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);
 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);
 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     if (getActionOption() == ACTION_OPTION_HIDE)
 395     {
 396       av.hideSelectedColumns();
 397     }
 398     av.sendSelection();
 399
 400     filterParams = null;
 401     av.setAnnotationColumnSelectionState(this);
 402     ap.paintAlignment(true);
 403   }
 404
 405   public HiddenColumns getOldHiddenColumns()
 406   {
 407     return oldHiddenColumns;
 408   }
 409
 410   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 411   {
 412     if (currentHiddenColumns != null)
 413     {
 414       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 415     }
 416   }
 417
 418   public FurtherActionPanel getCurrentFutherActionPanel()
 419   {
 420     return currentFurtherActionPanel;
 421   }
 422
 423   public void setCurrentFutherActionPanel(
 424           FurtherActionPanel currentFutherActionPanel)
 425   {
 426     this.currentFurtherActionPanel = currentFutherActionPanel;
 427   }
 428
 429   public SearchPanel getCurrentSearchPanel()
 430   {
 431     return currentSearchPanel;
 432   }
 433
 434   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 435   {
 436     this.currentSearchPanel = currentSearchPanel;
 437   }
 438
 439   public int getActionOption()
 440   {
 441     return actionOption;
 442   }
 443
 444   public void setActionOption(int actionOption)
 445   {
 446     this.actionOption = actionOption;
 447   }
 448
 449   public StructureFilterPanel getCurrentStructureFilterPanel()
 450   {
 451     return currentStructureFilterPanel;
 452   }
 453
 454   public void setCurrentStructureFilterPanel(
 455           StructureFilterPanel currentStructureFilterPanel)
 456   {
 457     this.currentStructureFilterPanel = currentStructureFilterPanel;
 458   }
 459
 460   public void select_action(ActionEvent actionEvent)
 461   {
 462     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 463     if (radioButton.isSelected())
 464     {
 465       setActionOption(ACTION_OPTION_SELECT);
 466       updateView();
 467     }
 468   }
 469
 470   public void hide_action(ActionEvent actionEvent)
 471   {
 472     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 473     if (radioButton.isSelected())
 474     {
 475       setActionOption(ACTION_OPTION_HIDE);
 476       updateView();
 477     }
 478   }
 479
 480   @Override
 481   public void itemStateChanged(ItemEvent e)
 482   {
 483     selectedAnnotationChanged();
 484   }
 485
 486   @Override
 487   public void selectedAnnotationChanged()
 488   {
 489     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 490     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 491             .getSelectedIndex()]].isQuantitative())
 492     {
 493       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 494     }
 495     saveCache();
 496     gSearchPanel.syncState();
 497     gFurtherActionPanel.syncState();
 498     gStructureFilterPanel.syncState();
 499
 500     ngSearchPanel.syncState();
 501     ngFurtherActionPanel.syncState();
 502     ngStructureFilterPanel.syncState();
 503
 504     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 505             .getLayout();
 506     switchableViewsLayout.show(switchableViewsPanel, currentView);
 507     updateView();
 508   }
 509
 510   public class FurtherActionPanel extends JPanel
 511   {
 512     private AnnotationColumnChooser aColChooser;
 513
 514     private JRadioButton hideOption = new JRadioButton();
 515
 516     private JRadioButton selectOption = new JRadioButton();
 517
 518     private ButtonGroup optionsGroup = new ButtonGroup();
 519
 520     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 521     {
 522       this.aColChooser = aColChooser;
 523       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 524       selectOption.addActionListener(new ActionListener()
 525       {
 526         @Override
 527         public void actionPerformed(ActionEvent actionEvent)
 528         {
 529           selectRadioAction(actionEvent);
 530         }
 531       });
 532
 533       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 534       hideOption.addActionListener(new ActionListener()
 535       {
 536         @Override
 537         public void actionPerformed(ActionEvent actionEvent)
 538         {
 539           hideRadioAction(actionEvent);
 540         }
 541       });
 542
 543       optionsGroup.add(selectOption);
 544       optionsGroup.add(hideOption);
 545       optionsGroup.setSelected(selectOption.getModel(), true);
 546
 547       JvSwingUtils.jvInitComponent(this);
 548       syncState();
 549
 550       this.add(selectOption);
 551       this.add(hideOption);
 552     }
 553
 554     public void selectRadioAction(ActionEvent actionEvent)
 555     {
 556       aColChooser.setCurrentFutherActionPanel(this);
 557       aColChooser.select_action(actionEvent);
 558     }
 559
 560     public void hideRadioAction(ActionEvent actionEvent)
 561     {
 562       aColChooser.setCurrentFutherActionPanel(this);
 563       aColChooser.hide_action(actionEvent);
 564     }
 565
 566     public void syncState()
 567     {
 568       if (aColChooser
 569               .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 570       {
 571         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 572       }
 573       else
 574       {
 575         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 576       }
 577     }
 578   }
 579
 580   public class StructureFilterPanel extends JPanel
 581   {
 582     private AnnotationColumnChooser aColChooser;
 583
 584     private JCheckBox alphaHelix = new JCheckBox();
 585
 586     private JCheckBox betaStrand = new JCheckBox();
 587
 588     private JCheckBox turn = new JCheckBox();
 589
 590     private JCheckBox all = new JCheckBox();
 591
 592     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 593     {
 594       this.aColChooser = aColChooser;
 595
 596       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 597       alphaHelix.addActionListener(new ActionListener()
 598       {
 599         @Override
 600         public void actionPerformed(ActionEvent actionEvent)
 601         {
 602           alphaHelix_actionPerformed();
 603         }
 604       });
 605
 606       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 607       betaStrand.addActionListener(new ActionListener()
 608       {
 609         @Override
 610         public void actionPerformed(ActionEvent actionEvent)
 611         {
 612           betaStrand_actionPerformed();
 613         }
 614       });
 615
 616       JvSwingUtils.jvInitComponent(turn, "label.turn");
 617       turn.addActionListener(new ActionListener()
 618       {
 619         @Override
 620         public void actionPerformed(ActionEvent actionEvent)
 621         {
 622           turn_actionPerformed();
 623         }
 624       });
 625
 626       JvSwingUtils.jvInitComponent(all, "label.select_all");
 627       all.addActionListener(new ActionListener()
 628       {
 629         @Override
 630         public void actionPerformed(ActionEvent actionEvent)
 631         {
 632           all_actionPerformed();
 633         }
 634       });
 635
 636       this.setBorder(new TitledBorder(
 637               MessageManager.getString("label.structures_filter")));
 638       JvSwingUtils.jvInitComponent(this);
 639
 640       this.add(all);
 641       this.add(alphaHelix);
 642       this.add(betaStrand);
 643       this.add(turn);
 644     }
 645
 646     public void alphaHelix_actionPerformed()
 647     {
 648       updateSelectAllState();
 649       aColChooser.setCurrentStructureFilterPanel(this);
 650       aColChooser.updateView();
 651     }
 652
 653     public void betaStrand_actionPerformed()
 654     {
 655       updateSelectAllState();
 656       aColChooser.setCurrentStructureFilterPanel(this);
 657       aColChooser.updateView();
 658     }
 659
 660     public void turn_actionPerformed()
 661     {
 662       updateSelectAllState();
 663       aColChooser.setCurrentStructureFilterPanel(this);
 664       aColChooser.updateView();
 665     }
 666
 667     public void all_actionPerformed()
 668     {
 669       if (all.isSelected())
 670       {
 671         alphaHelix.setSelected(true);
 672         betaStrand.setSelected(true);
 673         turn.setSelected(true);
 674       }
 675       else
 676       {
 677         alphaHelix.setSelected(false);
 678         betaStrand.setSelected(false);
 679         turn.setSelected(false);
 680       }
 681       aColChooser.setCurrentStructureFilterPanel(this);
 682       aColChooser.updateView();
 683     }
 684
 685     public void updateSelectAllState()
 686     {
 687       if (alphaHelix.isSelected() && betaStrand.isSelected()
 688               && turn.isSelected())
 689       {
 690         all.setSelected(true);
 691       }
 692       else
 693       {
 694         all.setSelected(false);
 695       }
 696     }
 697
 698     public void syncState()
 699     {
 700       StructureFilterPanel sfp = aColChooser
 701               .getCurrentStructureFilterPanel();
 702       if (sfp != null)
 703       {
 704         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 705         betaStrand.setSelected(sfp.betaStrand.isSelected());
 706         turn.setSelected(sfp.turn.isSelected());
 707         if (sfp.all.isSelected())
 708         {
 709           all.setSelected(true);
 710           alphaHelix.setSelected(true);
 711           betaStrand.setSelected(true);
 712           turn.setSelected(true);
 713         }
 714       }
 715
 716     }
 717   }
 718
 719   public class SearchPanel extends JPanel
 720   {
 721     private AnnotationColumnChooser aColChooser;
 722
 723     private JCheckBox displayName = new JCheckBox();
 724
 725     private JCheckBox description = new JCheckBox();
 726
 727     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 728
 729     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
 730             FILTER_BY_ANN_CACHE_KEY);
 731
 732     public SearchPanel(AnnotationColumnChooser aColChooser)
 733     {
 734
 735       this.aColChooser = aColChooser;
 736       JvSwingUtils.jvInitComponent(this);
 737       this.setBorder(new TitledBorder(
 738               MessageManager.getString("label.search_filter")));
 739
 740       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
 741       searchBox.setToolTipText(
 742               MessageManager.getString("info.enter_search_text_here"));
 743       searchBox.getEditor().getEditorComponent()
 744               .addKeyListener(new java.awt.event.KeyAdapter()
 745               {
 746                 @Override
 747                 public void keyPressed(KeyEvent e)
 748                 {
 749                   if (e.getKeyCode() == KeyEvent.VK_ENTER)
 750                   {
 751                     e.consume();
 752                     searchStringAction();
 753                   }
 754                 }
 755               });
 756
 757       JvSwingUtils.jvInitComponent(displayName, "label.label");
 758       displayName.addActionListener(new ActionListener()
 759       {
 760         @Override
 761         public void actionPerformed(ActionEvent actionEvent)
 762         {
 763           displayNameCheckboxAction();
 764         }
 765       });
 766
 767       JvSwingUtils.jvInitComponent(description, "label.description");
 768       description.addActionListener(new ActionListener()
 769       {
 770         @Override
 771         public void actionPerformed(ActionEvent actionEvent)
 772         {
 773           discriptionCheckboxAction();
 774         }
 775       });
 776
 777       syncState();
 778       this.add(searchBox);
 779       this.add(displayName);
 780       this.add(description);
 781     }
 782
 783     public void displayNameCheckboxAction()
 784     {
 785       aColChooser.setCurrentSearchPanel(this);
 786       aColChooser.updateView();
 787     }
 788
 789     public void discriptionCheckboxAction()
 790     {
 791       aColChooser.setCurrentSearchPanel(this);
 792       aColChooser.updateView();
 793     }
 794
 795     public void searchStringAction()
 796     {
 797       aColChooser.setCurrentSearchPanel(this);
 798       aColChooser.updateView();
 799       updateSearchPanelToolTips();
 800       searchBox.updateCache();
 801     }
 802
 803     public void syncState()
 804     {
 805       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 806       if (sp != null)
 807       {
 808         description.setEnabled(sp.description.isEnabled());
 809         description.setSelected(sp.description.isSelected());
 810
 811         displayName.setEnabled(sp.displayName.isEnabled());
 812         displayName.setSelected(sp.displayName.isSelected());
 813
 814         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 815       }
 816       updateSearchPanelToolTips();
 817     }
 818
 819     public void updateSearchPanelToolTips()
 820     {
 821       String defaultTtip = MessageManager
 822               .getString("info.enter_search_text_to_enable");
 823       String labelTtip = MessageManager.formatMessage(
 824               "info.search_in_annotation_label",
 825               annotations.getSelectedItem().toString());
 826       String descTtip = MessageManager.formatMessage(
 827               "info.search_in_annotation_description",
 828               annotations.getSelectedItem().toString());
 829       displayName.setToolTipText(
 830               displayName.isEnabled() ? labelTtip : defaultTtip);
 831       description.setToolTipText(
 832               description.isEnabled() ? descTtip : defaultTtip);
 833     }
 834   }
 835
 836   @Override
 837   public void ok_actionPerformed()
 838   {
 839     saveCache();
 840     super.ok_actionPerformed();
 841   }
 842
 843   @Override
 844   public void cancel_actionPerformed()
 845   {
 846     saveCache();
 847     super.cancel_actionPerformed();
 848   }
 849
 850   private void saveCache()
 851   {
 852     gSearchPanel.searchBox.persistCache();
 853     ngSearchPanel.searchBox.persistCache();
 854     gSearchPanel.searchBox.updateCache();
 855     ngSearchPanel.searchBox.updateCache();
 856   }
 857 }