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.JCheckBox;
  15 import javax.swing.JComboBox;
  16 import javax.swing.JInternalFrame;
  17 import javax.swing.JPanel;
  18 import javax.swing.JSlider;
  19 import javax.swing.JTextField;
  20 import javax.swing.event.ChangeEvent;
  21 import javax.swing.event.ChangeListener;
  22
  23 @SuppressWarnings("serial")
  24 public abstract class AnnotationRowFilter extends JPanel
  25 {
  26   protected AlignViewport av;
  27
  28   protected AlignmentPanel ap;
  29
  30   protected int[] annmap;
  31
  32   protected boolean enableSeqAss = false;
  33
  34   private jalview.datamodel.AlignmentAnnotation currentAnnotation;
  35
  36   protected boolean adjusting = false;
  37
  38   protected JCheckBox currentColours = new JCheckBox();
  39
  40   protected JPanel minColour = new JPanel();
  41
  42   protected JPanel maxColour = new JPanel();
  43
  44   protected JCheckBox seqAssociated = new JCheckBox();
  45
  46   protected JCheckBox thresholdIsMin = new JCheckBox();
  47
  48   protected JSlider slider = new JSlider();
  49
  50   protected JTextField thresholdValue = new JTextField(20);
  51
  52   protected JInternalFrame frame;
  53   /**
  54    * enabled if the user is dragging the slider - try to keep updates to a
  55    * minimun
  56    */
  57   protected boolean sliderDragging = false;
  58
  59   protected void addSliderChangeListener()
  60   {
  61
  62     slider.addChangeListener(new ChangeListener()
  63     {
  64       @Override
  65       public void stateChanged(ChangeEvent evt)
  66       {
  67         if (!adjusting)
  68         {
  69           thresholdValue.setText((slider.getValue() / 1000f) + "");
  70           valueChanged(!sliderDragging);
  71         }
  72       }
  73     });
  74   }
  75
  76   protected void addSliderMouseListeners()
  77   {
  78
  79     slider.addMouseListener(new MouseAdapter()
  80     {
  81       @Override
  82       public void mousePressed(MouseEvent e)
  83       {
  84         sliderDragging = true;
  85         super.mousePressed(e);
  86       }
  87
  88       @Override
  89       public void mouseDragged(MouseEvent e)
  90       {
  91         sliderDragging = true;
  92         super.mouseDragged(e);
  93       }
  94
  95       @Override
  96       public void mouseReleased(MouseEvent evt)
  97       {
  98         if (sliderDragging)
  99         {
 100           sliderDragging = false;
 101           valueChanged(true);
 102         }
 103         ap.paintAlignment(true);
 104       }
 105     });
 106   }
 107
 108
 109   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
 110   {
 111     this.av = av;
 112     this.ap = ap;
 113   }
 114
 115   public AnnotationRowFilter()
 116   {
 117
 118   }
 119
 120   public Vector<String> getAnnotationItems(boolean isSeqAssociated)
 121   {
 122     Vector<String> list = new Vector<String>();
 123     int index = 1;
 124     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 125     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 126     {
 127       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 128       {
 129         if (isSeqAssociated)
 130         {
 131           continue;
 132         }
 133       }
 134       else
 135       {
 136         enableSeqAss = true;
 137       }
 138       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 139       if (!list.contains(label))
 140       {
 141         anmap[list.size()] = i;
 142         list.add(label);
 143
 144       }
 145       else
 146       {
 147         if (!isSeqAssociated)
 148         {
 149           anmap[list.size()] = i;
 150           list.add(label + "_" + (index++));
 151         }
 152       }
 153     }
 154     this.annmap = new int[list.size()];
 155     System.arraycopy(anmap, 0, this.annmap, 0, this.annmap.length);
 156     return list;
 157   }
 158
 159   protected int getSelectedThresholdItem(int indexValue)
 160   {
 161     int selectedThresholdItem = -1;
 162     if (indexValue == 1)
 163     {
 164       selectedThresholdItem = AnnotationColourGradient.ABOVE_THRESHOLD;
 165     }
 166     else if (indexValue == 2)
 167     {
 168       selectedThresholdItem = AnnotationColourGradient.BELOW_THRESHOLD;
 169     }
 170     return selectedThresholdItem;
 171   }
 172
 173   public void modelChanged()
 174   {
 175     seqAssociated.setEnabled(enableSeqAss);
 176   }
 177
 178   public void ok_actionPerformed(ActionEvent e)
 179   {
 180     updateView();
 181     try
 182     {
 183       frame.setClosed(true);
 184     } catch (Exception ex)
 185     {
 186     }
 187   }
 188
 189   public void cancel_actionPerformed(ActionEvent e)
 190   {
 191     reset();
 192     ap.paintAlignment(true);
 193     try
 194     {
 195       frame.setClosed(true);
 196     } catch (Exception ex)
 197     {
 198     }
 199   }
 200
 201   public void thresholdCheck_actionPerformed(ActionEvent e)
 202   {
 203     updateView();
 204   }
 205
 206   public void annotations_actionPerformed(ActionEvent e)
 207   {
 208     updateView();
 209   }
 210
 211   public void threshold_actionPerformed(ActionEvent e)
 212   {
 213     updateView();
 214   }
 215
 216   public void thresholdValue_actionPerformed(ActionEvent e)
 217   {
 218     try
 219     {
 220       float f = Float.parseFloat(thresholdValue.getText());
 221       slider.setValue((int) (f * 1000));
 222       updateView();
 223     } catch (NumberFormatException ex)
 224     {
 225     }
 226   }
 227
 228   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 229   {
 230     updateView();
 231   }
 232
 233   protected void populateThresholdComboBox(JComboBox<String> threshold)
 234   {
 235     threshold.addItem(MessageManager
 236             .getString("label.threshold_feature_no_thereshold"));
 237     threshold.addItem(MessageManager
 238             .getString("label.threshold_feature_above_thereshold"));
 239     threshold.addItem(MessageManager
 240             .getString("label.threshold_feature_below_thereshold"));
 241   }
 242
 243   protected void seqAssociated_actionPerformed(ActionEvent arg0,
 244           JComboBox<String> annotations, JCheckBox seqAssociated)
 245   {
 246     adjusting = true;
 247     String cursel = (String) annotations.getSelectedItem();
 248     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 249     annotations.removeAllItems();
 250     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 251     {
 252       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 253       {
 254         isvalid = true;
 255         cursel = anitem;
 256       }
 257       annotations.addItem(anitem);
 258     }
 259     adjusting = false;
 260     if (isvalid)
 261     {
 262       annotations.setSelectedItem(cursel);
 263     }
 264     else
 265     {
 266       if (annotations.getItemCount() > 0)
 267       {
 268         annotations.setSelectedIndex(0);
 269       }
 270     }
 271   }
 272
 273   protected void propagateSeqAssociatedThreshold(boolean allAnnotation,
 274           AlignmentAnnotation annotation)
 275   {
 276     if (annotation.sequenceRef == null || annotation.threshold == null)
 277     {
 278       return;
 279     }
 280
 281     float thr = annotation.threshold.value;
 282     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 283     {
 284       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 285       if (aa.label.equals(annotation.label)
 286               && (annotation.getCalcId() == null ? aa.getCalcId() == null
 287                       : annotation.getCalcId().equals(aa.getCalcId())))
 288       {
 289         if (aa.threshold == null)
 290         {
 291           aa.threshold = new GraphLine(annotation.threshold);
 292         }
 293         else
 294         {
 295           aa.threshold.value = thr;
 296         }
 297       }
 298     }
 299   }
 300
 301   protected boolean colorAlignmContaining(
 302           AlignmentAnnotation currentAnnotation, int selectedThresholdItem)
 303   {
 304
 305     AnnotationColourGradient acg = null;
 306     if (currentColours.isSelected())
 307     {
 308       acg = new AnnotationColourGradient(currentAnnotation,
 309               av.getGlobalColourScheme(), selectedThresholdItem);
 310     }
 311     else
 312     {
 313       acg = new AnnotationColourGradient(currentAnnotation,
 314               minColour.getBackground(), maxColour.getBackground(),
 315               selectedThresholdItem);
 316     }
 317     acg.setSeqAssociated(seqAssociated.isSelected());
 318
 319     if (currentAnnotation.graphMin == 0f
 320             && currentAnnotation.graphMax == 0f)
 321     {
 322       acg.setPredefinedColours(true);
 323     }
 324
 325     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 326
 327     av.setGlobalColourScheme(acg);
 328
 329     if (av.getAlignment().getGroups() != null)
 330     {
 331
 332       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 333       {
 334         if (sg.cs == null)
 335         {
 336           continue;
 337         }
 338
 339         if (currentColours.isSelected())
 340         {
 341           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 342                   selectedThresholdItem);
 343           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 344                   .isSelected());
 345
 346         }
 347         else
 348         {
 349           sg.cs = new AnnotationColourGradient(currentAnnotation,
 350                   minColour.getBackground(), maxColour.getBackground(),
 351                   selectedThresholdItem);
 352           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 353                   .isSelected());
 354         }
 355
 356       }
 357     }
 358     return false;
 359   }
 360
 361
 362   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
 363   {
 364     return currentAnnotation;
 365   }
 366
 367   public void setCurrentAnnotation(
 368           jalview.datamodel.AlignmentAnnotation currentAnnotation)
 369   {
 370     this.currentAnnotation = currentAnnotation;
 371   }
 372
 373   public abstract void valueChanged(boolean updateAllAnnotation);
 374
 375   public abstract void updateView();
 376
 377   public abstract void reset();
 378 }