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
 150               .setText(String.valueOf(acg.getAnnotationThreshold()));
 151     }
 152
 153     jbInit();
 154     adjusting = false;
 155
 156     updateView();
 157     frame.invalidate();
 158     frame.pack();
 159   }
 160
 161   @Override
 162   protected void jbInit()
 163   {
 164     super.jbInit();
 165
 166     minColour.setFont(JvSwingUtils.getLabelFont());
 167     minColour.setBorder(BorderFactory.createEtchedBorder());
 168     minColour.setPreferredSize(new Dimension(40, 20));
 169     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 170     minColour.addMouseListener(new MouseAdapter()
 171     {
 172       @Override
 173       public void mousePressed(MouseEvent e)
 174       {
 175         if (minColour.isEnabled())
 176         {
 177           showColourChooser(minColour, "label.select_colour_minimum_value");
 178         }
 179       }
 180     });
 181     maxColour.setFont(JvSwingUtils.getLabelFont());
 182     maxColour.setBorder(BorderFactory.createEtchedBorder());
 183     maxColour.setPreferredSize(new Dimension(40, 20));
 184     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 185     maxColour.addMouseListener(new MouseAdapter()
 186     {
 187       @Override
 188       public void mousePressed(MouseEvent e)
 189       {
 190         if (maxColour.isEnabled())
 191         {
 192           showColourChooser(maxColour, "label.select_colour_maximum_value");
 193         }
 194       }
 195     });
 196
 197     defColours = new JButton();
 198     defColours.setOpaque(false);
 199     defColours.setText(MessageManager.getString("action.set_defaults"));
 200     defColours.setToolTipText(MessageManager
 201             .getString("label.reset_min_max_colours_to_defaults"));
 202     defColours.addActionListener(new ActionListener()
 203     {
 204
 205       @Override
 206       public void actionPerformed(ActionEvent arg0)
 207       {
 208         resetColours_actionPerformed();
 209       }
 210     });
 211
 212     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 213     useOriginalColours.setOpaque(false);
 214     useOriginalColours.setText(
 215             MessageManager.getString("label.use_original_colours"));
 216     useOriginalColours.addActionListener(new ActionListener()
 217     {
 218       @Override
 219       public void actionPerformed(ActionEvent e)
 220       {
 221         originalColours_actionPerformed();
 222       }
 223     });
 224     thresholdIsMin.setBackground(Color.white);
 225     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 226     thresholdIsMin
 227             .setText(MessageManager.getString("label.threshold_minmax"));
 228     thresholdIsMin.addActionListener(new ActionListener()
 229     {
 230       @Override
 231       public void actionPerformed(ActionEvent actionEvent)
 232       {
 233         thresholdIsMin_actionPerformed();
 234       }
 235     });
 236     seqAssociated.setBackground(Color.white);
 237     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 238     seqAssociated
 239             .setText(MessageManager.getString("label.per_sequence_only"));
 240     seqAssociated.addActionListener(new ActionListener()
 241     {
 242
 243       @Override
 244       public void actionPerformed(ActionEvent arg0)
 245       {
 246         seqAssociated_actionPerformed(annotations);
 247       }
 248     });
 249
 250     transparency.setBackground(Color.white);
 251     transparency.setFont(JvSwingUtils.getLabelFont());
 252     transparency
 253             .setText(MessageManager.getString("Use Transparency"));
 254     transparency.addActionListener(new ActionListener()
 255     {
 256
 257       @Override
 258       public void actionPerformed(ActionEvent arg0)
 259       {
 260         transparency_actionPerformed();
 261       }
 262     });
 263     this.setLayout(new BorderLayout());
 264     JPanel jPanel1 = new JPanel();
 265     JPanel jPanel2 = new JPanel();
 266     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 267     jPanel1.setBackground(Color.white);
 268     jPanel2.setBackground(Color.white);
 269
 270     jPanel1.add(ok);
 271     jPanel1.add(cancel);
 272     jPanel2.add(annotations, "grow, wrap");
 273     jPanel2.add(seqAssociated);
 274     jPanel2.add(useOriginalColours);
 275     jPanel2.add(transparency);
 276     JPanel colpanel = new JPanel(new FlowLayout());
 277     colpanel.setBackground(Color.white);
 278     colpanel.add(minColour);
 279     colpanel.add(maxColour);
 280     jPanel2.add(colpanel, "wrap");
 281     jPanel2.add(getThreshold());
 282     jPanel2.add(defColours, "skip 1, wrap");
 283     jPanel2.add(thresholdIsMin);
 284     jPanel2.add(slider, "grow");
 285     jPanel2.add(thresholdValue, "grow");
 286     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 287     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 288     this.validate();
 289   }
 290
 291   protected void transparency_actionPerformed()
 292   {
 293     updateView();
 294   }
 295   protected void resetColours_actionPerformed()
 296   {
 297     setDefaultMinMax();
 298     updateView();
 299   }
 300
 301   private void setDefaultMinMax()
 302   {
 303     minColour.setBackground(
 304             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 305     maxColour.setBackground(
 306             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 307   }
 308
 309   protected void showColourChooser(JPanel colourPanel, String titleKey)
 310   {
 311     String ttl = MessageManager.getString(titleKey);
 312     ColourChooserListener listener = new ColourChooserListener()
 313     {
 314       @Override
 315       public void colourSelected(Color c)
 316       {
 317         colourPanel.setBackground(c);
 318         colourPanel.repaint();
 319         updateView();
 320       }
 321     };
 322     JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), ttl,
 323             colourPanel.getBackground(), listener);
 324   }
 325
 326   @Override
 327   public void reset()
 328   {
 329     this.ap.alignFrame.changeColour(oldcs);
 330     if (av.getAlignment().getGroups() != null)
 331     {
 332
 333       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 334       {
 335         sg.setColourScheme(oldgroupColours.get(sg));
 336       }
 337     }
 338   }
 339
 340   @Override
 341   public void valueChanged(boolean updateAllAnnotation)
 342   {
 343     if (slider.isEnabled())
 344     {
 345       if (useOriginalColours.isSelected() && !(av
 346               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 347       {
 348         updateView();
 349       }
 350       getCurrentAnnotation().threshold.value = getSliderValue();
 351       propagateSeqAssociatedThreshold(updateAllAnnotation,
 352               getCurrentAnnotation());
 353       ap.paintAlignment(false, false);
 354     }
 355   }
 356
 357   public void originalColours_actionPerformed()
 358   {
 359     boolean selected = useOriginalColours.isSelected();
 360     if (selected)
 361     {
 362       reset();
 363     }
 364     maxColour.setEnabled(!selected);
 365     minColour.setEnabled(!selected);
 366     thresholdIsMin.setEnabled(!selected);
 367     updateView();
 368   }
 369
 370   @Override
 371   public void updateView()
 372   {
 373     // Check if combobox is still adjusting
 374     if (adjusting)
 375     {
 376       return;
 377     }
 378
 379     setCurrentAnnotation(
 380             av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 381                     .getSelectedIndex()]]);
 382
 383     int selectedThresholdItem = getSelectedThresholdItem(
 384             getThreshold().getSelectedIndex());
 385
 386     slider.setEnabled(true);
 387     thresholdValue.setEnabled(true);
 388     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 389
 390     final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
 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             && currentAnnotation.threshold == null)
 400     {
 401       currentAnnotation.setThreshold(new GraphLine(
 402               (currentAnnotation.graphMax - currentAnnotation.graphMin)
 403                       / 2f,
 404               "Threshold", Color.black));
 405     }
 406
 407     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 408     {
 409       adjusting = true;
 410       setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
 411               currentAnnotation.threshold.value);
 412       slider.setEnabled(true);
 413
 414       setThresholdValueText();
 415       thresholdValue.setEnabled(true);
 416       adjusting = false;
 417     }
 418     colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 419
 420     ap.alignmentChanged();
 421   }
 422
 423   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 424           int selectedThresholdOption)
 425   {
 426
 427     AnnotationColourGradient acg = null;
 428     if (useOriginalColours.isSelected())
 429     {
 430       acg = new AnnotationColourGradient(currentAnn,
 431               av.getGlobalColourScheme(), selectedThresholdOption);
 432     }
 433     else
 434     {
 435       acg = new AnnotationColourGradient(currentAnn,
 436               minColour.getBackground(), maxColour.getBackground(),
 437               selectedThresholdOption);
 438     }
 439     acg.setSeqAssociated(seqAssociated.isSelected());
 440
 441     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 442     {
 443       acg.setPredefinedColours(true);
 444     }
 445
 446     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 447
 448     acg.setPositionToTransparency(transparency.isSelected());
 449
 450     this.ap.alignFrame.changeColour(acg);
 451
 452     if (av.getAlignment().getGroups() != null)
 453     {
 454
 455       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 456       {
 457         if (sg.cs == null)
 458         {
 459           continue;
 460         }
 461         sg.setColourScheme(
 462                 acg.getInstance(av, sg));
 463       }
 464     }
 465   }
 466
 467   @Override
 468   protected void sliderDragReleased()
 469   {
 470     super.sliderDragReleased();
 471     ap.paintAlignment(true, true);
 472   }
 473 }