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   protected static final int MIN_WIDTH = 500;
  73
  74   protected static final int MIN_HEIGHT = 240;
  75
  76   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  77   {
  78     super(av, ap);
  79     oldcs = av.getGlobalColourScheme();
  80     if (av.getAlignment().getGroups() != null)
  81     {
  82       oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
  83       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  84       {
  85         if (sg.getColourScheme() != null)
  86         {
  87           oldgroupColours.put(sg, sg.getColourScheme());
  88         }
  89       }
  90     }
  91     frame = new JInternalFrame();
  92     frame.setContentPane(this);
  93     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  94     Desktop.addInternalFrame(frame,
  95             MessageManager.getString("label.colour_by_annotation"), 520,
  96             215);
  97     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
  98     addSliderChangeListener();
  99     addSliderMouseListeners();
 100
 101     if (av.getAlignment().getAlignmentAnnotation() == null)
 102     {
 103       return;
 104     }
 105
 106     // Always get default shading from preferences.
 107     setDefaultMinMax();
 108
 109     adjusting = true;
 110     if (oldcs instanceof AnnotationColourGradient)
 111     {
 112       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 113       useOriginalColours.setSelected(acg.isPredefinedColours()
 114               || acg.getBaseColour() != null);
 115       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 116       {
 117         minColour.setBackground(acg.getMinColour());
 118         maxColour.setBackground(acg.getMaxColour());
 119       }
 120       seqAssociated.setSelected(acg.isSeqAssociated());
 121
 122     }
 123     Vector<String> annotItems = getAnnotationItems(seqAssociated
 124             .isSelected());
 125     annotations = new JComboBox<String>(annotItems);
 126
 127     populateThresholdComboBox(threshold);
 128
 129     if (oldcs instanceof AnnotationColourGradient)
 130     {
 131       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 132       String label = getAnnotationMenuLabel(acg.getAnnotation());
 133       annotations.setSelectedItem(label);
 134       switch (acg.getAboveThreshold())
 135       {
 136       case AnnotationColourGradient.NO_THRESHOLD:
 137         getThreshold().setSelectedIndex(0);
 138         break;
 139       case AnnotationColourGradient.ABOVE_THRESHOLD:
 140         getThreshold().setSelectedIndex(1);
 141         break;
 142       case AnnotationColourGradient.BELOW_THRESHOLD:
 143         getThreshold().setSelectedIndex(2);
 144         break;
 145       default:
 146         throw new Error(
 147                 MessageManager
 148                         .getString("error.implementation_error_dont_know_about_threshold_setting"));
 149       }
 150       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 151       thresholdValue.setText("" + acg.getAnnotationThreshold());
 152     }
 153
 154     jbInit();
 155     adjusting = false;
 156
 157     updateView();
 158     frame.invalidate();
 159     frame.pack();
 160   }
 161
 162   @Override
 163   protected void jbInit()
 164   {
 165     super.jbInit();
 166
 167     minColour.setFont(JvSwingUtils.getLabelFont());
 168     minColour.setBorder(BorderFactory.createEtchedBorder());
 169     minColour.setPreferredSize(new Dimension(40, 20));
 170     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 171     minColour.addMouseListener(new MouseAdapter()
 172     {
 173       @Override
 174       public void mousePressed(MouseEvent e)
 175       {
 176         if (minColour.isEnabled())
 177         {
 178           minColour_actionPerformed();
 179         }
 180       }
 181     });
 182     maxColour.setFont(JvSwingUtils.getLabelFont());
 183     maxColour.setBorder(BorderFactory.createEtchedBorder());
 184     maxColour.setPreferredSize(new Dimension(40, 20));
 185     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 186     maxColour.addMouseListener(new MouseAdapter()
 187     {
 188       @Override
 189       public void mousePressed(MouseEvent e)
 190       {
 191         if (maxColour.isEnabled())
 192         {
 193           maxColour_actionPerformed();
 194         }
 195       }
 196     });
 197
 198     defColours = new JButton();
 199     defColours.setOpaque(false);
 200     defColours.setText(MessageManager.getString("action.set_defaults"));
 201     defColours.setToolTipText(MessageManager
 202             .getString("label.reset_min_max_colours_to_defaults"));
 203     defColours.addActionListener(new ActionListener()
 204     {
 205
 206       @Override
 207       public void actionPerformed(ActionEvent arg0)
 208       {
 209         resetColours_actionPerformed();
 210       }
 211     });
 212
 213     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 214     useOriginalColours.setOpaque(false);
 215     useOriginalColours.setText(MessageManager
 216             .getString("label.use_original_colours"));
 217     useOriginalColours.addActionListener(new ActionListener()
 218     {
 219       @Override
 220       public void actionPerformed(ActionEvent e)
 221       {
 222         originalColours_actionPerformed();
 223       }
 224     });
 225     thresholdIsMin.setBackground(Color.white);
 226     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 227     thresholdIsMin.setText(MessageManager
 228             .getString("label.threshold_minmax"));
 229     thresholdIsMin.addActionListener(new ActionListener()
 230     {
 231       @Override
 232       public void actionPerformed(ActionEvent actionEvent)
 233       {
 234         thresholdIsMin_actionPerformed();
 235       }
 236     });
 237     seqAssociated.setBackground(Color.white);
 238     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 239     seqAssociated.setText(MessageManager
 240             .getString("label.per_sequence_only"));
 241     seqAssociated.addActionListener(new ActionListener()
 242     {
 243
 244       @Override
 245       public void actionPerformed(ActionEvent arg0)
 246       {
 247         seqAssociated_actionPerformed(annotations);
 248       }
 249     });
 250
 251     this.setLayout(new BorderLayout());
 252     JPanel jPanel1 = new JPanel();
 253     JPanel jPanel2 = new JPanel();
 254     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 255     jPanel1.setBackground(Color.white);
 256     jPanel2.setBackground(Color.white);
 257
 258     jPanel1.add(ok);
 259     jPanel1.add(cancel);
 260     jPanel2.add(annotations, "grow, wrap");
 261     jPanel2.add(seqAssociated);
 262     jPanel2.add(useOriginalColours);
 263     JPanel colpanel = new JPanel(new FlowLayout());
 264     colpanel.setBackground(Color.white);
 265     colpanel.add(minColour);
 266     colpanel.add(maxColour);
 267     jPanel2.add(colpanel, "wrap");
 268     jPanel2.add(getThreshold());
 269     jPanel2.add(defColours, "skip 1, wrap");
 270     jPanel2.add(thresholdIsMin);
 271     jPanel2.add(slider, "grow");
 272     jPanel2.add(thresholdValue, "grow");
 273     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 274     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 275     this.validate();
 276   }
 277
 278   protected void resetColours_actionPerformed()
 279   {
 280     setDefaultMinMax();
 281     updateView();
 282   }
 283
 284   private void setDefaultMinMax()
 285   {
 286     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 287             Color.orange));
 288     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 289             Color.red));
 290   }
 291
 292   public void minColour_actionPerformed()
 293   {
 294     Color col = JColorChooser.showDialog(this,
 295             MessageManager.getString("label.select_colour_minimum_value"),
 296             minColour.getBackground());
 297     if (col != null)
 298     {
 299       minColour.setBackground(col);
 300     }
 301     minColour.repaint();
 302     updateView();
 303   }
 304
 305   public void maxColour_actionPerformed()
 306   {
 307     Color col = JColorChooser.showDialog(this,
 308             MessageManager.getString("label.select_colour_maximum_value"),
 309             maxColour.getBackground());
 310     if (col != null)
 311     {
 312       maxColour.setBackground(col);
 313     }
 314     maxColour.repaint();
 315     updateView();
 316   }
 317
 318   @Override
 319   public void reset()
 320   {
 321     av.setGlobalColourScheme(oldcs);
 322     if (av.getAlignment().getGroups() != null)
 323     {
 324
 325       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 326       {
 327         sg.setColourScheme(oldgroupColours.get(sg));
 328       }
 329     }
 330   }
 331
 332   @Override
 333   public void valueChanged(boolean updateAllAnnotation)
 334   {
 335     if (slider.isEnabled())
 336     {
 337       if (useOriginalColours.isSelected()
 338               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 339       {
 340         updateView();
 341       }
 342       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 343       propagateSeqAssociatedThreshold(updateAllAnnotation,
 344               getCurrentAnnotation());
 345       ap.paintAlignment(false);
 346     }
 347   }
 348
 349   public void originalColours_actionPerformed()
 350   {
 351     boolean selected = useOriginalColours.isSelected();
 352     if (selected)
 353     {
 354       reset();
 355     }
 356     maxColour.setEnabled(!selected);
 357     minColour.setEnabled(!selected);
 358     thresholdIsMin.setEnabled(!selected);
 359     updateView();
 360   }
 361
 362   @Override
 363   public void updateView()
 364   {
 365     // Check if combobox is still adjusting
 366     if (adjusting)
 367     {
 368       return;
 369     }
 370
 371     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 372             .getSelectedIndex()]]);
 373
 374     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 375             .getSelectedIndex());
 376
 377     slider.setEnabled(true);
 378     thresholdValue.setEnabled(true);
 379     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 380
 381     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 382     {
 383       slider.setEnabled(false);
 384       thresholdValue.setEnabled(false);
 385       thresholdValue.setText("");
 386       thresholdIsMin.setEnabled(false);
 387     }
 388     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 389             && getCurrentAnnotation().threshold == null)
 390     {
 391       getCurrentAnnotation()
 392               .setThreshold(
 393                       new GraphLine(
 394                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 395                               "Threshold", Color.black));
 396     }
 397
 398     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 399     {
 400       adjusting = true;
 401       float range = getCurrentAnnotation().graphMax * ONETHOUSAND
 402               - getCurrentAnnotation().graphMin * ONETHOUSAND;
 403
 404       slider.setMinimum((int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
 405       slider.setMaximum((int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
 406       slider.setValue((int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
 407       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 408       slider.setMajorTickSpacing((int) (range / 10f));
 409       slider.setEnabled(true);
 410       thresholdValue.setEnabled(true);
 411       adjusting = false;
 412     }
 413     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 414
 415     ap.alignmentChanged();
 416     // ensure all associated views (overviews, structures, etc) are notified of
 417     // updated colours.
 418     ap.paintAlignment(true);
 419   }
 420
 421   protected boolean colorAlignmentContaining(AlignmentAnnotation currentAnn, int selectedThresholdOption)
 422   {
 423
 424     AnnotationColourGradient acg = null;
 425     if (useOriginalColours.isSelected())
 426     {
 427       acg = new AnnotationColourGradient(currentAnn,
 428               av.getGlobalColourScheme(), selectedThresholdOption);
 429     }
 430     else
 431     {
 432       acg = new AnnotationColourGradient(currentAnn,
 433               minColour.getBackground(), maxColour.getBackground(),
 434               selectedThresholdOption);
 435     }
 436     acg.setSeqAssociated(seqAssociated.isSelected());
 437
 438     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 439     {
 440       acg.setPredefinedColours(true);
 441     }
 442
 443     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 444
 445     av.setGlobalColourScheme(acg);
 446
 447     if (av.getAlignment().getGroups() != null)
 448     {
 449
 450       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 451       {
 452         if (sg.cs == null)
 453         {
 454           continue;
 455         }
 456
 457         if (useOriginalColours.isSelected())
 458         {
 459           sg.setColourScheme(new AnnotationColourGradient(currentAnn, sg
 460                   .getColourScheme(), selectedThresholdOption));
 461           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 462                   .isSelected());
 463         }
 464         else
 465         {
 466           sg.setColourScheme(new AnnotationColourGradient(currentAnn,
 467                   minColour.getBackground(), maxColour.getBackground(),
 468                   selectedThresholdOption));
 469           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 470                   .isSelected());
 471         }
 472       }
 473     }
 474     return false;
 475   }
 476
 477 }