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.AlignmentAnnotation;
  25 import jalview.datamodel.ColumnSelection;
  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.util.Iterator;
  39
  40 import javax.swing.ButtonGroup;
  41 import javax.swing.JCheckBox;
  42 import javax.swing.JComboBox;
  43 import javax.swing.JInternalFrame;
  44 import javax.swing.JLayeredPane;
  45 import javax.swing.JPanel;
  46 import javax.swing.JRadioButton;
  47 import javax.swing.JTextField;
  48 import javax.swing.border.TitledBorder;
  49 import javax.swing.event.DocumentEvent;
  50 import javax.swing.event.DocumentListener;
  51
  52 import net.miginfocom.swing.MigLayout;
  53
  54 @SuppressWarnings("serial")
  55 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  56         ItemListener
  57 {
  58   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  59
  60   private JPanel annotationComboBoxPanel = new JPanel();
  61
  62   private StructureFilterPanel gStructureFilterPanel;
  63
  64   private StructureFilterPanel ngStructureFilterPanel;
  65
  66   private StructureFilterPanel currentStructureFilterPanel;
  67
  68   private SearchPanel currentSearchPanel;
  69
  70   private SearchPanel gSearchPanel;
  71
  72   private SearchPanel ngSearchPanel;
  73
  74   private FurtherActionPanel currentFurtherActionPanel;
  75
  76   private FurtherActionPanel gFurtherActionPanel;
  77
  78   private FurtherActionPanel ngFurtherActionPanel;
  79
  80   public static final int ACTION_OPTION_SELECT = 1;
  81
  82   public static int ACTION_OPTION_HIDE = 2;
  83
  84   public static String NO_GRAPH_VIEW = "0";
  85
  86   public static String GRAPH_VIEW = "1";
  87
  88   private int actionOption = ACTION_OPTION_SELECT;
  89
  90   private ColumnSelection oldColumnSelection;
  91
  92   protected int MIN_WIDTH = 420;
  93
  94   protected int MIN_HEIGHT = 430;
  95
  96   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  97   {
  98     super(av, ap);
  99     frame = new JInternalFrame();
 100     frame.setContentPane(this);
 101     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 102     Desktop.addInternalFrame(frame,
 103             MessageManager.getString("label.select_by_annotation"), 520,
 104             215);
 105     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 106
 107     addSliderChangeListener();
 108     addSliderMouseListeners();
 109
 110     if (av.getAlignment().getAlignmentAnnotation() == null)
 111     {
 112       return;
 113     }
 114     setOldColumnSelection(av.getColumnSelection());
 115     adjusting = true;
 116
 117     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 118     populateThresholdComboBox(threshold);
 119
 120     // restore Object state from the previous session if one exists
 121     if (av.getAnnotationColumnSelectionState() != null)
 122     {
 123       currentSearchPanel = av.getAnnotationColumnSelectionState()
 124               .getCurrentSearchPanel();
 125       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 126               .getCurrentStructureFilterPanel();
 127       annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
 128               .getAnnotations().getSelectedIndex());
 129       threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
 130               .getThreshold().getSelectedIndex());
 131       actionOption = av.getAnnotationColumnSelectionState()
 132               .getActionOption();
 133     }
 134
 135     try
 136     {
 137       jbInit();
 138     } catch (Exception ex)
 139     {
 140     }
 141     adjusting = false;
 142
 143     updateView();
 144     frame.invalidate();
 145     frame.pack();
 146   }
 147
 148   @Override
 149   protected void jbInit()
 150   {
 151     super.jbInit();
 152
 153     JPanel thresholdPanel = new JPanel();
 154     thresholdPanel.setBorder(new TitledBorder(MessageManager
 155             .getString("label.threshold_filter")));
 156     thresholdPanel.setBackground(Color.white);
 157     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 158     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 159
 160     JPanel actionPanel = new JPanel();
 161     actionPanel.setBackground(Color.white);
 162     actionPanel.setFont(JvSwingUtils.getLabelFont());
 163
 164     JPanel graphFilterView = new JPanel();
 165     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 166     graphFilterView.setBackground(Color.white);
 167
 168     JPanel noGraphFilterView = new JPanel();
 169     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 170     noGraphFilterView.setBackground(Color.white);
 171
 172     annotationComboBoxPanel.setBackground(Color.white);
 173     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 174
 175     gSearchPanel = new SearchPanel(this);
 176     ngSearchPanel = new SearchPanel(this);
 177     gFurtherActionPanel = new FurtherActionPanel(this);
 178     ngFurtherActionPanel = new FurtherActionPanel(this);
 179     gStructureFilterPanel = new StructureFilterPanel(this);
 180     ngStructureFilterPanel = new StructureFilterPanel(this);
 181
 182     thresholdPanel.add(getThreshold());
 183     thresholdPanel.add(thresholdValue, "wrap");
 184     thresholdPanel.add(slider, "grow, span, wrap");
 185
 186     actionPanel.add(ok);
 187     actionPanel.add(cancel);
 188
 189     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 190     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 191     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 192     graphFilterView.add(gFurtherActionPanel);
 193
 194     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 195     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 196     noGraphFilterView.add(ngFurtherActionPanel);
 197
 198     annotationComboBoxPanel.add(getAnnotations());
 199     switchableViewsPanel.add(noGraphFilterView,
 200             AnnotationColumnChooser.NO_GRAPH_VIEW);
 201     switchableViewsPanel.add(graphFilterView,
 202             AnnotationColumnChooser.GRAPH_VIEW);
 203
 204     this.setLayout(new BorderLayout());
 205     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 206     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 207     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 208
 209     selectedAnnotationChanged();
 210     updateThresholdPanelToolTip();
 211     this.validate();
 212   }
 213
 214   protected void updateThresholdPanelToolTip()
 215   {
 216     thresholdValue.setToolTipText("");
 217     slider.setToolTipText("");
 218
 219     String defaultTtip = MessageManager
 220             .getString("info.change_threshold_mode_to_enable");
 221
 222     String thresh = getThreshold().getSelectedItem().toString();
 223     if (thresh.equalsIgnoreCase("No Threshold"))
 224     {
 225       thresholdValue.setToolTipText(defaultTtip);
 226       slider.setToolTipText(defaultTtip);
 227     }
 228   }
 229
 230   @Override
 231   protected void reset()
 232   {
 233     if (this.getOldColumnSelection() != null)
 234     {
 235       av.getColumnSelection().clear();
 236
 237       if (av.getAnnotationColumnSelectionState() != null)
 238       {
 239         ColumnSelection oldSelection = av
 240                 .getAnnotationColumnSelectionState()
 241                 .getOldColumnSelection();
 242         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 243                 && !oldSelection.getHiddenColumns().isEmpty())
 244         {
 245           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 246                   .iterator(); itr.hasNext();)
 247           {
 248             int positions[] = itr.next();
 249             av.hideColumns(positions[0], positions[1]);
 250           }
 251         }
 252         av.setColumnSelection(oldSelection);
 253       }
 254       ap.paintAlignment(true);
 255     }
 256
 257   }
 258
 259   @Override
 260   public void valueChanged(boolean updateAllAnnotation)
 261   {
 262     if (slider.isEnabled())
 263     {
 264       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 265       updateView();
 266       propagateSeqAssociatedThreshold(updateAllAnnotation,
 267               getCurrentAnnotation());
 268       ap.paintAlignment(false);
 269     }
 270   }
 271
 272   @Override
 273   public void updateView()
 274   {
 275     // Check if combobox is still adjusting
 276     if (adjusting)
 277     {
 278       return;
 279     }
 280
 281     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 282
 283     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 284             .getSelectedIndex()]]);
 285
 286     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 287             .getSelectedIndex());
 288
 289     slider.setEnabled(true);
 290     thresholdValue.setEnabled(true);
 291
 292     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 293     {
 294       slider.setEnabled(false);
 295       thresholdValue.setEnabled(false);
 296       thresholdValue.setText("");
 297       // build filter params
 298     }
 299     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 300     {
 301       if (getCurrentAnnotation().threshold == null)
 302       {
 303         getCurrentAnnotation()
 304                 .setThreshold(
 305                         new jalview.datamodel.GraphLine(
 306                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 307                                 "Threshold", Color.black));
 308       }
 309
 310       adjusting = true;
 311       float range = getCurrentAnnotation().graphMax * 1000
 312               - getCurrentAnnotation().graphMin * 1000;
 313
 314       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 315       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 316       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 317       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 318       slider.setMajorTickSpacing((int) (range / 10f));
 319       slider.setEnabled(true);
 320       thresholdValue.setEnabled(true);
 321       adjusting = false;
 322
 323       // build filter params
 324       filterParams
 325               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 326       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 327       {
 328         filterParams
 329                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 330
 331         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 332         {
 333           filterParams
 334                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 335         }
 336         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 337         {
 338           filterParams
 339                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 340         }
 341       }
 342     }
 343
 344     updateThresholdPanelToolTip();
 345     if (currentStructureFilterPanel != null)
 346     {
 347       if (currentStructureFilterPanel.alphaHelix.isSelected())
 348       {
 349         filterParams.setFilterAlphaHelix(true);
 350       }
 351       if (currentStructureFilterPanel.betaStrand.isSelected())
 352       {
 353         filterParams.setFilterBetaSheet(true);
 354       }
 355       if (currentStructureFilterPanel.turn.isSelected())
 356       {
 357         filterParams.setFilterTurn(true);
 358       }
 359     }
 360
 361     if (currentSearchPanel != null)
 362     {
 363
 364       if (!currentSearchPanel.searchBox.getText().isEmpty())
 365       {
 366         currentSearchPanel.description.setEnabled(true);
 367         currentSearchPanel.displayName.setEnabled(true);
 368         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 369         if (currentSearchPanel.displayName.isSelected())
 370         {
 371           filterParams
 372                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 373         }
 374         if (currentSearchPanel.description.isSelected())
 375         {
 376           filterParams
 377                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 378         }
 379       }
 380       else
 381       {
 382         currentSearchPanel.description.setEnabled(false);
 383         currentSearchPanel.displayName.setEnabled(false);
 384       }
 385     }
 386
 387     av.getColumnSelection().filterAnnotations(
 388             getCurrentAnnotation().annotations, filterParams);
 389
 390     av.showAllHiddenColumns();
 391     if (getActionOption() == ACTION_OPTION_HIDE)
 392     {
 393       av.hideSelectedColumns();
 394     }
 395
 396     filterParams = null;
 397     av.setAnnotationColumnSelectionState(this);
 398     ap.paintAlignment(true);
 399   }
 400
 401   public ColumnSelection getOldColumnSelection()
 402   {
 403     return oldColumnSelection;
 404   }
 405
 406   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 407   {
 408     if (currentColumnSelection != null)
 409     {
 410       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 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()]].graph != AlignmentAnnotation.NO_GRAPH)
 488     {
 489       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 490     }
 491
 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.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 565       {
 566         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 567       }
 568       else
 569       {
 570         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 571       }
 572     }
 573   }
 574
 575   public class StructureFilterPanel extends JPanel
 576   {
 577     private AnnotationColumnChooser aColChooser;
 578
 579     private JCheckBox alphaHelix = new JCheckBox();
 580
 581     private JCheckBox betaStrand = new JCheckBox();
 582
 583     private JCheckBox turn = new JCheckBox();
 584
 585     private JCheckBox all = new JCheckBox();
 586
 587     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 588     {
 589       this.aColChooser = aColChooser;
 590
 591       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 592       alphaHelix.addActionListener(new ActionListener()
 593       {
 594         @Override
 595         public void actionPerformed(ActionEvent actionEvent)
 596         {
 597           alphaHelix_actionPerformed();
 598         }
 599       });
 600
 601       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 602       betaStrand.addActionListener(new ActionListener()
 603       {
 604         @Override
 605         public void actionPerformed(ActionEvent actionEvent)
 606         {
 607           betaStrand_actionPerformed();
 608         }
 609       });
 610
 611       JvSwingUtils.jvInitComponent(turn, "label.turn");
 612       turn.addActionListener(new ActionListener()
 613       {
 614         @Override
 615         public void actionPerformed(ActionEvent actionEvent)
 616         {
 617           turn_actionPerformed();
 618         }
 619       });
 620
 621       JvSwingUtils.jvInitComponent(all, "label.select_all");
 622       all.addActionListener(new ActionListener()
 623       {
 624         @Override
 625         public void actionPerformed(ActionEvent actionEvent)
 626         {
 627           all_actionPerformed();
 628         }
 629       });
 630
 631       this.setBorder(new TitledBorder(MessageManager
 632               .getString("label.structures_filter")));
 633       JvSwingUtils.jvInitComponent(this);
 634
 635       this.add(all);
 636       this.add(alphaHelix);
 637       this.add(betaStrand);
 638       this.add(turn);
 639     }
 640
 641     public void alphaHelix_actionPerformed()
 642     {
 643       updateSelectAllState();
 644       aColChooser.setCurrentStructureFilterPanel(this);
 645       aColChooser.updateView();
 646     }
 647
 648     public void betaStrand_actionPerformed()
 649     {
 650       updateSelectAllState();
 651       aColChooser.setCurrentStructureFilterPanel(this);
 652       aColChooser.updateView();
 653     }
 654
 655     public void turn_actionPerformed()
 656     {
 657       updateSelectAllState();
 658       aColChooser.setCurrentStructureFilterPanel(this);
 659       aColChooser.updateView();
 660     }
 661
 662     public void all_actionPerformed()
 663     {
 664       if (all.isSelected())
 665       {
 666         alphaHelix.setSelected(true);
 667         betaStrand.setSelected(true);
 668         turn.setSelected(true);
 669       }
 670       else
 671       {
 672         alphaHelix.setSelected(false);
 673         betaStrand.setSelected(false);
 674         turn.setSelected(false);
 675       }
 676       aColChooser.setCurrentStructureFilterPanel(this);
 677       aColChooser.updateView();
 678     }
 679
 680     public void updateSelectAllState()
 681     {
 682       if (alphaHelix.isSelected() && betaStrand.isSelected()
 683               && turn.isSelected())
 684       {
 685         all.setSelected(true);
 686       }
 687       else
 688       {
 689         all.setSelected(false);
 690       }
 691     }
 692
 693     public void syncState()
 694     {
 695       StructureFilterPanel sfp = aColChooser
 696               .getCurrentStructureFilterPanel();
 697       if (sfp != null)
 698       {
 699         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 700         betaStrand.setSelected(sfp.betaStrand.isSelected());
 701         turn.setSelected(sfp.turn.isSelected());
 702         if (sfp.all.isSelected())
 703         {
 704           all.setSelected(true);
 705           alphaHelix.setSelected(true);
 706           betaStrand.setSelected(true);
 707           turn.setSelected(true);
 708         }
 709       }
 710
 711     }
 712   }
 713
 714   public class SearchPanel extends JPanel
 715   {
 716     private AnnotationColumnChooser aColChooser;
 717
 718     private JCheckBox displayName = new JCheckBox();
 719
 720     private JCheckBox description = new JCheckBox();
 721
 722     private JTextField searchBox = new JTextField(10);
 723
 724     public SearchPanel(AnnotationColumnChooser aColChooser)
 725     {
 726
 727       this.aColChooser = aColChooser;
 728       JvSwingUtils.jvInitComponent(this);
 729       this.setBorder(new TitledBorder(MessageManager
 730               .getString("label.search_filter")));
 731
 732       JvSwingUtils.jvInitComponent(searchBox);
 733       searchBox.setToolTipText(MessageManager
 734               .getString("info.enter_search_text_here"));
 735       searchBox.getDocument().addDocumentListener(new DocumentListener()
 736       {
 737         @Override
 738         public void insertUpdate(DocumentEvent e)
 739         {
 740           searchStringAction();
 741         }
 742
 743         @Override
 744         public void removeUpdate(DocumentEvent e)
 745         {
 746           searchStringAction();
 747         }
 748
 749         @Override
 750         public void changedUpdate(DocumentEvent e)
 751         {
 752           searchStringAction();
 753         }
 754       });
 755
 756       JvSwingUtils.jvInitComponent(displayName, "label.label");
 757       displayName.setEnabled(false);
 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.setEnabled(false);
 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     }
 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.setText(sp.searchBox.getText());
 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", annotations
 825                       .getSelectedItem().toString());
 826       String descTtip = MessageManager.formatMessage(
 827               "info.search_in_annotation_description", annotations
 828                       .getSelectedItem().toString());
 829       displayName.setToolTipText(displayName.isEnabled() ? labelTtip
 830               : defaultTtip);
 831       description.setToolTipText(description.isEnabled() ? descTtip
 832               : defaultTtip);
 833     }
 834   }
 835
 836 }