src/jalview/gui/AnnotationRowFilter.java

   1 package jalview.gui;
   2
   3 import jalview.datamodel.AlignmentAnnotation;
   4 import jalview.datamodel.GraphLine;
   5 import jalview.datamodel.SequenceGroup;
   6 import jalview.schemes.AnnotationColourGradient;
   7 import jalview.util.MessageManager;
   8
   9 import java.awt.event.ActionEvent;
  10 import java.awt.event.MouseAdapter;
  11 import java.awt.event.MouseEvent;
  12 import java.util.Vector;
  13
  14 import javax.swing.JButton;
  15 import javax.swing.JCheckBox;
  16 import javax.swing.JComboBox;
  17 import javax.swing.JInternalFrame;
  18 import javax.swing.JPanel;
  19 import javax.swing.JSlider;
  20 import javax.swing.JTextField;
  21 import javax.swing.event.ChangeEvent;
  22 import javax.swing.event.ChangeListener;
  23
  24 @SuppressWarnings("serial")
  25 public abstract class AnnotationRowFilter extends JPanel
  26 {
  27   protected AlignViewport av;
  28
  29   protected AlignmentPanel ap;
  30
  31   protected int[] annmap;
  32
  33   protected boolean enableSeqAss = false;
  34
  35   private jalview.datamodel.AlignmentAnnotation currentAnnotation;
  36
  37   protected boolean adjusting = false;
  38
  39   protected JCheckBox currentColours = new JCheckBox();
  40
  41   protected JPanel minColour = new JPanel();
  42
  43   protected JPanel maxColour = new JPanel();
  44
  45   protected JCheckBox seqAssociated = new JCheckBox();
  46
  47   protected JCheckBox thresholdIsMin = new JCheckBox();
  48
  49   protected JSlider slider = new JSlider();
  50
  51   protected JTextField thresholdValue = new JTextField(20);
  52
  53   protected JInternalFrame frame;
  54
  55   protected JButton ok = new JButton();
  56
  57   protected JButton cancel = new JButton();
  58
  59   /**
  60    * enabled if the user is dragging the slider - try to keep updates to a
  61    * minimun
  62    */
  63   protected boolean sliderDragging = false;
  64
  65   protected void addSliderChangeListener()
  66   {
  67
  68     slider.addChangeListener(new ChangeListener()
  69     {
  70       @Override
  71       public void stateChanged(ChangeEvent evt)
  72       {
  73         if (!adjusting)
  74         {
  75           thresholdValue.setText((slider.getValue() / 1000f) + "");
  76           valueChanged(!sliderDragging);
  77         }
  78       }
  79     });
  80   }
  81
  82   protected void addSliderMouseListeners()
  83   {
  84
  85     slider.addMouseListener(new MouseAdapter()
  86     {
  87       @Override
  88       public void mousePressed(MouseEvent e)
  89       {
  90         sliderDragging = true;
  91         super.mousePressed(e);
  92       }
  93
  94       @Override
  95       public void mouseDragged(MouseEvent e)
  96       {
  97         sliderDragging = true;
  98         super.mouseDragged(e);
  99       }
 100
 101       @Override
 102       public void mouseReleased(MouseEvent evt)
 103       {
 104         if (sliderDragging)
 105         {
 106           sliderDragging = false;
 107           valueChanged(true);
 108         }
 109         ap.paintAlignment(true);
 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     try
 186     {
 187       frame.setClosed(true);
 188     } catch (Exception ex)
 189     {
 190     }
 191   }
 192
 193   public void cancel_actionPerformed(ActionEvent e)
 194   {
 195     reset();
 196     ap.paintAlignment(true);
 197     try
 198     {
 199       frame.setClosed(true);
 200     } catch (Exception ex)
 201     {
 202     }
 203   }
 204
 205   public void thresholdCheck_actionPerformed(ActionEvent e)
 206   {
 207     updateView();
 208   }
 209
 210   public void annotations_actionPerformed(ActionEvent e)
 211   {
 212     updateView();
 213   }
 214
 215   public void threshold_actionPerformed(ActionEvent e)
 216   {
 217     updateView();
 218   }
 219
 220   public void thresholdValue_actionPerformed(ActionEvent e)
 221   {
 222     try
 223     {
 224       float f = Float.parseFloat(thresholdValue.getText());
 225       slider.setValue((int) (f * 1000));
 226       updateView();
 227     } catch (NumberFormatException ex)
 228     {
 229     }
 230   }
 231
 232   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 233   {
 234     updateView();
 235   }
 236
 237   protected void populateThresholdComboBox(JComboBox<String> threshold)
 238   {
 239     threshold.addItem(MessageManager
 240             .getString("label.threshold_feature_no_thereshold"));
 241     threshold.addItem(MessageManager
 242             .getString("label.threshold_feature_above_thereshold"));
 243     threshold.addItem(MessageManager
 244             .getString("label.threshold_feature_below_thereshold"));
 245   }
 246
 247   protected void seqAssociated_actionPerformed(ActionEvent arg0,
 248           JComboBox<String> annotations, JCheckBox seqAssociated)
 249   {
 250     adjusting = true;
 251     String cursel = (String) annotations.getSelectedItem();
 252     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 253     annotations.removeAllItems();
 254     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 255     {
 256       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 257       {
 258         isvalid = true;
 259         cursel = anitem;
 260       }
 261       annotations.addItem(anitem);
 262     }
 263     adjusting = false;
 264     if (isvalid)
 265     {
 266       annotations.setSelectedItem(cursel);
 267     }
 268     else
 269     {
 270       if (annotations.getItemCount() > 0)
 271       {
 272         annotations.setSelectedIndex(0);
 273       }
 274     }
 275   }
 276
 277   protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
 278           AlignmentAnnotation annotation)
 279   {
 280     if (annotation.sequenceRef == null || annotation.threshold == null)
 281     {
 282       return;
 283     }
 284
 285     float thr = annotation.threshold.value;
 286     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 287     {
 288       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 289       if (aa.label.equals(annotation.label)
 290               && (annotation.getCalcId() == null ? aa.getCalcId() == null
 291                       : annotation.getCalcId().equals(aa.getCalcId())))
 292       {
 293         if (aa.threshold == null)
 294         {
 295           aa.threshold = new GraphLine(annotation.threshold);
 296         }
 297         else
 298         {
 299           aa.threshold.value = thr;
 300         }
 301       }
 302     }
 303   }
 304
 305   protected boolean colorAlignmContaining(
 306           AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
 307   {
 308
 309     AnnotationColourGradient acg = null;
 310     if (currentColours.isSelected())
 311     {
 312       acg = new AnnotationColourGradient(currentAnnotation,
 313               av.getGlobalColourScheme(), selectedThresholdItem);
 314     }
 315     else
 316     {
 317       acg = new AnnotationColourGradient(currentAnnotation,
 318               minColour.getBackground(), maxColour.getBackground(),
 319               selectedThresholdItem);
 320     }
 321     acg.setSeqAssociated(seqAssociated.isSelected());
 322
 323     if (currentAnnotation.graphMin == 0f
 324             && currentAnnotation.graphMax == 0f)
 325     {
 326       acg.setPredefinedColours(true);
 327     }
 328
 329     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 330
 331     av.setGlobalColourScheme(acg);
 332
 333     if (av.getAlignment().getGroups() != null)
 334     {
 335
 336       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 337       {
 338         if (sg.cs == null)
 339         {
 340           continue;
 341         }
 342
 343         if (currentColours.isSelected())
 344         {
 345           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 346                   selectedThresholdItem);
 347           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 348                   .isSelected());
 349
 350         }
 351         else
 352         {
 353           sg.cs = new AnnotationColourGradient(currentAnnotation,
 354                   minColour.getBackground(), maxColour.getBackground(),
 355                   selectedThresholdItem);
 356           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 357                   .isSelected());
 358         }
 359
 360       }
 361     }
 362     return false;
 363   }
 364
 365   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
 366   {
 367     return currentAnnotation;
 368   }
 369
 370   public void setCurrentAnnotation(
 371           jalview.datamodel.AlignmentAnnotation currentAnnotation)
 372   {
 373     this.currentAnnotation = currentAnnotation;
 374   }
 375
 376   public abstract void valueChanged(boolean updateAllAnnotation);
 377
 378   public abstract void updateView();
 379
 380   public abstract void reset();
 381 }