 281     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 282             .getSelectedIndex()]]);
 283
 284     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 285             .getSelectedIndex());
 286
 287     slider.setEnabled(true);
 288     thresholdValue.setEnabled(true);
 289     percentThreshold.setEnabled(true);
 290
 291     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 292     {
 293       slider.setEnabled(false);
 294       thresholdValue.setEnabled(false);
 295       thresholdValue.setText("");
 296       percentThreshold.setEnabled(false);
 297       // build filter params
 298     }
 299     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 300     {
 301       if (getCurrentAnnotation().threshold == null)
 302       {
 303         getCurrentAnnotation()
 304                 .setThreshold(
 305                         new jalview.datamodel.GraphLine(
 306                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 307                                 "Threshold", Color.black));
 308       }
 309
 310       adjusting = true;
 311       float range = getCurrentAnnotation().graphMax * 1000
 312               - getCurrentAnnotation().graphMin * 1000;
 313
 314       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 315       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 316       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 317
 318       if (percentThreshold.isSelected())
 319       {
 320         thresholdValue
 321                 .setText(""
 322                         + ((getCurrentAnnotation().threshold.value - getCurrentAnnotation().graphMin) * 100f / (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin)));
 323       }
 324       else
 325       {
 326         thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 327       }
 328
 329       slider.setMajorTickSpacing((int) (range / 10f));
 330       slider.setEnabled(true);
 331       thresholdValue.setEnabled(true);
 332       adjusting = false;
 333
 334       // build filter params
 335       filterParams
 336               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 337       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 338       {
 339         filterParams
 340                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 341
 342         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 343         {
 344           filterParams
 345                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 346         }
 347         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 348         {
 349           filterParams
 350                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 351         }
 352       }
 353     }
 354
 355     updateThresholdPanelToolTip();
 356     if (currentStructureFilterPanel != null)
 357     {
 358       if (currentStructureFilterPanel.alphaHelix.isSelected())
 359       {
 360         filterParams.setFilterAlphaHelix(true);
 361       }
 362       if (currentStructureFilterPanel.betaStrand.isSelected())
 363       {
 364         filterParams.setFilterBetaSheet(true);
 365       }
 366       if (currentStructureFilterPanel.turn.isSelected())
 367       {
 368         filterParams.setFilterTurn(true);
 369       }
 370     }
 371
 372     if (currentSearchPanel != null)
 373     {
 374
 375       if (!currentSearchPanel.searchBox.getText().isEmpty())
 376       {
 377         currentSearchPanel.description.setEnabled(true);
 378         currentSearchPanel.displayName.setEnabled(true);
 379         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 380         if (currentSearchPanel.displayName.isSelected())
 381         {
 382           filterParams
 383                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 384         }
 385         if (currentSearchPanel.description.isSelected())
 386         {
 387           filterParams
 388                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 389         }
 390       }
 391       else
 392       {
 393         currentSearchPanel.description.setEnabled(false);
 394         currentSearchPanel.displayName.setEnabled(false);
 395       }
 396     }
 397
 398     av.getColumnSelection().filterAnnotations(
 399             getCurrentAnnotation().annotations, filterParams);
 400
 401     av.showAllHiddenColumns();
 402     if (getActionOption() == ACTION_OPTION_HIDE)
 403     {
 404       av.hideSelectedColumns();
 405     }
 406
 407     filterParams = null;
 408     av.setAnnotationColumnSelectionState(this);
 409     ap.paintAlignment(true);
 410   }
 411
 412
 413   public ColumnSelection getOldColumnSelection()
 414   {
 415     return oldColumnSelection;
 416   }
 417
 418   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 419   {
 420     if (currentColumnSelection != null)
 421     {
 422       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 423     }
 424   }
 425
 426   public FurtherActionPanel getCurrentFutherActionPanel()
 427   {
 428     return currentFurtherActionPanel;
 429   }
 430
 431   public void setCurrentFutherActionPanel(
 432           FurtherActionPanel currentFutherActionPanel)
 433   {
 434     this.currentFurtherActionPanel = currentFutherActionPanel;
 435   }
 436
 437   public SearchPanel getCurrentSearchPanel()
 438   {
 439     return currentSearchPanel;
 440   }
 441
 442   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 443   {
 444     this.currentSearchPanel = currentSearchPanel;
 445   }
 446
 447   public int getActionOption()
 448   {
 449     return actionOption;
 450   }
 451
 452   public void setActionOption(int actionOption)
 453   {
 454     this.actionOption = actionOption;
 455   }
 456
 457   public StructureFilterPanel getCurrentStructureFilterPanel()
 458   {
 459     return currentStructureFilterPanel;
 460   }
 461
 462   public void setCurrentStructureFilterPanel(
 463           StructureFilterPanel currentStructureFilterPanel)
 464   {
 465     this.currentStructureFilterPanel = currentStructureFilterPanel;
 466   }
 467
 468   public void select_action(ActionEvent actionEvent)
 469   {
 470     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 471     if (radioButton.isSelected())
 472     {
 473       setActionOption(ACTION_OPTION_SELECT);
 474       updateView();
 475     }
 476   }
 477
 478   public void hide_action(ActionEvent actionEvent)
 479   {
 480     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 481     if (radioButton.isSelected())
 482     {
 483       setActionOption(ACTION_OPTION_HIDE);
 484       updateView();
 485     }
 486   }
 487
 488   @Override
 489   public void itemStateChanged(ItemEvent e)
 490   {
 491     selectedAnnotationChanged();
 492   }
 493
 494   @Override
 495   public void selectedAnnotationChanged()
 496   {
 497     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 498     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 499             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 500     {
 501       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 502     }
 503
 504     gSearchPanel.syncState();
 505     gFurtherActionPanel.syncState();
 506     gStructureFilterPanel.syncState();
 507
 508     ngSearchPanel.syncState();
 509     ngFurtherActionPanel.syncState();
 510     ngStructureFilterPanel.syncState();
 511
 512     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 513             .getLayout();
 514     switchableViewsLayout.show(switchableViewsPanel, currentView);
 515     updateView();
 516   }
 517
 518   public class FurtherActionPanel extends JPanel
 519   {
 520     private AnnotationColumnChooser aColChooser;
 521
 522     private JRadioButton hideOption = new JRadioButton();
 523
 524     private JRadioButton selectOption = new JRadioButton();
 525
 526     private ButtonGroup optionsGroup = new ButtonGroup();
 527
 528     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 529     {
 530       this.aColChooser = aColChooser;
 531       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 532       selectOption.addActionListener(new ActionListener()
 533       {
 534         @Override
 535         public void actionPerformed(ActionEvent actionEvent)
 536         {
 537           selectRadioAction(actionEvent);
 538         }
 539       });
 540
 541       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 542       hideOption.addActionListener(new ActionListener()
 543       {
 544         @Override
 545         public void actionPerformed(ActionEvent actionEvent)
 546         {
 547           hideRadioAction(actionEvent);
 548         }
 549       });
 550
 551       optionsGroup.add(selectOption);
 552       optionsGroup.add(hideOption);
 553       optionsGroup.setSelected(selectOption.getModel(), true);
 554
 555       JvSwingUtils.jvInitComponent(this);
 556       syncState();
 557
 558       this.add(selectOption);
 559       this.add(hideOption);
 560     }
 561
 562     public void selectRadioAction(ActionEvent actionEvent)
 563     {
 564       aColChooser.setCurrentFutherActionPanel(this);
 565       aColChooser.select_action(actionEvent);
 566     }
 567
 568     public void hideRadioAction(ActionEvent actionEvent)
 569     {
 570       aColChooser.setCurrentFutherActionPanel(this);
 571       aColChooser.hide_action(actionEvent);
 572     }
 573
 574     public void syncState()
 575     {
 576       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 577       {
 578         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 579       }
 580       else
 581       {
 582         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 583       }
 584     }
 585   }
 586
 587   public class StructureFilterPanel extends JPanel
 588   {
 589     private AnnotationColumnChooser aColChooser;
 590
 591     private JCheckBox alphaHelix = new JCheckBox();
 592
 593     private JCheckBox betaStrand = new JCheckBox();
 594
 595     private JCheckBox turn = new JCheckBox();
 596
 597     private JCheckBox all = new JCheckBox();
 598
 599     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 600     {
 601       this.aColChooser = aColChooser;
 602
 603       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 604       alphaHelix.addActionListener(new ActionListener()
 605       {
 606         @Override
 607         public void actionPerformed(ActionEvent actionEvent)
 608         {
 609           alphaHelix_actionPerformed();
 610         }
 611       });
 612
 613       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 614       betaStrand.addActionListener(new ActionListener()
 615       {
 616         @Override
 617         public void actionPerformed(ActionEvent actionEvent)
 618         {
 619           betaStrand_actionPerformed();
 620         }
 621       });
 622
 623       JvSwingUtils.jvInitComponent(turn, "label.turn");
 624       turn.addActionListener(new ActionListener()
 625       {
 626         @Override
 627         public void actionPerformed(ActionEvent actionEvent)
 628         {
 629           turn_actionPerformed();
 630         }
 631       });
 632
 633       JvSwingUtils.jvInitComponent(all, "label.select_all");
 634       all.addActionListener(new ActionListener()
 635       {
 636         @Override
 637         public void actionPerformed(ActionEvent actionEvent)
 638         {
 639           all_actionPerformed();
 640         }
 641       });
 642
 643       this.setBorder(new TitledBorder(MessageManager
 644               .getString("label.structures_filter")));
 645       JvSwingUtils.jvInitComponent(this);
 646
 647       this.add(all);
 648       this.add(alphaHelix);
 649       this.add(betaStrand);
 650       this.add(turn);
 651     }
 652
 653     public void alphaHelix_actionPerformed()
 654     {
 655       updateSelectAllState();
 656       aColChooser.setCurrentStructureFilterPanel(this);
 657       aColChooser.updateView();
 658     }
 659
 660     public void betaStrand_actionPerformed()
 661     {
 662       updateSelectAllState();
 663       aColChooser.setCurrentStructureFilterPanel(this);
 664       aColChooser.updateView();
 665     }
 666
 667     public void turn_actionPerformed()
 668     {
 669       updateSelectAllState();
 670       aColChooser.setCurrentStructureFilterPanel(this);
 671       aColChooser.updateView();
 672     }
 673
 674     public void all_actionPerformed()
 675     {
 676       if (all.isSelected())
 677       {
 678         alphaHelix.setSelected(true);
 679         betaStrand.setSelected(true);
 680         turn.setSelected(true);
 681       }
 682       else
 683       {
 684         alphaHelix.setSelected(false);
 685         betaStrand.setSelected(false);
 686         turn.setSelected(false);
 687       }
 688       aColChooser.setCurrentStructureFilterPanel(this);
 689       aColChooser.updateView();
 690     }
 691
 692     public void updateSelectAllState()
 693     {
 694       if (alphaHelix.isSelected() && betaStrand.isSelected()
 695               && turn.isSelected())
 696       {
 697         all.setSelected(true);
 698       }
 699       else
 700       {
 701         all.setSelected(false);
 702       }
 703     }
 704
 705     public void syncState()
 706     {
 707       StructureFilterPanel sfp = aColChooser
 708               .getCurrentStructureFilterPanel();
 709       if (sfp != null)
 710       {
 711         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 712         betaStrand.setSelected(sfp.betaStrand.isSelected());
 713         turn.setSelected(sfp.turn.isSelected());
 714         if (sfp.all.isSelected())
 715         {
 716           all.setSelected(true);
 717           alphaHelix.setSelected(true);
 718           betaStrand.setSelected(true);
 719           turn.setSelected(true);
 720         }
 721       }
 722
 723     }
 724   }
 725
 726   public class SearchPanel extends JPanel
 727   {
 728     private AnnotationColumnChooser aColChooser;
 729
 730     private JCheckBox displayName = new JCheckBox();
 731
 732     private JCheckBox description = new JCheckBox();
 733
 734     private JTextField searchBox = new JTextField(10);
 735
 736     public SearchPanel(AnnotationColumnChooser aColChooser)
 737     {
 738
 739       this.aColChooser = aColChooser;
 740       JvSwingUtils.jvInitComponent(this);
 741       this.setBorder(new TitledBorder(MessageManager
 742               .getString("label.search_filter")));
 743
 744       JvSwingUtils.jvInitComponent(searchBox);
 745       searchBox.setToolTipText(MessageManager
 746               .getString("info.enter_search_text_here"));
 747       searchBox.getDocument().addDocumentListener(new DocumentListener()
 748       {
 749         @Override
 750         public void insertUpdate(DocumentEvent e)
 751         {
 752           searchStringAction();
 753         }
 754
 755         @Override
 756         public void removeUpdate(DocumentEvent e)
 757         {
 758           searchStringAction();
 759         }
 760
 761         @Override
 762         public void changedUpdate(DocumentEvent e)
 763         {
 764           searchStringAction();
 765         }
 766       });
 767
 768       JvSwingUtils.jvInitComponent(displayName, "label.label");
 769       displayName.setEnabled(false);
 770       displayName.addActionListener(new ActionListener()
 771       {
 772         @Override
 773         public void actionPerformed(ActionEvent actionEvent)
 774         {
 775           displayNameCheckboxAction();
 776         }
 777       });
 778
 779       JvSwingUtils.jvInitComponent(description, "label.description");
 780       description.setEnabled(false);
 781       description.addActionListener(new ActionListener()
 782       {
 783         @Override
 784         public void actionPerformed(ActionEvent actionEvent)
 785         {
 786           discriptionCheckboxAction();
 787         }
 788       });
 789
 790       syncState();
 791       this.add(searchBox);
 792       this.add(displayName);
 793       this.add(description);
 794     }
 795
 796     public void displayNameCheckboxAction()
 797     {
 798       aColChooser.setCurrentSearchPanel(this);
 799       aColChooser.updateView();
 800     }
 801
 802     public void discriptionCheckboxAction()
 803     {
 804       aColChooser.setCurrentSearchPanel(this);
 805       aColChooser.updateView();
 806     }
 807
 808     public void searchStringAction()
 809     {
 810       aColChooser.setCurrentSearchPanel(this);
 811       aColChooser.updateView();
 812       updateSearchPanelToolTips();
 813     }
 814
 815     public void syncState()
 816     {
 817       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 818       if (sp != null)
 819       {
 820         description.setEnabled(sp.description.isEnabled());
 821         description.setSelected(sp.description.isSelected());
 822
 823         displayName.setEnabled(sp.displayName.isEnabled());
 824         displayName.setSelected(sp.displayName.isSelected());
 825
 826         searchBox.setText(sp.searchBox.getText());
 827       }
 828       updateSearchPanelToolTips();
 829     }
 830
 831     public void updateSearchPanelToolTips()
 832     {
 833       String defaultTtip = MessageManager
 834               .getString("info.enter_search_text_to_enable");
 835       String labelTtip = MessageManager.formatMessage(
 836               "info.search_in_annotation_label", annotations
 837                       .getSelectedItem().toString());
 838       String descTtip = MessageManager.formatMessage(
 839               "info.search_in_annotation_description", annotations
 840                       .getSelectedItem().toString());
 841       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 842               : defaultTtip);
 843       description.setToolTipText(description.isEnabled() ? descTtip
 844               : defaultTtip);
 845     }
 846   }
 847
 848 }