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