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       ap.paintAlignment(true);
 260     }
 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
 401     filterParams = null;
 402     av.setAnnotationColumnSelectionState(this);
 403     ap.paintAlignment(true);
 404   }
 405
 406   public HiddenColumns getOldHiddenColumns()
 407   {
 408     return oldHiddenColumns;
 409   }
 410
 411   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 412   {
 413     if (currentHiddenColumns != null)
 414     {
 415       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 416     }
 417   }
 418
 419   public FurtherActionPanel getCurrentFutherActionPanel()
 420   {
 421     return currentFurtherActionPanel;
 422   }
 423
 424   public void setCurrentFutherActionPanel(
 425           FurtherActionPanel currentFutherActionPanel)
 426   {
 427     this.currentFurtherActionPanel = currentFutherActionPanel;
 428   }
 429
 430   public SearchPanel getCurrentSearchPanel()
 431   {
 432     return currentSearchPanel;
 433   }
 434
 435   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 436   {
 437     this.currentSearchPanel = currentSearchPanel;
 438   }
 439
 440   public int getActionOption()
 441   {
 442     return actionOption;
 443   }
 444
 445   public void setActionOption(int actionOption)
 446   {
 447     this.actionOption = actionOption;
 448   }
 449
 450   public StructureFilterPanel getCurrentStructureFilterPanel()
 451   {
 452     return currentStructureFilterPanel;
 453   }
 454
 455   public void setCurrentStructureFilterPanel(
 456           StructureFilterPanel currentStructureFilterPanel)
 457   {
 458     this.currentStructureFilterPanel = currentStructureFilterPanel;
 459   }
 460
 461   public void select_action(ActionEvent actionEvent)
 462   {
 463     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 464     if (radioButton.isSelected())
 465     {
 466       setActionOption(ACTION_OPTION_SELECT);
 467       updateView();
 468     }
 469   }
 470
 471   public void hide_action(ActionEvent actionEvent)
 472   {
 473     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 474     if (radioButton.isSelected())
 475     {
 476       setActionOption(ACTION_OPTION_HIDE);
 477       updateView();
 478     }
 479   }
 480
 481   @Override
 482   public void itemStateChanged(ItemEvent e)
 483   {
 484     selectedAnnotationChanged();
 485   }
 486
 487   @Override
 488   public void selectedAnnotationChanged()
 489   {
 490     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 491     if (av.getAlignment()
 492             .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.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 571       {
 572         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 573       }
 574       else
 575       {
 576         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 577       }
 578     }
 579   }
 580
 581   public class StructureFilterPanel extends JPanel
 582   {
 583     private AnnotationColumnChooser aColChooser;
 584
 585     private JCheckBox alphaHelix = new JCheckBox();
 586
 587     private JCheckBox betaStrand = new JCheckBox();
 588
 589     private JCheckBox turn = new JCheckBox();
 590
 591     private JCheckBox all = new JCheckBox();
 592
 593     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 594     {
 595       this.aColChooser = aColChooser;
 596
 597       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 598       alphaHelix.addActionListener(new ActionListener()
 599       {
 600         @Override
 601         public void actionPerformed(ActionEvent actionEvent)
 602         {
 603           alphaHelix_actionPerformed();
 604         }
 605       });
 606
 607       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 608       betaStrand.addActionListener(new ActionListener()
 609       {
 610         @Override
 611         public void actionPerformed(ActionEvent actionEvent)
 612         {
 613           betaStrand_actionPerformed();
 614         }
 615       });
 616
 617       JvSwingUtils.jvInitComponent(turn, "label.turn");
 618       turn.addActionListener(new ActionListener()
 619       {
 620         @Override
 621         public void actionPerformed(ActionEvent actionEvent)
 622         {
 623           turn_actionPerformed();
 624         }
 625       });
 626
 627       JvSwingUtils.jvInitComponent(all, "label.select_all");
 628       all.addActionListener(new ActionListener()
 629       {
 630         @Override
 631         public void actionPerformed(ActionEvent actionEvent)
 632         {
 633           all_actionPerformed();
 634         }
 635       });
 636
 637       this.setBorder(new TitledBorder(MessageManager
 638               .getString("label.structures_filter")));
 639       JvSwingUtils.jvInitComponent(this);
 640
 641       this.add(all);
 642       this.add(alphaHelix);
 643       this.add(betaStrand);
 644       this.add(turn);
 645     }
 646
 647     public void alphaHelix_actionPerformed()
 648     {
 649       updateSelectAllState();
 650       aColChooser.setCurrentStructureFilterPanel(this);
 651       aColChooser.updateView();
 652     }
 653
 654     public void betaStrand_actionPerformed()
 655     {
 656       updateSelectAllState();
 657       aColChooser.setCurrentStructureFilterPanel(this);
 658       aColChooser.updateView();
 659     }
 660
 661     public void turn_actionPerformed()
 662     {
 663       updateSelectAllState();
 664       aColChooser.setCurrentStructureFilterPanel(this);
 665       aColChooser.updateView();
 666     }
 667
 668     public void all_actionPerformed()
 669     {
 670       if (all.isSelected())
 671       {
 672         alphaHelix.setSelected(true);
 673         betaStrand.setSelected(true);
 674         turn.setSelected(true);
 675       }
 676       else
 677       {
 678         alphaHelix.setSelected(false);
 679         betaStrand.setSelected(false);
 680         turn.setSelected(false);
 681       }
 682       aColChooser.setCurrentStructureFilterPanel(this);
 683       aColChooser.updateView();
 684     }
 685
 686     public void updateSelectAllState()
 687     {
 688       if (alphaHelix.isSelected() && betaStrand.isSelected()
 689               && turn.isSelected())
 690       {
 691         all.setSelected(true);
 692       }
 693       else
 694       {
 695         all.setSelected(false);
 696       }
 697     }
 698
 699     public void syncState()
 700     {
 701       StructureFilterPanel sfp = aColChooser
 702               .getCurrentStructureFilterPanel();
 703       if (sfp != null)
 704       {
 705         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 706         betaStrand.setSelected(sfp.betaStrand.isSelected());
 707         turn.setSelected(sfp.turn.isSelected());
 708         if (sfp.all.isSelected())
 709         {
 710           all.setSelected(true);
 711           alphaHelix.setSelected(true);
 712           betaStrand.setSelected(true);
 713           turn.setSelected(true);
 714         }
 715       }
 716
 717     }
 718   }
 719
 720   public class SearchPanel extends JPanel
 721   {
 722     private AnnotationColumnChooser aColChooser;
 723
 724     private JCheckBox displayName = new JCheckBox();
 725
 726     private JCheckBox description = new JCheckBox();
 727
 728     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 729
 730     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
 731             FILTER_BY_ANN_CACHE_KEY);
 732
 733     public SearchPanel(AnnotationColumnChooser aColChooser)
 734     {
 735
 736       this.aColChooser = aColChooser;
 737       JvSwingUtils.jvInitComponent(this);
 738       this.setBorder(new TitledBorder(MessageManager
 739               .getString("label.search_filter")));
 740
 741       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
 742       searchBox.setToolTipText(MessageManager
 743               .getString("info.enter_search_text_here"));
 744       searchBox.getEditor().getEditorComponent()
 745               .addKeyListener(new java.awt.event.KeyAdapter()
 746               {
 747                 @Override
 748                 public void keyPressed(KeyEvent e)
 749                 {
 750                   if (e.getKeyCode() == KeyEvent.VK_ENTER)
 751                   {
 752                     e.consume();
 753                     searchStringAction();
 754                   }
 755                 }
 756               });
 757
 758
 759
 760       JvSwingUtils.jvInitComponent(displayName, "label.label");
 761       displayName.addActionListener(new ActionListener()
 762       {
 763         @Override
 764         public void actionPerformed(ActionEvent actionEvent)
 765         {
 766           displayNameCheckboxAction();
 767         }
 768       });
 769
 770       JvSwingUtils.jvInitComponent(description, "label.description");
 771       description.addActionListener(new ActionListener()
 772       {
 773         @Override
 774         public void actionPerformed(ActionEvent actionEvent)
 775         {
 776           discriptionCheckboxAction();
 777         }
 778       });
 779
 780       syncState();
 781       this.add(searchBox);
 782       this.add(displayName);
 783       this.add(description);
 784     }
 785
 786     public void displayNameCheckboxAction()
 787     {
 788       aColChooser.setCurrentSearchPanel(this);
 789       aColChooser.updateView();
 790     }
 791
 792     public void discriptionCheckboxAction()
 793     {
 794       aColChooser.setCurrentSearchPanel(this);
 795       aColChooser.updateView();
 796     }
 797
 798     public void searchStringAction()
 799     {
 800       aColChooser.setCurrentSearchPanel(this);
 801       aColChooser.updateView();
 802       updateSearchPanelToolTips();
 803       searchBox.updateCache();
 804     }
 805
 806     public void syncState()
 807     {
 808       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 809       if (sp != null)
 810       {
 811         description.setEnabled(sp.description.isEnabled());
 812         description.setSelected(sp.description.isSelected());
 813
 814         displayName.setEnabled(sp.displayName.isEnabled());
 815         displayName.setSelected(sp.displayName.isSelected());
 816
 817         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 818       }
 819       updateSearchPanelToolTips();
 820     }
 821
 822     public void updateSearchPanelToolTips()
 823     {
 824       String defaultTtip = MessageManager
 825               .getString("info.enter_search_text_to_enable");
 826       String labelTtip = MessageManager.formatMessage(
 827               "info.search_in_annotation_label", annotations
 828                       .getSelectedItem().toString());
 829       String descTtip = MessageManager.formatMessage(
 830               "info.search_in_annotation_description", annotations
 831                       .getSelectedItem().toString());
 832       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 833               : defaultTtip);
 834       description.setToolTipText(description.isEnabled() ? descTtip
 835               : defaultTtip);
 836     }
 837   }
 838
 839   @Override
 840   public void ok_actionPerformed()
 841   {
 842     saveCache();
 843     super.ok_actionPerformed();
 844   }
 845
 846   @Override
 847   public void cancel_actionPerformed()
 848   {
 849     saveCache();
 850     super.cancel_actionPerformed();
 851   }
 852
 853   private void saveCache()
 854   {
 855     gSearchPanel.searchBox.persistCache();
 856     ngSearchPanel.searchBox.persistCache();
 857     gSearchPanel.searchBox.updateCache();
 858     ngSearchPanel.searchBox.updateCache();
 859   }
 860 }