src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.gui;
  22
  23 import jalview.bin.Cache;
  24 import jalview.datamodel.AlignmentAnnotation;
  25 import jalview.datamodel.GraphLine;
  26 import jalview.datamodel.SequenceGroup;
  27 import jalview.schemes.AnnotationColourGradient;
  28 import jalview.schemes.ColourSchemeI;
  29 import jalview.util.MessageManager;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Color;
  33 import java.awt.Dimension;
  34 import java.awt.FlowLayout;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.awt.event.MouseAdapter;
  38 import java.awt.event.MouseEvent;
  39 import java.util.Hashtable;
  40 import java.util.Vector;
  41
  42 import javax.swing.BorderFactory;
  43 import javax.swing.JButton;
  44 import javax.swing.JCheckBox;
  45 import javax.swing.JColorChooser;
  46 import javax.swing.JComboBox;
  47 import javax.swing.JInternalFrame;
  48 import javax.swing.JLayeredPane;
  49 import javax.swing.JPanel;
  50
  51 import net.miginfocom.swing.MigLayout;
  52
  53 @SuppressWarnings("serial")
  54 public class AnnotationColourChooser extends AnnotationRowFilter
  55 {
  56   private static final int ONETHOUSAND = 1000;
  57
  58   private ColourSchemeI oldcs;
  59
  60   private JButton defColours;
  61
  62   private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  63
  64   private JCheckBox useOriginalColours = new JCheckBox();
  65
  66   private JPanel minColour = new JPanel();
  67
  68   private JPanel maxColour = new JPanel();
  69
  70   private JCheckBox thresholdIsMin = new JCheckBox();
  71
  72   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  73   {
  74     super(av, ap);
  75     oldcs = av.getGlobalColourScheme();
  76     if (av.getAlignment().getGroups() != null)
  77     {
  78       oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
  79       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  80       {
  81         if (sg.getColourScheme() != null)
  82         {
  83           oldgroupColours.put(sg, sg.getColourScheme());
  84         }
  85       }
  86     }
  87     frame = new JInternalFrame();
  88     frame.setContentPane(this);
  89     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  90     Desktop.addInternalFrame(frame,
  91             MessageManager.getString("label.colour_by_annotation"), 520,
  92             215);
  93
  94     addSliderChangeListener();
  95     addSliderMouseListeners();
  96
  97     if (av.getAlignment().getAlignmentAnnotation() == null)
  98     {
  99       return;
 100     }
 101
 102     // Always get default shading from preferences.
 103     setDefaultMinMax();
 104
 105     adjusting = true;
 106     if (oldcs instanceof AnnotationColourGradient)
 107     {
 108       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 109       useOriginalColours.setSelected(acg.isPredefinedColours()
 110               || acg.getBaseColour() != null);
 111       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 112       {
 113         minColour.setBackground(acg.getMinColour());
 114         maxColour.setBackground(acg.getMaxColour());
 115       }
 116       seqAssociated.setSelected(acg.isSeqAssociated());
 117
 118     }
 119     Vector<String> annotItems = getAnnotationItems(seqAssociated
 120             .isSelected());
 121     annotations = new JComboBox<String>(annotItems);
 122
 123     populateThresholdComboBox(threshold);
 124
 125     if (oldcs instanceof AnnotationColourGradient)
 126     {
 127       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 128       String label = getAnnotationMenuLabel(acg.getAnnotation());
 129       annotations.setSelectedItem(label);
 130       switch (acg.getAboveThreshold())
 131       {
 132       case AnnotationColourGradient.NO_THRESHOLD:
 133         getThreshold().setSelectedIndex(0);
 134         break;
 135       case AnnotationColourGradient.ABOVE_THRESHOLD:
 136         getThreshold().setSelectedIndex(1);
 137         break;
 138       case AnnotationColourGradient.BELOW_THRESHOLD:
 139         getThreshold().setSelectedIndex(2);
 140         break;
 141       default:
 142         throw new Error(
 143                 MessageManager
 144                         .getString("error.implementation_error_dont_know_about_threshold_setting"));
 145       }
 146       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 147       thresholdValue.setText("" + acg.getAnnotationThreshold());
 148     }
 149
 150     jbInit();
 151     adjusting = false;
 152
 153     updateView();
 154     frame.invalidate();
 155     frame.pack();
 156   }
 157
 158   @Override
 159   protected void jbInit()
 160   {
 161     super.jbInit();
 162
 163     minColour.setFont(JvSwingUtils.getLabelFont());
 164     minColour.setBorder(BorderFactory.createEtchedBorder());
 165     minColour.setPreferredSize(new Dimension(40, 20));
 166     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 167     minColour.addMouseListener(new MouseAdapter()
 168     {
 169       @Override
 170       public void mousePressed(MouseEvent e)
 171       {
 172         if (minColour.isEnabled())
 173         {
 174           minColour_actionPerformed();
 175         }
 176       }
 177     });
 178     maxColour.setFont(JvSwingUtils.getLabelFont());
 179     maxColour.setBorder(BorderFactory.createEtchedBorder());
 180     maxColour.setPreferredSize(new Dimension(40, 20));
 181     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 182     maxColour.addMouseListener(new MouseAdapter()
 183     {
 184       @Override
 185       public void mousePressed(MouseEvent e)
 186       {
 187         if (maxColour.isEnabled())
 188         {
 189           maxColour_actionPerformed();
 190         }
 191       }
 192     });
 193
 194     defColours = new JButton();
 195     defColours.setOpaque(false);
 196     defColours.setText(MessageManager.getString("action.set_defaults"));
 197     defColours.setToolTipText(MessageManager
 198             .getString("label.reset_min_max_colours_to_defaults"));
 199     defColours.addActionListener(new ActionListener()
 200     {
 201
 202       @Override
 203       public void actionPerformed(ActionEvent arg0)
 204       {
 205         resetColours_actionPerformed();
 206       }
 207     });
 208
 209     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 210     useOriginalColours.setOpaque(false);
 211     useOriginalColours.setText(MessageManager
 212             .getString("label.use_original_colours"));
 213     useOriginalColours.addActionListener(new ActionListener()
 214     {
 215       @Override
 216       public void actionPerformed(ActionEvent e)
 217       {
 218         originalColours_actionPerformed();
 219       }
 220     });
 221     thresholdIsMin.setBackground(Color.white);
 222     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 223     thresholdIsMin.setText(MessageManager
 224             .getString("label.threshold_minmax"));
 225     thresholdIsMin.addActionListener(new ActionListener()
 226     {
 227       @Override
 228       public void actionPerformed(ActionEvent actionEvent)
 229       {
 230         thresholdIsMin_actionPerformed();
 231       }
 232     });
 233     seqAssociated.setBackground(Color.white);
 234     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 235     seqAssociated.setText(MessageManager
 236             .getString("label.per_sequence_only"));
 237     seqAssociated.addActionListener(new ActionListener()
 238     {
 239
 240       @Override
 241       public void actionPerformed(ActionEvent arg0)
 242       {
 243         seqAssociated_actionPerformed(annotations);
 244       }
 245     });
 246
 247     this.setLayout(new BorderLayout());
 248     JPanel jPanel1 = new JPanel();
 249     JPanel jPanel2 = new JPanel();
 250     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 251     jPanel1.setBackground(Color.white);
 252     jPanel2.setBackground(Color.white);
 253
 254     jPanel1.add(ok);
 255     jPanel1.add(cancel);
 256     jPanel2.add(annotations, "grow, wrap");
 257     jPanel2.add(seqAssociated);
 258     jPanel2.add(useOriginalColours);
 259     JPanel colpanel = new JPanel(new FlowLayout());
 260     colpanel.setBackground(Color.white);
 261     colpanel.add(minColour);
 262     colpanel.add(maxColour);
 263     jPanel2.add(colpanel, "wrap");
 264     jPanel2.add(getThreshold());
 265     jPanel2.add(defColours, "skip 1, wrap");
 266     jPanel2.add(thresholdIsMin);
 267     jPanel2.add(slider, "grow");
 268     jPanel2.add(thresholdValue, "grow");
 269     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 270     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 271     this.validate();
 272   }
 273
 274   protected void resetColours_actionPerformed()
 275   {
 276     setDefaultMinMax();
 277     updateView();
 278   }
 279
 280   private void setDefaultMinMax()
 281   {
 282     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 283             Color.orange));
 284     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 285             Color.red));
 286   }
 287
 288   public void minColour_actionPerformed()
 289   {
 290     Color col = JColorChooser.showDialog(this,
 291             MessageManager.getString("label.select_colour_minimum_value"),
 292             minColour.getBackground());
 293     if (col != null)
 294     {
 295       minColour.setBackground(col);
 296     }
 297     minColour.repaint();
 298     updateView();
 299   }
 300
 301   public void maxColour_actionPerformed()
 302   {
 303     Color col = JColorChooser.showDialog(this,
 304             MessageManager.getString("label.select_colour_maximum_value"),
 305             maxColour.getBackground());
 306     if (col != null)
 307     {
 308       maxColour.setBackground(col);
 309     }
 310     maxColour.repaint();
 311     updateView();
 312   }
 313
 314   @Override
 315   public void reset()
 316   {
 317     av.setGlobalColourScheme(oldcs);
 318     if (av.getAlignment().getGroups() != null)
 319     {
 320
 321       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 322       {
 323         sg.setColourScheme(oldgroupColours.get(sg));
 324       }
 325     }
 326   }
 327
 328   @Override
 329   public void valueChanged(boolean updateAllAnnotation)
 330   {
 331     if (slider.isEnabled())
 332     {
 333       if (useOriginalColours.isSelected()
 334               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 335       {
 336         updateView();
 337       }
 338       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 339       propagateSeqAssociatedThreshold(updateAllAnnotation,
 340               getCurrentAnnotation());
 341       ap.paintAlignment(false);
 342     }
 343   }
 344
 345   public void originalColours_actionPerformed()
 346   {
 347     boolean selected = useOriginalColours.isSelected();
 348     if (selected)
 349     {
 350       reset();
 351     }
 352     maxColour.setEnabled(!selected);
 353     minColour.setEnabled(!selected);
 354     thresholdIsMin.setEnabled(!selected);
 355     updateView();
 356   }
 357
 358   @Override
 359   public void updateView()
 360   {
 361     // Check if combobox is still adjusting
 362     if (adjusting)
 363     {
 364       return;
 365     }
 366
 367     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 368             .getSelectedIndex()]]);
 369
 370     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 371             .getSelectedIndex());
 372
 373     slider.setEnabled(true);
 374     thresholdValue.setEnabled(true);
 375     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 376
 377     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 378     {
 379       slider.setEnabled(false);
 380       thresholdValue.setEnabled(false);
 381       thresholdValue.setText("");
 382       thresholdIsMin.setEnabled(false);
 383     }
 384     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 385             && getCurrentAnnotation().threshold == null)
 386     {
 387       getCurrentAnnotation()
 388               .setThreshold(
 389                       new GraphLine(
 390                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 391                               "Threshold", Color.black));
 392     }
 393
 394     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 395     {
 396       adjusting = true;
 397       float range = getCurrentAnnotation().graphMax * ONETHOUSAND
 398               - getCurrentAnnotation().graphMin * ONETHOUSAND;
 399
 400       slider.setMinimum((int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
 401       slider.setMaximum((int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
 402       slider.setValue((int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
 403       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 404       slider.setMajorTickSpacing((int) (range / 10f));
 405       slider.setEnabled(true);
 406       thresholdValue.setEnabled(true);
 407       adjusting = false;
 408     }
 409     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 410
 411     ap.alignmentChanged();
 412     // ensure all associated views (overviews, structures, etc) are notified of
 413     // updated colours.
 414     ap.paintAlignment(true);
 415   }
 416
 417   protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption)
 418   {
 419
 420     AnnotationColourGradient acg = null;
 421     if (useOriginalColours.isSelected())
 422     {
 423       acg = new AnnotationColourGradient(currentAnn,
 424               av.getGlobalColourScheme(), selectedThresholdOption);
 425     }
 426     else
 427     {
 428       acg = new AnnotationColourGradient(currentAnn,
 429               minColour.getBackground(), maxColour.getBackground(),
 430               selectedThresholdOption);
 431     }
 432     acg.setSeqAssociated(seqAssociated.isSelected());
 433
 434     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 435     {
 436       acg.setPredefinedColours(true);
 437     }
 438
 439     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 440
 441     av.setGlobalColourScheme(acg);
 442
 443     if (av.getAlignment().getGroups() != null)
 444     {
 445
 446       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 447       {
 448         if (sg.cs == null)
 449         {
 450           continue;
 451         }
 452
 453         if (useOriginalColours.isSelected())
 454         {
 455           sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg
 456                   .getColourScheme(), selectedThresholdOption));
 457           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 458                   .isSelected());
 459         }
 460         else
 461         {
 462           sg.setColourScheme(new AnnotationColourGradient(currentAnn,
 463                   minColour.getBackground(), maxColour.getBackground(),
 464                   selectedThresholdOption));
 465           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 466                   .isSelected());
 467         }
 468       }
 469     }
 470     return false;
 471   }
 472
 473 }