unused/appletgui/AnnotationColumnChooser.java

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