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
 115   public AnnotationRowFilter(AlignViewport av, final AlignmentPanel ap)
 116   {
 117     this.av = av;
 118     this.ap = ap;
 119   }
 120
 121   public AnnotationRowFilter()
 122   {
 123
 124   }
 125
 126   public Vector<String> getAnnotationItems(boolean isSeqAssociated)
 127   {
 128     Vector<String> list = new Vector<String>();
 129     int index = 1;
 130     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 131     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 132     {
 133       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 134       {
 135         if (isSeqAssociated)
 136         {
 137           continue;
 138         }
 139       }
 140       else
 141       {
 142         enableSeqAss = true;
 143       }
 144       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 145       if (!list.contains(label))
 146       {
 147         anmap[list.size()] = i;
 148         list.add(label);
 149
 150       }
 151       else
 152       {
 153         if (!isSeqAssociated)
 154         {
 155           anmap[list.size()] = i;
 156           list.add(label + "_" + (index++));
 157         }
 158       }
 159     }
 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     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
 367   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
 368   {
 369     return currentAnnotation;
 370   }
 371
 372   public void setCurrentAnnotation(
 373           jalview.datamodel.AlignmentAnnotation currentAnnotation)
 374   {
 375     this.currentAnnotation = currentAnnotation;
 376   }
 377
 378   public abstract void valueChanged(boolean updateAllAnnotation);
 379
 380   public abstract void updateView();
 381
 382   public abstract void reset();
 383 }