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.ColumnSelection;
   7 import jalview.datamodel.GraphLine;
   8 import jalview.datamodel.SequenceGroup;
   9 import jalview.schemes.AnnotationColourGradient;
  10 import jalview.util.MessageManager;
  11
  12 import java.awt.event.ActionEvent;
  13 import java.awt.event.MouseAdapter;
  14 import java.awt.event.MouseEvent;
  15 import java.util.Vector;
  16
  17 import javax.swing.JCheckBox;
  18 import javax.swing.JComboBox;
  19 import javax.swing.JInternalFrame;
  20 import javax.swing.JPanel;
  21 import javax.swing.JSlider;
  22 import javax.swing.JTextField;
  23 import javax.swing.event.ChangeEvent;
  24 import javax.swing.event.ChangeListener;
  25
  26 @SuppressWarnings("serial")
  27 public abstract class AnnotationRowFilter extends JPanel implements
  28         AnnotationRowFilterI
  29 {
  30   protected AlignViewport av;
  31
  32   protected AlignmentPanel ap;
  33
  34   protected int[] annmap;
  35
  36   protected boolean enableSeqAss = false;
  37
  38   private jalview.datamodel.AlignmentAnnotation currentAnnotation;
  39
  40   protected boolean adjusting = false;
  41
  42   protected JCheckBox currentColours = new JCheckBox();
  43
  44   protected JPanel minColour = new JPanel();
  45
  46   protected JPanel maxColour = new JPanel();
  47
  48   protected JCheckBox seqAssociated = new JCheckBox();
  49
  50   protected JCheckBox thresholdIsMin = new JCheckBox();
  51
  52   protected JSlider slider = new JSlider();
  53
  54   protected JTextField thresholdValue = new JTextField(20);
  55
  56   protected JInternalFrame frame;
  57   /**
  58    * enabled if the user is dragging the slider - try to keep updates to a
  59    * minimun
  60    */
  61   protected boolean sliderDragging = false;
  62
  63   protected void addSliderChangeListener()
  64   {
  65
  66     slider.addChangeListener(new ChangeListener()
  67     {
  68       @Override
  69       public void stateChanged(ChangeEvent evt)
  70       {
  71         if (!adjusting)
  72         {
  73           thresholdValue.setText((slider.getValue() / 1000f) + "");
  74           valueChanged(!sliderDragging);
  75         }
  76       }
  77     });
  78   }
  79
  80   protected void addSliderMouseListeners()
  81   {
  82
  83     slider.addMouseListener(new MouseAdapter()
  84     {
  85       @Override
  86       public void mousePressed(MouseEvent e)
  87       {
  88         sliderDragging = true;
  89         super.mousePressed(e);
  90       }
  91
  92       @Override
  93       public void mouseDragged(MouseEvent e)
  94       {
  95         sliderDragging = true;
  96         super.mouseDragged(e);
  97       }
  98
  99       @Override
 100       public void mouseReleased(MouseEvent evt)
 101       {
 102         if (sliderDragging)
 103         {
 104           sliderDragging = false;
 105           valueChanged(true);
 106         }
 107         ap.paintAlignment(true);
 108       }
 109     });
 110   }
 111
 112
 113   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
 114   {
 115     this.av = av;
 116     this.ap = ap;
 117   }
 118
 119   public AnnotationRowFilter()
 120   {
 121
 122   }
 123
 124   @Override
 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     // seqAssociated.setEnabled(enableSeqAss);
 160     this.annmap = new int[list.size()];
 161     System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
 162     return list;
 163   }
 164
 165   protected int getSelectedThresholdItem(int indexValue)
 166   {
 167     int selectedThresholdItem = -1;
 168     if (indexValue == 1)
 169     {
 170       selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
 171     }
 172     else if (indexValue == 2)
 173     {
 174       selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
 175     }
 176     return selectedThresholdItem;
 177   }
 178
 179   public void modelChanged()
 180   {
 181     seqAssociated.setEnabled(enableSeqAss);
 182   }
 183
 184   public void ok_actionPerformed(ActionEvent e)
 185   {
 186     updateView();
 187     try
 188     {
 189       frame.setClosed(true);
 190     } catch (Exception ex)
 191     {
 192     }
 193   }
 194
 195   public void cancel_actionPerformed(ActionEvent e)
 196   {
 197     reset();
 198     ap.paintAlignment(true);
 199     try
 200     {
 201       frame.setClosed(true);
 202     } catch (Exception ex)
 203     {
 204     }
 205   }
 206
 207   public void thresholdCheck_actionPerformed(ActionEvent e)
 208   {
 209     updateView();
 210   }
 211
 212   public void annotations_actionPerformed(ActionEvent e)
 213   {
 214     updateView();
 215   }
 216
 217   public void threshold_actionPerformed(ActionEvent e)
 218   {
 219     updateView();
 220   }
 221
 222   public void thresholdValue_actionPerformed(ActionEvent e)
 223   {
 224     try
 225     {
 226       float f = Float.parseFloat(thresholdValue.getText());
 227       slider.setValue((int) (f * 1000));
 228       updateView();
 229     } catch (NumberFormatException ex)
 230     {
 231     }
 232   }
 233
 234   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 235   {
 236     updateView();
 237   }
 238
 239   protected void populateThresholdComboBox(JComboBox<String> threshold)
 240   {
 241     threshold.addItem(MessageManager
 242             .getString("label.threshold_feature_no_thereshold"));
 243     threshold.addItem(MessageManager
 244             .getString("label.threshold_feature_above_thereshold"));
 245     threshold.addItem(MessageManager
 246             .getString("label.threshold_feature_below_thereshold"));
 247   }
 248
 249   protected void seqAssociated_actionPerformed(ActionEvent arg0,
 250           JComboBox<String> annotations, JCheckBox seqAssociated)
 251   {
 252     adjusting = true;
 253     String cursel = (String) annotations.getSelectedItem();
 254     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 255     annotations.removeAllItems();
 256     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 257     {
 258       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 259       {
 260         isvalid = true;
 261         cursel = anitem;
 262       }
 263       annotations.addItem(anitem);
 264     }
 265     adjusting = false;
 266     if (isvalid)
 267     {
 268       annotations.setSelectedItem(cursel);
 269     }
 270     else
 271     {
 272       if (annotations.getItemCount() > 0)
 273       {
 274         annotations.setSelectedIndex(0);
 275       }
 276     }
 277   }
 278
 279   protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
 280           AlignmentAnnotation annotation)
 281   {
 282     if (annotation.sequenceRef == null || annotation.threshold == null)
 283     {
 284       return;
 285     }
 286
 287     float thr = annotation.threshold.value;
 288     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 289     {
 290       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 291       if (aa.label.equals(annotation.label)
 292               && (annotation.getCalcId() == null ? aa.getCalcId() == null
 293                       : annotation.getCalcId().equals(aa.getCalcId())))
 294       {
 295         if (aa.threshold == null)
 296         {
 297           aa.threshold = new GraphLine(annotation.threshold);
 298         }
 299         else
 300         {
 301           aa.threshold.value = thr;
 302         }
 303       }
 304     }
 305   }
 306
 307   protected boolean colorAlignmContaining(
 308           AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
 309   {
 310
 311     AnnotationColourGradient acg = null;
 312     if (currentColours.isSelected())
 313     {
 314       acg = new AnnotationColourGradient(currentAnnotation,
 315               av.getGlobalColourScheme(), selectedThresholdItem);
 316     }
 317     else
 318     {
 319       acg = new AnnotationColourGradient(currentAnnotation,
 320               minColour.getBackground(), maxColour.getBackground(),
 321               selectedThresholdItem);
 322     }
 323     acg.setSeqAssociated(seqAssociated.isSelected());
 324
 325     if (currentAnnotation.graphMin == 0f
 326             && currentAnnotation.graphMax == 0f)
 327     {
 328       acg.setPredefinedColours(true);
 329     }
 330
 331     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 332
 333     av.setGlobalColourScheme(acg);
 334
 335     if (av.getAlignment().getGroups() != null)
 336     {
 337
 338       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 339       {
 340         if (sg.cs == null)
 341         {
 342           continue;
 343         }
 344
 345         if (currentColours.isSelected())
 346         {
 347           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 348                   selectedThresholdItem);
 349           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 350                   .isSelected());
 351
 352         }
 353         else
 354         {
 355           sg.cs = new AnnotationColourGradient(currentAnnotation,
 356                   minColour.getBackground(), maxColour.getBackground(),
 357                   selectedThresholdItem);
 358           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 359                   .isSelected());
 360         }
 361
 362       }
 363     }
 364     return false;
 365   }
 366
 367   protected boolean markColumnsContaining(
 368           AlignmentAnnotation currentAnnotation, int thresholdComparisonType)
 369   {
 370     try
 371     {
 372       if (currentAnnotation != null)
 373       {
 374         Annotation[] annotations = currentAnnotation.annotations;
 375         ColumnSelection cs = av.getColumnSelection();
 376         cs.clear();
 377         if (thresholdComparisonType == AnnotationColourGradient.NO_THRESHOLD)
 378         {
 379           int count = 0;
 380           do
 381           {
 382             if (annotations[count] != null)
 383             {
 384               if (currentAnnotation.label.equals("Secondary Structure")
 385                       && annotations[count].secondaryStructure != ' ')
 386               {
 387                 cs.addElement(count);
 388               }
 389               else if (currentAnnotation.label
 390                       .equals("Iron Sulphur Contacts"))
 391               {
 392                 cs.addElement(count);
 393               }
 394               else if (annotations[count].value != 0.0)
 395               {
 396                 cs.addElement(count);
 397               }
 398
 399             }
 400             count++;
 401           } while (count < annotations.length);
 402         }
 403         else
 404         {
 405           int count = 0;
 406           do
 407           {
 408             if (annotations[count] != null)
 409             {
 410               if (thresholdComparisonType == AnnotationColourGradient.ABOVE_THRESHOLD)
 411               {
 412                 if (annotations[count].value > currentAnnotation.threshold.value)
 413                 {
 414                   cs.addElement(count);
 415                 }
 416               }
 417               else if (thresholdComparisonType == AnnotationColourGradient.BELOW_THRESHOLD)
 418               {
 419                 if (annotations[count].value < currentAnnotation.threshold.value)
 420                 {
 421                   cs.addElement(count);
 422                 }
 423               }
 424
 425             }
 426             count++;
 427           } while (count < annotations.length);
 428         }
 429       }
 430
 431       return true;
 432     } catch (Exception e)
 433     {
 434       e.printStackTrace();
 435       return false;
 436     }
 437   }
 438
 439   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
 440   {
 441     return currentAnnotation;
 442   }
 443
 444   public void setCurrentAnnotation(
 445           jalview.datamodel.AlignmentAnnotation currentAnnotation)
 446   {
 447     this.currentAnnotation = currentAnnotation;
 448   }
 449
 450 }