src/jalview/gui/AnnotationColumnSelection.java

   1 package jalview.gui;
   2
   3 import jalview.bin.Cache;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.Annotation;
   6 import jalview.datamodel.ColumnSelection;
   7 import jalview.datamodel.GraphLine;
   8 import jalview.schemes.AnnotationColourGradient;
   9 import jalview.schemes.ColourSchemeI;
  10 import jalview.util.MessageManager;
  11
  12 import java.awt.BorderLayout;
  13 import java.awt.Color;
  14 import java.awt.Dimension;
  15 import java.awt.event.ActionEvent;
  16 import java.awt.event.ActionListener;
  17 import java.awt.event.MouseAdapter;
  18 import java.awt.event.MouseEvent;
  19 import java.util.Hashtable;
  20 import java.util.Vector;
  21
  22 import javax.swing.JButton;
  23 import javax.swing.JCheckBox;
  24 import javax.swing.JComboBox;
  25 import javax.swing.JInternalFrame;
  26 import javax.swing.JLayeredPane;
  27 import javax.swing.JPanel;
  28 import javax.swing.JSlider;
  29 import javax.swing.JTextField;
  30 import javax.swing.event.ChangeEvent;
  31 import javax.swing.event.ChangeListener;
  32
  33 import net.miginfocom.swing.MigLayout;
  34
  35 public class AnnotationColumnSelection extends JPanel
  36 {
  37   JInternalFrame frame;
  38
  39   AlignViewport av;
  40
  41   AlignmentPanel ap;
  42
  43   ColourSchemeI oldcs;
  44
  45   Hashtable oldgroupColours;
  46
  47   private JComboBox annotations;
  48
  49   int[] annmap;
  50
  51   JPanel minColour = new JPanel();
  52
  53   JPanel maxColour = new JPanel();
  54
  55   JButton defColours = new JButton();
  56
  57   JButton ok = new JButton();
  58
  59   JButton cancel = new JButton();
  60
  61   JPanel jPanel1 = new JPanel();
  62
  63   JPanel jPanel2 = new JPanel();
  64
  65   BorderLayout borderLayout1 = new BorderLayout();
  66
  67   private JComboBox threshold = new JComboBox();
  68
  69   JSlider slider = new JSlider();
  70
  71   JTextField thresholdValue = new JTextField(20);
  72
  73   JCheckBox currentColours = new JCheckBox();
  74
  75   JCheckBox thresholdIsMin = new JCheckBox();
  76
  77   JCheckBox seqAssociated = new JCheckBox();
  78
  79   private jalview.datamodel.AlignmentAnnotation currentAnnotation;
  80
  81   boolean adjusting = false;
  82
  83   /**
  84    * enabled if the user is dragging the slider - try to keep updates to a
  85    * minimun
  86    */
  87   boolean sliderDragging = false;
  88
  89   public AnnotationColumnSelection(AlignViewport av, final AlignmentPanel ap)
  90   {
  91
  92     this.av = av;
  93     this.ap = ap;
  94     frame = new JInternalFrame();
  95     frame.setContentPane(this);
  96     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  97     Desktop.addInternalFrame(frame, "Select By Annotation", 520, 215);
  98
  99     slider.addChangeListener(new ChangeListener()
 100     {
 101       @Override
 102       public void stateChanged(ChangeEvent evt)
 103       {
 104         if (!adjusting)
 105         {
 106           thresholdValue.setText((slider.getValue() / 1000f) + "");
 107           valueChanged(!sliderDragging);
 108         }
 109       }
 110     });
 111     slider.addMouseListener(new MouseAdapter()
 112     {
 113       @Override
 114       public void mousePressed(MouseEvent e)
 115       {
 116         sliderDragging = true;
 117         super.mousePressed(e);
 118       }
 119
 120       @Override
 121       public void mouseDragged(MouseEvent e)
 122       {
 123         sliderDragging = true;
 124         super.mouseDragged(e);
 125       }
 126
 127       @Override
 128       public void mouseReleased(MouseEvent evt)
 129       {
 130         if (sliderDragging)
 131         {
 132           sliderDragging = false;
 133           valueChanged(true);
 134         }
 135         ap.paintAlignment(true);
 136       }
 137     });
 138
 139     if (av.getAlignment().getAlignmentAnnotation() == null)
 140     {
 141       return;
 142     }
 143
 144     // Always get default shading from preferences.
 145     setDefaultMinMax();
 146
 147     adjusting = true;
 148
 149     setAnnotations(new JComboBox(
 150             getAnnotationItems(seqAssociated.isSelected())));
 151
 152     threshold.addItem(MessageManager
 153             .getString("label.threshold_feature_no_thereshold"));
 154     threshold.addItem(MessageManager
 155             .getString("label.threshold_feature_above_thereshold"));
 156     threshold.addItem(MessageManager
 157             .getString("label.threshold_feature_below_thereshold"));
 158
 159     if (av.getCurrentAnnotationColumnSelectionState() != null)
 160     {
 161       annotations.setSelectedIndex(av
 162               .getCurrentAnnotationColumnSelectionState().getAnnotations()
 163               .getSelectedIndex());
 164       threshold.setSelectedIndex(av
 165               .getCurrentAnnotationColumnSelectionState().getThreshold()
 166               .getSelectedIndex());
 167       System.out.println("selected annotation : "
 168               + av.getCurrentAnnotationColumnSelectionState()
 169                       .getAnnotations().getSelectedIndex());
 170       System.out.println("selected threshold : "
 171               + av.getCurrentAnnotationColumnSelectionState()
 172                       .getThreshold().getSelectedIndex());
 173     }
 174
 175     try
 176     {
 177       jbInit();
 178     } catch (Exception ex)
 179     {
 180     }
 181
 182     adjusting = false;
 183
 184     changeColumnSelection();
 185     frame.invalidate();
 186     frame.pack();
 187
 188   }
 189
 190   private Vector<String> getAnnotationItems(boolean isSeqAssociated)
 191   {
 192     Vector<String> list = new Vector<String>();
 193     int index = 1;
 194     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 195     boolean enableSeqAss = false;
 196     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 197     {
 198       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 199       {
 200         if (isSeqAssociated)
 201         {
 202           continue;
 203         }
 204       }
 205       else
 206       {
 207         enableSeqAss = true;
 208       }
 209       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 210       if (!list.contains(label))
 211       {
 212         anmap[list.size()] = i;
 213         list.add(label);
 214
 215       }
 216       else
 217       {
 218         if (!isSeqAssociated)
 219         {
 220           anmap[list.size()] = i;
 221           list.add(label + "_" + (index++));
 222         }
 223       }
 224     }
 225     seqAssociated.setEnabled(enableSeqAss);
 226     this.annmap = new int[list.size()];
 227     System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
 228     return list;
 229   }
 230
 231   private void setDefaultMinMax()
 232   {
 233     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 234             Color.orange));
 235     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 236             Color.red));
 237   }
 238
 239   public AnnotationColumnSelection()
 240   {
 241     try
 242     {
 243       jbInit();
 244     } catch (Exception ex)
 245     {
 246       ex.printStackTrace();
 247     }
 248   }
 249
 250   private void jbInit() throws Exception
 251   {
 252     ok.setOpaque(false);
 253     ok.setText(MessageManager.getString("action.ok"));
 254     ok.addActionListener(new ActionListener()
 255     {
 256       @Override
 257       public void actionPerformed(ActionEvent e)
 258       {
 259         ok_actionPerformed(e);
 260       }
 261     });
 262     cancel.setOpaque(false);
 263     cancel.setText(MessageManager.getString("action.cancel"));
 264     cancel.addActionListener(new ActionListener()
 265     {
 266       @Override
 267       public void actionPerformed(ActionEvent e)
 268       {
 269         cancel_actionPerformed(e);
 270       }
 271     });
 272
 273     getAnnotations().addActionListener(new ActionListener()
 274     {
 275       @Override
 276       public void actionPerformed(ActionEvent e)
 277       {
 278         annotations_actionPerformed(e);
 279       }
 280     });
 281     getThreshold().addActionListener(new ActionListener()
 282     {
 283       @Override
 284       public void actionPerformed(ActionEvent e)
 285       {
 286         threshold_actionPerformed(e);
 287       }
 288     });
 289     thresholdValue.addActionListener(new ActionListener()
 290     {
 291       @Override
 292       public void actionPerformed(ActionEvent e)
 293       {
 294         thresholdValue_actionPerformed(e);
 295       }
 296     });
 297     slider.setPaintLabels(false);
 298     slider.setPaintTicks(true);
 299     slider.setBackground(Color.white);
 300     slider.setEnabled(false);
 301     slider.setOpaque(false);
 302     slider.setPreferredSize(new Dimension(100, 32));
 303     thresholdValue.setEnabled(false);
 304     thresholdValue.setColumns(7);
 305     thresholdIsMin.setBackground(Color.white);
 306     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 307     thresholdIsMin.setText(MessageManager
 308             .getString("label.threshold_minmax"));
 309     thresholdIsMin.addActionListener(new ActionListener()
 310     {
 311       @Override
 312       public void actionPerformed(ActionEvent actionEvent)
 313       {
 314         thresholdIsMin_actionPerformed(actionEvent);
 315       }
 316     });
 317     seqAssociated.setBackground(Color.white);
 318     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 319     seqAssociated.setText(MessageManager
 320             .getString("label.per_sequence_only"));
 321     seqAssociated.addActionListener(new ActionListener()
 322     {
 323
 324       @Override
 325       public void actionPerformed(ActionEvent arg0)
 326       {
 327         seqAssociated_actionPerformed(arg0);
 328       }
 329     });
 330
 331     this.setLayout(borderLayout1);
 332     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 333     jPanel1.setBackground(Color.white);
 334     jPanel2.setBackground(Color.white);
 335
 336     jPanel1.add(ok);
 337     jPanel1.add(cancel);
 338     jPanel2.add(getAnnotations(), "grow, wrap");
 339     jPanel2.add(seqAssociated, "wrap");
 340     jPanel2.add(getThreshold(), "grow, wrap");
 341     jPanel2.add(thresholdIsMin, "wrap");
 342     jPanel2.add(slider, "grow");
 343     jPanel2.add(thresholdValue, "grow");
 344     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 345     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 346     this.validate();
 347   }
 348
 349   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 350   {
 351     adjusting = true;
 352     String cursel = (String) getAnnotations().getSelectedItem();
 353     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 354     this.getAnnotations().removeAllItems();
 355     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 356     {
 357       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 358       {
 359         isvalid = true;
 360         cursel = anitem;
 361       }
 362       this.getAnnotations().addItem(anitem);
 363     }
 364     adjusting = false;
 365     if (isvalid)
 366     {
 367       this.getAnnotations().setSelectedItem(cursel);
 368     }
 369     else
 370     {
 371       if (getAnnotations().getItemCount() > 0)
 372       {
 373         getAnnotations().setSelectedIndex(0);
 374       }
 375     }
 376   }
 377
 378
 379   void changeColumnSelection()
 380   {
 381     // Check if combobox is still adjusting
 382     if (adjusting)
 383     {
 384       return;
 385     }
 386
 387     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[getAnnotations()
 388             .getSelectedIndex()]]);
 389
 390     int aboveThreshold = -1;
 391     if (getThreshold().getSelectedIndex() == 1)
 392     {
 393       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 394     }
 395     else if (getThreshold().getSelectedIndex() == 2)
 396     {
 397       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 398     }
 399
 400     slider.setEnabled(true);
 401     thresholdValue.setEnabled(true);
 402     thresholdIsMin.setEnabled(true);
 403
 404     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 405     {
 406       slider.setEnabled(false);
 407       thresholdValue.setEnabled(false);
 408       thresholdValue.setText("");
 409       thresholdIsMin.setEnabled(false);
 410     }
 411     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 412             && getCurrentAnnotation().threshold == null)
 413     {
 414       getCurrentAnnotation()
 415               .setThreshold(new jalview.datamodel.GraphLine(
 416                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 417                       "Threshold", Color.black));
 418     }
 419
 420     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 421     {
 422       adjusting = true;
 423       float range = getCurrentAnnotation().graphMax * 1000
 424               - getCurrentAnnotation().graphMin * 1000;
 425
 426       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 427       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 428       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 429       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 430       slider.setMajorTickSpacing((int) (range / 10f));
 431       slider.setEnabled(true);
 432       thresholdValue.setEnabled(true);
 433       adjusting = false;
 434     }
 435
 436     markColumnsContaining(getCurrentAnnotation(), aboveThreshold);
 437     av.setCurrentAnnotationColumnSelectionState(this);
 438     ap.alignmentChanged();
 439     // ensure all associated views (overviews, structures, etc) are notified of
 440     // updated colours.
 441     ap.paintAlignment(true);
 442   }
 443
 444   public boolean markColumnsContaining(
 445           AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
 446   {
 447     try
 448     {
 449       if (currentAnnotation != null)
 450       {
 451         Annotation[] annotations = currentAnnotation.annotations;
 452         ColumnSelection cs = av.getColumnSelection();
 453         cs.clear();
 454         if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
 455         {
 456           int count = 0;
 457           do
 458           {
 459             if (annotations[count] != null)
 460             {
 461               if (currentAnnotation.label.equals("Secondary Structure")
 462                       && annotations[count].secondaryStructure != ' ')
 463               {
 464                 cs.addElement(count);
 465               }
 466               else if (currentAnnotation.label
 467                       .equals("Iron Sulphur Contacts"))
 468               {
 469                 cs.addElement(count);
 470               }
 471               else if (annotations[count].value != 0.0)
 472               {
 473                 cs.addElement(count);
 474               }
 475
 476             }
 477             count++;
 478           } while (count < annotations.length);
 479         }
 480         else
 481         {
 482           int count = 0;
 483           do
 484           {
 485             if (annotations[count] != null)
 486             {
 487               if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
 488               {
 489                 if (annotations[count].value > currentAnnotation.threshold.value)
 490                 {
 491                   cs.addElement(count);
 492                 }
 493               }
 494               else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
 495               {
 496                 if (annotations[count].value < currentAnnotation.threshold.value)
 497                 {
 498                   cs.addElement(count);
 499                 }
 500               }
 501
 502             }
 503             count++;
 504           } while (count < annotations.length);
 505         }
 506       }
 507
 508       return true;
 509     } catch (Exception e)
 510     {
 511       e.printStackTrace();
 512       return false;
 513     }
 514   }
 515
 516   public void ok_actionPerformed(ActionEvent e)
 517   {
 518     changeColumnSelection();
 519     try
 520     {
 521       frame.setClosed(true);
 522     } catch (Exception ex)
 523     {
 524     }
 525   }
 526
 527   public void cancel_actionPerformed(ActionEvent e)
 528   {
 529     reset();
 530     // ensure all original colouring is propagated to listeners.
 531     ap.paintAlignment(true);
 532     try
 533     {
 534       frame.setClosed(true);
 535     } catch (Exception ex)
 536     {
 537     }
 538   }
 539
 540   void reset()
 541   {
 542     av.getColumnSelection().clear();
 543   }
 544
 545   public void thresholdCheck_actionPerformed(ActionEvent e)
 546   {
 547     changeColumnSelection();
 548   }
 549
 550   public void annotations_actionPerformed(ActionEvent e)
 551   {
 552     changeColumnSelection();
 553   }
 554
 555   public void threshold_actionPerformed(ActionEvent e)
 556   {
 557     changeColumnSelection();
 558   }
 559
 560   public void thresholdValue_actionPerformed(ActionEvent e)
 561   {
 562     try
 563     {
 564       float f = Float.parseFloat(thresholdValue.getText());
 565       slider.setValue((int) (f * 1000));
 566       changeColumnSelection();
 567     } catch (NumberFormatException ex)
 568     {
 569     }
 570   }
 571
 572   public void valueChanged(boolean updateAllAnnotation)
 573   {
 574     getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 575     changeColumnSelection();
 576     // propagateSeqAssociatedThreshold(updateAllAnnotation);
 577     ap.paintAlignment(false);
 578   }
 579
 580   private void propagateSeqAssociatedThreshold(boolean allAnnotation)
 581   {
 582     if (getCurrentAnnotation().sequenceRef == null
 583             || getCurrentAnnotation().threshold == null)
 584     {
 585       return;
 586     }
 587
 588
 589     float thr = getCurrentAnnotation().threshold.value;
 590     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 591     {
 592       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 593       if (aa.label.equals(getCurrentAnnotation().label)
 594               && (getCurrentAnnotation().getCalcId() == null ? aa
 595                       .getCalcId() == null : getCurrentAnnotation()
 596                       .getCalcId()
 597                               .equals(aa.getCalcId())))
 598       {
 599         if (aa.threshold == null)
 600         {
 601           aa.threshold = new GraphLine(getCurrentAnnotation().threshold);
 602         }
 603         else
 604         {
 605           aa.threshold.value = thr;
 606         }
 607       }
 608     }
 609   }
 610
 611   public void currentColours_actionPerformed(ActionEvent e)
 612   {
 613     if (currentColours.isSelected())
 614     {
 615       reset();
 616     }
 617
 618     maxColour.setEnabled(!currentColours.isSelected());
 619     minColour.setEnabled(!currentColours.isSelected());
 620
 621     changeColumnSelection();
 622   }
 623
 624   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 625   {
 626     changeColumnSelection();
 627   }
 628
 629   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
 630   {
 631     return currentAnnotation;
 632   }
 633
 634   public void setCurrentAnnotation(
 635           jalview.datamodel.AlignmentAnnotation currentAnnotation)
 636   {
 637     this.currentAnnotation = currentAnnotation;
 638   }
 639
 640   public JComboBox getThreshold()
 641   {
 642     return threshold;
 643   }
 644
 645   public void setThreshold(JComboBox threshold)
 646   {
 647     this.threshold = threshold;
 648   }
 649
 650   public JComboBox getAnnotations()
 651   {
 652     return annotations;
 653   }
 654
 655   public void setAnnotations(JComboBox annotations)
 656   {
 657     this.annotations = annotations;
 658   }
 659
 660 }