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.gui.JalviewColourChooser.ColourChooserListener;
  28 import jalview.schemes.AnnotationColourGradient;
  29 import jalview.schemes.ColourSchemeI;
  30 import jalview.util.MessageManager;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.FlowLayout;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.MouseAdapter;
  39 import java.awt.event.MouseEvent;
  40 import java.util.Hashtable;
  41 import java.util.Vector;
  42
  43 import javax.swing.BorderFactory;
  44 import javax.swing.JButton;
  45 import javax.swing.JCheckBox;
  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 ColourSchemeI oldcs;
  57
  58   private JButton defColours;
  59
  60   private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  61
  62   private JCheckBox useOriginalColours = new JCheckBox();
  63
  64   JPanel minColour = new JPanel();
  65
  66   JPanel maxColour = new JPanel();
  67
  68   private JCheckBox thresholdIsMin = new JCheckBox();
  69   private JCheckBox transparency = new JCheckBox();
  70
  71   protected static final int MIN_WIDTH = 500;
  72
  73   protected static final int MIN_HEIGHT = 240;
  74
  75   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  76   {
  77     super(av, ap);
  78     oldcs = av.getGlobalColourScheme();
  79     if (av.getAlignment().getGroups() != null)
  80     {
  81       oldgroupColours = new Hashtable<>();
  82       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  83       {
  84         if (sg.getColourScheme() != null)
  85         {
  86           oldgroupColours.put(sg, sg.getColourScheme());
  87         }
  88       }
  89     }
  90     frame = new JInternalFrame();
  91     frame.setContentPane(this);
  92     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  93     Desktop.addInternalFrame(frame,
  94             MessageManager.getString("label.colour_by_annotation"), 520,
  95             215);
  96     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
  97     addSliderChangeListener();
  98     addSliderMouseListeners();
  99
 100     if (av.getAlignment().getAlignmentAnnotation() == null)
 101     {
 102       return;
 103     }
 104
 105     // Always get default shading from preferences.
 106     setDefaultMinMax();
 107
 108     adjusting = true;
 109     if (oldcs instanceof AnnotationColourGradient)
 110     {
 111       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 112       useOriginalColours.setSelected(
 113               acg.isPredefinedColours() || acg.getBaseColour() != null);
 114       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 115       {
 116         minColour.setBackground(acg.getMinColour());
 117         maxColour.setBackground(acg.getMaxColour());
 118       }
 119       seqAssociated.setSelected(acg.isSeqAssociated());
 120
 121     }
 122     Vector<String> annotItems = getAnnotationItems(
 123             seqAssociated.isSelected());
 124     annotations = new JComboBox<>(annotItems);
 125
 126     populateThresholdComboBox(threshold);
 127
 128     if (oldcs instanceof AnnotationColourGradient)
 129     {
 130       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 131       String label = getAnnotationMenuLabel(acg.getAnnotation());
 132       annotations.setSelectedItem(label);
 133       switch (acg.getAboveThreshold())
 134       {
 135       case AnnotationColourGradient.NO_THRESHOLD:
 136         getThreshold().setSelectedIndex(0);
 137         break;
 138       case AnnotationColourGradient.ABOVE_THRESHOLD:
 139         getThreshold().setSelectedIndex(1);
 140         break;
 141       case AnnotationColourGradient.BELOW_THRESHOLD:
 142         getThreshold().setSelectedIndex(2);
 143         break;
 144       default:
 145         throw new Error(MessageManager.getString(
 146                 "error.implementation_error_dont_know_about_threshold_setting"));
 147       }
 148       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 149       thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
 150     }
 151
 152     jbInit();
 153     adjusting = false;
 154
 155     updateView();
 156     frame.invalidate();
 157     frame.pack();
 158   }
 159
 160   @Override
 161   protected void jbInit()
 162   {
 163     super.jbInit();
 164
 165     minColour.setFont(JvSwingUtils.getLabelFont());
 166     minColour.setBorder(BorderFactory.createEtchedBorder());
 167     minColour.setPreferredSize(new Dimension(40, 20));
 168     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 169     minColour.addMouseListener(new MouseAdapter()
 170     {
 171       @Override
 172       public void mousePressed(MouseEvent e)
 173       {
 174         if (minColour.isEnabled())
 175         {
 176           showColourChooser(minColour, "label.select_colour_minimum_value");
 177         }
 178       }
 179     });
 180     maxColour.setFont(JvSwingUtils.getLabelFont());
 181     maxColour.setBorder(BorderFactory.createEtchedBorder());
 182     maxColour.setPreferredSize(new Dimension(40, 20));
 183     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 184     maxColour.addMouseListener(new MouseAdapter()
 185     {
 186       @Override
 187       public void mousePressed(MouseEvent e)
 188       {
 189         if (maxColour.isEnabled())
 190         {
 191           showColourChooser(maxColour, "label.select_colour_maximum_value");
 192         }
 193       }
 194     });
 195
 196     defColours = new JButton();
 197     defColours.setOpaque(false);
 198     defColours.setText(MessageManager.getString("action.set_defaults"));
 199     defColours.setToolTipText(MessageManager
 200             .getString("label.reset_min_max_colours_to_defaults"));
 201     defColours.addActionListener(new ActionListener()
 202     {
 203
 204       @Override
 205       public void actionPerformed(ActionEvent arg0)
 206       {
 207         resetColours_actionPerformed();
 208       }
 209     });
 210
 211     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 212     useOriginalColours.setOpaque(false);
 213     useOriginalColours.setText(
 214             MessageManager.getString("label.use_original_colours"));
 215     useOriginalColours.addActionListener(new ActionListener()
 216     {
 217       @Override
 218       public void actionPerformed(ActionEvent e)
 219       {
 220         originalColours_actionPerformed();
 221       }
 222     });
 223     thresholdIsMin.setBackground(Color.white);
 224     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 225     thresholdIsMin
 226             .setText(MessageManager.getString("label.threshold_minmax"));
 227     thresholdIsMin.addActionListener(new ActionListener()
 228     {
 229       @Override
 230       public void actionPerformed(ActionEvent actionEvent)
 231       {
 232         thresholdIsMin_actionPerformed();
 233       }
 234     });
 235     seqAssociated.setBackground(Color.white);
 236     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 237     seqAssociated
 238             .setText(MessageManager.getString("label.per_sequence_only"));
 239     seqAssociated.addActionListener(new ActionListener()
 240     {
 241
 242       @Override
 243       public void actionPerformed(ActionEvent arg0)
 244       {
 245         seqAssociated_actionPerformed(annotations);
 246       }
 247     });
 248
 249     transparency.setBackground(Color.white);
 250     transparency.setFont(JvSwingUtils.getLabelFont());
 251     transparency
 252             .setText(MessageManager.getString("Use Transparency"));
 253     transparency.addActionListener(new ActionListener()
 254     {
 255
 256       @Override
 257       public void actionPerformed(ActionEvent arg0)
 258       {
 259         transparency_actionPerformed();
 260       }
 261     });
 262     this.setLayout(new BorderLayout());
 263     JPanel jPanel1 = new JPanel();
 264     JPanel jPanel2 = new JPanel();
 265     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 266     jPanel1.setBackground(Color.white);
 267     jPanel2.setBackground(Color.white);
 268
 269     jPanel1.add(ok);
 270     jPanel1.add(cancel);
 271     jPanel2.add(annotations, "grow, wrap");
 272     jPanel2.add(seqAssociated);
 273     jPanel2.add(useOriginalColours);
 274     jPanel2.add(transparency);
 275     JPanel colpanel = new JPanel(new FlowLayout());
 276     colpanel.setBackground(Color.white);
 277     colpanel.add(minColour);
 278     colpanel.add(maxColour);
 279     jPanel2.add(colpanel, "wrap");
 280     jPanel2.add(getThreshold());
 281     jPanel2.add(defColours, "skip 1, wrap");
 282     jPanel2.add(thresholdIsMin);
 283     jPanel2.add(slider, "grow");
 284     jPanel2.add(thresholdValue, "grow");
 285     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 286     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 287     this.validate();
 288   }
 289
 290   protected void transparency_actionPerformed()
 291   {
 292     updateView();
 293   }
 294   protected void resetColours_actionPerformed()
 295   {
 296     setDefaultMinMax();
 297     updateView();
 298   }
 299
 300   private void setDefaultMinMax()
 301   {
 302     minColour.setBackground(
 303             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 304     maxColour.setBackground(
 305             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 306   }
 307
 308   protected void showColourChooser(JPanel colourPanel, String titleKey)
 309   {
 310     String ttl = MessageManager.getString(titleKey);
 311     ColourChooserListener listener = new ColourChooserListener()
 312     {
 313       @Override
 314       public void colourSelected(Color c)
 315       {
 316         colourPanel.setBackground(c);
 317         colourPanel.repaint();
 318         updateView();
 319       }
 320     };
 321     JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), ttl,
 322             colourPanel.getBackground(), listener);
 323   }
 324
 325   @Override
 326   public void reset()
 327   {
 328     this.ap.alignFrame.changeColour(oldcs);
 329     if (av.getAlignment().getGroups() != null)
 330     {
 331
 332       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 333       {
 334         sg.setColourScheme(oldgroupColours.get(sg));
 335       }
 336     }
 337   }
 338
 339   @Override
 340   public void valueChanged(boolean updateAllAnnotation)
 341   {
 342     if (slider.isEnabled())
 343     {
 344       if (useOriginalColours.isSelected() && !(av
 345               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 346       {
 347         updateView();
 348       }
 349       getCurrentAnnotation().threshold.value = getSliderValue();
 350       propagateSeqAssociatedThreshold(updateAllAnnotation,
 351               getCurrentAnnotation());
 352       ap.paintAlignment(false, false);
 353     }
 354   }
 355
 356   public void originalColours_actionPerformed()
 357   {
 358     boolean selected = useOriginalColours.isSelected();
 359     if (selected)
 360     {
 361       reset();
 362     }
 363     maxColour.setEnabled(!selected);
 364     minColour.setEnabled(!selected);
 365     thresholdIsMin.setEnabled(!selected);
 366     updateView();
 367   }
 368
 369   @Override
 370   public void updateView()
 371   {
 372     // Check if combobox is still adjusting
 373     if (adjusting)
 374     {
 375       return;
 376     }
 377
 378     setCurrentAnnotation(
 379             av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 380                     .getSelectedIndex()]]);
 381
 382     int selectedThresholdItem = getSelectedThresholdItem(
 383             getThreshold().getSelectedIndex());
 384
 385     slider.setEnabled(true);
 386     thresholdValue.setEnabled(true);
 387     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 388
 389     final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
 390     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 391     {
 392       slider.setEnabled(false);
 393       thresholdValue.setEnabled(false);
 394       thresholdValue.setText("");
 395       thresholdIsMin.setEnabled(false);
 396     }
 397     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 398             && currentAnnotation.threshold == null)
 399     {
 400       currentAnnotation.setThreshold(new GraphLine(
 401               (currentAnnotation.graphMax - currentAnnotation.graphMin)
 402                       / 2f,
 403               "Threshold", Color.black));
 404     }
 405
 406     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 407     {
 408       adjusting = true;
 409       setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
 410               currentAnnotation.threshold.value);
 411       slider.setEnabled(true);
 412
 413       setThresholdValueText();
 414       thresholdValue.setEnabled(true);
 415       adjusting = false;
 416     }
 417     colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 418
 419     ap.alignmentChanged();
 420   }
 421
 422   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 423           int selectedThresholdOption)
 424   {
 425
 426     AnnotationColourGradient acg = null;
 427     if (useOriginalColours.isSelected())
 428     {
 429       acg = new AnnotationColourGradient(currentAnn,
 430               av.getGlobalColourScheme(), selectedThresholdOption);
 431     }
 432     else
 433     {
 434       acg = new AnnotationColourGradient(currentAnn,
 435               minColour.getBackground(), maxColour.getBackground(),
 436               selectedThresholdOption);
 437     }
 438     acg.setSeqAssociated(seqAssociated.isSelected());
 439
 440     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 441     {
 442       acg.setPredefinedColours(true);
 443     }
 444
 445     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 446
 447     acg.setPositionToTransparency(transparency.isSelected());
 448
 449     this.ap.alignFrame.changeColour(acg);
 450
 451     if (av.getAlignment().getGroups() != null)
 452     {
 453
 454       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 455       {
 456         if (sg.cs == null)
 457         {
 458           continue;
 459         }
 460         sg.setColourScheme(acg.getInstance(av, sg));
 461       }
 462     }
 463   }
 464
 465   @Override
 466   protected void sliderDragReleased()
 467   {
 468     super.sliderDragReleased();
 469     ap.paintAlignment(true, true);
 470   }
 471 }