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
 102   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap,
 103           AlignmentAnnotation selectedAnnotation)
 104   {
 105     super(av, ap);
 106     frame = new JInternalFrame();
 107     frame.setFrameIcon(null);
 108     frame.setContentPane(this);
 109     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 110     Desktop.addInternalFrame(frame,
 111             MessageManager.getString("label.select_by_annotation"), 0, 0);
 112     // BH note: MIGLayout ignores this completely,
 113     // possibly creating a frame smaller than specified:
 114     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 115
 116     addSliderChangeListener();
 117     addSliderMouseListeners();
 118
 119     if (av.getAlignment().getAlignmentAnnotation() == null)
 120     {
 121       return;
 122     }
 123     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 124     adjusting = true;
 125
 126     setAnnotations(new JComboBox<>(getAnnotationItems(false)));
 127     populateThresholdComboBox(threshold);
 128     AnnotationColumnChooser lastChooser = av
 129             .getAnnotationColumnSelectionState();
 130     // restore Object state from the previous session if one exists
 131     if (lastChooser != null)
 132     {
 133       currentSearchPanel = lastChooser.getCurrentSearchPanel();
 134       currentStructureFilterPanel = lastChooser
 135               .getCurrentStructureFilterPanel();
 136       annotations.setSelectedIndex(
 137               lastChooser.getAnnotations().getSelectedIndex());
 138       threshold.setSelectedIndex(
 139               lastChooser.getThreshold().getSelectedIndex());
 140       actionOption = lastChooser.getActionOption();
 141       percentThreshold
 142               .setSelected(lastChooser.percentThreshold.isSelected());
 143     }
 144     if (selectedAnnotation != null)
 145     {
 146       try
 147       {
 148         setCurrentAnnotation(selectedAnnotation);
 149         annotations.setSelectedItem(
 150                 getAnnotationMenuLabel(selectedAnnotation));
 151       } catch (Exception x)
 152       {
 153         Console.error("Couldn't select annotation in column chooser", x);
 154       }
 155     }
 156
 157     try
 158     {
 159       jbInit();
 160     } catch (Exception ex)
 161     {
 162     }
 163     adjusting = false;
 164
 165     updateView();
 166     frame.invalidate();
 167     frame.pack();
 168   }
 169
 170   @Override
 171   protected void jbInit()
 172   {
 173     super.jbInit();
 174
 175     JPanel thresholdPanel = new JPanel();
 176     thresholdPanel.setBorder(new TitledBorder(
 177             MessageManager.getString("label.threshold_filter")));
 178     thresholdPanel.setBackground(Color.white);
 179     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 180     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 181
 182     percentThreshold.setBackground(Color.white);
 183     percentThreshold.setFont(JvSwingUtils.getLabelFont());
 184
 185     JPanel actionPanel = new JPanel();
 186     actionPanel.setBackground(Color.white);
 187     actionPanel.setFont(JvSwingUtils.getLabelFont());
 188
 189     JPanel graphFilterView = new JPanel();
 190     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 191     graphFilterView.setBackground(Color.white);
 192
 193     JPanel noGraphFilterView = new JPanel();
 194     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 195     noGraphFilterView.setBackground(Color.white);
 196
 197     annotationComboBoxPanel.setBackground(Color.white);
 198     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 199
 200     gSearchPanel = new SearchPanel(this);
 201     ngSearchPanel = new SearchPanel(this);
 202     gFurtherActionPanel = new FurtherActionPanel(this);
 203     ngFurtherActionPanel = new FurtherActionPanel(this);
 204     gStructureFilterPanel = new StructureFilterPanel(this);
 205     ngStructureFilterPanel = new StructureFilterPanel(this);
 206
 207     thresholdPanel.add(getThreshold());
 208     thresholdPanel.add(percentThreshold, "wrap");
 209     thresholdPanel.add(slider, "grow");
 210     thresholdPanel.add(thresholdValue, "span, wrap");
 211
 212     actionPanel.add(ok);
 213     actionPanel.add(cancel);
 214
 215     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 216     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 217     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 218     graphFilterView.add(gFurtherActionPanel);
 219
 220     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 221     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 222     noGraphFilterView.add(ngFurtherActionPanel);
 223
 224     annotationComboBoxPanel.add(getAnnotations());
 225     switchableViewsPanel.add(noGraphFilterView,
 226             AnnotationColumnChooser.NO_GRAPH_VIEW);
 227     switchableViewsPanel.add(graphFilterView,
 228             AnnotationColumnChooser.GRAPH_VIEW);
 229     this.setLayout(new BorderLayout());
 230     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 231     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 232     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 233
 234     selectedAnnotationChanged();
 235     updateThresholdPanelToolTip();
 236     this.validate();
 237   }
 238
 239   protected void updateThresholdPanelToolTip()
 240   {
 241     thresholdValue.setToolTipText("");
 242     slider.setToolTipText("");
 243
 244     String defaultTtip = MessageManager
 245             .getString("info.change_threshold_mode_to_enable");
 246
 247     String thresh = getThreshold().getSelectedItem().toString();
 248     if (thresh.equalsIgnoreCase("No Threshold"))
 249     {
 250       thresholdValue.setToolTipText(defaultTtip);
 251       slider.setToolTipText(defaultTtip);
 252     }
 253   }
 254
 255   @Override
 256   protected void reset()
 257   {
 258     if (this.getOldHiddenColumns() != null)
 259     {
 260       av.getColumnSelection().clear();
 261
 262       if (av.getAnnotationColumnSelectionState() != null)
 263       {
 264         HiddenColumns oldHidden = av.getAnnotationColumnSelectionState()
 265                 .getOldHiddenColumns();
 266         av.getAlignment().setHiddenColumns(oldHidden);
 267       }
 268       av.sendSelection();
 269       ap.paintAlignment(true, true);
 270     }
 271   }
 272
 273   @Override
 274   public void valueChanged(boolean updateAllAnnotation)
 275   {
 276     if (slider.isEnabled())
 277     {
 278       getCurrentAnnotation().threshold.value = getSliderValue();
 279       updateView();
 280       propagateSeqAssociatedThreshold(updateAllAnnotation,
 281               getCurrentAnnotation());
 282       ap.paintAlignment(false, false);
 283     }
 284   }
 285
 286   @Override
 287   public void updateView()
 288   {
 289     // Check if combobox is still adjusting
 290     if (adjusting)
 291     {
 292       return;
 293     }
 294
 295     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 296
 297     setCurrentAnnotation(av.getAlignment()
 298             .getAlignmentAnnotation()[annmap[getAnnotations()
 299                     .getSelectedIndex()]]);
 300
 301     int selectedThresholdItem = getSelectedThresholdItem(
 302             getThreshold().getSelectedIndex());
 303
 304     slider.setEnabled(true);
 305     thresholdValue.setEnabled(true);
 306     percentThreshold.setEnabled(true);
 307
 308     final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
 309     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 310     {
 311       slider.setEnabled(false);
 312       thresholdValue.setEnabled(false);
 313       thresholdValue.setText("");
 314       percentThreshold.setEnabled(false);
 315       // build filter params
 316     }
 317     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 318     {
 319       if (currentAnnotation.threshold == null)
 320       {
 321         currentAnnotation.setThreshold(new jalview.datamodel.GraphLine(
 322                 (currentAnnotation.graphMax - currentAnnotation.graphMin)
 323                         / 2f,
 324                 "Threshold", Color.black));
 325       }
 326
 327       adjusting = true;
 328
 329       setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
 330               currentAnnotation.threshold.value);
 331
 332       setThresholdValueText();
 333
 334       slider.setEnabled(true);
 335       thresholdValue.setEnabled(true);
 336       adjusting = false;
 337
 338       // build filter params
 339       filterParams.setThresholdType(
 340               AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 341       if (currentAnnotation.isQuantitative())
 342       {
 343         filterParams.setThresholdValue(currentAnnotation.threshold.value);
 344
 345         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 346         {
 347           filterParams.setThresholdType(
 348                   AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 349         }
 350         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 351         {
 352           filterParams.setThresholdType(
 353                   AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 354         }
 355       }
 356     }
 357
 358     updateThresholdPanelToolTip();
 359     if (currentStructureFilterPanel != null)
 360     {
 361       if (currentStructureFilterPanel.alphaHelix.isSelected())
 362       {
 363         filterParams.setFilterAlphaHelix(true);
 364       }
 365       if (currentStructureFilterPanel.betaStrand.isSelected())
 366       {
 367         filterParams.setFilterBetaSheet(true);
 368       }
 369       if (currentStructureFilterPanel.turn.isSelected())
 370       {
 371         filterParams.setFilterTurn(true);
 372       }
 373     }
 374
 375     if (currentSearchPanel != null)
 376     {
 377       if (!currentSearchPanel.searchBox.getUserInput().isEmpty())
 378       {
 379         filterParams.setRegexString(
 380                 currentSearchPanel.searchBox.getUserInput());
 381         if (currentSearchPanel.displayName.isSelected())
 382         {
 383           filterParams.addRegexSearchField(
 384                   AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 385         }
 386         if (currentSearchPanel.description.isSelected())
 387         {
 388           filterParams.addRegexSearchField(
 389                   AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 390         }
 391       }
 392     }
 393
 394     // show hidden columns here, before changing the column selection in
 395     // filterAnnotations, because showing hidden columns has the side effect of
 396     // adding them to the selection
 397     av.showAllHiddenColumns();
 398     av.getColumnSelection().filterAnnotations(currentAnnotation,
 399             filterParams);
 400
 401     boolean hideCols = getActionOption() == ACTION_OPTION_HIDE;
 402     if (hideCols)
 403     {
 404       av.hideSelectedColumns();
 405     }
 406     av.sendSelection();
 407
 408     filterParams = null;
 409     av.setAnnotationColumnSelectionState(this);
 410     // only update overview and structures if columns were hidden
 411     ap.paintAlignment(hideCols, hideCols);
 412   }
 413
 414   public HiddenColumns getOldHiddenColumns()
 415   {
 416     return oldHiddenColumns;
 417   }
 418
 419   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 420   {
 421     if (currentHiddenColumns != null)
 422     {
 423       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 424     }
 425   }
 426
 427   public FurtherActionPanel getCurrentFutherActionPanel()
 428   {
 429     return currentFurtherActionPanel;
 430   }
 431
 432   public void setCurrentFutherActionPanel(
 433           FurtherActionPanel currentFutherActionPanel)
 434   {
 435     this.currentFurtherActionPanel = currentFutherActionPanel;
 436   }
 437
 438   public SearchPanel getCurrentSearchPanel()
 439   {
 440     return currentSearchPanel;
 441   }
 442
 443   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 444   {
 445     this.currentSearchPanel = currentSearchPanel;
 446   }
 447
 448   public int getActionOption()
 449   {
 450     return actionOption;
 451   }
 452
 453   public void setActionOption(int actionOption)
 454   {
 455     this.actionOption = actionOption;
 456   }
 457
 458   public StructureFilterPanel getCurrentStructureFilterPanel()
 459   {
 460     return currentStructureFilterPanel;
 461   }
 462
 463   public void setCurrentStructureFilterPanel(
 464           StructureFilterPanel currentStructureFilterPanel)
 465   {
 466     this.currentStructureFilterPanel = currentStructureFilterPanel;
 467   }
 468
 469   public void select_action(ActionEvent actionEvent)
 470   {
 471     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 472     if (radioButton.isSelected())
 473     {
 474       setActionOption(ACTION_OPTION_SELECT);
 475       updateView();
 476     }
 477   }
 478
 479   public void hide_action(ActionEvent actionEvent)
 480   {
 481     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 482     if (radioButton.isSelected())
 483     {
 484       setActionOption(ACTION_OPTION_HIDE);
 485       updateView();
 486     }
 487   }
 488
 489   @Override
 490   public void itemStateChanged(ItemEvent e)
 491   {
 492     selectedAnnotationChanged();
 493   }
 494
 495   @Override
 496   public void selectedAnnotationChanged()
 497   {
 498     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 499     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 500             .getSelectedIndex()]].isQuantitative())
 501     {
 502       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 503     }
 504     saveCache();
 505     gSearchPanel.syncState();
 506     gFurtherActionPanel.syncState();
 507     gStructureFilterPanel.syncState();
 508
 509     ngSearchPanel.syncState();
 510     ngFurtherActionPanel.syncState();
 511     ngStructureFilterPanel.syncState();
 512
 513     CardLayout switchableViewsLayout = (CardLayout) switchableViewsPanel
 514             .getLayout();
 515     switchableViewsLayout.show(switchableViewsPanel, currentView);
 516     updateView();
 517   }
 518
 519   public class FurtherActionPanel extends JPanel
 520   {
 521     private AnnotationColumnChooser aColChooser;
 522
 523     private JRadioButton hideOption = new JRadioButton();
 524
 525     private JRadioButton selectOption = new JRadioButton();
 526
 527     private ButtonGroup optionsGroup = new ButtonGroup();
 528
 529     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 530     {
 531       this.aColChooser = aColChooser;
 532       JvSwingUtils.jvInitComponent(selectOption, "action.select");
 533       selectOption.addActionListener(new ActionListener()
 534       {
 535         @Override
 536         public void actionPerformed(ActionEvent actionEvent)
 537         {
 538           selectRadioAction(actionEvent);
 539         }
 540       });
 541
 542       JvSwingUtils.jvInitComponent(hideOption, "action.hide");
 543       hideOption.addActionListener(new ActionListener()
 544       {
 545         @Override
 546         public void actionPerformed(ActionEvent actionEvent)
 547         {
 548           hideRadioAction(actionEvent);
 549         }
 550       });
 551
 552       optionsGroup.add(selectOption);
 553       optionsGroup.add(hideOption);
 554       optionsGroup.setSelected(selectOption.getModel(), true);
 555
 556       JvSwingUtils.jvInitComponent(this);
 557       syncState();
 558
 559       this.add(selectOption);
 560       this.add(hideOption);
 561     }
 562
 563     public void selectRadioAction(ActionEvent actionEvent)
 564     {
 565       aColChooser.setCurrentFutherActionPanel(this);
 566       aColChooser.select_action(actionEvent);
 567     }
 568
 569     public void hideRadioAction(ActionEvent actionEvent)
 570     {
 571       aColChooser.setCurrentFutherActionPanel(this);
 572       aColChooser.hide_action(actionEvent);
 573     }
 574
 575     public void syncState()
 576     {
 577       if (aColChooser
 578               .getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 579       {
 580         this.optionsGroup.setSelected(this.hideOption.getModel(), true);
 581       }
 582       else
 583       {
 584         this.optionsGroup.setSelected(this.selectOption.getModel(), true);
 585       }
 586     }
 587   }
 588
 589   public class StructureFilterPanel extends JPanel
 590   {
 591     private AnnotationColumnChooser aColChooser;
 592
 593     private JCheckBox alphaHelix = new JCheckBox();
 594
 595     private JCheckBox betaStrand = new JCheckBox();
 596
 597     private JCheckBox turn = new JCheckBox();
 598
 599     private JCheckBox all = new JCheckBox();
 600
 601     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 602     {
 603       this.aColChooser = aColChooser;
 604
 605       JvSwingUtils.jvInitComponent(alphaHelix, "label.alpha_helix");
 606       alphaHelix.addActionListener(new ActionListener()
 607       {
 608         @Override
 609         public void actionPerformed(ActionEvent actionEvent)
 610         {
 611           alphaHelix_actionPerformed();
 612         }
 613       });
 614
 615       JvSwingUtils.jvInitComponent(betaStrand, "label.beta_strand");
 616       betaStrand.addActionListener(new ActionListener()
 617       {
 618         @Override
 619         public void actionPerformed(ActionEvent actionEvent)
 620         {
 621           betaStrand_actionPerformed();
 622         }
 623       });
 624
 625       JvSwingUtils.jvInitComponent(turn, "label.turn");
 626       turn.addActionListener(new ActionListener()
 627       {
 628         @Override
 629         public void actionPerformed(ActionEvent actionEvent)
 630         {
 631           turn_actionPerformed();
 632         }
 633       });
 634
 635       JvSwingUtils.jvInitComponent(all, "label.select_all");
 636       all.addActionListener(new ActionListener()
 637       {
 638         @Override
 639         public void actionPerformed(ActionEvent actionEvent)
 640         {
 641           all_actionPerformed();
 642         }
 643       });
 644
 645       this.setBorder(new TitledBorder(
 646               MessageManager.getString("label.structures_filter")));
 647       JvSwingUtils.jvInitComponent(this);
 648
 649       this.add(all);
 650       this.add(alphaHelix);
 651       this.add(betaStrand);
 652       this.add(turn);
 653     }
 654
 655     public void alphaHelix_actionPerformed()
 656     {
 657       updateSelectAllState();
 658       aColChooser.setCurrentStructureFilterPanel(this);
 659       aColChooser.updateView();
 660     }
 661
 662     public void betaStrand_actionPerformed()
 663     {
 664       updateSelectAllState();
 665       aColChooser.setCurrentStructureFilterPanel(this);
 666       aColChooser.updateView();
 667     }
 668
 669     public void turn_actionPerformed()
 670     {
 671       updateSelectAllState();
 672       aColChooser.setCurrentStructureFilterPanel(this);
 673       aColChooser.updateView();
 674     }
 675
 676     public void all_actionPerformed()
 677     {
 678       if (all.isSelected())
 679       {
 680         alphaHelix.setSelected(true);
 681         betaStrand.setSelected(true);
 682         turn.setSelected(true);
 683       }
 684       else
 685       {
 686         alphaHelix.setSelected(false);
 687         betaStrand.setSelected(false);
 688         turn.setSelected(false);
 689       }
 690       aColChooser.setCurrentStructureFilterPanel(this);
 691       aColChooser.updateView();
 692     }
 693
 694     public void updateSelectAllState()
 695     {
 696       if (alphaHelix.isSelected() && betaStrand.isSelected()
 697               && turn.isSelected())
 698       {
 699         all.setSelected(true);
 700       }
 701       else
 702       {
 703         all.setSelected(false);
 704       }
 705     }
 706
 707     public void syncState()
 708     {
 709       StructureFilterPanel sfp = aColChooser
 710               .getCurrentStructureFilterPanel();
 711       if (sfp != null)
 712       {
 713         alphaHelix.setSelected(sfp.alphaHelix.isSelected());
 714         betaStrand.setSelected(sfp.betaStrand.isSelected());
 715         turn.setSelected(sfp.turn.isSelected());
 716         if (sfp.all.isSelected())
 717         {
 718           all.setSelected(true);
 719           alphaHelix.setSelected(true);
 720           betaStrand.setSelected(true);
 721           turn.setSelected(true);
 722         }
 723       }
 724
 725     }
 726   }
 727
 728   public class SearchPanel extends JPanel
 729   {
 730     private AnnotationColumnChooser aColChooser;
 731
 732     private JCheckBox displayName = new JCheckBox();
 733
 734     private JCheckBox description = new JCheckBox();
 735
 736     private static final String FILTER_BY_ANN_CACHE_KEY = "CACHE.SELECT_FILTER_BY_ANNOT";
 737
 738     public JvCacheableInputBox<String> searchBox = new JvCacheableInputBox<>(
 739             FILTER_BY_ANN_CACHE_KEY, 23);
 740
 741     public SearchPanel(AnnotationColumnChooser aColChooser)
 742     {
 743
 744       this.aColChooser = aColChooser;
 745       JvSwingUtils.jvInitComponent(this);
 746       this.setBorder(new TitledBorder(
 747               MessageManager.getString("label.search_filter")));
 748
 749       searchBox.getComponent().setToolTipText(
 750               MessageManager.getString("info.enter_search_text_here"));
 751       searchBox.addKeyListener(new java.awt.event.KeyAdapter()
 752       {
 753         @Override
 754         public void keyPressed(KeyEvent e)
 755         {
 756           if (e.getKeyCode() == KeyEvent.VK_ENTER)
 757           {
 758             e.consume();
 759             searchStringAction();
 760           }
 761         }
 762       });
 763       searchBox.addFocusListener(new FocusAdapter()
 764       {
 765         @Override
 766         public void focusLost(FocusEvent e)
 767         {
 768           searchStringAction();
 769         }
 770       });
 771
 772       JvSwingUtils.jvInitComponent(displayName, "label.label");
 773       displayName.addActionListener(new ActionListener()
 774       {
 775         @Override
 776         public void actionPerformed(ActionEvent actionEvent)
 777         {
 778           displayNameCheckboxAction();
 779         }
 780       });
 781
 782       JvSwingUtils.jvInitComponent(description, "label.description");
 783       description.addActionListener(new ActionListener()
 784       {
 785         @Override
 786         public void actionPerformed(ActionEvent actionEvent)
 787         {
 788           descriptionCheckboxAction();
 789         }
 790       });
 791
 792       syncState();
 793       this.add(searchBox.getComponent());
 794       this.add(displayName);
 795       this.add(description);
 796     }
 797
 798     public void displayNameCheckboxAction()
 799     {
 800       aColChooser.setCurrentSearchPanel(this);
 801       aColChooser.updateView();
 802     }
 803
 804     public void descriptionCheckboxAction()
 805     {
 806       aColChooser.setCurrentSearchPanel(this);
 807       aColChooser.updateView();
 808     }
 809
 810     public void searchStringAction()
 811     {
 812       aColChooser.setCurrentSearchPanel(this);
 813       aColChooser.updateView();
 814       updateSearchPanelToolTips();
 815       searchBox.updateCache();
 816     }
 817
 818     public void syncState()
 819     {
 820       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 821       if (sp != null)
 822       {
 823         description.setEnabled(sp.description.isEnabled());
 824         description.setSelected(sp.description.isSelected());
 825
 826         displayName.setEnabled(sp.displayName.isEnabled());
 827         displayName.setSelected(sp.displayName.isSelected());
 828
 829         searchBox.setSelectedItem(sp.searchBox.getUserInput());
 830       }
 831       updateSearchPanelToolTips();
 832     }
 833
 834     public void updateSearchPanelToolTips()
 835     {
 836       String defaultTtip = MessageManager
 837               .getString("info.enter_search_text_to_enable");
 838       String labelTtip = MessageManager.formatMessage(
 839               "info.search_in_annotation_label",
 840               annotations.getSelectedItem().toString());
 841       String descTtip = MessageManager.formatMessage(
 842               "info.search_in_annotation_description",
 843               annotations.getSelectedItem().toString());
 844       displayName.setToolTipText(
 845               displayName.isEnabled() ? labelTtip : defaultTtip);
 846       description.setToolTipText(
 847               description.isEnabled() ? descTtip : defaultTtip);
 848     }
 849   }
 850
 851   @Override
 852   public void ok_actionPerformed()
 853   {
 854     saveCache();
 855     super.ok_actionPerformed();
 856   }
 857
 858   @Override
 859   public void cancel_actionPerformed()
 860   {
 861     saveCache();
 862     super.cancel_actionPerformed();
 863   }
 864
 865   private void saveCache()
 866   {
 867     gSearchPanel.searchBox.persistCache();
 868     ngSearchPanel.searchBox.persistCache();
 869     gSearchPanel.searchBox.updateCache();
 870     ngSearchPanel.searchBox.updateCache();
 871   }
 872
 873   public static void displayFor(AlignViewport av, AlignmentPanel ap,
 874           AlignmentAnnotation alignmentAnnotation)
 875   {
 876     AnnotationColumnChooser colchooser = new AnnotationColumnChooser(av, ap,
 877             alignmentAnnotation);
 878   }
 879 }