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.ColumnSelection;
  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.Iterator;
  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 ColumnSelection oldColumnSelection;
 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     setOldColumnSelection(av.getColumnSelection());
 144     adjusting = true;
 145     Vector<String> list = new Vector<String>();
 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     }
 186
 187     try
 188     {
 189       jbInit();
 190     } catch (Exception ex)
 191     {
 192     }
 193     adjusting = false;
 194
 195     updateView();
 196     frame.invalidate();
 197     frame.pack();
 198   }
 199
 200   private void jbInit() throws Exception
 201   {
 202     ok.setLabel(MessageManager.getString("action.ok"));
 203
 204     cancel.setLabel(MessageManager.getString("action.cancel"));
 205
 206     thresholdValue.setEnabled(false);
 207     thresholdValue.setColumns(7);
 208     thresholdValue.setCaretPosition(0);
 209
 210     ok.addActionListener(this);
 211     cancel.addActionListener(this);
 212     annotations.addItemListener(this);
 213     thresholdValue.addActionListener(this);
 214     threshold.addItemListener(this);
 215
 216     slider.setBackground(Color.white);
 217     slider.setEnabled(false);
 218     slider.setPreferredSize(new Dimension(100, 32));
 219
 220     thresholdPanel.setBackground(Color.white);
 221     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 222     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 223
 224     percentThreshold.setLabel("As percentage");
 225     percentThreshold.addItemListener(this);
 226
 227     actionPanel.setBackground(Color.white);
 228     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 229
 230     graphFilterView.setLayout(gBorderLayout);
 231     graphFilterView.setBackground(Color.white);
 232
 233     noGraphFilterView.setLayout(ngBorderLayout);
 234     noGraphFilterView.setBackground(Color.white);
 235
 236     annotationComboBoxPanel.setBackground(Color.white);
 237     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 238
 239     gSearchPanel = new SearchPanel(this);
 240     ngSearchPanel = new SearchPanel(this);
 241     gFurtherActionPanel = new FurtherActionPanel(this);
 242     ngFurtherActionPanel = new FurtherActionPanel(this);
 243     gStructureFilterPanel = new StructureFilterPanel(this);
 244     ngStructureFilterPanel = new StructureFilterPanel(this);
 245
 246     thresholdPanel.setTitle("Threshold Filter");
 247     thresholdPanel.add(percentThreshold);
 248     thresholdPanel.add(getThreshold());
 249     thresholdPanel.add(slider);
 250     thresholdPanel.add(thresholdValue);
 251
 252     actionPanel.add(ok);
 253     actionPanel.add(cancel);
 254
 255     Panel staticPanel = new Panel();
 256     staticPanel.setLayout(new BorderLayout());
 257     staticPanel.setBackground(Color.white);
 258
 259     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 260     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 261
 262     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 263     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 264     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 265
 266     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 267     noGraphFilterView.add(ngStructureFilterPanel,
 268             java.awt.BorderLayout.CENTER);
 269     noGraphFilterView.add(ngFurtherActionPanel,
 270             java.awt.BorderLayout.CENTER);
 271
 272     annotationComboBoxPanel.add(getAnnotations());
 273     switchableViewsPanel.add(noGraphFilterView,
 274             AnnotationColumnChooser.NO_GRAPH_VIEW);
 275     switchableViewsPanel.add(graphFilterView,
 276             AnnotationColumnChooser.GRAPH_VIEW);
 277
 278     this.setLayout(borderLayout1);
 279     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 280     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 281     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 282
 283     selectedAnnotationChanged();
 284     this.validate();
 285   }
 286
 287   @Override
 288   @SuppressWarnings("unchecked")
 289   public void reset()
 290   {
 291     if (this.getOldColumnSelection() != null)
 292     {
 293       av.getColumnSelection().clear();
 294
 295       if (av.getAnnotationColumnSelectionState() != null)
 296       {
 297         ColumnSelection oldSelection = av
 298                 .getAnnotationColumnSelectionState()
 299                 .getOldColumnSelection();
 300         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 301                 && !oldSelection.getHiddenColumns().isEmpty())
 302         {
 303           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 304                   .iterator(); itr.hasNext();)
 305           {
 306             int positions[] = itr.next();
 307             av.hideColumns(positions[0], positions[1]);
 308           }
 309         }
 310         av.setColumnSelection(oldSelection);
 311       }
 312       ap.paintAlignment(true);
 313     }
 314
 315   }
 316
 317   @Override
 318   public void adjustmentValueChanged(AdjustmentEvent evt)
 319   {
 320     if (!adjusting)
 321     {
 322       thresholdValue.setText((slider.getValue() / 1000f) + "");
 323       valueChanged(!sliderDragging);
 324     }
 325   }
 326
 327   protected void addSliderMouseListeners()
 328   {
 329
 330     slider.addMouseListener(new MouseAdapter()
 331     {
 332       @Override
 333       public void mousePressed(MouseEvent e)
 334       {
 335         sliderDragging = true;
 336         super.mousePressed(e);
 337       }
 338
 339       @Override
 340       public void mouseDragged(MouseEvent e)
 341       {
 342         sliderDragging = true;
 343         super.mouseDragged(e);
 344       }
 345
 346       @Override
 347       public void mouseReleased(MouseEvent evt)
 348       {
 349         if (sliderDragging)
 350         {
 351           sliderDragging = false;
 352           valueChanged(true);
 353         }
 354         ap.paintAlignment(true);
 355       }
 356     });
 357   }
 358
 359   @Override
 360   public void valueChanged(boolean updateAllAnnotation)
 361   {
 362     if (slider.isEnabled())
 363     {
 364       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 365       updateView();
 366       ap.paintAlignment(false);
 367     }
 368   }
 369
 370   public Choice getThreshold()
 371   {
 372     return threshold;
 373   }
 374
 375   public void setThreshold(Choice threshold)
 376   {
 377     this.threshold = threshold;
 378   }
 379
 380   public Choice getAnnotations()
 381   {
 382     return annotations;
 383   }
 384
 385   public void setAnnotations(Choice annotations)
 386   {
 387     this.annotations = annotations;
 388   }
 389
 390   @Override
 391   public void updateView()
 392   {
 393     // Check if combobox is still adjusting
 394     if (adjusting)
 395     {
 396       return;
 397     }
 398
 399     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 400     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 401             .getSelectedIndex()]);
 402
 403     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 404             .getSelectedIndex());
 405
 406     slider.setEnabled(true);
 407     thresholdValue.setEnabled(true);
 408
 409     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 410     {
 411       slider.setEnabled(false);
 412       thresholdValue.setEnabled(false);
 413       thresholdValue.setText("");
 414       // build filter params
 415     }
 416     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 417     {
 418       if (getCurrentAnnotation().threshold == null)
 419       {
 420         getCurrentAnnotation()
 421                 .setThreshold(
 422                         new jalview.datamodel.GraphLine(
 423                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 424                                 "Threshold", Color.black));
 425       }
 426
 427       adjusting = true;
 428       float range = getCurrentAnnotation().graphMax * 1000
 429               - getCurrentAnnotation().graphMin * 1000;
 430
 431       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 432       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 433       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 434       setThresholdValueText();
 435       // slider.setMajorTickSpacing((int) (range / 10f));
 436       slider.setEnabled(true);
 437       thresholdValue.setEnabled(true);
 438       adjusting = false;
 439
 440       // build filter params
 441       filterParams
 442               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 443       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 444       {
 445         filterParams
 446                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 447
 448         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 449         {
 450           filterParams
 451                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 452         }
 453         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 454         {
 455           filterParams
 456                   .setThresholdType(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
 488                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 489         }
 490         if (currentSearchPanel.description.getState())
 491         {
 492           filterParams
 493                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 494         }
 495       }
 496       else
 497       {
 498         currentSearchPanel.description.setEnabled(false);
 499         currentSearchPanel.displayName.setEnabled(false);
 500       }
 501     }
 502
 503     av.getColumnSelection().filterAnnotations(
 504             getCurrentAnnotation().annotations, filterParams);
 505
 506     av.showAllHiddenColumns();
 507     if (getActionOption() == ACTION_OPTION_HIDE)
 508     {
 509       av.hideSelectedColumns();
 510     }
 511
 512     filterParams = null;
 513     av.setAnnotationColumnSelectionState(this);
 514     ap.paintAlignment(true);
 515   }
 516
 517   public ColumnSelection getOldColumnSelection()
 518   {
 519     return oldColumnSelection;
 520   }
 521
 522   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 523   {
 524     if (currentColumnSelection != null)
 525     {
 526       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 527     }
 528   }
 529
 530   public FurtherActionPanel getCurrentFutherActionPanel()
 531   {
 532     return currentFurtherActionPanel;
 533   }
 534
 535   public void setCurrentFutherActionPanel(
 536           FurtherActionPanel currentFutherActionPanel)
 537   {
 538     this.currentFurtherActionPanel = currentFutherActionPanel;
 539   }
 540
 541   public SearchPanel getCurrentSearchPanel()
 542   {
 543     return currentSearchPanel;
 544   }
 545
 546   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 547   {
 548     this.currentSearchPanel = currentSearchPanel;
 549   }
 550
 551   public int getActionOption()
 552   {
 553     return actionOption;
 554   }
 555
 556   public void setActionOption(int actionOption)
 557   {
 558     this.actionOption = actionOption;
 559   }
 560
 561   public StructureFilterPanel getCurrentStructureFilterPanel()
 562   {
 563     return currentStructureFilterPanel;
 564   }
 565
 566   public void setCurrentStructureFilterPanel(
 567           StructureFilterPanel currentStructureFilterPanel)
 568   {
 569     this.currentStructureFilterPanel = currentStructureFilterPanel;
 570   }
 571
 572   @Override
 573   public void itemStateChanged(ItemEvent e)
 574   {
 575     if (e.getSource() == annotations)
 576     {
 577       selectedAnnotationChanged();
 578     }
 579     else if (e.getSource() == threshold)
 580     {
 581       threshold_actionPerformed(null);
 582     }
 583     else if (e.getSource() == percentThreshold)
 584     {
 585       if (!adjusting)
 586       {
 587         percentageValue_actionPerformed();
 588       }
 589
 590     }
 591   }
 592
 593   public void selectedAnnotationChanged()
 594   {
 595     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 596     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 597             .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
 598     {
 599       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 600     }
 601
 602     gSearchPanel.syncState();
 603     gFurtherActionPanel.syncState();
 604     gStructureFilterPanel.syncState();
 605
 606     ngSearchPanel.syncState();
 607     ngFurtherActionPanel.syncState();
 608     ngStructureFilterPanel.syncState();
 609
 610     switchableViewsLayout.show(switchableViewsPanel, currentView);
 611     updateView();
 612   }
 613
 614   public class FurtherActionPanel extends Panel implements ItemListener
 615   {
 616     private AnnotationColumnChooser aColChooser;
 617
 618     private Choice furtherAction = new Choice();
 619
 620     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 621     {
 622       this.aColChooser = aColChooser;
 623       furtherAction.addItem("Select");
 624       furtherAction.addItem("Hide");
 625       furtherAction.addItemListener(this);
 626       syncState();
 627
 628       // this.setTitle("Filter Actions");
 629       // this.setFont(JvSwingUtils.getLabelFont());
 630
 631       this.add(furtherAction);
 632     }
 633
 634     public void syncState()
 635     {
 636       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 637       {
 638         furtherAction.select("Hide");
 639       }
 640       else
 641       {
 642         furtherAction.select("Select");
 643       }
 644     }
 645
 646     @Override
 647     public void itemStateChanged(ItemEvent e)
 648     {
 649       aColChooser.setCurrentFutherActionPanel(this);
 650       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 651       {
 652         setActionOption(ACTION_OPTION_SELECT);
 653         updateView();
 654       }
 655       else
 656       {
 657         setActionOption(ACTION_OPTION_HIDE);
 658         updateView();
 659       }
 660
 661     }
 662   }
 663
 664   public class StructureFilterPanel extends TitledPanel implements
 665           ItemListener
 666   {
 667     private AnnotationColumnChooser aColChooser;
 668
 669     private Checkbox alphaHelix = new Checkbox();
 670
 671     private Checkbox betaStrand = new Checkbox();
 672
 673     private Checkbox turn = new Checkbox();
 674
 675     private Checkbox all = new Checkbox();
 676
 677     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 678     {
 679       this.aColChooser = aColChooser;
 680
 681       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 682       alphaHelix.setBackground(Color.white);
 683
 684       alphaHelix.addItemListener(this);
 685
 686       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 687       betaStrand.setBackground(Color.white);
 688       betaStrand.addItemListener(this);
 689
 690       turn.setLabel(MessageManager.getString("label.turn"));
 691       turn.setBackground(Color.white);
 692       turn.addItemListener(this);
 693
 694       all.setLabel(MessageManager.getString("label.select_all"));
 695       all.setBackground(Color.white);
 696       all.addItemListener(this);
 697
 698       this.setBackground(Color.white);
 699       this.setTitle("Structure Filter");
 700       // this.setFont(JvSwingUtils.getLabelFont());
 701
 702       this.add(all);
 703       this.add(alphaHelix);
 704       this.add(betaStrand);
 705       this.add(turn);
 706     }
 707
 708     public void alphaHelix_actionPerformed()
 709     {
 710       updateSelectAllState();
 711       aColChooser.setCurrentStructureFilterPanel(this);
 712       aColChooser.updateView();
 713     }
 714
 715     public void betaStrand_actionPerformed()
 716     {
 717       updateSelectAllState();
 718       aColChooser.setCurrentStructureFilterPanel(this);
 719       aColChooser.updateView();
 720     }
 721
 722     public void turn_actionPerformed()
 723     {
 724       updateSelectAllState();
 725       aColChooser.setCurrentStructureFilterPanel(this);
 726       aColChooser.updateView();
 727     }
 728
 729     public void all_actionPerformed()
 730     {
 731       if (all.getState())
 732       {
 733         alphaHelix.setState(true);
 734         betaStrand.setState(true);
 735         turn.setState(true);
 736       }
 737       else
 738       {
 739         alphaHelix.setState(false);
 740         betaStrand.setState(false);
 741         turn.setState(false);
 742       }
 743       aColChooser.setCurrentStructureFilterPanel(this);
 744       aColChooser.updateView();
 745     }
 746
 747     public void updateSelectAllState()
 748     {
 749       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 750       {
 751         all.setState(true);
 752       }
 753       else
 754       {
 755         all.setState(false);
 756       }
 757     }
 758
 759     public void syncState()
 760     {
 761       StructureFilterPanel sfp = aColChooser
 762               .getCurrentStructureFilterPanel();
 763       if (sfp != null)
 764       {
 765         alphaHelix.setState(sfp.alphaHelix.getState());
 766         betaStrand.setState(sfp.betaStrand.getState());
 767         turn.setState(sfp.turn.getState());
 768         if (sfp.all.getState())
 769         {
 770           all.setState(true);
 771           alphaHelix.setState(true);
 772           betaStrand.setState(true);
 773           turn.setState(true);
 774         }
 775       }
 776
 777     }
 778
 779     @Override
 780     public void itemStateChanged(ItemEvent e)
 781     {
 782       if (e.getSource() == alphaHelix)
 783       {
 784         alphaHelix_actionPerformed();
 785       }
 786       else if (e.getSource() == betaStrand)
 787       {
 788         betaStrand_actionPerformed();
 789       }
 790       else if (e.getSource() == turn)
 791       {
 792         turn_actionPerformed();
 793       }
 794       else if (e.getSource() == all)
 795       {
 796         all_actionPerformed();
 797       }
 798     }
 799   }
 800
 801   public class SearchPanel extends TitledPanel implements ItemListener
 802   {
 803     private AnnotationColumnChooser aColChooser;
 804
 805     private Checkbox displayName = new Checkbox();
 806
 807     private Checkbox description = new Checkbox();
 808
 809     private TextField searchBox = new TextField(10);
 810
 811     public SearchPanel(AnnotationColumnChooser aColChooser)
 812     {
 813
 814       this.aColChooser = aColChooser;
 815       searchBox.addTextListener(new TextListener()
 816       {
 817
 818         @Override
 819         public void textValueChanged(TextEvent e)
 820         {
 821           searchStringAction();
 822
 823         }
 824
 825       });
 826
 827       displayName.setLabel(MessageManager.getString("label.label"));
 828       displayName.setEnabled(false);
 829       displayName.addItemListener(this);
 830
 831       description.setLabel(MessageManager.getString("label.description"));
 832       description.setEnabled(false);
 833       description.addItemListener(this);
 834       this.setTitle("Search Filter");
 835       // this.setFont(JvSwingUtils.getLabelFont());
 836
 837       syncState();
 838       this.add(searchBox);
 839       this.add(displayName);
 840       this.add(description);
 841     }
 842
 843     public void displayNameCheckboxAction()
 844     {
 845       aColChooser.setCurrentSearchPanel(this);
 846       aColChooser.updateView();
 847     }
 848
 849     public void discriptionCheckboxAction()
 850     {
 851       aColChooser.setCurrentSearchPanel(this);
 852       aColChooser.updateView();
 853     }
 854
 855     public void searchStringAction()
 856     {
 857       aColChooser.setCurrentSearchPanel(this);
 858       aColChooser.updateView();
 859     }
 860
 861     public void syncState()
 862     {
 863       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 864       if (sp != null)
 865       {
 866         description.setEnabled(sp.description.isEnabled());
 867         description.setState(sp.description.getState());
 868
 869         displayName.setEnabled(sp.displayName.isEnabled());
 870         displayName.setState(sp.displayName.getState());
 871
 872         searchBox.setText(sp.searchBox.getText());
 873       }
 874     }
 875
 876     @Override
 877     public void itemStateChanged(ItemEvent e)
 878     {
 879       if (e.getSource() == displayName)
 880       {
 881         displayNameCheckboxAction();
 882       }
 883       else if (e.getSource() == description)
 884       {
 885         discriptionCheckboxAction();
 886       }
 887
 888     }
 889   }
 890
 891   @Override
 892   public void actionPerformed(ActionEvent evt)
 893   {
 894     if (evt.getSource() == thresholdValue)
 895     {
 896       try
 897       {
 898         float f = new Float(thresholdValue.getText()).floatValue();
 899         slider.setValue((int) (f * 1000));
 900         adjustmentValueChanged(null);
 901       } catch (NumberFormatException ex)
 902       {
 903       }
 904     }
 905
 906     else if (evt.getSource() == ok)
 907     {
 908       ok_actionPerformed(null);
 909     }
 910     else if (evt.getSource() == cancel)
 911     {
 912       cancel_actionPerformed(null);
 913     }
 914     else if (evt.getSource() == thresholdValue)
 915     {
 916       thresholdValue_actionPerformed(null);
 917     }
 918     else
 919     {
 920       updateView();
 921     }
 922   }
 923
 924   @Override
 925   public void mouseClicked(MouseEvent e)
 926   {
 927     // TODO Auto-generated method stub
 928
 929   }
 930
 931   @Override
 932   public void mousePressed(MouseEvent e)
 933   {
 934     if (e.getSource() == slider)
 935     {
 936       updateView();
 937     }
 938
 939   }
 940
 941   @Override
 942   public void mouseReleased(MouseEvent e)
 943   {
 944     if (e.getSource() == slider)
 945     {
 946       updateView();
 947     }
 948   }
 949
 950   @Override
 951   public void mouseEntered(MouseEvent e)
 952   {
 953     if (e.getSource() == slider)
 954     {
 955       updateView();
 956     }
 957   }
 958
 959   @Override
 960   public void mouseExited(MouseEvent e)
 961   {
 962     if (e.getSource() == slider)
 963     {
 964       updateView();
 965     }
 966   }
 967
 968 }