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