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
 171     // restore Object state from the previous session if one exists
 172     if (av.getAnnotationColumnSelectionState() != null)
 173     {
 174       currentSearchPanel = av.getAnnotationColumnSelectionState()
 175               .getCurrentSearchPanel();
 176       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 177               .getCurrentStructureFilterPanel();
 178       annotations.select(av.getAnnotationColumnSelectionState()
 179               .getAnnotations().getSelectedIndex());
 180       threshold.select(av.getAnnotationColumnSelectionState()
 181               .getThreshold().getSelectedIndex());
 182       actionOption = av.getAnnotationColumnSelectionState()
 183               .getActionOption();
 184     }
 185
 186     try
 187     {
 188       jbInit();
 189     } catch (Exception ex)
 190     {
 191     }
 192     adjusting = false;
 193
 194     updateView();
 195     frame.invalidate();
 196     frame.pack();
 197   }
 198
 199   private void jbInit() throws Exception
 200   {
 201     ok.setLabel(MessageManager.getString("action.ok"));
 202
 203     cancel.setLabel(MessageManager.getString("action.cancel"));
 204
 205     thresholdValue.setEnabled(false);
 206     thresholdValue.setColumns(7);
 207
 208     ok.addActionListener(this);
 209     cancel.addActionListener(this);
 210     annotations.addItemListener(this);
 211     thresholdValue.addActionListener(this);
 212     threshold.addItemListener(this);
 213
 214     slider.setBackground(Color.white);
 215     slider.setEnabled(false);
 216     slider.setPreferredSize(new Dimension(100, 32));
 217
 218     thresholdPanel.setBackground(Color.white);
 219     // thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 220     // thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 221
 222     actionPanel.setBackground(Color.white);
 223     // actionPanel.setFont(JvSwingUtils.getLabelFont());
 224
 225     graphFilterView.setLayout(gBorderLayout);
 226     graphFilterView.setBackground(Color.white);
 227
 228     noGraphFilterView.setLayout(ngBorderLayout);
 229     noGraphFilterView.setBackground(Color.white);
 230
 231     annotationComboBoxPanel.setBackground(Color.white);
 232     // annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 233
 234     gSearchPanel = new SearchPanel(this);
 235     ngSearchPanel = new SearchPanel(this);
 236     gFurtherActionPanel = new FurtherActionPanel(this);
 237     ngFurtherActionPanel = new FurtherActionPanel(this);
 238     gStructureFilterPanel = new StructureFilterPanel(this);
 239     ngStructureFilterPanel = new StructureFilterPanel(this);
 240
 241     thresholdPanel.setTitle("Threshold Filter");
 242     thresholdPanel.add(getThreshold());
 243     thresholdPanel.add(slider);
 244     thresholdPanel.add(thresholdValue);
 245
 246     actionPanel.add(ok);
 247     actionPanel.add(cancel);
 248
 249     Panel staticPanel = new Panel();
 250     staticPanel.setLayout(new BorderLayout());
 251     staticPanel.setBackground(Color.white);
 252
 253     staticPanel.add(gSearchPanel, java.awt.BorderLayout.NORTH);
 254     staticPanel.add(gStructureFilterPanel, java.awt.BorderLayout.SOUTH);
 255
 256     graphFilterView.add(staticPanel, java.awt.BorderLayout.NORTH);
 257     graphFilterView.add(thresholdPanel, java.awt.BorderLayout.CENTER);
 258     graphFilterView.add(gFurtherActionPanel, java.awt.BorderLayout.SOUTH);
 259
 260     noGraphFilterView.add(ngSearchPanel, java.awt.BorderLayout.PAGE_START);
 261     noGraphFilterView.add(ngStructureFilterPanel,
 262             java.awt.BorderLayout.CENTER);
 263     noGraphFilterView.add(ngFurtherActionPanel,
 264             java.awt.BorderLayout.CENTER);
 265
 266     annotationComboBoxPanel.add(getAnnotations());
 267     switchableViewsPanel.add(noGraphFilterView,
 268             AnnotationColumnChooser.NO_GRAPH_VIEW);
 269     switchableViewsPanel.add(graphFilterView,
 270             AnnotationColumnChooser.GRAPH_VIEW);
 271
 272     this.setLayout(borderLayout1);
 273     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 274     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 275     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 276
 277     selectedAnnotationChanged();
 278     this.validate();
 279   }
 280
 281   @Override
 282   @SuppressWarnings("unchecked")
 283   public void reset()
 284   {
 285     if (this.getOldColumnSelection() != null)
 286     {
 287       av.getColumnSelection().clear();
 288
 289       if (av.getAnnotationColumnSelectionState() != null)
 290       {
 291         ColumnSelection oldSelection = av
 292                 .getAnnotationColumnSelectionState()
 293                 .getOldColumnSelection();
 294         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 295                 && !oldSelection.getHiddenColumns().isEmpty())
 296         {
 297           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 298                   .iterator(); itr.hasNext();)
 299           {
 300             int positions[] = itr.next();
 301             av.hideColumns(positions[0], positions[1]);
 302           }
 303         }
 304         av.setColumnSelection(oldSelection);
 305       }
 306       ap.paintAlignment(true);
 307     }
 308
 309   }
 310
 311   @Override
 312   public void adjustmentValueChanged(AdjustmentEvent evt)
 313   {
 314     if (!adjusting)
 315     {
 316       thresholdValue.setText((slider.getValue() / 1000f) + "");
 317       valueChanged(!sliderDragging);
 318     }
 319   }
 320
 321   protected void addSliderMouseListeners()
 322   {
 323
 324     slider.addMouseListener(new MouseAdapter()
 325     {
 326       @Override
 327       public void mousePressed(MouseEvent e)
 328       {
 329         sliderDragging = true;
 330         super.mousePressed(e);
 331       }
 332
 333       @Override
 334       public void mouseDragged(MouseEvent e)
 335       {
 336         sliderDragging = true;
 337         super.mouseDragged(e);
 338       }
 339
 340       @Override
 341       public void mouseReleased(MouseEvent evt)
 342       {
 343         if (sliderDragging)
 344         {
 345           sliderDragging = false;
 346           valueChanged(true);
 347         }
 348         ap.paintAlignment(true);
 349       }
 350     });
 351   }
 352
 353   @Override
 354   public void valueChanged(boolean updateAllAnnotation)
 355   {
 356     if (slider.isEnabled())
 357     {
 358       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 359       updateView();
 360       ap.paintAlignment(false);
 361     }
 362   }
 363
 364   public Choice getThreshold()
 365   {
 366     return threshold;
 367   }
 368
 369   public void setThreshold(Choice threshold)
 370   {
 371     this.threshold = threshold;
 372   }
 373
 374   public Choice getAnnotations()
 375   {
 376     return annotations;
 377   }
 378
 379   public void setAnnotations(Choice annotations)
 380   {
 381     this.annotations = annotations;
 382   }
 383
 384   @Override
 385   public void updateView()
 386   {
 387     // Check if combobox is still adjusting
 388     if (adjusting)
 389     {
 390       return;
 391     }
 392
 393     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 394     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 395             .getSelectedIndex()]);
 396
 397     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 398             .getSelectedIndex());
 399
 400     slider.setEnabled(true);
 401     thresholdValue.setEnabled(true);
 402
 403     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 404     {
 405       slider.setEnabled(false);
 406       thresholdValue.setEnabled(false);
 407       thresholdValue.setText("");
 408       // build filter params
 409     }
 410     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 411     {
 412       if (getCurrentAnnotation().threshold == null)
 413       {
 414         getCurrentAnnotation()
 415                 .setThreshold(
 416                         new jalview.datamodel.GraphLine(
 417                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 418                                 "Threshold", Color.black));
 419       }
 420
 421       adjusting = true;
 422       float range = getCurrentAnnotation().graphMax * 1000
 423               - getCurrentAnnotation().graphMin * 1000;
 424
 425       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 426       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 427       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 428       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 429       // slider.setMajorTickSpacing((int) (range / 10f));
 430       slider.setEnabled(true);
 431       thresholdValue.setEnabled(true);
 432       adjusting = false;
 433
 434       // build filter params
 435       filterParams
 436               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 437       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 438       {
 439         filterParams
 440                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 441
 442         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 443         {
 444           filterParams
 445                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 446         }
 447         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 448         {
 449           filterParams
 450                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 451         }
 452       }
 453     }
 454
 455     if (currentStructureFilterPanel != null)
 456     {
 457       if (currentStructureFilterPanel.alphaHelix.getState())
 458       {
 459         filterParams.setFilterAlphaHelix(true);
 460       }
 461       if (currentStructureFilterPanel.betaStrand.getState())
 462       {
 463         filterParams.setFilterBetaSheet(true);
 464       }
 465       if (currentStructureFilterPanel.turn.getState())
 466       {
 467         filterParams.setFilterTurn(true);
 468       }
 469     }
 470
 471     if (currentSearchPanel != null)
 472     {
 473
 474       if (!currentSearchPanel.searchBox.getText().isEmpty())
 475       {
 476         currentSearchPanel.description.setEnabled(true);
 477         currentSearchPanel.displayName.setEnabled(true);
 478         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 479         if (currentSearchPanel.displayName.getState())
 480         {
 481           filterParams
 482                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 483         }
 484         if (currentSearchPanel.description.getState())
 485         {
 486           filterParams
 487                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 488         }
 489       }
 490       else
 491       {
 492         currentSearchPanel.description.setEnabled(false);
 493         currentSearchPanel.displayName.setEnabled(false);
 494       }
 495     }
 496
 497     av.getColumnSelection().filterAnnotations(
 498             getCurrentAnnotation().annotations, filterParams);
 499
 500     av.showAllHiddenColumns();
 501     if (getActionOption() == ACTION_OPTION_HIDE)
 502     {
 503       av.hideSelectedColumns();
 504     }
 505
 506     filterParams = null;
 507     av.setAnnotationColumnSelectionState(this);
 508     ap.paintAlignment(true);
 509   }
 510
 511   public ColumnSelection getOldColumnSelection()
 512   {
 513     return oldColumnSelection;
 514   }
 515
 516   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 517   {
 518     if (currentColumnSelection != null)
 519     {
 520       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 521     }
 522   }
 523
 524   public FurtherActionPanel getCurrentFutherActionPanel()
 525   {
 526     return currentFurtherActionPanel;
 527   }
 528
 529   public void setCurrentFutherActionPanel(
 530           FurtherActionPanel currentFutherActionPanel)
 531   {
 532     this.currentFurtherActionPanel = currentFutherActionPanel;
 533   }
 534
 535   public SearchPanel getCurrentSearchPanel()
 536   {
 537     return currentSearchPanel;
 538   }
 539
 540   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 541   {
 542     this.currentSearchPanel = currentSearchPanel;
 543   }
 544
 545   public int getActionOption()
 546   {
 547     return actionOption;
 548   }
 549
 550   public void setActionOption(int actionOption)
 551   {
 552     this.actionOption = actionOption;
 553   }
 554
 555   public StructureFilterPanel getCurrentStructureFilterPanel()
 556   {
 557     return currentStructureFilterPanel;
 558   }
 559
 560   public void setCurrentStructureFilterPanel(
 561           StructureFilterPanel currentStructureFilterPanel)
 562   {
 563     this.currentStructureFilterPanel = currentStructureFilterPanel;
 564   }
 565
 566   @Override
 567   public void itemStateChanged(ItemEvent e)
 568   {
 569     if (e.getSource() == annotations)
 570     {
 571       selectedAnnotationChanged();
 572     }
 573     else if (e.getSource() == threshold)
 574     {
 575       threshold_actionPerformed(null);
 576     }
 577   }
 578
 579   public void selectedAnnotationChanged()
 580   {
 581     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 582     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 583             .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
 584     {
 585       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 586     }
 587
 588     gSearchPanel.syncState();
 589     gFurtherActionPanel.syncState();
 590     gStructureFilterPanel.syncState();
 591
 592     ngSearchPanel.syncState();
 593     ngFurtherActionPanel.syncState();
 594     ngStructureFilterPanel.syncState();
 595
 596     switchableViewsLayout.show(switchableViewsPanel, currentView);
 597     updateView();
 598   }
 599
 600   public class FurtherActionPanel extends Panel implements ItemListener
 601   {
 602     private AnnotationColumnChooser aColChooser;
 603
 604     private Choice furtherAction = new Choice();
 605
 606     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 607     {
 608       this.aColChooser = aColChooser;
 609       furtherAction.addItem("Select");
 610       furtherAction.addItem("Hide");
 611       furtherAction.addItemListener(this);
 612       syncState();
 613
 614       // this.setTitle("Filter Actions");
 615       // this.setFont(JvSwingUtils.getLabelFont());
 616
 617       this.add(furtherAction);
 618     }
 619
 620     public void syncState()
 621     {
 622       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 623       {
 624         furtherAction.select("Hide");
 625       }
 626       else
 627       {
 628         furtherAction.select("Select");
 629       }
 630     }
 631
 632     @Override
 633     public void itemStateChanged(ItemEvent e)
 634     {
 635       aColChooser.setCurrentFutherActionPanel(this);
 636       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 637       {
 638         setActionOption(ACTION_OPTION_SELECT);
 639         updateView();
 640       }
 641       else
 642       {
 643         setActionOption(ACTION_OPTION_HIDE);
 644         updateView();
 645       }
 646
 647     }
 648   }
 649
 650   public class StructureFilterPanel extends TitledPanel implements
 651           ItemListener
 652   {
 653     private AnnotationColumnChooser aColChooser;
 654
 655     private Checkbox alphaHelix = new Checkbox();
 656
 657     private Checkbox betaStrand = new Checkbox();
 658
 659     private Checkbox turn = new Checkbox();
 660
 661     private Checkbox all = new Checkbox();
 662
 663     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 664     {
 665       this.aColChooser = aColChooser;
 666
 667       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 668       alphaHelix.setBackground(Color.white);
 669
 670       alphaHelix.addItemListener(this);
 671
 672       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 673       betaStrand.setBackground(Color.white);
 674       betaStrand.addItemListener(this);
 675
 676       turn.setLabel(MessageManager.getString("label.turn"));
 677       turn.setBackground(Color.white);
 678       turn.addItemListener(this);
 679
 680       all.setLabel(MessageManager.getString("label.select_all"));
 681       all.setBackground(Color.white);
 682       all.addItemListener(this);
 683
 684       this.setBackground(Color.white);
 685       this.setTitle("Structure Filter");
 686       // this.setFont(JvSwingUtils.getLabelFont());
 687
 688       this.add(all);
 689       this.add(alphaHelix);
 690       this.add(betaStrand);
 691       this.add(turn);
 692     }
 693
 694     public void alphaHelix_actionPerformed()
 695     {
 696       updateSelectAllState();
 697       aColChooser.setCurrentStructureFilterPanel(this);
 698       aColChooser.updateView();
 699     }
 700
 701     public void betaStrand_actionPerformed()
 702     {
 703       updateSelectAllState();
 704       aColChooser.setCurrentStructureFilterPanel(this);
 705       aColChooser.updateView();
 706     }
 707
 708     public void turn_actionPerformed()
 709     {
 710       updateSelectAllState();
 711       aColChooser.setCurrentStructureFilterPanel(this);
 712       aColChooser.updateView();
 713     }
 714
 715     public void all_actionPerformed()
 716     {
 717       if (all.getState())
 718       {
 719         alphaHelix.setState(true);
 720         betaStrand.setState(true);
 721         turn.setState(true);
 722       }
 723       else
 724       {
 725         alphaHelix.setState(false);
 726         betaStrand.setState(false);
 727         turn.setState(false);
 728       }
 729       aColChooser.setCurrentStructureFilterPanel(this);
 730       aColChooser.updateView();
 731     }
 732
 733     public void updateSelectAllState()
 734     {
 735       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 736       {
 737         all.setState(true);
 738       }
 739       else
 740       {
 741         all.setState(false);
 742       }
 743     }
 744
 745     public void syncState()
 746     {
 747       StructureFilterPanel sfp = aColChooser
 748               .getCurrentStructureFilterPanel();
 749       if (sfp != null)
 750       {
 751         alphaHelix.setState(sfp.alphaHelix.getState());
 752         betaStrand.setState(sfp.betaStrand.getState());
 753         turn.setState(sfp.turn.getState());
 754         if (sfp.all.getState())
 755         {
 756           all.setState(true);
 757           alphaHelix.setState(true);
 758           betaStrand.setState(true);
 759           turn.setState(true);
 760         }
 761       }
 762
 763     }
 764
 765     @Override
 766     public void itemStateChanged(ItemEvent e)
 767     {
 768       if (e.getSource() == alphaHelix)
 769       {
 770         alphaHelix_actionPerformed();
 771       }
 772       else if (e.getSource() == betaStrand)
 773       {
 774         betaStrand_actionPerformed();
 775       }
 776       else if (e.getSource() == turn)
 777       {
 778         turn_actionPerformed();
 779       }
 780       else if (e.getSource() == all)
 781       {
 782         all_actionPerformed();
 783       }
 784     }
 785   }
 786
 787   public class SearchPanel extends TitledPanel implements ItemListener
 788   {
 789     private AnnotationColumnChooser aColChooser;
 790
 791     private Checkbox displayName = new Checkbox();
 792
 793     private Checkbox description = new Checkbox();
 794
 795     private TextField searchBox = new TextField(10);
 796
 797     public SearchPanel(AnnotationColumnChooser aColChooser)
 798     {
 799
 800       this.aColChooser = aColChooser;
 801       searchBox.addTextListener(new TextListener()
 802       {
 803
 804         @Override
 805         public void textValueChanged(TextEvent e)
 806         {
 807           searchStringAction();
 808
 809         }
 810
 811       });
 812
 813       displayName.setLabel(MessageManager.getString("label.label"));
 814       displayName.setEnabled(false);
 815       displayName.addItemListener(this);
 816
 817       description.setLabel(MessageManager.getString("label.description"));
 818       description.setEnabled(false);
 819       description.addItemListener(this);
 820       this.setTitle("Search Filter");
 821       // this.setFont(JvSwingUtils.getLabelFont());
 822
 823       syncState();
 824       this.add(searchBox);
 825       this.add(displayName);
 826       this.add(description);
 827     }
 828
 829     public void displayNameCheckboxAction()
 830     {
 831       aColChooser.setCurrentSearchPanel(this);
 832       aColChooser.updateView();
 833     }
 834
 835     public void discriptionCheckboxAction()
 836     {
 837       aColChooser.setCurrentSearchPanel(this);
 838       aColChooser.updateView();
 839     }
 840
 841     public void searchStringAction()
 842     {
 843       aColChooser.setCurrentSearchPanel(this);
 844       aColChooser.updateView();
 845     }
 846
 847     public void syncState()
 848     {
 849       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 850       if (sp != null)
 851       {
 852         description.setEnabled(sp.description.isEnabled());
 853         description.setState(sp.description.getState());
 854
 855         displayName.setEnabled(sp.displayName.isEnabled());
 856         displayName.setState(sp.displayName.getState());
 857
 858         searchBox.setText(sp.searchBox.getText());
 859       }
 860     }
 861
 862     @Override
 863     public void itemStateChanged(ItemEvent e)
 864     {
 865       if (e.getSource() == displayName)
 866       {
 867         displayNameCheckboxAction();
 868       }
 869       else if (e.getSource() == description)
 870       {
 871         discriptionCheckboxAction();
 872       }
 873
 874     }
 875   }
 876
 877   @Override
 878   public void actionPerformed(ActionEvent evt)
 879   {
 880     if (evt.getSource() == thresholdValue)
 881     {
 882       try
 883       {
 884         float f = new Float(thresholdValue.getText()).floatValue();
 885         slider.setValue((int) (f * 1000));
 886         adjustmentValueChanged(null);
 887       } catch (NumberFormatException ex)
 888       {
 889       }
 890     }
 891
 892     else if (evt.getSource() == ok)
 893     {
 894       ok_actionPerformed(null);
 895     }
 896     else if (evt.getSource() == cancel)
 897     {
 898       cancel_actionPerformed(null);
 899     }
 900     else if (evt.getSource() == thresholdValue)
 901     {
 902       thresholdValue_actionPerformed(null);
 903     }
 904     else
 905     {
 906       updateView();
 907     }
 908   }
 909
 910   @Override
 911   public void mouseClicked(MouseEvent e)
 912   {
 913     // TODO Auto-generated method stub
 914
 915   }
 916
 917   @Override
 918   public void mousePressed(MouseEvent e)
 919   {
 920     if (e.getSource() == slider)
 921     {
 922       updateView();
 923     }
 924
 925   }
 926
 927   @Override
 928   public void mouseReleased(MouseEvent e)
 929   {
 930     if (e.getSource() == slider)
 931     {
 932       updateView();
 933     }
 934   }
 935
 936   @Override
 937   public void mouseEntered(MouseEvent e)
 938   {
 939     if (e.getSource() == slider)
 940     {
 941       updateView();
 942     }
 943   }
 944
 945   @Override
 946   public void mouseExited(MouseEvent e)
 947   {
 948     if (e.getSource() == slider)
 949     {
 950       updateView();
 951     }
 952   }
 953
 954 }