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
  54         implements 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.getCurrentSearchPanel();
 123       currentStructureFilterPanel = lastChooser
 124               .getCurrentStructureFilterPanel();
 125       annotations.setSelectedIndex(
 126               lastChooser.getAnnotations().getSelectedIndex());
 127       threshold.setSelectedIndex(
 128               lastChooser.getThreshold().getSelectedIndex());
 129       actionOption = lastChooser.getActionOption();
 130       percentThreshold
 131               .setSelected(lastChooser.percentThreshold.isSelected());
 132     }
 133
 134     try
 135     {
 136       jbInit();
 137     } catch (Exception ex)
 138     {
 139     }
 140     adjusting = false;
 141
 142     updateView();
 143     frame.invalidate();
 144     frame.pack();
 145   }
 146
 147   @Override
 148   protected void jbInit()
 149   {
 150     super.jbInit();
 151
 152     JPanel thresholdPanel = new JPanel();
 153     thresholdPanel.setBorder(new TitledBorder(
 154             MessageManager.getString("label.threshold_filter")));
 155     thresholdPanel.setBackground(Color.white);
 156     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 157     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 158
 159     percentThreshold.setBackground(Color.white);
 160     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 161
 162     JPanel actionPanel = new JPanel();
 163     actionPanel.setBackground(Color.white);
 164     actionPanel.setFont(JvSwingUtils.getLabelFont());
 165
 166     JPanel graphFilterView = new JPanel();
 167     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 168     graphFilterView.setBackground(Color.white);
 169
 170     JPanel noGraphFilterView = new JPanel();
 171     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 172     noGraphFilterView.setBackground(Color.white);
 173
 174     annotationComboBoxPanel.setBackground(Color.white);
 175     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 176
 177     gSearchPanel = new SearchPanel(this);
 178     ngSearchPanel = new SearchPanel(this);
 179     gFurtherActionPanel = new FurtherActionPanel(this);
 180     ngFurtherActionPanel = new FurtherActionPanel(this);
 181     gStructureFilterPanel = new StructureFilterPanel(this);
 182     ngStructureFilterPanel = new StructureFilterPanel(this);
 183
 184     thresholdPanel.add(getThreshold());
 185     thresholdPanel.add(percentThreshold, "wrap");
 186     thresholdPanel.add(slider, "grow");
 187     thresholdPanel.add(thresholdValue, "span, wrap");
 188
 189     actionPanel.add(ok);
 190     actionPanel.add(cancel);
 191
 192     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 193     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 194     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 195     graphFilterView.add(gFurtherActionPanel);
 196
 197     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 198     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 199     noGraphFilterView.add(ngFurtherActionPanel);
 200
 201     annotationComboBoxPanel.add(getAnnotations());
 202     switchableViewsPanel.add(noGraphFilterView,
 203             AnnotationColumnChooser.NO_GRAPH_VIEW);
 204     switchableViewsPanel.add(graphFilterView,
 205             AnnotationColumnChooser.GRAPH_VIEW);
 206
 207     this.setLayout(new BorderLayout());
 208     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 209     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 210     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 211
 212     selectedAnnotationChanged();
 213     updateThresholdPanelToolTip();
 214     this.validate();
 215   }
 216
 217   protected void updateThresholdPanelToolTip()
 218   {
 219     thresholdValue.setToolTipText("");
 220     slider.setToolTipText("");
 221
 222     String defaultTtip = MessageManager
 223             .getString("info.change_threshold_mode_to_enable");
 224
 225     String thresh = getThreshold().getSelectedItem().toString();
 226     if (thresh.equalsIgnoreCase("No Threshold"))
 227     {
 228       thresholdValue.setToolTipText(defaultTtip);
 229       slider.setToolTipText(defaultTtip);
 230     }
 231   }
 232
 233   @Override
 234   protected void reset()
 235   {
 236     if (this.getOldHiddenColumns() != null)
 237     {
 238       av.getColumnSelection().clear();
 239
 240       if (av.getAnnotationColumnSelectionState() != null)
 241       {
 242         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
 243                 .getOldHiddenColumns();
 244         if (oldHidden != null)
 245         {
 246           ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
 247           for (int[] positions : regions)
 248           {
 249             av.hideColumns(positions[0], positions[1]);
 250           }
 251         }
 252         // TODO not clear why we need to hide all the columns (above) if we are
 253         // going to copy the hidden columns over wholesale anyway
 254         av.getAlignment().setHiddenColumns(oldHidden);
 255       }
 256       av.sendSelection();
 257       ap.paintAlignment(true, true);
 258     }
 259   }
 260
 261   @Override
 262   public void valueChanged(boolean updateAllAnnotation)
 263   {
 264     if (slider.isEnabled())
 265     {
 266       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 267       updateView();
 268       propagateSeqAssociatedThreshold(updateAllAnnotation,
 269               getCurrentAnnotation());
 270       ap.paintAlignment(false, false);
 271     }
 272   }
 273
 274   @Override
 275   public void updateView()
 276   {
 277     // Check if combobox is still adjusting
 278     if (adjusting)
 279     {
 280       return;
 281     }
 282
 283     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 284
 285     setCurrentAnnotation(av.getAlignment()
 286             .getAlignmentAnnotation()[annmap[getAnnotations()
 287                     .getSelectedIndex()]]);
 288
 289     int selectedThresholdItem = getSelectedThresholdItem(
 290             getThreshold().getSelectedIndex());
 291
 292     slider.setEnabled(true);
 293     thresholdValue.setEnabled(true);
 294     percentThreshold.setEnabled(true);
 295
 296     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 297     {
 298       slider.setEnabled(false);
 299       thresholdValue.setEnabled(false);
 300       thresholdValue.setText("");
 301       percentThreshold.setEnabled(false);
 302       // build filter params
 303     }
 304     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 305     {
 306       if (getCurrentAnnotation().threshold == null)
 307       {
 308         getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
 309                 (getCurrentAnnotation().graphMax
 310                         - getCurrentAnnotation().graphMin) / 2f,
 311                 "Threshold", Color.black));
 312       }
 313
 314       adjusting = true;
 315       float range = getCurrentAnnotation().graphMax * 1000
 316               - getCurrentAnnotation().graphMin * 1000;
 317
 318       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 319       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 320       slider.setValue(
 321               (int) (getCurrentAnnotation().threshold.value * 1000));
 322
 323       setThresholdValueText();
 324
 325       slider.setMajorTickSpacing((int) (range / 10f));
 326       slider.setEnabled(true);
 327       thresholdValue.setEnabled(true);
 328       adjusting = false;
 329
 330       // build filter params
 331       filterParams.setThresholdType(
 332               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 333       if (getCurrentAnnotation().isQuantitative())
 334       {
 335         filterParams
 336                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 337
 338         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 339         {
 340           filterParams.setThresholdType(
 341                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 342         }
 343         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 344         {
 345           filterParams.setThresholdType(
 346                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 347         }
 348       }
 349     }
 350
 351     updateThresholdPanelToolTip();
 352     if (currentStructureFilterPanel != null)
 353     {
 354       if (currentStructureFilterPanel.alphaHelix.isSelected())
 355       {
 356         filterParams.setFilterAlphaHelix(true);
 357       }
 358       if (currentStructureFilterPanel.betaStrand.isSelected())
 359       {
 360         filterParams.setFilterBetaSheet(true);
 361       }
 362       if (currentStructureFilterPanel.turn.isSelected())
 363       {
 364         filterParams.setFilterTurn(true);
 365       }
 366     }
 367
 368     if (currentSearchPanel != null)
 369     {
 370       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
 371       {
 372         filterParams.setRegexString(
 373                 currentSearchPanel.searchBox.getUserInput());
 374         if (currentSearchPanel.displayName.isSelected())
 375         {
 376           filterParams.addRegexSearchField(
 377                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 378         }
 379         if (currentSearchPanel.description.isSelected())
 380         {
 381           filterParams.addRegexSearchField(
 382                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 383         }
 384       }
 385     }
 386
 387     // show hidden columns here, before changing the column selection in
 388     // filterAnnotations, because showing hidden columns has the side effect of
 389     // adding them to the selection
 390     av.showAllHiddenColumns();
 391     av.getColumnSelection().filterAnnotations(
 392             getCurrentAnnotation().annotations, filterParams);
 393
 394     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
 395     if (hideCols)
 396     {
 397       av.hideSelectedColumns();
 398     }
 399     av.sendSelection();
 400
 401     filterParams = null;
 402     av.setAnnotationColumnSelectionState(this);
 403     // only update overview and structures if columns were hidden
 404     ap.paintAlignment(hideCols, hideCols);
 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().getAlignmentAnnotation()[annmap[getAnnotations()
 493             .getSelectedIndex()]].isQuantitative())
 494     {
 495       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 496     }
 497     saveCache();
 498     gSearchPanel.syncState();
 499     gFurtherActionPanel.syncState();
 500     gStructureFilterPanel.syncState();
 501
 502     ngSearchPanel.syncState();
 503     ngFurtherActionPanel.syncState();
 504     ngStructureFilterPanel.syncState();
 505
 506     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 507             .getLayout();
 508     switchableViewsLayout.show(switchableViewsPanel, currentView);
 509     updateView();
 510   }
 511
 512   public class FurtherActionPanel extends JPanel
 513   {
 514     private AnnotationColumnChooser aColChooser;
 515
 516     private JRadioButton hideOption = new JRadioButton();
 517
 518     private JRadioButton selectOption = new JRadioButton();
 519
 520     private ButtonGroup optionsGroup = new ButtonGroup();
 521
 522     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 523     {
 524       this.aColChooser = aColChooser;
 525       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 526       selectOption.addActionListener(new ActionListener()
 527       {
 528         @Override
 529         public void actionPerformed(ActionEvent actionEvent)
 530         {
 531           selectRadioAction(actionEvent);
 532         }
 533       });
 534
 535       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 536       hideOption.addActionListener(new ActionListener()
 537       {
 538         @Override
 539         public void actionPerformed(ActionEvent actionEvent)
 540         {
 541           hideRadioAction(actionEvent);
 542         }
 543       });
 544
 545       optionsGroup.add(selectOption);
 546       optionsGroup.add(hideOption);
 547       optionsGroup.setSelected(selectOption.getModel(), true);
 548
 549       JvSwingUtils.jvInitComponent(this);
 550       syncState();
 551
 552       this.add(selectOption);
 553       this.add(hideOption);
 554     }
 555
 556     public void selectRadioAction(ActionEvent actionEvent)
 557     {
 558       aColChooser.setCurrentFutherActionPanel(this);
 559       aColChooser.select_action(actionEvent);
 560     }
 561
 562     public void hideRadioAction(ActionEvent actionEvent)
 563     {
 564       aColChooser.setCurrentFutherActionPanel(this);
 565       aColChooser.hide_action(actionEvent);
 566     }
 567
 568     public void syncState()
 569     {
 570       if (aColChooser
 571               .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(
 639               MessageManager.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(
 740               MessageManager.getString("label.search_filter")));
 741
 742       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
 743       searchBox.setToolTipText(
 744               MessageManager.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       JvSwingUtils.jvInitComponent(displayName, "label.label");
 760       displayName.addActionListener(new ActionListener()
 761       {
 762         @Override
 763         public void actionPerformed(ActionEvent actionEvent)
 764         {
 765           displayNameCheckboxAction();
 766         }
 767       });
 768
 769       JvSwingUtils.jvInitComponent(description, "label.description");
 770       description.addActionListener(new ActionListener()
 771       {
 772         @Override
 773         public void actionPerformed(ActionEvent actionEvent)
 774         {
 775           discriptionCheckboxAction();
 776         }
 777       });
 778
 779       syncState();
 780       this.add(searchBox);
 781       this.add(displayName);
 782       this.add(description);
 783     }
 784
 785     public void displayNameCheckboxAction()
 786     {
 787       aColChooser.setCurrentSearchPanel(this);
 788       aColChooser.updateView();
 789     }
 790
 791     public void discriptionCheckboxAction()
 792     {
 793       aColChooser.setCurrentSearchPanel(this);
 794       aColChooser.updateView();
 795     }
 796
 797     public void searchStringAction()
 798     {
 799       aColChooser.setCurrentSearchPanel(this);
 800       aColChooser.updateView();
 801       updateSearchPanelToolTips();
 802       searchBox.updateCache();
 803     }
 804
 805     public void syncState()
 806     {
 807       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 808       if (sp != null)
 809       {
 810         description.setEnabled(sp.description.isEnabled());
 811         description.setSelected(sp.description.isSelected());
 812
 813         displayName.setEnabled(sp.displayName.isEnabled());
 814         displayName.setSelected(sp.displayName.isSelected());
 815
 816         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 817       }
 818       updateSearchPanelToolTips();
 819     }
 820
 821     public void updateSearchPanelToolTips()
 822     {
 823       String defaultTtip = MessageManager
 824               .getString("info.enter_search_text_to_enable");
 825       String labelTtip = MessageManager.formatMessage(
 826               "info.search_in_annotation_label",
 827               annotations.getSelectedItem().toString());
 828       String descTtip = MessageManager.formatMessage(
 829               "info.search_in_annotation_description",
 830               annotations.getSelectedItem().toString());
 831       displayName.setToolTipText(
 832               displayName.isEnabled() ? labelTtip : defaultTtip);
 833       description.setToolTipText(
 834               description.isEnabled() ? descTtip : defaultTtip);
 835     }
 836   }
 837
 838   @Override
 839   public void ok_actionPerformed()
 840   {
 841     saveCache();
 842     super.ok_actionPerformed();
 843   }
 844
 845   @Override
 846   public void cancel_actionPerformed()
 847   {
 848     saveCache();
 849     super.cancel_actionPerformed();
 850   }
 851
 852   private void saveCache()
 853   {
 854     gSearchPanel.searchBox.persistCache();
 855     ngSearchPanel.searchBox.persistCache();
 856     gSearchPanel.searchBox.updateCache();
 857     ngSearchPanel.searchBox.updateCache();
 858   }
 859 }