src/jalview/appletgui/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 package jalview.appletgui;
  22
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.HiddenColumns;
  25 import jalview.schemes.AnnotationColourGradient;
  26 import jalview.util.MessageManager;
  27 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.CardLayout;
  31 import java.awt.Checkbox;
  32 import java.awt.Choice;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.Frame;
  36 import java.awt.Panel;
  37 import java.awt.TextField;
  38 import java.awt.event.ActionEvent;
  39 import java.awt.event.ActionListener;
  40 import java.awt.event.AdjustmentEvent;
  41 import java.awt.event.AdjustmentListener;
  42 import java.awt.event.ItemEvent;
  43 import java.awt.event.ItemListener;
  44 import java.awt.event.MouseAdapter;
  45 import java.awt.event.MouseEvent;
  46 import java.awt.event.MouseListener;
  47 import java.awt.event.TextEvent;
  48 import java.awt.event.TextListener;
  49 import java.util.ArrayList;
  50 import java.util.Vector;
  51
  52 //import javax.swing.JPanel;
  53
  54 //import net.miginfocom.swing.MigLayout;
  55
  56 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  57         ActionListener, AdjustmentListener, ItemListener, MouseListener
  58 {
  59
  60   private Choice annotations = new Choice();
  61
  62   private Panel actionPanel = new Panel();
  63
  64   private TitledPanel thresholdPanel = new TitledPanel();
  65
  66   private Panel switchableViewsPanel = new Panel(new CardLayout());
  67
  68   private CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  69           .getLayout());
  70
  71   private Panel noGraphFilterView = new Panel();
  72
  73   private Panel graphFilterView = new Panel();
  74
  75   private Panel annotationComboBoxPanel = new Panel();
  76
  77   private BorderLayout borderLayout1 = new BorderLayout();
  78
  79   private BorderLayout gBorderLayout = new BorderLayout();
  80
  81   private BorderLayout ngBorderLayout = new BorderLayout();
  82
  83   private Choice threshold = new Choice();
  84
  85   private StructureFilterPanel gStructureFilterPanel;
  86
  87   private StructureFilterPanel ngStructureFilterPanel;
  88
  89   private StructureFilterPanel currentStructureFilterPanel;
  90
  91   private SearchPanel currentSearchPanel;
  92
  93   private SearchPanel gSearchPanel;
  94
  95   private SearchPanel ngSearchPanel;
  96
  97   private FurtherActionPanel currentFurtherActionPanel;
  98
  99   private FurtherActionPanel gFurtherActionPanel;
 100
 101   private FurtherActionPanel ngFurtherActionPanel;
 102
 103   public static final int ACTION_OPTION_SELECT = 1;
 104
 105   public static int ACTION_OPTION_HIDE = 2;
 106
 107   public static String NO_GRAPH_VIEW = "0";
 108
 109   public static String GRAPH_VIEW = "1";
 110
 111   private int actionOption = ACTION_OPTION_SELECT;
 112
 113   private HiddenColumns oldHiddenColumns;
 114
 115   public AnnotationColumnChooser()
 116   {
 117     try
 118     {
 119       jbInit();
 120     } catch (Exception ex)
 121     {
 122       ex.printStackTrace();
 123     }
 124   }
 125
 126   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
 127   {
 128     super(av, ap);
 129     frame = new Frame();
 130     frame.add(this);
 131     jalview.bin.JalviewLite.addFrame(frame,
 132             MessageManager.getString("label.select_by_annotation"), 520,
 133             215);
 134
 135     slider.addAdjustmentListener(this);
 136     slider.addMouseListener(this);
 137
 138     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 139     if (anns == null)
 140     {
 141       return;
 142     }
 143     setOldHiddenColumns(av.getAlignment().getHiddenColumns());
 144     adjusting = true;
 145     Vector<String> list = new Vector<>();
 146     int index = 1;
 147     for (int i = 0; i < anns.length; i++)
 148     {
 149       String label = anns[i].label;
 150       if (anns[i].sequenceRef != null)
 151       {
 152         label = label + "_" + anns[i].sequenceRef.getName();
 153       }
 154       if (!list.contains(label))
 155       {
 156         list.addElement(label);
 157       }
 158       else
 159       {
 160         list.addElement(label + "_" + (index++));
 161       }
 162     }
 163
 164     for (int i = 0; i < list.size(); i++)
 165     {
 166       annotations.addItem(list.elementAt(i).toString());
 167     }
 168
 169     populateThresholdComboBox(threshold);
 170     AnnotationColumnChooser lastChooser = av
 171             .getAnnotationColumnSelectionState();
 172     // restore Object state from the previous session if one exists
 173     if (lastChooser != null)
 174     {
 175       currentSearchPanel = lastChooser
 176               .getCurrentSearchPanel();
 177       currentStructureFilterPanel = lastChooser
 178               .getCurrentStructureFilterPanel();
 179       annotations.select(lastChooser
 180               .getAnnotations().getSelectedIndex());
 181       threshold.select(lastChooser
 182               .getThreshold().getSelectedIndex());
 183       actionOption = lastChooser
 184               .getActionOption();
 185       percentThreshold.setState(lastChooser.percentThreshold.getState());
 186     }
 187
 188     try
 189     {
 190       jbInit();
 191     } catch (Exception ex)
 192     {
 193     }
 194     adjusting = false;
 195
 196     updateView();
 197     frame.invalidate();
 198     frame.pack();
 199   }
 200
 201   private void jbInit() throws Exception
 202   {
 203     ok.setLabel(MessageManager.getString("action.ok"));
 204
 205     cancel.setLabel(MessageManager.getString("action.cancel"));
 206
 207     thresholdValue.setEnabled(false);
 208     thresholdValue.setColumns(7);
 209     thresholdValue.setCaretPosition(0);
 210
 211     ok.addActionListener(this);
 212     cancel.addActionListener(this);
 213     annotations.addItemListener(this);
 214     thresholdValue.addActionListener(this);
 215     threshold.addItemListener(this);
 216
 217     slider.setBackground(Color.white);
 218     slider.setEnabled(false);
 219     slider.setPreferredSize(new Dimension(100, 32));
 220
 221     thresholdPanel.setBackground(Color.white);
 222     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 223     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 224
 225     percentThreshold.setLabel("As percentage");
 226     percentThreshold.addItemListener(this);
 227
 228     actionPanel.setBackground(Color.white);
 229     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 230
 231     graphFilterView.setLayout(gBorderLayout);
 232     graphFilterView.setBackground(Color.white);
 233
 234     noGraphFilterView.setLayout(ngBorderLayout);
 235     noGraphFilterView.setBackground(Color.white);
 236
 237     annotationComboBoxPanel.setBackground(Color.white);
 238     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 239
 240     gSearchPanel = new SearchPanel(this);
 241     ngSearchPanel = new SearchPanel(this);
 242     gFurtherActionPanel = new FurtherActionPanel(this);
 243     ngFurtherActionPanel = new FurtherActionPanel(this);
 244     gStructureFilterPanel = new StructureFilterPanel(this);
 245     ngStructureFilterPanel = new StructureFilterPanel(this);
 246
 247     thresholdPanel.setTitle("Threshold Filter");
 248     thresholdPanel.add(getThreshold());
 249     thresholdPanel.add(slider);
 250     thresholdPanel.add(thresholdValue);
 251     thresholdPanel.add(percentThreshold);
 252
 253     actionPanel.add(ok);
 254     actionPanel.add(cancel);
 255
 256     Panel staticPanel = new Panel();
 257     staticPanel.setLayout(new BorderLayout());
 258     staticPanel.setBackground(Color.white);
 259
 260     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 261     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 262
 263     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 264     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 265     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 266
 267     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 268     noGraphFilterView.add(ngStructureFilterPanel,
 269             java.awt.BorderLayout.CENTER);
 270     noGraphFilterView.add(ngFurtherActionPanel,
 271             java.awt.BorderLayout.CENTER);
 272
 273     annotationComboBoxPanel.add(getAnnotations());
 274     switchableViewsPanel.add(noGraphFilterView,
 275             AnnotationColumnChooser.NO_GRAPH_VIEW);
 276     switchableViewsPanel.add(graphFilterView,
 277             AnnotationColumnChooser.GRAPH_VIEW);
 278
 279     this.setLayout(borderLayout1);
 280     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 281     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 282     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 283
 284     selectedAnnotationChanged();
 285     this.validate();
 286   }
 287
 288   @Override
 289   @SuppressWarnings("unchecked")
 290   public void reset()
 291   {
 292     if (this.getOldHiddenColumns() != null)
 293     {
 294       av.getColumnSelection().clear();
 295
 296       if (av.getAnnotationColumnSelectionState() != null)
 297       {
 298         HiddenColumns oldHidden = av
 299                 .getAnnotationColumnSelectionState()
 300                 .getOldHiddenColumns();
 301         if (oldHidden != null)
 302         {
 303           ArrayList<int[]> regions = oldHidden.getHiddenColumnsCopy();
 304           for (int[] positions : regions)
 305           {
 306             av.hideColumns(positions[0], positions[1]);
 307           }
 308         }
 309         // TODO not clear why we need to hide all the columns (above) if we are
 310         // going to copy the hidden columns over wholesale anyway
 311         av.getAlignment().setHiddenColumns(oldHidden);
 312       }
 313       av.sendSelection();
 314       ap.paintAlignment(true);
 315     }
 316
 317   }
 318
 319   @Override
 320   public void adjustmentValueChanged(AdjustmentEvent evt)
 321   {
 322     if (!adjusting)
 323     {
 324       setThresholdValueText();
 325       valueChanged(!sliderDragging);
 326     }
 327   }
 328
 329   protected void addSliderMouseListeners()
 330   {
 331
 332     slider.addMouseListener(new MouseAdapter()
 333     {
 334       @Override
 335       public void mousePressed(MouseEvent e)
 336       {
 337         sliderDragging = true;
 338         super.mousePressed(e);
 339       }
 340
 341       @Override
 342       public void mouseDragged(MouseEvent e)
 343       {
 344         sliderDragging = true;
 345         super.mouseDragged(e);
 346       }
 347
 348       @Override
 349       public void mouseReleased(MouseEvent evt)
 350       {
 351         if (sliderDragging)
 352         {
 353           sliderDragging = false;
 354           valueChanged(true);
 355         }
 356         ap.paintAlignment(true);
 357       }
 358     });
 359   }
 360
 361   @Override
 362   public void valueChanged(boolean updateAllAnnotation)
 363   {
 364     if (slider.isEnabled())
 365     {
 366       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 367       updateView();
 368       ap.paintAlignment(false);
 369     }
 370   }
 371
 372   public Choice getThreshold()
 373   {
 374     return threshold;
 375   }
 376
 377   public void setThreshold(Choice threshold)
 378   {
 379     this.threshold = threshold;
 380   }
 381
 382   public Choice getAnnotations()
 383   {
 384     return annotations;
 385   }
 386
 387   public void setAnnotations(Choice annotations)
 388   {
 389     this.annotations = annotations;
 390   }
 391
 392   @Override
 393   public void updateView()
 394   {
 395     // Check if combobox is still adjusting
 396     if (adjusting)
 397     {
 398       return;
 399     }
 400
 401     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 402     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 403             .getSelectedIndex()]);
 404
 405     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 406             .getSelectedIndex());
 407
 408     slider.setEnabled(true);
 409     thresholdValue.setEnabled(true);
 410     percentThreshold.setEnabled(true);
 411
 412     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 413     {
 414       slider.setEnabled(false);
 415       thresholdValue.setEnabled(false);
 416       thresholdValue.setText("");
 417       percentThreshold.setEnabled(false);
 418       // build filter params
 419     }
 420     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 421     {
 422       if (getCurrentAnnotation().threshold == null)
 423       {
 424         getCurrentAnnotation()
 425                 .setThreshold(
 426                         new jalview.datamodel.GraphLine(
 427                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 428                                 "Threshold", Color.black));
 429       }
 430
 431       adjusting = true;
 432       // float range = getCurrentAnnotation().graphMax * 1000
 433       // - getCurrentAnnotation().graphMin * 1000;
 434
 435       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 436       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 437       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 438       setThresholdValueText();
 439       // slider.setMajorTickSpacing((int) (range / 10f));
 440       slider.setEnabled(true);
 441       thresholdValue.setEnabled(true);
 442       percentThreshold.setEnabled(true);
 443       adjusting = false;
 444
 445       // build filter params
 446       filterParams
 447               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 448       if (getCurrentAnnotation().isQuantitative())
 449       {
 450         filterParams
 451                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 452
 453         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 454         {
 455           filterParams
 456                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 457         }
 458         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 459         {
 460           filterParams
 461                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 462         }
 463       }
 464     }
 465
 466     if (currentStructureFilterPanel != null)
 467     {
 468       if (currentStructureFilterPanel.alphaHelix.getState())
 469       {
 470         filterParams.setFilterAlphaHelix(true);
 471       }
 472       if (currentStructureFilterPanel.betaStrand.getState())
 473       {
 474         filterParams.setFilterBetaSheet(true);
 475       }
 476       if (currentStructureFilterPanel.turn.getState())
 477       {
 478         filterParams.setFilterTurn(true);
 479       }
 480     }
 481
 482     if (currentSearchPanel != null)
 483     {
 484
 485       if (!currentSearchPanel.searchBox.getText().isEmpty())
 486       {
 487         currentSearchPanel.description.setEnabled(true);
 488         currentSearchPanel.displayName.setEnabled(true);
 489         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 490         if (currentSearchPanel.displayName.getState())
 491         {
 492           filterParams
 493                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 494         }
 495         if (currentSearchPanel.description.getState())
 496         {
 497           filterParams
 498                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 499         }
 500       }
 501       else
 502       {
 503         currentSearchPanel.description.setEnabled(false);
 504         currentSearchPanel.displayName.setEnabled(false);
 505       }
 506     }
 507
 508     // show hidden columns here, before changing the column selection in
 509     // filterAnnotations, because showing hidden columns has the side effect of
 510     // adding them to the selection
 511     av.showAllHiddenColumns();
 512     av.getColumnSelection().filterAnnotations(
 513             getCurrentAnnotation().annotations, filterParams);
 514
 515     if (getActionOption() == ACTION_OPTION_HIDE)
 516     {
 517       av.hideSelectedColumns();
 518     }
 519
 520     filterParams = null;
 521     av.setAnnotationColumnSelectionState(this);
 522     av.sendSelection();
 523     ap.paintAlignment(true);
 524   }
 525
 526   public HiddenColumns getOldHiddenColumns()
 527   {
 528     return oldHiddenColumns;
 529   }
 530
 531   public void setOldHiddenColumns(HiddenColumns currentHiddenColumns)
 532   {
 533     if (currentHiddenColumns != null)
 534     {
 535       this.oldHiddenColumns = new HiddenColumns(currentHiddenColumns);
 536     }
 537   }
 538
 539   public FurtherActionPanel getCurrentFutherActionPanel()
 540   {
 541     return currentFurtherActionPanel;
 542   }
 543
 544   public void setCurrentFutherActionPanel(
 545           FurtherActionPanel currentFutherActionPanel)
 546   {
 547     this.currentFurtherActionPanel = currentFutherActionPanel;
 548   }
 549
 550   public SearchPanel getCurrentSearchPanel()
 551   {
 552     return currentSearchPanel;
 553   }
 554
 555   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 556   {
 557     this.currentSearchPanel = currentSearchPanel;
 558   }
 559
 560   public int getActionOption()
 561   {
 562     return actionOption;
 563   }
 564
 565   public void setActionOption(int actionOption)
 566   {
 567     this.actionOption = actionOption;
 568   }
 569
 570   public StructureFilterPanel getCurrentStructureFilterPanel()
 571   {
 572     return currentStructureFilterPanel;
 573   }
 574
 575   public void setCurrentStructureFilterPanel(
 576           StructureFilterPanel currentStructureFilterPanel)
 577   {
 578     this.currentStructureFilterPanel = currentStructureFilterPanel;
 579   }
 580
 581   @Override
 582   public void itemStateChanged(ItemEvent e)
 583   {
 584     if (e.getSource() == annotations)
 585     {
 586       selectedAnnotationChanged();
 587     }
 588     else if (e.getSource() == threshold)
 589     {
 590       threshold_actionPerformed(null);
 591     }
 592     else if (e.getSource() == percentThreshold)
 593     {
 594       if (!adjusting)
 595       {
 596         percentageValue_actionPerformed();
 597       }
 598
 599     }
 600   }
 601
 602   public void selectedAnnotationChanged()
 603   {
 604     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 605     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 606             .getSelectedIndex()].isQuantitative())
 607     {
 608       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 609     }
 610
 611     gSearchPanel.syncState();
 612     gFurtherActionPanel.syncState();
 613     gStructureFilterPanel.syncState();
 614
 615     ngSearchPanel.syncState();
 616     ngFurtherActionPanel.syncState();
 617     ngStructureFilterPanel.syncState();
 618
 619     switchableViewsLayout.show(switchableViewsPanel, currentView);
 620     updateView();
 621   }
 622
 623   public class FurtherActionPanel extends Panel implements ItemListener
 624   {
 625     private AnnotationColumnChooser aColChooser;
 626
 627     private Choice furtherAction = new Choice();
 628
 629     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 630     {
 631       this.aColChooser = aColChooser;
 632       furtherAction.addItem("Select");
 633       furtherAction.addItem("Hide");
 634       furtherAction.addItemListener(this);
 635       syncState();
 636
 637       // this.setTitle("Filter Actions");
 638       // this.setFont(JvSwingUtils.getLabelFont());
 639
 640       this.add(furtherAction);
 641     }
 642
 643     public void syncState()
 644     {
 645       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 646       {
 647         furtherAction.select("Hide");
 648       }
 649       else
 650       {
 651         furtherAction.select("Select");
 652       }
 653     }
 654
 655     @Override
 656     public void itemStateChanged(ItemEvent e)
 657     {
 658       aColChooser.setCurrentFutherActionPanel(this);
 659       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 660       {
 661         setActionOption(ACTION_OPTION_SELECT);
 662         updateView();
 663       }
 664       else
 665       {
 666         setActionOption(ACTION_OPTION_HIDE);
 667         updateView();
 668       }
 669
 670     }
 671   }
 672
 673   public class StructureFilterPanel extends TitledPanel implements
 674           ItemListener
 675   {
 676     private AnnotationColumnChooser aColChooser;
 677
 678     private Checkbox alphaHelix = new Checkbox();
 679
 680     private Checkbox betaStrand = new Checkbox();
 681
 682     private Checkbox turn = new Checkbox();
 683
 684     private Checkbox all = new Checkbox();
 685
 686     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 687     {
 688       this.aColChooser = aColChooser;
 689
 690       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 691       alphaHelix.setBackground(Color.white);
 692
 693       alphaHelix.addItemListener(this);
 694
 695       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 696       betaStrand.setBackground(Color.white);
 697       betaStrand.addItemListener(this);
 698
 699       turn.setLabel(MessageManager.getString("label.turn"));
 700       turn.setBackground(Color.white);
 701       turn.addItemListener(this);
 702
 703       all.setLabel(MessageManager.getString("label.select_all"));
 704       all.setBackground(Color.white);
 705       all.addItemListener(this);
 706
 707       this.setBackground(Color.white);
 708       this.setTitle("Structure Filter");
 709       // this.setFont(JvSwingUtils.getLabelFont());
 710
 711       this.add(all);
 712       this.add(alphaHelix);
 713       this.add(betaStrand);
 714       this.add(turn);
 715     }
 716
 717     public void alphaHelix_actionPerformed()
 718     {
 719       updateSelectAllState();
 720       aColChooser.setCurrentStructureFilterPanel(this);
 721       aColChooser.updateView();
 722     }
 723
 724     public void betaStrand_actionPerformed()
 725     {
 726       updateSelectAllState();
 727       aColChooser.setCurrentStructureFilterPanel(this);
 728       aColChooser.updateView();
 729     }
 730
 731     public void turn_actionPerformed()
 732     {
 733       updateSelectAllState();
 734       aColChooser.setCurrentStructureFilterPanel(this);
 735       aColChooser.updateView();
 736     }
 737
 738     public void all_actionPerformed()
 739     {
 740       if (all.getState())
 741       {
 742         alphaHelix.setState(true);
 743         betaStrand.setState(true);
 744         turn.setState(true);
 745       }
 746       else
 747       {
 748         alphaHelix.setState(false);
 749         betaStrand.setState(false);
 750         turn.setState(false);
 751       }
 752       aColChooser.setCurrentStructureFilterPanel(this);
 753       aColChooser.updateView();
 754     }
 755
 756     public void updateSelectAllState()
 757     {
 758       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 759       {
 760         all.setState(true);
 761       }
 762       else
 763       {
 764         all.setState(false);
 765       }
 766     }
 767
 768     public void syncState()
 769     {
 770       StructureFilterPanel sfp = aColChooser
 771               .getCurrentStructureFilterPanel();
 772       if (sfp != null)
 773       {
 774         alphaHelix.setState(sfp.alphaHelix.getState());
 775         betaStrand.setState(sfp.betaStrand.getState());
 776         turn.setState(sfp.turn.getState());
 777         if (sfp.all.getState())
 778         {
 779           all.setState(true);
 780           alphaHelix.setState(true);
 781           betaStrand.setState(true);
 782           turn.setState(true);
 783         }
 784       }
 785
 786     }
 787
 788     @Override
 789     public void itemStateChanged(ItemEvent e)
 790     {
 791       if (e.getSource() == alphaHelix)
 792       {
 793         alphaHelix_actionPerformed();
 794       }
 795       else if (e.getSource() == betaStrand)
 796       {
 797         betaStrand_actionPerformed();
 798       }
 799       else if (e.getSource() == turn)
 800       {
 801         turn_actionPerformed();
 802       }
 803       else if (e.getSource() == all)
 804       {
 805         all_actionPerformed();
 806       }
 807     }
 808   }
 809
 810   public class SearchPanel extends TitledPanel implements ItemListener
 811   {
 812     private AnnotationColumnChooser aColChooser;
 813
 814     private Checkbox displayName = new Checkbox();
 815
 816     private Checkbox description = new Checkbox();
 817
 818     private TextField searchBox = new TextField(10);
 819
 820     public SearchPanel(AnnotationColumnChooser aColChooser)
 821     {
 822
 823       this.aColChooser = aColChooser;
 824       searchBox.addTextListener(new TextListener()
 825       {
 826
 827         @Override
 828         public void textValueChanged(TextEvent e)
 829         {
 830           searchStringAction();
 831
 832         }
 833
 834       });
 835
 836       displayName.setLabel(MessageManager.getString("label.label"));
 837       displayName.setEnabled(false);
 838       displayName.addItemListener(this);
 839
 840       description.setLabel(MessageManager.getString("label.description"));
 841       description.setEnabled(false);
 842       description.addItemListener(this);
 843       this.setTitle("Search Filter");
 844       // this.setFont(JvSwingUtils.getLabelFont());
 845
 846       syncState();
 847       this.add(searchBox);
 848       this.add(displayName);
 849       this.add(description);
 850     }
 851
 852     public void displayNameCheckboxAction()
 853     {
 854       aColChooser.setCurrentSearchPanel(this);
 855       aColChooser.updateView();
 856     }
 857
 858     public void discriptionCheckboxAction()
 859     {
 860       aColChooser.setCurrentSearchPanel(this);
 861       aColChooser.updateView();
 862     }
 863
 864     public void searchStringAction()
 865     {
 866       aColChooser.setCurrentSearchPanel(this);
 867       aColChooser.updateView();
 868     }
 869
 870     public void syncState()
 871     {
 872       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 873       if (sp != null)
 874       {
 875         description.setEnabled(sp.description.isEnabled());
 876         description.setState(sp.description.getState());
 877
 878         displayName.setEnabled(sp.displayName.isEnabled());
 879         displayName.setState(sp.displayName.getState());
 880
 881         searchBox.setText(sp.searchBox.getText());
 882       }
 883     }
 884
 885     @Override
 886     public void itemStateChanged(ItemEvent e)
 887     {
 888       if (e.getSource() == displayName)
 889       {
 890         displayNameCheckboxAction();
 891       }
 892       else if (e.getSource() == description)
 893       {
 894         discriptionCheckboxAction();
 895       }
 896
 897     }
 898   }
 899
 900   @Override
 901   public void actionPerformed(ActionEvent evt)
 902   {
 903
 904     if (evt.getSource() == ok)
 905     {
 906       ok_actionPerformed(null);
 907     }
 908     else if (evt.getSource() == cancel)
 909     {
 910       cancel_actionPerformed(null);
 911     }
 912     else if (evt.getSource() == thresholdValue)
 913     {
 914       thresholdValue_actionPerformed(null);
 915     }
 916     else
 917     {
 918       updateView();
 919     }
 920   }
 921
 922   @Override
 923   public void mouseClicked(MouseEvent e)
 924   {
 925     // TODO Auto-generated method stub
 926
 927   }
 928
 929   @Override
 930   public void mousePressed(MouseEvent e)
 931   {
 932     if (e.getSource() == slider)
 933     {
 934       updateView();
 935     }
 936
 937   }
 938
 939   @Override
 940   public void mouseReleased(MouseEvent e)
 941   {
 942     if (e.getSource() == slider)
 943     {
 944       updateView();
 945     }
 946   }
 947
 948   @Override
 949   public void mouseEntered(MouseEvent e)
 950   {
 951     if (e.getSource() == slider)
 952     {
 953       updateView();
 954     }
 955   }
 956
 957   @Override
 958   public void mouseExited(MouseEvent e)
 959   {
 960     if (e.getSource() == slider)
 961     {
 962       updateView();
 963     }
 964   }
 965
 966 }