src/jalview/gui/AnnotationRowFilter.java

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