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.FocusAdapter;
  37 import java.awt.event.FocusEvent;
  38 import java.awt.event.ItemEvent;
  39 import java.awt.event.ItemListener;
  40 import java.awt.event.KeyEvent;
  41
  42 import javax.swing.ButtonGroup;
  43 import javax.swing.JCheckBox;
  44 import javax.swing.JComboBox;
  45 import javax.swing.JInternalFrame;
  46 import javax.swing.JLayeredPane;
  47 import javax.swing.JPanel;
  48 import javax.swing.JRadioButton;
  49 import javax.swing.border.TitledBorder;
  50
  51 import net.miginfocom.swing.MigLayout;
  52
  53 @SuppressWarnings("serial")
  54 public class AnnotationColumnChooser extends AnnotationRowFilter
  55         implements ItemListener
  56 {
  57   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  58
  59   private JPanel annotationComboBoxPanel = new JPanel();
  60
  61   private StructureFilterPanel gStructureFilterPanel;
  62
  63   private StructureFilterPanel ngStructureFilterPanel;
  64
  65   private StructureFilterPanel currentStructureFilterPanel;
  66
  67   private SearchPanel currentSearchPanel;
  68
  69   private SearchPanel gSearchPanel;
  70
  71   private SearchPanel ngSearchPanel;
  72
  73   private FurtherActionPanel currentFurtherActionPanel;
  74
  75   private FurtherActionPanel gFurtherActionPanel;
  76
  77   private FurtherActionPanel ngFurtherActionPanel;
  78
  79   public static final int ACTION_OPTION_SELECT = 1;
  80
  81   public static int ACTION_OPTION_HIDE = 2;
  82
  83   public static String NO_GRAPH_VIEW = "0";
  84
  85   public static String GRAPH_VIEW = "1";
  86
  87   private int actionOption = ACTION_OPTION_SELECT;
  88
  89   private HiddenColumns oldHiddenColumns;
  90
  91   // J2SHIDDENCODE
  92   protected static int MIN_WIDTH = (/** @j2sNative 370||*/420);
  93
  94   // J2SHIDDENCODE
  95   protected static int MIN_HEIGHT = (/** @j2sNative 370||*/430);
  96
  97   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  98   {
  99     super(av, ap);
 100     frame = new JInternalFrame();
 101     frame.setContentPane(this);
 102     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 103     Desktop.addInternalFrame(frame,
 104             MessageManager.getString("label.select_by_annotation"), 0,
 105             0);
 106     // BH note: MIGLayout ignores this completely,
 107     // possibly creating a frame smaller than specified:
 108     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 109
 110     addSliderChangeListener();
 111     addSliderMouseListeners();
 112
 113     if (av.getAlignment().getAlignmentAnnotation() == null)
 114     {
 115       return;
 116     }
 117     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 118     adjusting = true;
 119
 120     setAnnotations(new JComboBox<>(getAnnotationItems(false)));
 121     populateThresholdComboBox(threshold);
 122     AnnotationColumnChooser lastChooser = av
 123             .getAnnotationColumnSelectionState();
 124     // restore Object state from the previous session if one exists
 125     if (lastChooser != null)
 126     {
 127       currentSearchPanel = lastChooser.getCurrentSearchPanel();
 128       currentStructureFilterPanel = lastChooser
 129               .getCurrentStructureFilterPanel();
 130       annotations.setSelectedIndex(
 131               lastChooser.getAnnotations().getSelectedIndex());
 132       threshold.setSelectedIndex(
 133               lastChooser.getThreshold().getSelectedIndex());
 134       actionOption = lastChooser.getActionOption();
 135       percentThreshold
 136               .setSelected(lastChooser.percentThreshold.isSelected());
 137     }
 138
 139     try
 140     {
 141       jbInit();
 142     } catch (Exception ex)
 143     {
 144     }
 145     adjusting = false;
 146
 147     updateView();
 148     frame.invalidate();
 149     frame.pack();
 150   }
 151
 152   @Override
 153   protected void jbInit()
 154   {
 155     super.jbInit();
 156
 157     JPanel thresholdPanel = new JPanel();
 158     thresholdPanel.setBorder(new TitledBorder(
 159             MessageManager.getString("label.threshold_filter")));
 160     thresholdPanel.setBackground(Color.white);
 161     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 162     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]") );
 163
 164     percentThreshold.setBackground(Color.white);
 165     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 166
 167     JPanel actionPanel = new JPanel();
 168     actionPanel.setBackground(Color.white);
 169     actionPanel.setFont(JvSwingUtils.getLabelFont());
 170
 171     JPanel graphFilterView = new JPanel();
 172     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 173     graphFilterView.setBackground(Color.white);
 174
 175     JPanel noGraphFilterView = new JPanel();
 176     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 177     noGraphFilterView.setBackground(Color.white);
 178
 179     annotationComboBoxPanel.setBackground(Color.white);
 180     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 181
 182     gSearchPanel = new SearchPanel(this);
 183     ngSearchPanel = new SearchPanel(this);
 184     gFurtherActionPanel = new FurtherActionPanel(this);
 185     ngFurtherActionPanel = new FurtherActionPanel(this);
 186     gStructureFilterPanel = new StructureFilterPanel(this);
 187     ngStructureFilterPanel = new StructureFilterPanel(this);
 188
 189     thresholdPanel.add(getThreshold());
 190     thresholdPanel.add(percentThreshold, "wrap");
 191     thresholdPanel.add(slider, "grow");
 192     thresholdPanel.add(thresholdValue, "span, wrap");
 193
 194     actionPanel.add(ok);
 195     actionPanel.add(cancel);
 196
 197     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 198     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 199     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 200     graphFilterView.add(gFurtherActionPanel);
 201
 202     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 203     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 204     noGraphFilterView.add(ngFurtherActionPanel);
 205
 206     annotationComboBoxPanel.add(getAnnotations());
 207     switchableViewsPanel.add(noGraphFilterView,
 208             AnnotationColumnChooser.NO_GRAPH_VIEW);
 209     switchableViewsPanel.add(graphFilterView,
 210             AnnotationColumnChooser.GRAPH_VIEW);
 211     this.setLayout(new BorderLayout());
 212     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 213     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 214     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 215
 216     selectedAnnotationChanged();
 217     updateThresholdPanelToolTip();
 218     this.validate();
 219   }
 220
 221   protected void updateThresholdPanelToolTip()
 222   {
 223     thresholdValue.setToolTipText("");
 224     slider.setToolTipText("");
 225
 226     String defaultTtip = MessageManager
 227             .getString("info.change_threshold_mode_to_enable");
 228
 229     String thresh = getThreshold().getSelectedItem().toString();
 230     if (thresh.equalsIgnoreCase("No Threshold"))
 231     {
 232       thresholdValue.setToolTipText(defaultTtip);
 233       slider.setToolTipText(defaultTtip);
 234     }
 235   }
 236
 237   @Override
 238   protected void reset()
 239   {
 240     if (this.getOldHiddenColumns() != null)
 241     {
 242       av.getColumnSelection().clear();
 243
 244       if (av.getAnnotationColumnSelectionState() != null)
 245       {
 246         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
 247                 .getOldHiddenColumns();
 248         av.getAlignment().setHiddenColumns(oldHidden);
 249       }
 250       av.sendSelection();
 251       ap.paintAlignment(true, true);
 252     }
 253   }
 254
 255   @Override
 256   public void valueChanged(boolean updateAllAnnotation)
 257   {
 258     if (slider.isEnabled())
 259     {
 260       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 261       updateView();
 262       propagateSeqAssociatedThreshold(updateAllAnnotation,
 263               getCurrentAnnotation());
 264       ap.paintAlignment(false, false);
 265     }
 266   }
 267
 268   @Override
 269   public void updateView()
 270   {
 271     // Check if combobox is still adjusting
 272     if (adjusting)
 273     {
 274       return;
 275     }
 276
 277     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 278
 279     setCurrentAnnotation(av.getAlignment()
 280             .getAlignmentAnnotation()[annmap[getAnnotations()
 281                     .getSelectedIndex()]]);
 282
 283     int selectedThresholdItem = getSelectedThresholdItem(
 284             getThreshold().getSelectedIndex());
 285
 286     slider.setEnabled(true);
 287     thresholdValue.setEnabled(true);
 288     percentThreshold.setEnabled(true);
 289
 290     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 291     {
 292       slider.setEnabled(false);
 293       thresholdValue.setEnabled(false);
 294       thresholdValue.setText("");
 295       percentThreshold.setEnabled(false);
 296       // build filter params
 297     }
 298     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 299     {
 300       if (getCurrentAnnotation().threshold == null)
 301       {
 302         getCurrentAnnotation().setThreshold(new jalview.datamodel.GraphLine(
 303                 (getCurrentAnnotation().graphMax
 304                         - getCurrentAnnotation().graphMin) / 2f,
 305                 "Threshold", Color.black));
 306       }
 307
 308       adjusting = true;
 309       float range = getCurrentAnnotation().graphMax * 1000
 310               - getCurrentAnnotation().graphMin * 1000;
 311
 312       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 313       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 314       slider.setValue(
 315               (int) (getCurrentAnnotation().threshold.value * 1000));
 316
 317       setThresholdValueText();
 318
 319       slider.setMajorTickSpacing((int) (range / 10f));
 320       slider.setEnabled(true);
 321       thresholdValue.setEnabled(true);
 322       adjusting = false;
 323
 324       // build filter params
 325       filterParams.setThresholdType(
 326               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 327       if (getCurrentAnnotation().isQuantitative())
 328       {
 329         filterParams
 330                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 331
 332         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 333         {
 334           filterParams.setThresholdType(
 335                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 336         }
 337         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 338         {
 339           filterParams.setThresholdType(
 340                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 341         }
 342       }
 343     }
 344
 345     updateThresholdPanelToolTip();
 346     if (currentStructureFilterPanel != null)
 347     {
 348       if (currentStructureFilterPanel.alphaHelix.isSelected())
 349       {
 350         filterParams.setFilterAlphaHelix(true);
 351       }
 352       if (currentStructureFilterPanel.betaStrand.isSelected())
 353       {
 354         filterParams.setFilterBetaSheet(true);
 355       }
 356       if (currentStructureFilterPanel.turn.isSelected())
 357       {
 358         filterParams.setFilterTurn(true);
 359       }
 360     }
 361
 362     if (currentSearchPanel != null)
 363     {
 364       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
 365       {
 366         filterParams.setRegexString(
 367                 currentSearchPanel.searchBox.getUserInput());
 368         if (currentSearchPanel.displayName.isSelected())
 369         {
 370           filterParams.addRegexSearchField(
 371                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 372         }
 373         if (currentSearchPanel.description.isSelected())
 374         {
 375           filterParams.addRegexSearchField(
 376                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 377         }
 378       }
 379     }
 380
 381     // show hidden columns here, before changing the column selection in
 382     // filterAnnotations, because showing hidden columns has the side effect of
 383     // adding them to the selection
 384     av.showAllHiddenColumns();
 385     av.getColumnSelection().filterAnnotations(
 386             getCurrentAnnotation().annotations, filterParams);
 387
 388     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
 389     if (hideCols)
 390     {
 391       av.hideSelectedColumns();
 392     }
 393     av.sendSelection();
 394
 395     filterParams = null;
 396     av.setAnnotationColumnSelectionState(this);
 397     // only update overview and structures if columns were hidden
 398     ap.paintAlignment(hideCols, hideCols);
 399   }
 400
 401   public HiddenColumns getOldHiddenColumns()
 402   {
 403     return oldHiddenColumns;
 404   }
 405
 406   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 407   {
 408     if (currentHiddenColumns != null)
 409     {
 410       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 411     }
 412   }
 413
 414   public FurtherActionPanel getCurrentFutherActionPanel()
 415   {
 416     return currentFurtherActionPanel;
 417   }
 418
 419   public void setCurrentFutherActionPanel(
 420           FurtherActionPanel currentFutherActionPanel)
 421   {
 422     this.currentFurtherActionPanel = currentFutherActionPanel;
 423   }
 424
 425   public SearchPanel getCurrentSearchPanel()
 426   {
 427     return currentSearchPanel;
 428   }
 429
 430   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 431   {
 432     this.currentSearchPanel = currentSearchPanel;
 433   }
 434
 435   public int getActionOption()
 436   {
 437     return actionOption;
 438   }
 439
 440   public void setActionOption(int actionOption)
 441   {
 442     this.actionOption = actionOption;
 443   }
 444
 445   public StructureFilterPanel getCurrentStructureFilterPanel()
 446   {
 447     return currentStructureFilterPanel;
 448   }
 449
 450   public void setCurrentStructureFilterPanel(
 451           StructureFilterPanel currentStructureFilterPanel)
 452   {
 453     this.currentStructureFilterPanel = currentStructureFilterPanel;
 454   }
 455
 456   public void select_action(ActionEvent actionEvent)
 457   {
 458     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 459     if (radioButton.isSelected())
 460     {
 461       setActionOption(ACTION_OPTION_SELECT);
 462       updateView();
 463     }
 464   }
 465
 466   public void hide_action(ActionEvent actionEvent)
 467   {
 468     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 469     if (radioButton.isSelected())
 470     {
 471       setActionOption(ACTION_OPTION_HIDE);
 472       updateView();
 473     }
 474   }
 475
 476   @Override
 477   public void itemStateChanged(ItemEvent e)
 478   {
 479     selectedAnnotationChanged();
 480   }
 481
 482   @Override
 483   public void selectedAnnotationChanged()
 484   {
 485     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 486     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 487             .getSelectedIndex()]].isQuantitative())
 488     {
 489       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 490     }
 491     saveCache();
 492     gSearchPanel.syncState();
 493     gFurtherActionPanel.syncState();
 494     gStructureFilterPanel.syncState();
 495
 496     ngSearchPanel.syncState();
 497     ngFurtherActionPanel.syncState();
 498     ngStructureFilterPanel.syncState();
 499
 500     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 501             .getLayout();
 502         switchableViewsLayout.show(switchableViewsPanel, currentView);
 503     updateView();
 504   }
 505
 506   public class FurtherActionPanel extends JPanel
 507   {
 508     private AnnotationColumnChooser aColChooser;
 509
 510     private JRadioButton hideOption = new JRadioButton();
 511
 512     private JRadioButton selectOption = new JRadioButton();
 513
 514     private ButtonGroup optionsGroup = new ButtonGroup();
 515
 516     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 517     {
 518       this.aColChooser = aColChooser;
 519       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 520       selectOption.addActionListener(new ActionListener()
 521       {
 522         @Override
 523         public void actionPerformed(ActionEvent actionEvent)
 524         {
 525           selectRadioAction(actionEvent);
 526         }
 527       });
 528
 529       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 530       hideOption.addActionListener(new ActionListener()
 531       {
 532         @Override
 533         public void actionPerformed(ActionEvent actionEvent)
 534         {
 535           hideRadioAction(actionEvent);
 536         }
 537       });
 538
 539       optionsGroup.add(selectOption);
 540       optionsGroup.add(hideOption);
 541       optionsGroup.setSelected(selectOption.getModel(), true);
 542
 543       JvSwingUtils.jvInitComponent(this);
 544       syncState();
 545
 546       this.add(selectOption);
 547       this.add(hideOption);
 548     }
 549
 550     public void selectRadioAction(ActionEvent actionEvent)
 551     {
 552       aColChooser.setCurrentFutherActionPanel(this);
 553       aColChooser.select_action(actionEvent);
 554     }
 555
 556     public void hideRadioAction(ActionEvent actionEvent)
 557     {
 558       aColChooser.setCurrentFutherActionPanel(this);
 559       aColChooser.hide_action(actionEvent);
 560     }
 561
 562     public void syncState()
 563     {
 564       if (aColChooser
 565               .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 566       {
 567         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 568       }
 569       else
 570       {
 571         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 572       }
 573     }
 574   }
 575
 576   public class StructureFilterPanel extends JPanel
 577   {
 578     private AnnotationColumnChooser aColChooser;
 579
 580     private JCheckBox alphaHelix = new JCheckBox();
 581
 582     private JCheckBox betaStrand = new JCheckBox();
 583
 584     private JCheckBox turn = new JCheckBox();
 585
 586     private JCheckBox all = new JCheckBox();
 587
 588     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 589     {
 590       this.aColChooser = aColChooser;
 591
 592       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 593       alphaHelix.addActionListener(new ActionListener()
 594       {
 595         @Override
 596         public void actionPerformed(ActionEvent actionEvent)
 597         {
 598           alphaHelix_actionPerformed();
 599         }
 600       });
 601
 602       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 603       betaStrand.addActionListener(new ActionListener()
 604       {
 605         @Override
 606         public void actionPerformed(ActionEvent actionEvent)
 607         {
 608           betaStrand_actionPerformed();
 609         }
 610       });
 611
 612       JvSwingUtils.jvInitComponent(turn, "label.turn");
 613       turn.addActionListener(new ActionListener()
 614       {
 615         @Override
 616         public void actionPerformed(ActionEvent actionEvent)
 617         {
 618           turn_actionPerformed();
 619         }
 620       });
 621
 622       JvSwingUtils.jvInitComponent(all, "label.select_all");
 623       all.addActionListener(new ActionListener()
 624       {
 625         @Override
 626         public void actionPerformed(ActionEvent actionEvent)
 627         {
 628           all_actionPerformed();
 629         }
 630       });
 631
 632       this.setBorder(new TitledBorder(
 633               MessageManager.getString("label.structures_filter")));
 634       JvSwingUtils.jvInitComponent(this);
 635
 636       this.add(all);
 637       this.add(alphaHelix);
 638       this.add(betaStrand);
 639       this.add(turn);
 640     }
 641
 642     public void alphaHelix_actionPerformed()
 643     {
 644       updateSelectAllState();
 645       aColChooser.setCurrentStructureFilterPanel(this);
 646       aColChooser.updateView();
 647     }
 648
 649     public void betaStrand_actionPerformed()
 650     {
 651       updateSelectAllState();
 652       aColChooser.setCurrentStructureFilterPanel(this);
 653       aColChooser.updateView();
 654     }
 655
 656     public void turn_actionPerformed()
 657     {
 658       updateSelectAllState();
 659       aColChooser.setCurrentStructureFilterPanel(this);
 660       aColChooser.updateView();
 661     }
 662
 663     public void all_actionPerformed()
 664     {
 665       if (all.isSelected())
 666       {
 667         alphaHelix.setSelected(true);
 668         betaStrand.setSelected(true);
 669         turn.setSelected(true);
 670       }
 671       else
 672       {
 673         alphaHelix.setSelected(false);
 674         betaStrand.setSelected(false);
 675         turn.setSelected(false);
 676       }
 677       aColChooser.setCurrentStructureFilterPanel(this);
 678       aColChooser.updateView();
 679     }
 680
 681     public void updateSelectAllState()
 682     {
 683       if (alphaHelix.isSelected() && betaStrand.isSelected()
 684               && turn.isSelected())
 685       {
 686         all.setSelected(true);
 687       }
 688       else
 689       {
 690         all.setSelected(false);
 691       }
 692     }
 693
 694     public void syncState()
 695     {
 696       StructureFilterPanel sfp = aColChooser
 697               .getCurrentStructureFilterPanel();
 698       if (sfp != null)
 699       {
 700         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 701         betaStrand.setSelected(sfp.betaStrand.isSelected());
 702         turn.setSelected(sfp.turn.isSelected());
 703         if (sfp.all.isSelected())
 704         {
 705           all.setSelected(true);
 706           alphaHelix.setSelected(true);
 707           betaStrand.setSelected(true);
 708           turn.setSelected(true);
 709         }
 710       }
 711
 712     }
 713   }
 714
 715   public class SearchPanel extends JPanel
 716   {
 717     private AnnotationColumnChooser aColChooser;
 718
 719     private JCheckBox displayName = new JCheckBox();
 720
 721     private JCheckBox description = new JCheckBox();
 722
 723     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 724
 725     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
 726             FILTER_BY_ANN_CACHE_KEY);
 727
 728     public SearchPanel(AnnotationColumnChooser aColChooser)
 729     {
 730
 731       this.aColChooser = aColChooser;
 732       JvSwingUtils.jvInitComponent(this);
 733       this.setBorder(new TitledBorder(
 734               MessageManager.getString("label.search_filter")));
 735
 736       searchBox.setPrototypeDisplayValue("XXXXXXXXXXXXXXXXXXXXXXX");
 737       searchBox.getComponent().setToolTipText(
 738               MessageManager.getString("info.enter_search_text_here"));
 739       searchBox.addKeyListener(new java.awt.event.KeyAdapter()
 740               {
 741                 @Override
 742                 public void keyPressed(KeyEvent e)
 743                 {
 744                   if (e.getKeyCode() == KeyEvent.VK_ENTER)
 745                   {
 746                     e.consume();
 747                     searchStringAction();
 748                   }
 749                 }
 750               });
 751       searchBox.addFocusListener(new FocusAdapter()
 752       {
 753         @Override
 754         public void focusLost(FocusEvent e)
 755         {
 756           searchStringAction();
 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           descriptionCheckboxAction();
 777         }
 778       });
 779
 780       syncState();
 781       this.add(searchBox.getComponent());
 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 descriptionCheckboxAction()
 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",
 828               annotations.getSelectedItem().toString());
 829       String descTtip = MessageManager.formatMessage(
 830               "info.search_in_annotation_description",
 831               annotations.getSelectedItem().toString());
 832       displayName.setToolTipText(
 833               displayName.isEnabled() ? labelTtip : defaultTtip);
 834       description.setToolTipText(
 835               description.isEnabled() ? descTtip : 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 }