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