src/jalview/gui/AnnotationColumnChooser.java

   1 package jalview.gui;
   2
   3 import jalview.datamodel.AlignmentAnnotation;
   4 import jalview.datamodel.AnnotationFilterParameter;
   5 import jalview.datamodel.ColumnSelection;
   6 import jalview.jbgui.FurtherActionPanel;
   7 import jalview.jbgui.SearchPanel;
   8 import jalview.jbgui.StructureFilterPanel;
   9 import jalview.schemes.AnnotationColourGradient;
  10 import jalview.util.MessageManager;
  11
  12 import java.awt.BorderLayout;
  13 import java.awt.CardLayout;
  14 import java.awt.Color;
  15 import java.awt.Dimension;
  16 import java.awt.event.ActionEvent;
  17 import java.awt.event.ActionListener;
  18 import java.awt.event.ItemEvent;
  19 import java.awt.event.ItemListener;
  20 import java.util.Iterator;
  21
  22 import javax.swing.JButton;
  23 import javax.swing.JComboBox;
  24 import javax.swing.JInternalFrame;
  25 import javax.swing.JLabel;
  26 import javax.swing.JLayeredPane;
  27 import javax.swing.JPanel;
  28 import javax.swing.JRadioButton;
  29 import javax.swing.border.TitledBorder;
  30
  31 import net.miginfocom.swing.MigLayout;
  32
  33 @SuppressWarnings("serial")
  34 public class AnnotationColumnChooser extends AnnotationRowFilter implements
  35         ItemListener
  36 {
  37
  38   private ColumnSelection oldColumnSelection;
  39
  40   private JComboBox<String> annotations;
  41
  42   JButton ok = new JButton();
  43
  44   JButton cancel = new JButton();
  45
  46   JPanel actionPanel = new JPanel();
  47
  48   JPanel thresholdPanel = new JPanel();
  49
  50   JPanel switchableViewsPanel = new JPanel(new CardLayout());
  51
  52   CardLayout switchableViewsLayout = (CardLayout) (switchableViewsPanel
  53           .getLayout());
  54
  55   JPanel noGraphFilterView = new JPanel();
  56
  57   JPanel graphFilterView = new JPanel();
  58
  59   JPanel annotationComboBoxPanel = new JPanel();
  60
  61   StructureFilterPanel gStructureFilterPanel;
  62
  63   StructureFilterPanel ngStructureFilterPanel;
  64
  65   private StructureFilterPanel currentStructureFilterPanel;
  66
  67   JLabel annotationLabel = new JLabel();
  68
  69   BorderLayout borderLayout1 = new BorderLayout();
  70
  71   private JComboBox<String> threshold = new JComboBox<String>();
  72
  73   private SearchPanel currentSearchPanel;
  74
  75   private SearchPanel gSearchPanel;
  76
  77   private SearchPanel ngSearchPanel;
  78
  79   private FurtherActionPanel currentFurtherActionPanel;
  80
  81   private FurtherActionPanel gFurtherActionPanel;
  82
  83   private FurtherActionPanel ngFurtherActionPanel;
  84
  85   public static final int ACTION_OPTION_SELECT = 1;
  86
  87   public static int ACTION_OPTION_HIDE = 2;
  88
  89   public static String NO_GRAPH_VIEW = "0";
  90
  91   public static String GRAPH_VIEW = "1";
  92
  93   private int actionOption = ACTION_OPTION_SELECT;
  94
  95   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap)
  96   {
  97     super(av, ap);
  98     frame = new JInternalFrame();
  99     frame.setContentPane(this);
 100     frame.setLayer(JLayeredPane.PALETTE_LAYER);
 101     Desktop.addInternalFrame(frame,
 102             MessageManager.getString("label.select_by_annotation"), 520,
 103             215);
 104
 105     addSliderChangeListener();
 106     addSliderMouseListeners();
 107
 108     if (av.getAlignment().getAlignmentAnnotation() == null)
 109     {
 110       return;
 111     }
 112     setOldColumnSelection(av.getColumnSelection());
 113     adjusting = true;
 114
 115     setAnnotations(new JComboBox<String>(getAnnotationItems(false)));
 116     populateThresholdComboBox(threshold);
 117
 118     // restore the Object state from the previous session if one exists
 119     if (av.getAnnotationColumnSelectionState() != null)
 120     {
 121       currentSearchPanel = av.getAnnotationColumnSelectionState()
 122               .getCurrentSearchPanel();
 123       currentStructureFilterPanel = av.getAnnotationColumnSelectionState()
 124               .getCurrentStructureFilterPanel();
 125       annotations.setSelectedIndex(av.getAnnotationColumnSelectionState()
 126               .getAnnotations().getSelectedIndex());
 127       threshold.setSelectedIndex(av.getAnnotationColumnSelectionState()
 128               .getThreshold().getSelectedIndex());
 129       actionOption = av.getAnnotationColumnSelectionState()
 130               .getActionOption();
 131
 132     }
 133
 134     try
 135     {
 136       jbInit();
 137     } catch (Exception ex)
 138     {
 139     }
 140     adjusting = false;
 141
 142     updateView();
 143     frame.invalidate();
 144     frame.pack();
 145   }
 146
 147   public AnnotationColumnChooser()
 148   {
 149     try
 150     {
 151       jbInit();
 152     } catch (Exception ex)
 153     {
 154       ex.printStackTrace();
 155     }
 156   }
 157
 158   private void jbInit() throws Exception
 159   {
 160     ok.setOpaque(false);
 161     ok.setText(MessageManager.getString("action.ok"));
 162     ok.addActionListener(new ActionListener()
 163     {
 164       @Override
 165       public void actionPerformed(ActionEvent e)
 166       {
 167         ok_actionPerformed(e);
 168       }
 169     });
 170     cancel.setOpaque(false);
 171     cancel.setText(MessageManager.getString("action.cancel"));
 172     cancel.addActionListener(new ActionListener()
 173     {
 174       @Override
 175       public void actionPerformed(ActionEvent e)
 176       {
 177         cancel_actionPerformed(e);
 178       }
 179     });
 180
 181     getAnnotations().addItemListener(this);
 182     getThreshold().addActionListener(new ActionListener()
 183     {
 184       @Override
 185       public void actionPerformed(ActionEvent e)
 186       {
 187         threshold_actionPerformed(e);
 188       }
 189     });
 190
 191     thresholdValue.addActionListener(new ActionListener()
 192     {
 193       @Override
 194       public void actionPerformed(ActionEvent e)
 195       {
 196         thresholdValue_actionPerformed(e);
 197       }
 198     });
 199     slider.setPaintLabels(false);
 200     slider.setPaintTicks(true);
 201     slider.setBackground(Color.white);
 202     slider.setEnabled(false);
 203     slider.setOpaque(false);
 204     slider.setPreferredSize(new Dimension(100, 32));
 205     thresholdValue.setEnabled(false);
 206     thresholdValue.setColumns(7);
 207
 208     annotationLabel.setBackground(Color.white);
 209     annotationLabel.setFont(JvSwingUtils.getLabelFont());
 210     annotationLabel.setText("Select Annotation : ");
 211
 212     thresholdPanel.setBorder(new TitledBorder("Threshold Filter"));
 213     thresholdPanel.setBackground(Color.white);
 214     thresholdPanel.setFont(JvSwingUtils.getLabelFont());
 215     thresholdPanel.setLayout(new MigLayout("", "[left][right]", "[][]"));
 216
 217     actionPanel.setBackground(Color.white);
 218     actionPanel.setFont(JvSwingUtils.getLabelFont());
 219
 220     this.setLayout(borderLayout1);
 221     graphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 222     graphFilterView.setBackground(Color.white);
 223
 224     noGraphFilterView.setLayout(new MigLayout("", "[left][right]", "[][]"));
 225     noGraphFilterView.setBackground(Color.white);
 226     annotationComboBoxPanel.setBackground(Color.white);
 227     annotationComboBoxPanel.setFont(JvSwingUtils.getLabelFont());
 228
 229     gSearchPanel = new SearchPanel(this);
 230     ngSearchPanel = new SearchPanel(this);
 231     gFurtherActionPanel = new FurtherActionPanel(this);
 232     ngFurtherActionPanel = new FurtherActionPanel(this);
 233     gStructureFilterPanel = new StructureFilterPanel(this);
 234     ngStructureFilterPanel = new StructureFilterPanel(this);
 235
 236
 237     thresholdPanel.add(getThreshold());
 238     thresholdPanel.add(thresholdValue, "wrap");
 239     thresholdPanel.add(slider, "grow, span, wrap");
 240
 241     actionPanel.add(ok);
 242     actionPanel.add(cancel);
 243
 244     graphFilterView.add(gSearchPanel, "grow, span, wrap");
 245     graphFilterView.add(gStructureFilterPanel, "grow, span, wrap");
 246     graphFilterView.add(thresholdPanel, "grow, span, wrap");
 247     graphFilterView.add(gFurtherActionPanel);
 248
 249     noGraphFilterView.add(ngSearchPanel, "grow, span, wrap");
 250     noGraphFilterView.add(ngStructureFilterPanel, "grow, span, wrap");
 251     noGraphFilterView.add(ngFurtherActionPanel);
 252
 253     annotationComboBoxPanel.add(getAnnotations());
 254     switchableViewsPanel.add(noGraphFilterView,
 255             AnnotationColumnChooser.NO_GRAPH_VIEW);
 256     switchableViewsPanel.add(graphFilterView,
 257             AnnotationColumnChooser.GRAPH_VIEW);
 258
 259     this.add(annotationComboBoxPanel, java.awt.BorderLayout.PAGE_START);
 260     this.add(switchableViewsPanel, java.awt.BorderLayout.CENTER);
 261     this.add(actionPanel, java.awt.BorderLayout.SOUTH);
 262
 263     selectedAnnotationChanged();
 264     this.validate();
 265   }
 266
 267   @SuppressWarnings("unchecked")
 268   public void reset()
 269   {
 270     if (this.getOldColumnSelection() != null)
 271     {
 272       av.getColumnSelection().clear();
 273
 274       if (av.getAnnotationColumnSelectionState() != null)
 275       {
 276         ColumnSelection oldSelection = av
 277                 .getAnnotationColumnSelectionState()
 278                 .getOldColumnSelection();
 279         if (oldSelection != null && oldSelection.getHiddenColumns() != null
 280                 && !oldSelection.getHiddenColumns().isEmpty())
 281         {
 282           for (Iterator<int[]> itr = oldSelection.getHiddenColumns()
 283                   .iterator(); itr.hasNext();)
 284           {
 285             int positions[] = itr.next();
 286             av.hideColumns(positions[0], positions[1]);
 287           }
 288         }
 289         av.setColumnSelection(oldSelection);
 290       }
 291       // ap.alignmentChanged();
 292       ap.paintAlignment(true);
 293     }
 294
 295   }
 296
 297   public void valueChanged(boolean updateAllAnnotation)
 298   {
 299     if (slider.isEnabled())
 300     {
 301       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 302       updateView();
 303       propagateSeqAssociatedThreshold(updateAllAnnotation,
 304               getCurrentAnnotation());
 305       ap.paintAlignment(false);
 306     }
 307   }
 308
 309   public JComboBox<String> getThreshold()
 310   {
 311     return threshold;
 312   }
 313
 314   public void setThreshold(JComboBox<String> threshold)
 315   {
 316     this.threshold = threshold;
 317   }
 318
 319   public JComboBox<String> getAnnotations()
 320   {
 321     return annotations;
 322   }
 323
 324   public void setAnnotations(JComboBox<String> annotations)
 325   {
 326     this.annotations = annotations;
 327   }
 328
 329   @Override
 330   public void updateView()
 331   {
 332     // Check if combobox is still adjusting
 333     if (adjusting)
 334     {
 335       return;
 336     }
 337
 338     AnnotationFilterParameter filterParams = new AnnotationFilterParameter();
 339
 340     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 341             .getSelectedIndex()]]);
 342
 343     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 344             .getSelectedIndex());
 345
 346     slider.setEnabled(true);
 347     thresholdValue.setEnabled(true);
 348
 349     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 350     {
 351       slider.setEnabled(false);
 352       thresholdValue.setEnabled(false);
 353       thresholdValue.setText("");
 354       // build filter params
 355     }
 356     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 357     {
 358       if (getCurrentAnnotation().threshold == null)
 359       {
 360         getCurrentAnnotation()
 361                 .setThreshold(
 362                         new jalview.datamodel.GraphLine(
 363                                 (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 364                                 "Threshold", Color.black));
 365       }
 366
 367       adjusting = true;
 368       float range = getCurrentAnnotation().graphMax * 1000
 369               - getCurrentAnnotation().graphMin * 1000;
 370
 371       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 372       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 373       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 374       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 375       slider.setMajorTickSpacing((int) (range / 10f));
 376       slider.setEnabled(true);
 377       thresholdValue.setEnabled(true);
 378       adjusting = false;
 379
 380       // build filter params
 381       filterParams
 382               .setThresholdType(AnnotationFilterParameter.ThresholdType.NO_THRESHOLD);
 383       if (getCurrentAnnotation().graph != AlignmentAnnotation.NO_GRAPH)
 384       {
 385
 386         if (selectedThresholdItem == AnnotationColourGradient.ABOVE_THRESHOLD)
 387         {
 388           filterParams
 389                   .setThresholdType(AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD);
 390         }
 391         else if (selectedThresholdItem == AnnotationColourGradient.BELOW_THRESHOLD)
 392         {
 393           filterParams
 394                   .setThresholdType(AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD);
 395         }
 396       }
 397     }
 398
 399     if (currentStructureFilterPanel != null)
 400     {
 401       if (currentStructureFilterPanel.getAlphaHelix().isSelected())
 402       {
 403         filterParams.setFilterAlphaHelix(true);
 404       }
 405       if (currentStructureFilterPanel.getBetaStrand().isSelected())
 406       {
 407         filterParams.setFilterBetaSheet(true);
 408       }
 409       if (currentStructureFilterPanel.getTurn().isSelected())
 410       {
 411         filterParams.setFilterTurn(true);
 412       }
 413     }
 414
 415     if (currentSearchPanel != null)
 416     {
 417       if (!currentSearchPanel.getSearchString().isEmpty())
 418       {
 419         currentSearchPanel.getDescription().setEnabled(true);
 420         currentSearchPanel.getDisplayName().setEnabled(true);
 421         filterParams.setRegexString(currentSearchPanel.getSearchString());
 422         if (currentSearchPanel.isDisplayNameChecked())
 423         {
 424           filterParams
 425                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DISPLAY_STRING);
 426         }
 427         if (currentSearchPanel.isDescriptionChecked())
 428         {
 429           filterParams
 430                   .addRegexSearchField(AnnotationFilterParameter.SearchableAnnotationField.DESCRIPTION);
 431         }
 432       }
 433       else
 434       {
 435         currentSearchPanel.getDescription().setEnabled(false);
 436         currentSearchPanel.getDisplayName().setEnabled(false);
 437       }
 438     }
 439
 440     filterAnnotations(getCurrentAnnotation().annotations, filterParams,
 441             av.getColumnSelection());
 442
 443     av.showAllHiddenColumns();
 444     if (getActionOption() == ACTION_OPTION_HIDE)
 445     {
 446       av.hideSelectedColumns();
 447     }
 448
 449     filterParams = null;
 450     av.setAnnotationColumnSelectionState(this);
 451     ap.paintAlignment(true);
 452   }
 453
 454   public ColumnSelection getOldColumnSelection()
 455   {
 456     return oldColumnSelection;
 457   }
 458
 459   public void setOldColumnSelection(ColumnSelection currentColumnSelection)
 460   {
 461     if (currentColumnSelection != null)
 462     {
 463       this.oldColumnSelection = new ColumnSelection(currentColumnSelection);
 464     }
 465   }
 466
 467
 468   public void select_action(ActionEvent actionEvent)
 469   {
 470     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 471     if (radioButton.isSelected())
 472     {
 473       setActionOption(ACTION_OPTION_SELECT);
 474       updateView();
 475     }
 476   }
 477
 478   public void hide_action(ActionEvent actionEvent)
 479   {
 480     JRadioButton radioButton = (JRadioButton) actionEvent.getSource();
 481     if (radioButton.isSelected())
 482     {
 483       setActionOption(ACTION_OPTION_HIDE);
 484       updateView();
 485     }
 486   }
 487
 488
 489   @Override
 490   public void itemStateChanged(ItemEvent e)
 491   {
 492     selectedAnnotationChanged();
 493   }
 494
 495   public void selectedAnnotationChanged()
 496   {
 497     String currentView = AnnotationColumnChooser.NO_GRAPH_VIEW;
 498     if (av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 499             .getSelectedIndex()]].graph != AlignmentAnnotation.NO_GRAPH)
 500     {
 501       currentView = AnnotationColumnChooser.GRAPH_VIEW;
 502     }
 503     // else{
 504     // threshold.setSelectedIndex(AlignmentAnnotation.NO_GRAPH);
 505     // }
 506
 507     gSearchPanel.syncState();
 508     gFurtherActionPanel.syncState();
 509     gFurtherActionPanel.syncState();
 510     gFurtherActionPanel.syncState();
 511
 512     ngSearchPanel.syncState();
 513     ngFurtherActionPanel.syncState();
 514     ngStructureFilterPanel.syncState();
 515     ngFurtherActionPanel.syncState();
 516
 517     switchableViewsLayout.show(switchableViewsPanel, currentView);
 518     updateView();
 519   }
 520
 521
 522   public FurtherActionPanel getCurrentFutherActionPanel()
 523   {
 524     return currentFurtherActionPanel;
 525   }
 526
 527   public void setCurrentFutherActionPanel(
 528           FurtherActionPanel currentFutherActionPanel)
 529   {
 530     this.currentFurtherActionPanel = currentFutherActionPanel;
 531   }
 532
 533   public SearchPanel getCurrentSearchPanel()
 534   {
 535     return currentSearchPanel;
 536   }
 537
 538   public void setCurrentSearchPanel(SearchPanel currentSearchPanel)
 539   {
 540     this.currentSearchPanel = currentSearchPanel;
 541   }
 542
 543   public int getActionOption()
 544   {
 545     return actionOption;
 546   }
 547
 548   public void setActionOption(int actionOption)
 549   {
 550     this.actionOption = actionOption;
 551   }
 552
 553   public StructureFilterPanel getCurrentStructureFilterPanel()
 554   {
 555     return currentStructureFilterPanel;
 556   }
 557
 558   public void setCurrentStructureFilterPanel(
 559           StructureFilterPanel currentStructureFilterPanel)
 560   {
 561     this.currentStructureFilterPanel = currentStructureFilterPanel;
 562   }
 563
 564 }