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 java.awt.BorderLayout;
  25 import java.awt.CardLayout;
  26 import java.awt.Color;
  27 import java.awt.Dimension;
  28 import java.awt.event.ActionEvent;
  29 import java.awt.event.ActionListener;
  30 import java.awt.event.FocusAdapter;
  31 import java.awt.event.FocusEvent;
  32 import java.awt.event.ItemEvent;
  33 import java.awt.event.ItemListener;
  34 import java.awt.event.KeyEvent;
  35
  36 import javax.swing.ButtonGroup;
  37 import javax.swing.JCheckBox;
  38 import javax.swing.JComboBox;
  39 import javax.swing.JInternalFrame;
  40 import javax.swing.JLayeredPane;
  41 import javax.swing.JPanel;
  42 import javax.swing.JRadioButton;
  43 import javax.swing.border.TitledBorder;
  44
  45 import jalview.bin.Console;
  46 import jalview.datamodel.AlignmentAnnotation;
  47 import jalview.datamodel.HiddenColumns;
  48 import jalview.io.cache.JvCacheableInputBox;
  49 import jalview.schemes.AnnotationColourGradient;
  50 import jalview.util.MessageManager;
  51 import jalview.util.Platform;
  52 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  53 import net.miginfocom.swing.MigLayout;
  54
  55 @SuppressWarnings("serial")
  56 public class AnnotationColumnChooser extends AnnotationRowFilter
  57         implements ItemListener
  58 {
  59   private JPanel switchableViewsPanel = new JPanel(new CardLayout());
  60
  61   private JPanel annotationComboBoxPanel = new JPanel();
  62
  63   private StructureFilterPanel gStructureFilterPanel;
  64
  65   private StructureFilterPanel ngStructureFilterPanel;
  66
  67   private StructureFilterPanel currentStructureFilterPanel;
  68
  69   private SearchPanel currentSearchPanel;
  70
  71   private SearchPanel gSearchPanel;
  72
  73   private SearchPanel ngSearchPanel;
  74
  75   private FurtherActionPanel currentFurtherActionPanel;
  76
  77   private FurtherActionPanel gFurtherActionPanel;
  78
  79   private FurtherActionPanel ngFurtherActionPanel;
  80
  81   public static final int ACTION_OPTION_SELECT = 1;
  82
  83   public static int ACTION_OPTION_HIDE = 2;
  84
  85   public static String NO_GRAPH_VIEW = "0";
  86
  87   public static String GRAPH_VIEW = "1";
  88
  89   private int actionOption = ACTION_OPTION_SELECT;
  90
  91   private HiddenColumns oldHiddenColumns;
  92
  93   protected static int MIN_WIDTH = (Platform.isJS() ? 370 : 420);
  94
  95   protected static int MIN_HEIGHT = (Platform.isJS() ? 370 : 430);
  96
  97   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  98   {
  99     this(av,ap,null);
 100   }
 101   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap, AlignmentAnnotation selectedAnnotation)
 102   {
 103     super(av, ap);
 104     frame = new JInternalFrame();
 105     frame.setFrameIcon(null);
 106     frame.setContentPane(this);
 107     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 108     Desktop.addInternalFrame(frame,
 109             MessageManager.getString("label.select_by_annotation"), 0, 0);
 110     // BH note: MIGLayout ignores this completely,
 111     // possibly creating a frame smaller than specified:
 112     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 113
 114     addSliderChangeListener();
 115     addSliderMouseListeners();
 116
 117     if (av.getAlignment().getAlignmentAnnotation() == null)
 118     {
 119       return;
 120     }
 121     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 122     adjusting = true;
 123
 124     setAnnotations(new JComboBox<>(getAnnotationItems(false)));
 125     populateThresholdComboBox(threshold);
 126     AnnotationColumnChooser lastChooser = av
 127             .getAnnotationColumnSelectionState();
 128     // restore Object state from the previous session if one exists
 129     if (lastChooser != null)
 130     {
 131       currentSearchPanel = lastChooser.getCurrentSearchPanel();
 132       currentStructureFilterPanel = lastChooser
 133               .getCurrentStructureFilterPanel();
 134       annotations.setSelectedIndex(
 135               lastChooser.getAnnotations().getSelectedIndex());
 136       threshold.setSelectedIndex(
 137               lastChooser.getThreshold().getSelectedIndex());
 138       actionOption = lastChooser.getActionOption();
 139       percentThreshold
 140               .setSelected(lastChooser.percentThreshold.isSelected());
 141     }
 142     if (selectedAnnotation!=null)
 143     {
 144       try {
 145         setCurrentAnnotation(selectedAnnotation);
 146         annotations.setSelectedItem(getAnnotationMenuLabel(selectedAnnotation));
 147       } catch (Exception x)
 148       {
 149         Console.error("Couldn't select annotation in column chooser",x);
 150       }
 151     }
 152
 153     try
 154     {
 155       jbInit();
 156     } catch (Exception ex)
 157     {
 158     }
 159     adjusting = false;
 160
 161     updateView();
 162     frame.invalidate();
 163     frame.pack();
 164   }
 165
 166   @Override
 167   protected void jbInit()
 168   {
 169     super.jbInit();
 170
 171     JPanel thresholdPanel = new JPanel();
 172     thresholdPanel.setBorder(new TitledBorder(
 173             MessageManager.getString("label.threshold_filter")));
 174     thresholdPanel.setBackground(Color.white);
 175     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 176     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 177
 178     percentThreshold.setBackground(Color.white);
 179     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 180
 181     JPanel actionPanel = new JPanel();
 182     actionPanel.setBackground(Color.white);
 183     actionPanel.setFont(JvSwingUtils.getLabelFont());
 184
 185     JPanel graphFilterView = new JPanel();
 186     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 187     graphFilterView.setBackground(Color.white);
 188
 189     JPanel noGraphFilterView = new JPanel();
 190     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 191     noGraphFilterView.setBackground(Color.white);
 192
 193     annotationComboBoxPanel.setBackground(Color.white);
 194     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 195
 196     gSearchPanel = new SearchPanel(this);
 197     ngSearchPanel = new SearchPanel(this);
 198     gFurtherActionPanel = new FurtherActionPanel(this);
 199     ngFurtherActionPanel = new FurtherActionPanel(this);
 200     gStructureFilterPanel = new StructureFilterPanel(this);
 201     ngStructureFilterPanel = new StructureFilterPanel(this);
 202
 203     thresholdPanel.add(getThreshold());
 204     thresholdPanel.add(percentThreshold, "wrap");
 205     thresholdPanel.add(slider, "grow");
 206     thresholdPanel.add(thresholdValue, "span, wrap");
 207
 208     actionPanel.add(ok);
 209     actionPanel.add(cancel);
 210
 211     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 212     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 213     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 214     graphFilterView.add(gFurtherActionPanel);
 215
 216     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 217     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 218     noGraphFilterView.add(ngFurtherActionPanel);
 219
 220     annotationComboBoxPanel.add(getAnnotations());
 221     switchableViewsPanel.add(noGraphFilterView,
 222             AnnotationColumnChooser.NO_GRAPH_VIEW);
 223     switchableViewsPanel.add(graphFilterView,
 224             AnnotationColumnChooser.GRAPH_VIEW);
 225     this.setLayout(new BorderLayout());
 226     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 227     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 228     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 229
 230     selectedAnnotationChanged();
 231     updateThresholdPanelToolTip();
 232     this.validate();
 233   }
 234
 235   protected void updateThresholdPanelToolTip()
 236   {
 237     thresholdValue.setToolTipText("");
 238     slider.setToolTipText("");
 239
 240     String defaultTtip = MessageManager
 241             .getString("info.change_threshold_mode_to_enable");
 242
 243     String thresh = getThreshold().getSelectedItem().toString();
 244     if (thresh.equalsIgnoreCase("No Threshold"))
 245     {
 246       thresholdValue.setToolTipText(defaultTtip);
 247       slider.setToolTipText(defaultTtip);
 248     }
 249   }
 250
 251   @Override
 252   protected void reset()
 253   {
 254     if (this.getOldHiddenColumns() != null)
 255     {
 256       av.getColumnSelection().clear();
 257
 258       if (av.getAnnotationColumnSelectionState() != null)
 259       {
 260         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
 261                 .getOldHiddenColumns();
 262         av.getAlignment().setHiddenColumns(oldHidden);
 263       }
 264       av.sendSelection();
 265       ap.paintAlignment(true, true);
 266     }
 267   }
 268
 269   @Override
 270   public void valueChanged(boolean updateAllAnnotation)
 271   {
 272     if (slider.isEnabled())
 273     {
 274       getCurrentAnnotation().threshold.value = getSliderValue();
 275       updateView();
 276       propagateSeqAssociatedThreshold(updateAllAnnotation,
 277               getCurrentAnnotation());
 278       ap.paintAlignment(false, false);
 279     }
 280   }
 281
 282   @Override
 283   public void updateView()
 284   {
 285     // Check if combobox is still adjusting
 286     if (adjusting)
 287     {
 288       return;
 289     }
 290
 291     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 292
 293     setCurrentAnnotation(av.getAlignment()
 294             .getAlignmentAnnotation()[annmap[getAnnotations()
 295                     .getSelectedIndex()]]);
 296
 297     int selectedThresholdItem = getSelectedThresholdItem(
 298             getThreshold().getSelectedIndex());
 299
 300     slider.setEnabled(true);
 301     thresholdValue.setEnabled(true);
 302     percentThreshold.setEnabled(true);
 303
 304     final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
 305     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 306     {
 307       slider.setEnabled(false);
 308       thresholdValue.setEnabled(false);
 309       thresholdValue.setText("");
 310       percentThreshold.setEnabled(false);
 311       // build filter params
 312     }
 313     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 314     {
 315       if (currentAnnotation.threshold == null)
 316       {
 317         currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
 318                 (currentAnnotation.graphMax - currentAnnotation.graphMin)
 319                         / 2f,
 320                 "Threshold", Color.black));
 321       }
 322
 323       adjusting = true;
 324
 325       setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
 326               currentAnnotation.threshold.value);
 327
 328       setThresholdValueText();
 329
 330       slider.setEnabled(true);
 331       thresholdValue.setEnabled(true);
 332       adjusting = false;
 333
 334       // build filter params
 335       filterParams.setThresholdType(
 336               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 337       if (currentAnnotation.isQuantitative())
 338       {
 339         filterParams.setThresholdValue(currentAnnotation.threshold.value);
 340
 341         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 342         {
 343           filterParams.setThresholdType(
 344                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 345         }
 346         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 347         {
 348           filterParams.setThresholdType(
 349                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 350         }
 351       }
 352     }
 353
 354     updateThresholdPanelToolTip();
 355     if (currentStructureFilterPanel != null)
 356     {
 357       if (currentStructureFilterPanel.alphaHelix.isSelected())
 358       {
 359         filterParams.setFilterAlphaHelix(true);
 360       }
 361       if (currentStructureFilterPanel.betaStrand.isSelected())
 362       {
 363         filterParams.setFilterBetaSheet(true);
 364       }
 365       if (currentStructureFilterPanel.turn.isSelected())
 366       {
 367         filterParams.setFilterTurn(true);
 368       }
 369     }
 370
 371     if (currentSearchPanel != null)
 372     {
 373       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
 374       {
 375         filterParams.setRegexString(
 376                 currentSearchPanel.searchBox.getUserInput());
 377         if (currentSearchPanel.displayName.isSelected())
 378         {
 379           filterParams.addRegexSearchField(
 380                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 381         }
 382         if (currentSearchPanel.description.isSelected())
 383         {
 384           filterParams.addRegexSearchField(
 385                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 386         }
 387       }
 388     }
 389
 390     // show hidden columns here, before changing the column selection in
 391     // filterAnnotations, because showing hidden columns has the side effect of
 392     // adding them to the selection
 393     av.showAllHiddenColumns();
 394     av.getColumnSelection().filterAnnotations(currentAnnotation,
 395             filterParams);
 396
 397     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
 398     if (hideCols)
 399     {
 400       av.hideSelectedColumns();
 401     }
 402     av.sendSelection();
 403
 404     filterParams = null;
 405     av.setAnnotationColumnSelectionState(this);
 406     // only update overview and structures if columns were hidden
 407     ap.paintAlignment(hideCols, hideCols);
 408   }
 409
 410   public HiddenColumns getOldHiddenColumns()
 411   {
 412     return oldHiddenColumns;
 413   }
 414
 415   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 416   {
 417     if (currentHiddenColumns != null)
 418     {
 419       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 420     }
 421   }
 422
 423   public FurtherActionPanel getCurrentFutherActionPanel()
 424   {
 425     return currentFurtherActionPanel;
 426   }
 427
 428   public void setCurrentFutherActionPanel(
 429           FurtherActionPanel currentFutherActionPanel)
 430   {
 431     this.currentFurtherActionPanel = currentFutherActionPanel;
 432   }
 433
 434   public SearchPanel getCurrentSearchPanel()
 435   {
 436     return currentSearchPanel;
 437   }
 438
 439   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 440   {
 441     this.currentSearchPanel = currentSearchPanel;
 442   }
 443
 444   public int getActionOption()
 445   {
 446     return actionOption;
 447   }
 448
 449   public void setActionOption(int actionOption)
 450   {
 451     this.actionOption = actionOption;
 452   }
 453
 454   public StructureFilterPanel getCurrentStructureFilterPanel()
 455   {
 456     return currentStructureFilterPanel;
 457   }
 458
 459   public void setCurrentStructureFilterPanel(
 460           StructureFilterPanel currentStructureFilterPanel)
 461   {
 462     this.currentStructureFilterPanel = currentStructureFilterPanel;
 463   }
 464
 465   public void select_action(ActionEvent actionEvent)
 466   {
 467     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 468     if (radioButton.isSelected())
 469     {
 470       setActionOption(ACTION_OPTION_SELECT);
 471       updateView();
 472     }
 473   }
 474
 475   public void hide_action(ActionEvent actionEvent)
 476   {
 477     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 478     if (radioButton.isSelected())
 479     {
 480       setActionOption(ACTION_OPTION_HIDE);
 481       updateView();
 482     }
 483   }
 484
 485   @Override
 486   public void itemStateChanged(ItemEvent e)
 487   {
 488     selectedAnnotationChanged();
 489   }
 490
 491   @Override
 492   public void selectedAnnotationChanged()
 493   {
 494     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 495     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 496             .getSelectedIndex()]].isQuantitative())
 497     {
 498       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 499     }
 500     saveCache();
 501     gSearchPanel.syncState();
 502     gFurtherActionPanel.syncState();
 503     gStructureFilterPanel.syncState();
 504
 505     ngSearchPanel.syncState();
 506     ngFurtherActionPanel.syncState();
 507     ngStructureFilterPanel.syncState();
 508
 509     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 510             .getLayout();
 511     switchableViewsLayout.show(switchableViewsPanel, currentView);
 512     updateView();
 513   }
 514
 515   public class FurtherActionPanel extends JPanel
 516   {
 517     private AnnotationColumnChooser aColChooser;
 518
 519     private JRadioButton hideOption = new JRadioButton();
 520
 521     private JRadioButton selectOption = new JRadioButton();
 522
 523     private ButtonGroup optionsGroup = new ButtonGroup();
 524
 525     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 526     {
 527       this.aColChooser = aColChooser;
 528       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 529       selectOption.addActionListener(new ActionListener()
 530       {
 531         @Override
 532         public void actionPerformed(ActionEvent actionEvent)
 533         {
 534           selectRadioAction(actionEvent);
 535         }
 536       });
 537
 538       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 539       hideOption.addActionListener(new ActionListener()
 540       {
 541         @Override
 542         public void actionPerformed(ActionEvent actionEvent)
 543         {
 544           hideRadioAction(actionEvent);
 545         }
 546       });
 547
 548       optionsGroup.add(selectOption);
 549       optionsGroup.add(hideOption);
 550       optionsGroup.setSelected(selectOption.getModel(), true);
 551
 552       JvSwingUtils.jvInitComponent(this);
 553       syncState();
 554
 555       this.add(selectOption);
 556       this.add(hideOption);
 557     }
 558
 559     public void selectRadioAction(ActionEvent actionEvent)
 560     {
 561       aColChooser.setCurrentFutherActionPanel(this);
 562       aColChooser.select_action(actionEvent);
 563     }
 564
 565     public void hideRadioAction(ActionEvent actionEvent)
 566     {
 567       aColChooser.setCurrentFutherActionPanel(this);
 568       aColChooser.hide_action(actionEvent);
 569     }
 570
 571     public void syncState()
 572     {
 573       if (aColChooser
 574               .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 575       {
 576         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 577       }
 578       else
 579       {
 580         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 581       }
 582     }
 583   }
 584
 585   public class StructureFilterPanel extends JPanel
 586   {
 587     private AnnotationColumnChooser aColChooser;
 588
 589     private JCheckBox alphaHelix = new JCheckBox();
 590
 591     private JCheckBox betaStrand = new JCheckBox();
 592
 593     private JCheckBox turn = new JCheckBox();
 594
 595     private JCheckBox all = new JCheckBox();
 596
 597     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 598     {
 599       this.aColChooser = aColChooser;
 600
 601       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 602       alphaHelix.addActionListener(new ActionListener()
 603       {
 604         @Override
 605         public void actionPerformed(ActionEvent actionEvent)
 606         {
 607           alphaHelix_actionPerformed();
 608         }
 609       });
 610
 611       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 612       betaStrand.addActionListener(new ActionListener()
 613       {
 614         @Override
 615         public void actionPerformed(ActionEvent actionEvent)
 616         {
 617           betaStrand_actionPerformed();
 618         }
 619       });
 620
 621       JvSwingUtils.jvInitComponent(turn, "label.turn");
 622       turn.addActionListener(new ActionListener()
 623       {
 624         @Override
 625         public void actionPerformed(ActionEvent actionEvent)
 626         {
 627           turn_actionPerformed();
 628         }
 629       });
 630
 631       JvSwingUtils.jvInitComponent(all, "label.select_all");
 632       all.addActionListener(new ActionListener()
 633       {
 634         @Override
 635         public void actionPerformed(ActionEvent actionEvent)
 636         {
 637           all_actionPerformed();
 638         }
 639       });
 640
 641       this.setBorder(new TitledBorder(
 642               MessageManager.getString("label.structures_filter")));
 643       JvSwingUtils.jvInitComponent(this);
 644
 645       this.add(all);
 646       this.add(alphaHelix);
 647       this.add(betaStrand);
 648       this.add(turn);
 649     }
 650
 651     public void alphaHelix_actionPerformed()
 652     {
 653       updateSelectAllState();
 654       aColChooser.setCurrentStructureFilterPanel(this);
 655       aColChooser.updateView();
 656     }
 657
 658     public void betaStrand_actionPerformed()
 659     {
 660       updateSelectAllState();
 661       aColChooser.setCurrentStructureFilterPanel(this);
 662       aColChooser.updateView();
 663     }
 664
 665     public void turn_actionPerformed()
 666     {
 667       updateSelectAllState();
 668       aColChooser.setCurrentStructureFilterPanel(this);
 669       aColChooser.updateView();
 670     }
 671
 672     public void all_actionPerformed()
 673     {
 674       if (all.isSelected())
 675       {
 676         alphaHelix.setSelected(true);
 677         betaStrand.setSelected(true);
 678         turn.setSelected(true);
 679       }
 680       else
 681       {
 682         alphaHelix.setSelected(false);
 683         betaStrand.setSelected(false);
 684         turn.setSelected(false);
 685       }
 686       aColChooser.setCurrentStructureFilterPanel(this);
 687       aColChooser.updateView();
 688     }
 689
 690     public void updateSelectAllState()
 691     {
 692       if (alphaHelix.isSelected() && betaStrand.isSelected()
 693               && turn.isSelected())
 694       {
 695         all.setSelected(true);
 696       }
 697       else
 698       {
 699         all.setSelected(false);
 700       }
 701     }
 702
 703     public void syncState()
 704     {
 705       StructureFilterPanel sfp = aColChooser
 706               .getCurrentStructureFilterPanel();
 707       if (sfp != null)
 708       {
 709         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 710         betaStrand.setSelected(sfp.betaStrand.isSelected());
 711         turn.setSelected(sfp.turn.isSelected());
 712         if (sfp.all.isSelected())
 713         {
 714           all.setSelected(true);
 715           alphaHelix.setSelected(true);
 716           betaStrand.setSelected(true);
 717           turn.setSelected(true);
 718         }
 719       }
 720
 721     }
 722   }
 723
 724   public class SearchPanel extends JPanel
 725   {
 726     private AnnotationColumnChooser aColChooser;
 727
 728     private JCheckBox displayName = new JCheckBox();
 729
 730     private JCheckBox description = new JCheckBox();
 731
 732     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 733
 734     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
 735             FILTER_BY_ANN_CACHE_KEY, 23);
 736
 737     public SearchPanel(AnnotationColumnChooser aColChooser)
 738     {
 739
 740       this.aColChooser = aColChooser;
 741       JvSwingUtils.jvInitComponent(this);
 742       this.setBorder(new TitledBorder(
 743               MessageManager.getString("label.search_filter")));
 744
 745       searchBox.getComponent().setToolTipText(
 746               MessageManager.getString("info.enter_search_text_here"));
 747       searchBox.addKeyListener(new java.awt.event.KeyAdapter()
 748       {
 749         @Override
 750         public void keyPressed(KeyEvent e)
 751         {
 752           if (e.getKeyCode() == KeyEvent.VK_ENTER)
 753           {
 754             e.consume();
 755             searchStringAction();
 756           }
 757         }
 758       });
 759       searchBox.addFocusListener(new FocusAdapter()
 760       {
 761         @Override
 762         public void focusLost(FocusEvent e)
 763         {
 764           searchStringAction();
 765         }
 766       });
 767
 768       JvSwingUtils.jvInitComponent(displayName, "label.label");
 769       displayName.addActionListener(new ActionListener()
 770       {
 771         @Override
 772         public void actionPerformed(ActionEvent actionEvent)
 773         {
 774           displayNameCheckboxAction();
 775         }
 776       });
 777
 778       JvSwingUtils.jvInitComponent(description, "label.description");
 779       description.addActionListener(new ActionListener()
 780       {
 781         @Override
 782         public void actionPerformed(ActionEvent actionEvent)
 783         {
 784           descriptionCheckboxAction();
 785         }
 786       });
 787
 788       syncState();
 789       this.add(searchBox.getComponent());
 790       this.add(displayName);
 791       this.add(description);
 792     }
 793
 794     public void displayNameCheckboxAction()
 795     {
 796       aColChooser.setCurrentSearchPanel(this);
 797       aColChooser.updateView();
 798     }
 799
 800     public void descriptionCheckboxAction()
 801     {
 802       aColChooser.setCurrentSearchPanel(this);
 803       aColChooser.updateView();
 804     }
 805
 806     public void searchStringAction()
 807     {
 808       aColChooser.setCurrentSearchPanel(this);
 809       aColChooser.updateView();
 810       updateSearchPanelToolTips();
 811       searchBox.updateCache();
 812     }
 813
 814     public void syncState()
 815     {
 816       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 817       if (sp != null)
 818       {
 819         description.setEnabled(sp.description.isEnabled());
 820         description.setSelected(sp.description.isSelected());
 821
 822         displayName.setEnabled(sp.displayName.isEnabled());
 823         displayName.setSelected(sp.displayName.isSelected());
 824
 825         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 826       }
 827       updateSearchPanelToolTips();
 828     }
 829
 830     public void updateSearchPanelToolTips()
 831     {
 832       String defaultTtip = MessageManager
 833               .getString("info.enter_search_text_to_enable");
 834       String labelTtip = MessageManager.formatMessage(
 835               "info.search_in_annotation_label",
 836               annotations.getSelectedItem().toString());
 837       String descTtip = MessageManager.formatMessage(
 838               "info.search_in_annotation_description",
 839               annotations.getSelectedItem().toString());
 840       displayName.setToolTipText(
 841               displayName.isEnabled() ? labelTtip : defaultTtip);
 842       description.setToolTipText(
 843               description.isEnabled() ? descTtip : defaultTtip);
 844     }
 845   }
 846
 847   @Override
 848   public void ok_actionPerformed()
 849   {
 850     saveCache();
 851     super.ok_actionPerformed();
 852   }
 853
 854   @Override
 855   public void cancel_actionPerformed()
 856   {
 857     saveCache();
 858     super.cancel_actionPerformed();
 859   }
 860
 861   private void saveCache()
 862   {
 863     gSearchPanel.searchBox.persistCache();
 864     ngSearchPanel.searchBox.persistCache();
 865     gSearchPanel.searchBox.updateCache();
 866     ngSearchPanel.searchBox.updateCache();
 867   }
 868
 869   public static void displayFor(AlignViewport av, AlignmentPanel ap,
 870           AlignmentAnnotation alignmentAnnotation)
 871   {
 872     AnnotationColumnChooser colchooser = new AnnotationColumnChooser(av, ap, alignmentAnnotation);
 873   }
 874 }