src/jalview/gui/AnnotationRowFilter.java

   1 package jalview.gui;
   2
   3 import jalview.api.analysis.AnnotationFilterParameter;
   4 import jalview.api.analysis.AnnotationFilterParameter.SearchableAnnotationField;
   5 import jalview.datamodel.AlignmentAnnotation;
   6 import jalview.datamodel.Annotation;
   7 import jalview.datamodel.ColumnSelection;
   8 import jalview.datamodel.GraphLine;
   9 import jalview.datamodel.SequenceGroup;
  10 import jalview.schemes.AnnotationColourGradient;
  11 import jalview.util.MessageManager;
  12
  13 import java.awt.event.ActionEvent;
  14 import java.awt.event.MouseAdapter;
  15 import java.awt.event.MouseEvent;
  16 import java.util.List;
  17 import java.util.Vector;
  18
  19 import javax.swing.JCheckBox;
  20 import javax.swing.JComboBox;
  21 import javax.swing.JInternalFrame;
  22 import javax.swing.JPanel;
  23 import javax.swing.JSlider;
  24 import javax.swing.JTextField;
  25 import javax.swing.event.ChangeEvent;
  26 import javax.swing.event.ChangeListener;
  27
  28 @SuppressWarnings("serial")
  29 public abstract class AnnotationRowFilter extends JPanel
  30 {
  31   protected AlignViewport av;
  32
  33   protected AlignmentPanel ap;
  34
  35   protected int[] annmap;
  36
  37   protected boolean enableSeqAss = false;
  38
  39   private jalview.datamodel.AlignmentAnnotation currentAnnotation;
  40
  41   protected boolean adjusting = false;
  42
  43   protected JCheckBox currentColours = new JCheckBox();
  44
  45   protected JPanel minColour = new JPanel();
  46
  47   protected JPanel maxColour = new JPanel();
  48
  49   protected JCheckBox seqAssociated = new JCheckBox();
  50
  51   protected JCheckBox thresholdIsMin = new JCheckBox();
  52
  53   protected JSlider slider = new JSlider();
  54
  55   protected JTextField thresholdValue = new JTextField(20);
  56
  57   protected JInternalFrame frame;
  58   /**
  59    * enabled if the user is dragging the slider - try to keep updates to a
  60    * minimun
  61    */
  62   protected boolean sliderDragging = false;
  63
  64   protected void addSliderChangeListener()
  65   {
  66
  67     slider.addChangeListener(new ChangeListener()
  68     {
  69       @Override
  70       public void stateChanged(ChangeEvent evt)
  71       {
  72         if (!adjusting)
  73         {
  74           thresholdValue.setText((slider.getValue() / 1000f) + "");
  75           valueChanged(!sliderDragging);
  76         }
  77       }
  78     });
  79   }
  80
  81   protected void addSliderMouseListeners()
  82   {
  83
  84     slider.addMouseListener(new MouseAdapter()
  85     {
  86       @Override
  87       public void mousePressed(MouseEvent e)
  88       {
  89         sliderDragging = true;
  90         super.mousePressed(e);
  91       }
  92
  93       @Override
  94       public void mouseDragged(MouseEvent e)
  95       {
  96         sliderDragging = true;
  97         super.mouseDragged(e);
  98       }
  99
 100       @Override
 101       public void mouseReleased(MouseEvent evt)
 102       {
 103         if (sliderDragging)
 104         {
 105           sliderDragging = false;
 106           valueChanged(true);
 107         }
 108         ap.paintAlignment(true);
 109       }
 110     });
 111   }
 112
 113
 114   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
 115   {
 116     this.av = av;
 117     this.ap = ap;
 118   }
 119
 120   public AnnotationRowFilter()
 121   {
 122
 123   }
 124
 125   public Vector<String> getAnnotationItems(boolean isSeqAssociated)
 126   {
 127     Vector<String> list = new Vector<String>();
 128     int index = 1;
 129     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 130     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 131     {
 132       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 133       {
 134         if (isSeqAssociated)
 135         {
 136           continue;
 137         }
 138       }
 139       else
 140       {
 141         enableSeqAss = true;
 142       }
 143       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 144       if (!list.contains(label))
 145       {
 146         anmap[list.size()] = i;
 147         list.add(label);
 148
 149       }
 150       else
 151       {
 152         if (!isSeqAssociated)
 153         {
 154           anmap[list.size()] = i;
 155           list.add(label + "_" + (index++));
 156         }
 157       }
 158     }
 159     this.annmap = new int[list.size()];
 160     System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
 161     return list;
 162   }
 163
 164   protected int getSelectedThresholdItem(int indexValue)
 165   {
 166     int selectedThresholdItem = -1;
 167     if (indexValue == 1)
 168     {
 169       selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
 170     }
 171     else if (indexValue == 2)
 172     {
 173       selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
 174     }
 175     return selectedThresholdItem;
 176   }
 177
 178   public void modelChanged()
 179   {
 180     seqAssociated.setEnabled(enableSeqAss);
 181   }
 182
 183   public void ok_actionPerformed(ActionEvent e)
 184   {
 185     updateView();
 186     try
 187     {
 188       frame.setClosed(true);
 189     } catch (Exception ex)
 190     {
 191     }
 192   }
 193
 194   public void cancel_actionPerformed(ActionEvent e)
 195   {
 196     reset();
 197     ap.paintAlignment(true);
 198     try
 199     {
 200       frame.setClosed(true);
 201     } catch (Exception ex)
 202     {
 203     }
 204   }
 205
 206   public void thresholdCheck_actionPerformed(ActionEvent e)
 207   {
 208     updateView();
 209   }
 210
 211   public void annotations_actionPerformed(ActionEvent e)
 212   {
 213     updateView();
 214   }
 215
 216   public void threshold_actionPerformed(ActionEvent e)
 217   {
 218     updateView();
 219   }
 220
 221   public void thresholdValue_actionPerformed(ActionEvent e)
 222   {
 223     try
 224     {
 225       float f = Float.parseFloat(thresholdValue.getText());
 226       slider.setValue((int) (f * 1000));
 227       updateView();
 228     } catch (NumberFormatException ex)
 229     {
 230     }
 231   }
 232
 233   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 234   {
 235     updateView();
 236   }
 237
 238   protected void populateThresholdComboBox(JComboBox<String> threshold)
 239   {
 240     threshold.addItem(MessageManager
 241             .getString("label.threshold_feature_no_thereshold"));
 242     threshold.addItem(MessageManager
 243             .getString("label.threshold_feature_above_thereshold"));
 244     threshold.addItem(MessageManager
 245             .getString("label.threshold_feature_below_thereshold"));
 246   }
 247
 248   protected void seqAssociated_actionPerformed(ActionEvent arg0,
 249           JComboBox<String> annotations, JCheckBox seqAssociated)
 250   {
 251     adjusting = true;
 252     String cursel = (String) annotations.getSelectedItem();
 253     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 254     annotations.removeAllItems();
 255     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 256     {
 257       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 258       {
 259         isvalid = true;
 260         cursel = anitem;
 261       }
 262       annotations.addItem(anitem);
 263     }
 264     adjusting = false;
 265     if (isvalid)
 266     {
 267       annotations.setSelectedItem(cursel);
 268     }
 269     else
 270     {
 271       if (annotations.getItemCount() > 0)
 272       {
 273         annotations.setSelectedIndex(0);
 274       }
 275     }
 276   }
 277
 278   protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
 279           AlignmentAnnotation annotation)
 280   {
 281     if (annotation.sequenceRef == null || annotation.threshold == null)
 282     {
 283       return;
 284     }
 285
 286     float thr = annotation.threshold.value;
 287     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 288     {
 289       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 290       if (aa.label.equals(annotation.label)
 291               && (annotation.getCalcId() == null ? aa.getCalcId() == null
 292                       : annotation.getCalcId().equals(aa.getCalcId())))
 293       {
 294         if (aa.threshold == null)
 295         {
 296           aa.threshold = new GraphLine(annotation.threshold);
 297         }
 298         else
 299         {
 300           aa.threshold.value = thr;
 301         }
 302       }
 303     }
 304   }
 305
 306   protected boolean colorAlignmContaining(
 307           AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
 308   {
 309
 310     AnnotationColourGradient acg = null;
 311     if (currentColours.isSelected())
 312     {
 313       acg = new AnnotationColourGradient(currentAnnotation,
 314               av.getGlobalColourScheme(), selectedThresholdItem);
 315     }
 316     else
 317     {
 318       acg = new AnnotationColourGradient(currentAnnotation,
 319               minColour.getBackground(), maxColour.getBackground(),
 320               selectedThresholdItem);
 321     }
 322     acg.setSeqAssociated(seqAssociated.isSelected());
 323
 324     if (currentAnnotation.graphMin == 0f
 325             && currentAnnotation.graphMax == 0f)
 326     {
 327       acg.setPredefinedColours(true);
 328     }
 329
 330     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 331
 332     av.setGlobalColourScheme(acg);
 333
 334     if (av.getAlignment().getGroups() != null)
 335     {
 336
 337       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 338       {
 339         if (sg.cs == null)
 340         {
 341           continue;
 342         }
 343
 344         if (currentColours.isSelected())
 345         {
 346           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 347                   selectedThresholdItem);
 348           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 349                   .isSelected());
 350
 351         }
 352         else
 353         {
 354           sg.cs = new AnnotationColourGradient(currentAnnotation,
 355                   minColour.getBackground(), maxColour.getBackground(),
 356                   selectedThresholdItem);
 357           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 358                   .isSelected());
 359         }
 360
 361       }
 362     }
 363     return false;
 364   }
 365
 366   protected boolean filterAnnotations(Annotation[] annotations,
 367           AnnotationFilterParameter filterParams, ColumnSelection cs)
 368   {
 369     av.showAllHiddenColumns();
 370     cs.clear();
 371     int count = 0;
 372     do
 373     {
 374       if (annotations[count] != null)
 375       {
 376
 377         boolean itemMatched = false;
 378
 379         if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
 380                 && annotations[count].value > currentAnnotation.threshold.value)
 381         {
 382           itemMatched = true;
 383         }
 384         if (filterParams.getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD
 385                 && annotations[count].value < currentAnnotation.threshold.value)
 386         {
 387           itemMatched = true;
 388         }
 389
 390         if (filterParams.isFilterAlphaHelix()
 391                 && annotations[count].secondaryStructure == 'H')
 392         {
 393           itemMatched = true;
 394         }
 395
 396         if (filterParams.isFilterBetaSheet()
 397                 && annotations[count].secondaryStructure == 'E')
 398         {
 399           itemMatched = true;
 400         }
 401
 402         if (filterParams.isFilterTurn()
 403                 && annotations[count].secondaryStructure == 'S')
 404         {
 405           itemMatched = true;
 406         }
 407
 408         String regexSearchString = filterParams.getRegexString();
 409         if (regexSearchString != null
 410                 && !filterParams.getRegexSearchFields().isEmpty())
 411         {
 412           List<SearchableAnnotationField> fields = filterParams
 413                   .getRegexSearchFields();
 414           try
 415           {
 416             if (fields.contains(SearchableAnnotationField.DISPLAY_STRING)
 417                     && annotations[count].displayCharacter
 418                             .matches(regexSearchString))
 419             {
 420               itemMatched = true;
 421             }
 422           } catch (java.util.regex.PatternSyntaxException pse)
 423           {
 424             if (annotations[count].displayCharacter
 425                     .equals(regexSearchString))
 426             {
 427               itemMatched = true;
 428             }
 429           }
 430           if (fields.contains(SearchableAnnotationField.DESCRIPTION)
 431                   && annotations[count].description != null
 432                   && annotations[count].description
 433                           .matches(regexSearchString))
 434           {
 435             itemMatched = true;
 436           }
 437         }
 438
 439         if (itemMatched)
 440         {
 441           cs.addElement(count);
 442         }
 443       }
 444       count++;
 445     } while (count < annotations.length);
 446     return false;
 447   }
 448
 449   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
 450   {
 451     return currentAnnotation;
 452   }
 453
 454   public void setCurrentAnnotation(
 455           jalview.datamodel.AlignmentAnnotation currentAnnotation)
 456   {
 457     this.currentAnnotation = currentAnnotation;
 458   }
 459
 460   public abstract void valueChanged(boolean updateAllAnnotation);
 461
 462   public abstract void updateView();
 463
 464   public abstract void reset();
 465 }