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.Iterator;
  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           for (Iterator<int[]> itr = oldHidden.iterator(); itr.hasNext();)
 250           {
 251             int positions[] = itr.next();
 252             av.hideColumns(positions[0], positions[1]);
 253           }
 254         }
 255         av.getAlignment().setHiddenColumns(oldHidden);
 256       }
 257       ap.paintAlignment(true);
 258     }
 259
 260   }
 261
 262   @Override
 263   public void valueChanged(boolean updateAllAnnotation)
 264   {
 265     if (slider.isEnabled())
 266     {
 267       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 268       updateView();
 269       propagateSeqAssociatedThreshold(updateAllAnnotation,
 270               getCurrentAnnotation());
 271       ap.paintAlignment(false);
 272     }
 273   }
 274
 275   @Override
 276   public void updateView()
 277   {
 278     // Check if combobox is still adjusting
 279     if (adjusting)
 280     {
 281       return;
 282     }
 283
 284     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 285
 286     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 287             .getSelectedIndex()]]);
 288
 289     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 290             .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()
 309                 .setThreshold(
 310                         new jalview.datamodel.GraphLine(
 311                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 312                                 "Threshold", Color.black));
 313       }
 314
 315       adjusting = true;
 316       float range = getCurrentAnnotation().graphMax * 1000
 317               - getCurrentAnnotation().graphMin * 1000;
 318
 319       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 320       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 321       slider.setValue((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
 332               .setThresholdType(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
 341                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 342         }
 343         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 344         {
 345           filterParams
 346                   .setThresholdType(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(currentSearchPanel.searchBox
 373                 .getUserInput());
 374         if (currentSearchPanel.displayName.isSelected())
 375         {
 376           filterParams
 377                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 378         }
 379         if (currentSearchPanel.description.isSelected())
 380         {
 381           filterParams
 382                   .addRegexSearchField(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
 399     filterParams = null;
 400     av.setAnnotationColumnSelectionState(this);
 401     ap.paintAlignment(true);
 402   }
 403
 404   public HiddenColumns getOldHiddenColumns()
 405   {
 406     return oldHiddenColumns;
 407   }
 408
 409   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 410   {
 411     if (currentHiddenColumns != null)
 412     {
 413       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 414     }
 415   }
 416
 417   public FurtherActionPanel getCurrentFutherActionPanel()
 418   {
 419     return currentFurtherActionPanel;
 420   }
 421
 422   public void setCurrentFutherActionPanel(
 423           FurtherActionPanel currentFutherActionPanel)
 424   {
 425     this.currentFurtherActionPanel = currentFutherActionPanel;
 426   }
 427
 428   public SearchPanel getCurrentSearchPanel()
 429   {
 430     return currentSearchPanel;
 431   }
 432
 433   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 434   {
 435     this.currentSearchPanel = currentSearchPanel;
 436   }
 437
 438   public int getActionOption()
 439   {
 440     return actionOption;
 441   }
 442
 443   public void setActionOption(int actionOption)
 444   {
 445     this.actionOption = actionOption;
 446   }
 447
 448   public StructureFilterPanel getCurrentStructureFilterPanel()
 449   {
 450     return currentStructureFilterPanel;
 451   }
 452
 453   public void setCurrentStructureFilterPanel(
 454           StructureFilterPanel currentStructureFilterPanel)
 455   {
 456     this.currentStructureFilterPanel = currentStructureFilterPanel;
 457   }
 458
 459   public void select_action(ActionEvent actionEvent)
 460   {
 461     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 462     if (radioButton.isSelected())
 463     {
 464       setActionOption(ACTION_OPTION_SELECT);
 465       updateView();
 466     }
 467   }
 468
 469   public void hide_action(ActionEvent actionEvent)
 470   {
 471     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 472     if (radioButton.isSelected())
 473     {
 474       setActionOption(ACTION_OPTION_HIDE);
 475       updateView();
 476     }
 477   }
 478
 479   @Override
 480   public void itemStateChanged(ItemEvent e)
 481   {
 482     selectedAnnotationChanged();
 483   }
 484
 485   @Override
 486   public void selectedAnnotationChanged()
 487   {
 488     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 489     if (av.getAlignment()
 490             .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.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 569       {
 570         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 571       }
 572       else
 573       {
 574         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 575       }
 576     }
 577   }
 578
 579   public class StructureFilterPanel extends JPanel
 580   {
 581     private AnnotationColumnChooser aColChooser;
 582
 583     private JCheckBox alphaHelix = new JCheckBox();
 584
 585     private JCheckBox betaStrand = new JCheckBox();
 586
 587     private JCheckBox turn = new JCheckBox();
 588
 589     private JCheckBox all = new JCheckBox();
 590
 591     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 592     {
 593       this.aColChooser = aColChooser;
 594
 595       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 596       alphaHelix.addActionListener(new ActionListener()
 597       {
 598         @Override
 599         public void actionPerformed(ActionEvent actionEvent)
 600         {
 601           alphaHelix_actionPerformed();
 602         }
 603       });
 604
 605       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 606       betaStrand.addActionListener(new ActionListener()
 607       {
 608         @Override
 609         public void actionPerformed(ActionEvent actionEvent)
 610         {
 611           betaStrand_actionPerformed();
 612         }
 613       });
 614
 615       JvSwingUtils.jvInitComponent(turn, "label.turn");
 616       turn.addActionListener(new ActionListener()
 617       {
 618         @Override
 619         public void actionPerformed(ActionEvent actionEvent)
 620         {
 621           turn_actionPerformed();
 622         }
 623       });
 624
 625       JvSwingUtils.jvInitComponent(all, "label.select_all");
 626       all.addActionListener(new ActionListener()
 627       {
 628         @Override
 629         public void actionPerformed(ActionEvent actionEvent)
 630         {
 631           all_actionPerformed();
 632         }
 633       });
 634
 635       this.setBorder(new TitledBorder(MessageManager
 636               .getString("label.structures_filter")));
 637       JvSwingUtils.jvInitComponent(this);
 638
 639       this.add(all);
 640       this.add(alphaHelix);
 641       this.add(betaStrand);
 642       this.add(turn);
 643     }
 644
 645     public void alphaHelix_actionPerformed()
 646     {
 647       updateSelectAllState();
 648       aColChooser.setCurrentStructureFilterPanel(this);
 649       aColChooser.updateView();
 650     }
 651
 652     public void betaStrand_actionPerformed()
 653     {
 654       updateSelectAllState();
 655       aColChooser.setCurrentStructureFilterPanel(this);
 656       aColChooser.updateView();
 657     }
 658
 659     public void turn_actionPerformed()
 660     {
 661       updateSelectAllState();
 662       aColChooser.setCurrentStructureFilterPanel(this);
 663       aColChooser.updateView();
 664     }
 665
 666     public void all_actionPerformed()
 667     {
 668       if (all.isSelected())
 669       {
 670         alphaHelix.setSelected(true);
 671         betaStrand.setSelected(true);
 672         turn.setSelected(true);
 673       }
 674       else
 675       {
 676         alphaHelix.setSelected(false);
 677         betaStrand.setSelected(false);
 678         turn.setSelected(false);
 679       }
 680       aColChooser.setCurrentStructureFilterPanel(this);
 681       aColChooser.updateView();
 682     }
 683
 684     public void updateSelectAllState()
 685     {
 686       if (alphaHelix.isSelected() && betaStrand.isSelected()
 687               && turn.isSelected())
 688       {
 689         all.setSelected(true);
 690       }
 691       else
 692       {
 693         all.setSelected(false);
 694       }
 695     }
 696
 697     public void syncState()
 698     {
 699       StructureFilterPanel sfp = aColChooser
 700               .getCurrentStructureFilterPanel();
 701       if (sfp != null)
 702       {
 703         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 704         betaStrand.setSelected(sfp.betaStrand.isSelected());
 705         turn.setSelected(sfp.turn.isSelected());
 706         if (sfp.all.isSelected())
 707         {
 708           all.setSelected(true);
 709           alphaHelix.setSelected(true);
 710           betaStrand.setSelected(true);
 711           turn.setSelected(true);
 712         }
 713       }
 714
 715     }
 716   }
 717
 718   public class SearchPanel extends JPanel
 719   {
 720     private AnnotationColumnChooser aColChooser;
 721
 722     private JCheckBox displayName = new JCheckBox();
 723
 724     private JCheckBox description = new JCheckBox();
 725
 726     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 727
 728     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
 729             FILTER_BY_ANN_CACHE_KEY);
 730
 731     public SearchPanel(AnnotationColumnChooser aColChooser)
 732     {
 733
 734       this.aColChooser = aColChooser;
 735       JvSwingUtils.jvInitComponent(this);
 736       this.setBorder(new TitledBorder(MessageManager
 737               .getString("label.search_filter")));
 738
 739       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
 740       searchBox.setToolTipText(MessageManager
 741               .getString("info.enter_search_text_here"));
 742       searchBox.getEditor().getEditorComponent()
 743               .addKeyListener(new java.awt.event.KeyAdapter()
 744               {
 745                 @Override
 746                 public void keyPressed(KeyEvent e)
 747                 {
 748                   if (e.getKeyCode() == KeyEvent.VK_ENTER)
 749                   {
 750                     e.consume();
 751                     searchStringAction();
 752                   }
 753                 }
 754               });
 755
 756
 757
 758       JvSwingUtils.jvInitComponent(displayName, "label.label");
 759       displayName.addActionListener(new ActionListener()
 760       {
 761         @Override
 762         public void actionPerformed(ActionEvent actionEvent)
 763         {
 764           displayNameCheckboxAction();
 765         }
 766       });
 767
 768       JvSwingUtils.jvInitComponent(description, "label.description");
 769       description.addActionListener(new ActionListener()
 770       {
 771         @Override
 772         public void actionPerformed(ActionEvent actionEvent)
 773         {
 774           discriptionCheckboxAction();
 775         }
 776       });
 777
 778       syncState();
 779       this.add(searchBox);
 780       this.add(displayName);
 781       this.add(description);
 782     }
 783
 784     public void displayNameCheckboxAction()
 785     {
 786       aColChooser.setCurrentSearchPanel(this);
 787       aColChooser.updateView();
 788     }
 789
 790     public void discriptionCheckboxAction()
 791     {
 792       aColChooser.setCurrentSearchPanel(this);
 793       aColChooser.updateView();
 794     }
 795
 796     public void searchStringAction()
 797     {
 798       aColChooser.setCurrentSearchPanel(this);
 799       aColChooser.updateView();
 800       updateSearchPanelToolTips();
 801       searchBox.updateCache();
 802     }
 803
 804     public void syncState()
 805     {
 806       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 807       if (sp != null)
 808       {
 809         description.setEnabled(sp.description.isEnabled());
 810         description.setSelected(sp.description.isSelected());
 811
 812         displayName.setEnabled(sp.displayName.isEnabled());
 813         displayName.setSelected(sp.displayName.isSelected());
 814
 815         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 816       }
 817       updateSearchPanelToolTips();
 818     }
 819
 820     public void updateSearchPanelToolTips()
 821     {
 822       String defaultTtip = MessageManager
 823               .getString("info.enter_search_text_to_enable");
 824       String labelTtip = MessageManager.formatMessage(
 825               "info.search_in_annotation_label", annotations
 826                       .getSelectedItem().toString());
 827       String descTtip = MessageManager.formatMessage(
 828               "info.search_in_annotation_description", annotations
 829                       .getSelectedItem().toString());
 830       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 831               : defaultTtip);
 832       description.setToolTipText(description.isEnabled() ? descTtip
 833               : defaultTtip);
 834     }
 835   }
 836
 837   @Override
 838   public void ok_actionPerformed()
 839   {
 840     saveCache();
 841     super.ok_actionPerformed();
 842   }
 843
 844   @Override
 845   public void cancel_actionPerformed()
 846   {
 847     saveCache();
 848     super.cancel_actionPerformed();
 849   }
 850
 851   private void saveCache()
 852   {
 853     gSearchPanel.searchBox.persistCache();
 854     ngSearchPanel.searchBox.persistCache();
 855     gSearchPanel.searchBox.updateCache();
 856     ngSearchPanel.searchBox.updateCache();
 857   }
 858 }