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       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.getOldColumnSelection() != null)
 293     {
 294       av.getColumnSelection().clear();
 295
 296       if (av.getAnnotationColumnSelectionState() != null)
 297       {
 298         ColumnSelection oldSelection = av
 299                 .getAnnotationColumnSelectionState()
 300                 .getOldColumnSelection();
 301         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 302                 && !oldSelection.getHiddenColumns().isEmpty())
 303         {
 304           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 305                   .iterator(); itr.hasNext();)
 306           {
 307             int positions[] = itr.next();
 308             av.hideColumns(positions[0], positions[1]);
 309           }
 310         }
 311         av.setColumnSelection(oldSelection);
 312       }
 313       ap.paintAlignment(true);
 314     }
 315
 316   }
 317
 318   @Override
 319   public void adjustmentValueChanged(AdjustmentEvent evt)
 320   {
 321     if (!adjusting)
 322     {
 323       thresholdValue.setText((slider.getValue() / 1000f) + "");
 324       valueChanged(!sliderDragging);
 325     }
 326   }
 327
 328   protected void addSliderMouseListeners()
 329   {
 330
 331     slider.addMouseListener(new MouseAdapter()
 332     {
 333       @Override
 334       public void mousePressed(MouseEvent e)
 335       {
 336         sliderDragging = true;
 337         super.mousePressed(e);
 338       }
 339
 340       @Override
 341       public void mouseDragged(MouseEvent e)
 342       {
 343         sliderDragging = true;
 344         super.mouseDragged(e);
 345       }
 346
 347       @Override
 348       public void mouseReleased(MouseEvent evt)
 349       {
 350         if (sliderDragging)
 351         {
 352           sliderDragging = false;
 353           valueChanged(true);
 354         }
 355         ap.paintAlignment(true);
 356       }
 357     });
 358   }
 359
 360   @Override
 361   public void valueChanged(boolean updateAllAnnotation)
 362   {
 363     if (slider.isEnabled())
 364     {
 365       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 366       updateView();
 367       ap.paintAlignment(false);
 368     }
 369   }
 370
 371   public Choice getThreshold()
 372   {
 373     return threshold;
 374   }
 375
 376   public void setThreshold(Choice threshold)
 377   {
 378     this.threshold = threshold;
 379   }
 380
 381   public Choice getAnnotations()
 382   {
 383     return annotations;
 384   }
 385
 386   public void setAnnotations(Choice annotations)
 387   {
 388     this.annotations = annotations;
 389   }
 390
 391   @Override
 392   public void updateView()
 393   {
 394     // Check if combobox is still adjusting
 395     if (adjusting)
 396     {
 397       return;
 398     }
 399
 400     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 401     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 402             .getSelectedIndex()]);
 403
 404     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 405             .getSelectedIndex());
 406
 407     slider.setEnabled(true);
 408     thresholdValue.setEnabled(true);
 409
 410     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 411     {
 412       slider.setEnabled(false);
 413       thresholdValue.setEnabled(false);
 414       thresholdValue.setText("");
 415       // build filter params
 416     }
 417     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 418     {
 419       if (getCurrentAnnotation().threshold == null)
 420       {
 421         getCurrentAnnotation()
 422                 .setThreshold(
 423                         new jalview.datamodel.GraphLine(
 424                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 425                                 "Threshold", Color.black));
 426       }
 427
 428       adjusting = true;
 429       float range = getCurrentAnnotation().graphMax * 1000
 430               - getCurrentAnnotation().graphMin * 1000;
 431
 432       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 433       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 434       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 435       setThresholdValueText();
 436       // slider.setMajorTickSpacing((int) (range / 10f));
 437       slider.setEnabled(true);
 438       thresholdValue.setEnabled(true);
 439       adjusting = false;
 440
 441       // build filter params
 442       filterParams
 443               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 444       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 445       {
 446         filterParams
 447                 .setThresholdValue(getCurrentAnnotation().threshold.value);
 448
 449         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 450         {
 451           filterParams
 452                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 453         }
 454         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 455         {
 456           filterParams
 457                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 458         }
 459       }
 460     }
 461
 462     if (currentStructureFilterPanel != null)
 463     {
 464       if (currentStructureFilterPanel.alphaHelix.getState())
 465       {
 466         filterParams.setFilterAlphaHelix(true);
 467       }
 468       if (currentStructureFilterPanel.betaStrand.getState())
 469       {
 470         filterParams.setFilterBetaSheet(true);
 471       }
 472       if (currentStructureFilterPanel.turn.getState())
 473       {
 474         filterParams.setFilterTurn(true);
 475       }
 476     }
 477
 478     if (currentSearchPanel != null)
 479     {
 480
 481       if (!currentSearchPanel.searchBox.getText().isEmpty())
 482       {
 483         currentSearchPanel.description.setEnabled(true);
 484         currentSearchPanel.displayName.setEnabled(true);
 485         filterParams.setRegexString(currentSearchPanel.searchBox.getText());
 486         if (currentSearchPanel.displayName.getState())
 487         {
 488           filterParams
 489                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 490         }
 491         if (currentSearchPanel.description.getState())
 492         {
 493           filterParams
 494                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 495         }
 496       }
 497       else
 498       {
 499         currentSearchPanel.description.setEnabled(false);
 500         currentSearchPanel.displayName.setEnabled(false);
 501       }
 502     }
 503
 504     av.getColumnSelection().filterAnnotations(
 505             getCurrentAnnotation().annotations, filterParams);
 506
 507     av.showAllHiddenColumns();
 508     if (getActionOption() == ACTION_OPTION_HIDE)
 509     {
 510       av.hideSelectedColumns();
 511     }
 512
 513     filterParams = null;
 514     av.setAnnotationColumnSelectionState(this);
 515     ap.paintAlignment(true);
 516   }
 517
 518   public ColumnSelection getOldColumnSelection()
 519   {
 520     return oldColumnSelection;
 521   }
 522
 523   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 524   {
 525     if (currentColumnSelection != null)
 526     {
 527       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 528     }
 529   }
 530
 531   public FurtherActionPanel getCurrentFutherActionPanel()
 532   {
 533     return currentFurtherActionPanel;
 534   }
 535
 536   public void setCurrentFutherActionPanel(
 537           FurtherActionPanel currentFutherActionPanel)
 538   {
 539     this.currentFurtherActionPanel = currentFutherActionPanel;
 540   }
 541
 542   public SearchPanel getCurrentSearchPanel()
 543   {
 544     return currentSearchPanel;
 545   }
 546
 547   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 548   {
 549     this.currentSearchPanel = currentSearchPanel;
 550   }
 551
 552   public int getActionOption()
 553   {
 554     return actionOption;
 555   }
 556
 557   public void setActionOption(int actionOption)
 558   {
 559     this.actionOption = actionOption;
 560   }
 561
 562   public StructureFilterPanel getCurrentStructureFilterPanel()
 563   {
 564     return currentStructureFilterPanel;
 565   }
 566
 567   public void setCurrentStructureFilterPanel(
 568           StructureFilterPanel currentStructureFilterPanel)
 569   {
 570     this.currentStructureFilterPanel = currentStructureFilterPanel;
 571   }
 572
 573   @Override
 574   public void itemStateChanged(ItemEvent e)
 575   {
 576     if (e.getSource() == annotations)
 577     {
 578       selectedAnnotationChanged();
 579     }
 580     else if (e.getSource() == threshold)
 581     {
 582       threshold_actionPerformed(null);
 583     }
 584     else if (e.getSource() == percentThreshold)
 585     {
 586       if (!adjusting)
 587       {
 588         percentageValue_actionPerformed();
 589       }
 590
 591     }
 592   }
 593
 594   public void selectedAnnotationChanged()
 595   {
 596     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 597     if (av.getAlignment().getAlignmentAnnotation()[getAnnotations()
 598             .getSelectedIndex()].graph != AlignmentAnnotation.NO_GRAPH)
 599     {
 600       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 601     }
 602
 603     gSearchPanel.syncState();
 604     gFurtherActionPanel.syncState();
 605     gStructureFilterPanel.syncState();
 606
 607     ngSearchPanel.syncState();
 608     ngFurtherActionPanel.syncState();
 609     ngStructureFilterPanel.syncState();
 610
 611     switchableViewsLayout.show(switchableViewsPanel, currentView);
 612     updateView();
 613   }
 614
 615   public class FurtherActionPanel extends Panel implements ItemListener
 616   {
 617     private AnnotationColumnChooser aColChooser;
 618
 619     private Choice furtherAction = new Choice();
 620
 621     public FurtherActionPanel(AnnotationColumnChooser aColChooser)
 622     {
 623       this.aColChooser = aColChooser;
 624       furtherAction.addItem("Select");
 625       furtherAction.addItem("Hide");
 626       furtherAction.addItemListener(this);
 627       syncState();
 628
 629       // this.setTitle("Filter Actions");
 630       // this.setFont(JvSwingUtils.getLabelFont());
 631
 632       this.add(furtherAction);
 633     }
 634
 635     public void syncState()
 636     {
 637       if (aColChooser.getActionOption() == AnnotationColumnChooser.ACTION_OPTION_HIDE)
 638       {
 639         furtherAction.select("Hide");
 640       }
 641       else
 642       {
 643         furtherAction.select("Select");
 644       }
 645     }
 646
 647     @Override
 648     public void itemStateChanged(ItemEvent e)
 649     {
 650       aColChooser.setCurrentFutherActionPanel(this);
 651       if (furtherAction.getSelectedItem().equalsIgnoreCase("Select"))
 652       {
 653         setActionOption(ACTION_OPTION_SELECT);
 654         updateView();
 655       }
 656       else
 657       {
 658         setActionOption(ACTION_OPTION_HIDE);
 659         updateView();
 660       }
 661
 662     }
 663   }
 664
 665   public class StructureFilterPanel extends TitledPanel implements
 666           ItemListener
 667   {
 668     private AnnotationColumnChooser aColChooser;
 669
 670     private Checkbox alphaHelix = new Checkbox();
 671
 672     private Checkbox betaStrand = new Checkbox();
 673
 674     private Checkbox turn = new Checkbox();
 675
 676     private Checkbox all = new Checkbox();
 677
 678     public StructureFilterPanel(AnnotationColumnChooser aColChooser)
 679     {
 680       this.aColChooser = aColChooser;
 681
 682       alphaHelix.setLabel(MessageManager.getString("label.alpha_helix"));
 683       alphaHelix.setBackground(Color.white);
 684
 685       alphaHelix.addItemListener(this);
 686
 687       betaStrand.setLabel(MessageManager.getString("label.beta_strand"));
 688       betaStrand.setBackground(Color.white);
 689       betaStrand.addItemListener(this);
 690
 691       turn.setLabel(MessageManager.getString("label.turn"));
 692       turn.setBackground(Color.white);
 693       turn.addItemListener(this);
 694
 695       all.setLabel(MessageManager.getString("label.select_all"));
 696       all.setBackground(Color.white);
 697       all.addItemListener(this);
 698
 699       this.setBackground(Color.white);
 700       this.setTitle("Structure Filter");
 701       // this.setFont(JvSwingUtils.getLabelFont());
 702
 703       this.add(all);
 704       this.add(alphaHelix);
 705       this.add(betaStrand);
 706       this.add(turn);
 707     }
 708
 709     public void alphaHelix_actionPerformed()
 710     {
 711       updateSelectAllState();
 712       aColChooser.setCurrentStructureFilterPanel(this);
 713       aColChooser.updateView();
 714     }
 715
 716     public void betaStrand_actionPerformed()
 717     {
 718       updateSelectAllState();
 719       aColChooser.setCurrentStructureFilterPanel(this);
 720       aColChooser.updateView();
 721     }
 722
 723     public void turn_actionPerformed()
 724     {
 725       updateSelectAllState();
 726       aColChooser.setCurrentStructureFilterPanel(this);
 727       aColChooser.updateView();
 728     }
 729
 730     public void all_actionPerformed()
 731     {
 732       if (all.getState())
 733       {
 734         alphaHelix.setState(true);
 735         betaStrand.setState(true);
 736         turn.setState(true);
 737       }
 738       else
 739       {
 740         alphaHelix.setState(false);
 741         betaStrand.setState(false);
 742         turn.setState(false);
 743       }
 744       aColChooser.setCurrentStructureFilterPanel(this);
 745       aColChooser.updateView();
 746     }
 747
 748     public void updateSelectAllState()
 749     {
 750       if (alphaHelix.getState() && betaStrand.getState() && turn.getState())
 751       {
 752         all.setState(true);
 753       }
 754       else
 755       {
 756         all.setState(false);
 757       }
 758     }
 759
 760     public void syncState()
 761     {
 762       StructureFilterPanel sfp = aColChooser
 763               .getCurrentStructureFilterPanel();
 764       if (sfp != null)
 765       {
 766         alphaHelix.setState(sfp.alphaHelix.getState());
 767         betaStrand.setState(sfp.betaStrand.getState());
 768         turn.setState(sfp.turn.getState());
 769         if (sfp.all.getState())
 770         {
 771           all.setState(true);
 772           alphaHelix.setState(true);
 773           betaStrand.setState(true);
 774           turn.setState(true);
 775         }
 776       }
 777
 778     }
 779
 780     @Override
 781     public void itemStateChanged(ItemEvent e)
 782     {
 783       if (e.getSource() == alphaHelix)
 784       {
 785         alphaHelix_actionPerformed();
 786       }
 787       else if (e.getSource() == betaStrand)
 788       {
 789         betaStrand_actionPerformed();
 790       }
 791       else if (e.getSource() == turn)
 792       {
 793         turn_actionPerformed();
 794       }
 795       else if (e.getSource() == all)
 796       {
 797         all_actionPerformed();
 798       }
 799     }
 800   }
 801
 802   public class SearchPanel extends TitledPanel implements ItemListener
 803   {
 804     private AnnotationColumnChooser aColChooser;
 805
 806     private Checkbox displayName = new Checkbox();
 807
 808     private Checkbox description = new Checkbox();
 809
 810     private TextField searchBox = new TextField(10);
 811
 812     public SearchPanel(AnnotationColumnChooser aColChooser)
 813     {
 814
 815       this.aColChooser = aColChooser;
 816       searchBox.addTextListener(new TextListener()
 817       {
 818
 819         @Override
 820         public void textValueChanged(TextEvent e)
 821         {
 822           searchStringAction();
 823
 824         }
 825
 826       });
 827
 828       displayName.setLabel(MessageManager.getString("label.label"));
 829       displayName.setEnabled(false);
 830       displayName.addItemListener(this);
 831
 832       description.setLabel(MessageManager.getString("label.description"));
 833       description.setEnabled(false);
 834       description.addItemListener(this);
 835       this.setTitle("Search Filter");
 836       // this.setFont(JvSwingUtils.getLabelFont());
 837
 838       syncState();
 839       this.add(searchBox);
 840       this.add(displayName);
 841       this.add(description);
 842     }
 843
 844     public void displayNameCheckboxAction()
 845     {
 846       aColChooser.setCurrentSearchPanel(this);
 847       aColChooser.updateView();
 848     }
 849
 850     public void discriptionCheckboxAction()
 851     {
 852       aColChooser.setCurrentSearchPanel(this);
 853       aColChooser.updateView();
 854     }
 855
 856     public void searchStringAction()
 857     {
 858       aColChooser.setCurrentSearchPanel(this);
 859       aColChooser.updateView();
 860     }
 861
 862     public void syncState()
 863     {
 864       SearchPanel sp = aColChooser.getCurrentSearchPanel();
 865       if (sp != null)
 866       {
 867         description.setEnabled(sp.description.isEnabled());
 868         description.setState(sp.description.getState());
 869
 870         displayName.setEnabled(sp.displayName.isEnabled());
 871         displayName.setState(sp.displayName.getState());
 872
 873         searchBox.setText(sp.searchBox.getText());
 874       }
 875     }
 876
 877     @Override
 878     public void itemStateChanged(ItemEvent e)
 879     {
 880       if (e.getSource() == displayName)
 881       {
 882         displayNameCheckboxAction();
 883       }
 884       else if (e.getSource() == description)
 885       {
 886         discriptionCheckboxAction();
 887       }
 888
 889     }
 890   }
 891
 892   @Override
 893   public void actionPerformed(ActionEvent evt)
 894   {
 895     if (evt.getSource() == thresholdValue)
 896     {
 897       try
 898       {
 899         float f = new Float(thresholdValue.getText()).floatValue();
 900         slider.setValue((int) (f * 1000));
 901         adjustmentValueChanged(null);
 902       } catch (NumberFormatException ex)
 903       {
 904       }
 905     }
 906
 907     else if (evt.getSource() == ok)
 908     {
 909       ok_actionPerformed(null);
 910     }
 911     else if (evt.getSource() == cancel)
 912     {
 913       cancel_actionPerformed(null);
 914     }
 915     else if (evt.getSource() == thresholdValue)
 916     {
 917       thresholdValue_actionPerformed(null);
 918     }
 919     else
 920     {
 921       updateView();
 922     }
 923   }
 924
 925   @Override
 926   public void mouseClicked(MouseEvent e)
 927   {
 928     // TODO Auto-generated method stub
 929
 930   }
 931
 932   @Override
 933   public void mousePressed(MouseEvent e)
 934   {
 935     if (e.getSource() == slider)
 936     {
 937       updateView();
 938     }
 939
 940   }
 941
 942   @Override
 943   public void mouseReleased(MouseEvent e)
 944   {
 945     if (e.getSource() == slider)
 946     {
 947       updateView();
 948     }
 949   }
 950
 951   @Override
 952   public void mouseEntered(MouseEvent e)
 953   {
 954     if (e.getSource() == slider)
 955     {
 956       updateView();
 957     }
 958   }
 959
 960   @Override
 961   public void mouseExited(MouseEvent e)
 962   {
 963     if (e.getSource() == slider)
 964     {
 965       updateView();
 966     }
 967   }
 968
 969 }