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 ColourSchemeI oldcs;
  57
  58   private JButton defColours;
  59
  60   private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  61
  62   private JCheckBox useOriginalColours = new JCheckBox();
  63
  64   private JPanel minColour = new JPanel();
  65
  66   private 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
 149               .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           minColour_actionPerformed();
 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           maxColour_actionPerformed();
 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     this.setLayout(new BorderLayout());
 250     JPanel jPanel1 = new JPanel();
 251     JPanel jPanel2 = new JPanel();
 252     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 253     jPanel1.setBackground(Color.white);
 254     jPanel2.setBackground(Color.white);
 255
 256     jPanel1.add(ok);
 257     jPanel1.add(cancel);
 258     jPanel2.add(annotations, "grow, wrap");
 259     jPanel2.add(seqAssociated);
 260     jPanel2.add(useOriginalColours);
 261     JPanel colpanel = new JPanel(new FlowLayout());
 262     colpanel.setBackground(Color.white);
 263     colpanel.add(minColour);
 264     colpanel.add(maxColour);
 265     jPanel2.add(colpanel, "wrap");
 266     jPanel2.add(getThreshold());
 267     jPanel2.add(defColours, "skip 1, wrap");
 268     jPanel2.add(thresholdIsMin);
 269     jPanel2.add(slider, "grow");
 270     jPanel2.add(thresholdValue, "grow");
 271     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 272     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 273     this.validate();
 274   }
 275
 276   protected void resetColours_actionPerformed()
 277   {
 278     setDefaultMinMax();
 279     updateView();
 280   }
 281
 282   private void setDefaultMinMax()
 283   {
 284     minColour.setBackground(
 285             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 286     maxColour.setBackground(
 287             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 288   }
 289
 290   public void minColour_actionPerformed()
 291   {
 292     Color col = JColorChooser.showDialog(this,
 293             MessageManager.getString("label.select_colour_minimum_value"),
 294             minColour.getBackground());
 295     if (col != null)
 296     {
 297       minColour.setBackground(col);
 298     }
 299     minColour.repaint();
 300     updateView();
 301   }
 302
 303   public void maxColour_actionPerformed()
 304   {
 305     Color col = JColorChooser.showDialog(this,
 306             MessageManager.getString("label.select_colour_maximum_value"),
 307             maxColour.getBackground());
 308     if (col != null)
 309     {
 310       maxColour.setBackground(col);
 311     }
 312     maxColour.repaint();
 313     updateView();
 314   }
 315
 316   @Override
 317   public void reset()
 318   {
 319     this.ap.alignFrame.changeColour(oldcs);
 320     if (av.getAlignment().getGroups() != null)
 321     {
 322
 323       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 324       {
 325         sg.setColourScheme(oldgroupColours.get(sg));
 326       }
 327     }
 328   }
 329
 330   @Override
 331   public void valueChanged(boolean updateAllAnnotation)
 332   {
 333     if (slider.isEnabled())
 334     {
 335       if (useOriginalColours.isSelected() && !(av
 336               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 337       {
 338         updateView();
 339       }
 340       getCurrentAnnotation().threshold.value = getSliderValue();
 341       propagateSeqAssociatedThreshold(updateAllAnnotation,
 342               getCurrentAnnotation());
 343       ap.paintAlignment(false, false);
 344     }
 345   }
 346
 347   public void originalColours_actionPerformed()
 348   {
 349     boolean selected = useOriginalColours.isSelected();
 350     if (selected)
 351     {
 352       reset();
 353     }
 354     maxColour.setEnabled(!selected);
 355     minColour.setEnabled(!selected);
 356     thresholdIsMin.setEnabled(!selected);
 357     updateView();
 358   }
 359
 360   @Override
 361   public void updateView()
 362   {
 363     // Check if combobox is still adjusting
 364     if (adjusting)
 365     {
 366       return;
 367     }
 368
 369     setCurrentAnnotation(
 370             av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 371                     .getSelectedIndex()]]);
 372
 373     int selectedThresholdItem = getSelectedThresholdItem(
 374             getThreshold().getSelectedIndex());
 375
 376     slider.setEnabled(true);
 377     thresholdValue.setEnabled(true);
 378     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 379
 380     final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
 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             && currentAnnotation.threshold == null)
 390     {
 391       currentAnnotation.setThreshold(new GraphLine(
 392               (currentAnnotation.graphMax - currentAnnotation.graphMin)
 393                       / 2f,
 394               "Threshold", Color.black));
 395     }
 396
 397     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 398     {
 399       adjusting = true;
 400       setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
 401               currentAnnotation.threshold.value);
 402       slider.setEnabled(true);
 403
 404       setThresholdValueText();
 405       thresholdValue.setEnabled(true);
 406       adjusting = false;
 407     }
 408     colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 409
 410     ap.alignmentChanged();
 411   }
 412
 413   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 414           int selectedThresholdOption)
 415   {
 416
 417     AnnotationColourGradient acg = null;
 418     if (useOriginalColours.isSelected())
 419     {
 420       acg = new AnnotationColourGradient(currentAnn,
 421               av.getGlobalColourScheme(), selectedThresholdOption);
 422     }
 423     else
 424     {
 425       acg = new AnnotationColourGradient(currentAnn,
 426               minColour.getBackground(), maxColour.getBackground(),
 427               selectedThresholdOption);
 428     }
 429     acg.setSeqAssociated(seqAssociated.isSelected());
 430
 431     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 432     {
 433       acg.setPredefinedColours(true);
 434     }
 435
 436     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 437
 438     this.ap.alignFrame.changeColour(acg);
 439
 440     if (av.getAlignment().getGroups() != null)
 441     {
 442
 443       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 444       {
 445         if (sg.cs == null)
 446         {
 447           continue;
 448         }
 449         sg.setColourScheme(
 450                 acg.getInstance(av, sg));
 451       }
 452     }
 453   }
 454
 455   @Override
 456   protected void sliderDragReleased()
 457   {
 458     super.sliderDragReleased();
 459     ap.paintAlignment(true, true);
 460   }
 461 }