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     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
 368   public jalview.datamodel.AlignmentAnnotation getCurrentAnnotation()
 369   {
 370     return currentAnnotation;
 371   }
 372
 373   public void setCurrentAnnotation(
 374           jalview.datamodel.AlignmentAnnotation currentAnnotation)
 375   {
 376     this.currentAnnotation = currentAnnotation;
 377   }
 378
 379   public abstract void valueChanged(boolean updateAllAnnotation);
 380
 381   public abstract void updateView();
 382
 383   public abstract void reset();
 384 }