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 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   JPanel minColour = new JPanel();
  67
  68   JPanel maxColour = new JPanel();
  69
  70   private JCheckBox thresholdIsMin = new JCheckBox();
  71   private JCheckBox transparency = new JCheckBox();
  72
  73   protected static final int MIN_WIDTH = 500;
  74
  75   protected static final int MIN_HEIGHT = 240;
  76
  77   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  78   {
  79     super(av, ap);
  80     oldcs = av.getGlobalColourScheme();
  81     if (av.getAlignment().getGroups() != null)
  82     {
  83       oldgroupColours = new Hashtable<>();
  84       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  85       {
  86         if (sg.getColourScheme() != null)
  87         {
  88           oldgroupColours.put(sg, sg.getColourScheme());
  89         }
  90       }
  91     }
  92     frame = new JInternalFrame();
  93     frame.setContentPane(this);
  94     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  95     Desktop.addInternalFrame(frame,
  96             MessageManager.getString("label.colour_by_annotation"), 520,
  97             215);
  98     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
  99     addSliderChangeListener();
 100     addSliderMouseListeners();
 101
 102     if (av.getAlignment().getAlignmentAnnotation() == null)
 103     {
 104       return;
 105     }
 106
 107     // Always get default shading from preferences.
 108     setDefaultMinMax();
 109
 110     adjusting = true;
 111     if (oldcs instanceof AnnotationColourGradient)
 112     {
 113       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 114       useOriginalColours.setSelected(
 115               acg.isPredefinedColours() || acg.getBaseColour() != null);
 116       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 117       {
 118         minColour.setBackground(acg.getMinColour());
 119         maxColour.setBackground(acg.getMaxColour());
 120       }
 121       seqAssociated.setSelected(acg.isSeqAssociated());
 122
 123     }
 124     Vector<String> annotItems = getAnnotationItems(
 125             seqAssociated.isSelected());
 126     annotations = new JComboBox<>(annotItems);
 127
 128     populateThresholdComboBox(threshold);
 129
 130     if (oldcs instanceof AnnotationColourGradient)
 131     {
 132       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 133       String label = getAnnotationMenuLabel(acg.getAnnotation());
 134       annotations.setSelectedItem(label);
 135       switch (acg.getAboveThreshold())
 136       {
 137       case AnnotationColourGradient.NO_THRESHOLD:
 138         getThreshold().setSelectedIndex(0);
 139         break;
 140       case AnnotationColourGradient.ABOVE_THRESHOLD:
 141         getThreshold().setSelectedIndex(1);
 142         break;
 143       case AnnotationColourGradient.BELOW_THRESHOLD:
 144         getThreshold().setSelectedIndex(2);
 145         break;
 146       default:
 147         throw new Error(MessageManager.getString(
 148                 "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           showColourChooser(minColour, "label.select_colour_minimum_value");
 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           showColourChooser(maxColour, "label.select_colour_maximum_value");
 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(
 216             MessageManager.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
 228             .setText(MessageManager.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
 240             .setText(MessageManager.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     transparency.setBackground(Color.white);
 252     transparency.setFont(JvSwingUtils.getLabelFont());
 253     transparency
 254             .setText(MessageManager.getString("Use Transparency"));
 255     transparency.addActionListener(new ActionListener()
 256     {
 257
 258       @Override
 259       public void actionPerformed(ActionEvent arg0)
 260       {
 261         transparency_actionPerformed();
 262       }
 263     });
 264     this.setLayout(new BorderLayout());
 265     JPanel jPanel1 = new JPanel();
 266     JPanel jPanel2 = new JPanel();
 267     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 268     jPanel1.setBackground(Color.white);
 269     jPanel2.setBackground(Color.white);
 270
 271     jPanel1.add(ok);
 272     jPanel1.add(cancel);
 273     jPanel2.add(annotations, "grow, wrap");
 274     jPanel2.add(seqAssociated);
 275     jPanel2.add(useOriginalColours);
 276     jPanel2.add(transparency);
 277     JPanel colpanel = new JPanel(new FlowLayout());
 278     colpanel.setBackground(Color.white);
 279     colpanel.add(minColour);
 280     colpanel.add(maxColour);
 281     jPanel2.add(colpanel, "wrap");
 282     jPanel2.add(getThreshold());
 283     jPanel2.add(defColours, "skip 1, wrap");
 284     jPanel2.add(thresholdIsMin);
 285     jPanel2.add(slider, "grow");
 286     jPanel2.add(thresholdValue, "grow");
 287     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 288     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 289     this.validate();
 290   }
 291
 292   protected void transparency_actionPerformed()
 293   {
 294     updateView();
 295   }
 296   protected void resetColours_actionPerformed()
 297   {
 298     setDefaultMinMax();
 299     updateView();
 300   }
 301
 302   private void setDefaultMinMax()
 303   {
 304     minColour.setBackground(
 305             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 306     maxColour.setBackground(
 307             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 308   }
 309
 310   protected void showColourChooser(JPanel colourPanel, String titleKey)
 311   {
 312     String ttl = MessageManager.getString(titleKey);
 313     ColourChooserListener listener = new ColourChooserListener()
 314     {
 315       @Override
 316       public void colourSelected(Color c)
 317       {
 318         colourPanel.setBackground(c);
 319         colourPanel.repaint();
 320         updateView();
 321       }
 322     };
 323     JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), ttl,
 324             colourPanel.getBackground(), listener);
 325   }
 326
 327   @Override
 328   public void reset()
 329   {
 330     this.ap.alignFrame.changeColour(oldcs);
 331     if (av.getAlignment().getGroups() != null)
 332     {
 333
 334       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 335       {
 336         sg.setColourScheme(oldgroupColours.get(sg));
 337       }
 338     }
 339   }
 340
 341   @Override
 342   public void valueChanged(boolean updateAllAnnotation)
 343   {
 344     if (slider.isEnabled())
 345     {
 346       if (useOriginalColours.isSelected() && !(av
 347               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 348       {
 349         updateView();
 350       }
 351       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 352       propagateSeqAssociatedThreshold(updateAllAnnotation,
 353               getCurrentAnnotation());
 354       ap.paintAlignment(false, false);
 355     }
 356   }
 357
 358   public void originalColours_actionPerformed()
 359   {
 360     boolean selected = useOriginalColours.isSelected();
 361     if (selected)
 362     {
 363       reset();
 364     }
 365     maxColour.setEnabled(!selected);
 366     minColour.setEnabled(!selected);
 367     thresholdIsMin.setEnabled(!selected);
 368     updateView();
 369   }
 370
 371   @Override
 372   public void updateView()
 373   {
 374     // Check if combobox is still adjusting
 375     if (adjusting)
 376     {
 377       return;
 378     }
 379
 380     setCurrentAnnotation(
 381             av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 382                     .getSelectedIndex()]]);
 383
 384     int selectedThresholdItem = getSelectedThresholdItem(
 385             getThreshold().getSelectedIndex());
 386
 387     slider.setEnabled(true);
 388     thresholdValue.setEnabled(true);
 389     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 390
 391     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 392     {
 393       slider.setEnabled(false);
 394       thresholdValue.setEnabled(false);
 395       thresholdValue.setText("");
 396       thresholdIsMin.setEnabled(false);
 397     }
 398     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 399             && getCurrentAnnotation().threshold == null)
 400     {
 401       getCurrentAnnotation().setThreshold(new GraphLine(
 402               (getCurrentAnnotation().graphMax
 403                       - getCurrentAnnotation().graphMin) / 2f,
 404               "Threshold", Color.black));
 405     }
 406
 407     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 408     {
 409       adjusting = true;
 410       float range = getCurrentAnnotation().graphMax * ONETHOUSAND
 411               - getCurrentAnnotation().graphMin * ONETHOUSAND;
 412
 413       slider.setMinimum(
 414               (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
 415       slider.setMaximum(
 416               (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
 417       slider.setValue(
 418               (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
 419       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 420       slider.setMajorTickSpacing((int) (range / 10f));
 421       slider.setEnabled(true);
 422       thresholdValue.setEnabled(true);
 423       adjusting = false;
 424     }
 425     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 426
 427     ap.alignmentChanged();
 428   }
 429
 430   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 431           int selectedThresholdOption)
 432   {
 433
 434     AnnotationColourGradient acg = null;
 435     if (useOriginalColours.isSelected())
 436     {
 437       acg = new AnnotationColourGradient(currentAnn,
 438               av.getGlobalColourScheme(), selectedThresholdOption);
 439     }
 440     else
 441     {
 442       acg = new AnnotationColourGradient(currentAnn,
 443               minColour.getBackground(), maxColour.getBackground(),
 444               selectedThresholdOption);
 445     }
 446     acg.setSeqAssociated(seqAssociated.isSelected());
 447
 448     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 449     {
 450       acg.setPredefinedColours(true);
 451     }
 452
 453     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 454
 455     acg.setPositionToTransparency(transparency.isSelected());
 456
 457     this.ap.alignFrame.changeColour(acg);
 458
 459     if (av.getAlignment().getGroups() != null)
 460     {
 461
 462       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 463       {
 464         if (sg.cs == null)
 465         {
 466           continue;
 467         }
 468         sg.setColourScheme(
 469                 acg.getInstance(av, sg));
 470       }
 471     }
 472   }
 473
 474   @Override
 475   protected void sliderDragReleased()
 476   {
 477     super.sliderDragReleased();
 478     ap.paintAlignment(true, true);
 479   }
 480 }