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 java.awt.BorderLayout;
  24 import java.awt.Color;
  25 import java.awt.Dimension;
  26 import java.awt.FlowLayout;
  27 import java.awt.event.ActionEvent;
  28 import java.awt.event.ActionListener;
  29 import java.awt.event.MouseAdapter;
  30 import java.awt.event.MouseEvent;
  31 import java.util.Hashtable;
  32 import java.util.Vector;
  33
  34 import javax.swing.BorderFactory;
  35 import javax.swing.JButton;
  36 import javax.swing.JCheckBox;
  37 import javax.swing.JComboBox;
  38 import javax.swing.JInternalFrame;
  39 import javax.swing.JLayeredPane;
  40 import javax.swing.JPanel;
  41
  42 import jalview.bin.Cache;
  43 import jalview.datamodel.AlignmentAnnotation;
  44 import jalview.datamodel.Annotation;
  45 import jalview.datamodel.GraphLine;
  46 import jalview.datamodel.SequenceGroup;
  47 import jalview.gui.JalviewColourChooser.ColourChooserListener;
  48 import jalview.schemes.AnnotationColourGradient;
  49 import jalview.schemes.ColourSchemeI;
  50 import jalview.util.MessageManager;
  51 import net.bytebuddy.dynamic.DynamicType.Builder.MethodDefinition.ParameterDefinition.Initial;
  52 import net.miginfocom.swing.MigLayout;
  53
  54 @SuppressWarnings("serial")
  55 public class AnnotationColourChooser extends AnnotationRowFilter
  56 {
  57   private ColourSchemeI oldcs;
  58
  59   private JButton defColours;
  60
  61   private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  62
  63   private JCheckBox useOriginalColours = new JCheckBox();
  64
  65   JPanel minColour = new JPanel();
  66
  67   JPanel maxColour = new JPanel();
  68
  69   private JCheckBox thresholdIsMin = 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     this(av,ap,null);
  78   }
  79   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,AnnotationColourGradient initSettings)
  80   {
  81     super(av, ap);
  82     oldcs = av.getGlobalColourScheme();
  83     if (av.getAlignment().getGroups() != null)
  84     {
  85       oldgroupColours = new Hashtable<>();
  86       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  87       {
  88         if (sg.getColourScheme() != null)
  89         {
  90           oldgroupColours.put(sg, sg.getColourScheme());
  91         }
  92       }
  93     }
  94     frame = new JInternalFrame();
  95     frame.setFrameIcon(null);
  96     frame.setContentPane(this);
  97     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  98     Desktop.addInternalFrame(frame,
  99             MessageManager.getString("label.colour_by_annotation"), 520,
 100             215);
 101     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 102     addSliderChangeListener();
 103     addSliderMouseListeners();
 104
 105     if (av.getAlignment().getAlignmentAnnotation() == null)
 106     {
 107       return;
 108     }
 109
 110     // Always get default shading from preferences.
 111     setDefaultMinMax();
 112
 113     adjusting = true;
 114     if (oldcs instanceof AnnotationColourGradient && initSettings==null)
 115     {
 116       // init from oldcs
 117       initialiseFrom((AnnotationColourGradient) oldcs);
 118     } else {
 119       // use initial colour gradient - if any..
 120       initialiseFrom(initSettings);
 121     }
 122
 123     jbInit();
 124     adjusting = false;
 125
 126     updateView();
 127     frame.invalidate();
 128     frame.pack();
 129   }
 130   private void initialiseFrom(AnnotationColourGradient acg)
 131   {
 132     if (acg!=null)
 133     {
 134       useOriginalColours.setSelected(
 135             acg.isPredefinedColours() || acg.getBaseColour() != null);
 136       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 137       {
 138         minColour.setBackground(acg.getMinColour());
 139         maxColour.setBackground(acg.getMaxColour());
 140       }
 141       seqAssociated.setSelected(acg.isSeqAssociated());
 142
 143     }
 144     Vector<String> annotItems = getAnnotationItems(
 145             seqAssociated.isSelected());
 146     annotations = new JComboBox<>(annotItems);
 147
 148     populateThresholdComboBox(threshold);
 149
 150     if (acg!=null)
 151     {
 152       String label = getAnnotationMenuLabel(acg.getAnnotation());
 153       // TODO: workaround below shouldn't be necessary - there's a bug in getAnnotationMenuLabel!
 154       if (acg.isSeqAssociated())
 155       {
 156         label = acg.getAnnotation().label;
 157       }
 158       annotations.setSelectedItem(label);
 159       switch (acg.getAboveThreshold())
 160       {
 161       case AnnotationColourGradient.NO_THRESHOLD:
 162         getThreshold().setSelectedIndex(0);
 163         break;
 164       case AnnotationColourGradient.ABOVE_THRESHOLD:
 165         getThreshold().setSelectedIndex(1);
 166         break;
 167       case AnnotationColourGradient.BELOW_THRESHOLD:
 168         getThreshold().setSelectedIndex(2);
 169         break;
 170       default:
 171         throw new Error(MessageManager.getString(
 172                 "error.implementation_error_dont_know_about_threshold_setting"));
 173       }
 174       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 175       thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
 176     }
 177   }
 178
 179   @Override
 180   protected void jbInit()
 181   {
 182     super.jbInit();
 183
 184     minColour.setFont(JvSwingUtils.getLabelFont());
 185     minColour.setBorder(BorderFactory.createEtchedBorder());
 186     minColour.setPreferredSize(new Dimension(40, 20));
 187     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 188     minColour.addMouseListener(new MouseAdapter()
 189     {
 190       @Override
 191       public void mousePressed(MouseEvent e)
 192       {
 193         if (minColour.isEnabled())
 194         {
 195           showColourChooser(minColour, "label.select_colour_minimum_value");
 196         }
 197       }
 198     });
 199     maxColour.setFont(JvSwingUtils.getLabelFont());
 200     maxColour.setBorder(BorderFactory.createEtchedBorder());
 201     maxColour.setPreferredSize(new Dimension(40, 20));
 202     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 203     maxColour.addMouseListener(new MouseAdapter()
 204     {
 205       @Override
 206       public void mousePressed(MouseEvent e)
 207       {
 208         if (maxColour.isEnabled())
 209         {
 210           showColourChooser(maxColour, "label.select_colour_maximum_value");
 211         }
 212       }
 213     });
 214
 215     defColours = new JButton();
 216     defColours.setOpaque(false);
 217     defColours.setText(MessageManager.getString("action.set_defaults"));
 218     defColours.setToolTipText(MessageManager
 219             .getString("label.reset_min_max_colours_to_defaults"));
 220     defColours.addActionListener(new ActionListener()
 221     {
 222
 223       @Override
 224       public void actionPerformed(ActionEvent arg0)
 225       {
 226         resetColours_actionPerformed();
 227       }
 228     });
 229
 230     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 231     useOriginalColours.setOpaque(false);
 232     useOriginalColours.setText(
 233             MessageManager.getString("label.use_original_colours"));
 234     useOriginalColours.addActionListener(new ActionListener()
 235     {
 236       @Override
 237       public void actionPerformed(ActionEvent e)
 238       {
 239         originalColours_actionPerformed();
 240       }
 241     });
 242     thresholdIsMin.setBackground(Color.white);
 243     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 244     thresholdIsMin
 245             .setText(MessageManager.getString("label.threshold_minmax"));
 246     thresholdIsMin.addActionListener(new ActionListener()
 247     {
 248       @Override
 249       public void actionPerformed(ActionEvent actionEvent)
 250       {
 251         thresholdIsMin_actionPerformed();
 252       }
 253     });
 254     seqAssociated.setBackground(Color.white);
 255     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 256     seqAssociated
 257             .setText(MessageManager.getString("label.per_sequence_only"));
 258     seqAssociated.addActionListener(new ActionListener()
 259     {
 260
 261       @Override
 262       public void actionPerformed(ActionEvent arg0)
 263       {
 264         seqAssociated_actionPerformed(annotations);
 265       }
 266     });
 267
 268     this.setLayout(new BorderLayout());
 269     JPanel jPanel1 = new JPanel();
 270     JPanel jPanel2 = new JPanel();
 271     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 272     jPanel1.setBackground(Color.white);
 273     jPanel2.setBackground(Color.white);
 274
 275     jPanel1.add(ok);
 276     jPanel1.add(cancel);
 277     jPanel2.add(annotations, "grow, wrap");
 278     jPanel2.add(seqAssociated);
 279     jPanel2.add(useOriginalColours);
 280     JPanel colpanel = new JPanel(new FlowLayout());
 281     colpanel.setBackground(Color.white);
 282     colpanel.add(minColour);
 283     colpanel.add(maxColour);
 284     jPanel2.add(colpanel, "wrap");
 285     jPanel2.add(getThreshold());
 286     jPanel2.add(defColours, "skip 1, wrap");
 287     jPanel2.add(thresholdIsMin);
 288     jPanel2.add(slider, "grow");
 289     jPanel2.add(thresholdValue, "grow");
 290     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 291     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 292     this.validate();
 293   }
 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.getDesktop(), 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     int selIndex = annotations
 380             .getSelectedIndex();
 381     int annIndex = annmap[selIndex];
 382     setCurrentAnnotation(
 383             av.getAlignment().getAlignmentAnnotation()[annIndex]);
 384
 385     int selectedThresholdItem = getSelectedThresholdItem(
 386             getThreshold().getSelectedIndex());
 387
 388     slider.setEnabled(true);
 389     thresholdValue.setEnabled(true);
 390     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 391
 392     final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
 393     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 394     {
 395       slider.setEnabled(false);
 396       thresholdValue.setEnabled(false);
 397       thresholdValue.setText("");
 398       thresholdIsMin.setEnabled(false);
 399     }
 400     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 401             && currentAnnotation.threshold == null)
 402     {
 403       currentAnnotation.setThreshold(new GraphLine(
 404               (currentAnnotation.graphMax - currentAnnotation.graphMin)
 405                       / 2f,
 406               "Threshold", Color.black));
 407     }
 408
 409     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 410     {
 411       adjusting = true;
 412       setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
 413               currentAnnotation.threshold.value);
 414       slider.setEnabled(true);
 415
 416       setThresholdValueText();
 417       thresholdValue.setEnabled(true);
 418       adjusting = false;
 419     }
 420     colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 421
 422     ap.alignmentChanged();
 423   }
 424
 425   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 426           int selectedThresholdOption)
 427   {
 428
 429     AnnotationColourGradient acg = null;
 430     if (useOriginalColours.isSelected())
 431     {
 432       acg = new AnnotationColourGradient(currentAnn,
 433               av.getGlobalColourScheme(), selectedThresholdOption);
 434     }
 435     else
 436     {
 437       acg = new AnnotationColourGradient(currentAnn,
 438               minColour.getBackground(), maxColour.getBackground(),
 439               selectedThresholdOption);
 440     }
 441     acg.setSeqAssociated(seqAssociated.isSelected());
 442
 443     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 444     {
 445       acg.setPredefinedColours(true);
 446     }
 447
 448     acg.setThresholdIsMinMax(thresholdIsMin.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(acg.getInstance(av, sg));
 462       }
 463     }
 464   }
 465
 466   @Override
 467   protected void sliderDragReleased()
 468   {
 469     super.sliderDragReleased();
 470     ap.paintAlignment(true, true);
 471   }
 472
 473   /**
 474    * construct and display a colourchooser for a given annotation row
 475    *
 476    * @param av
 477    * @param ap
 478    * @param alignmentAnnotation
 479    * @param perseq - when true, enable per-sequence if alignment annotation is per sequence
 480    */
 481   public static void displayFor(AlignViewport av, AlignmentPanel ap,
 482           AlignmentAnnotation alignmentAnnotation, boolean perSeq)
 483   {
 484     ColourSchemeI global = av.getGlobalColourScheme();
 485     AnnotationColourGradient newCS = new AnnotationColourGradient(alignmentAnnotation, global, alignmentAnnotation.threshold!=null ? AnnotationColourGradient.ABOVE_THRESHOLD:AnnotationColourGradient.NO_THRESHOLD);
 486     if (alignmentAnnotation.sequenceRef!=null)
 487     {
 488       newCS.setSeqAssociated(perSeq);
 489     }
 490     for (int i=0;i<alignmentAnnotation.annotations.length;i++)
 491     {
 492       Annotation ann = alignmentAnnotation.annotations[i];
 493       if (ann!=null && ann.colour!=null && !ann.colour.equals(Color.white))
 494       {
 495         newCS.setPredefinedColours(true);
 496         break;
 497       }
 498     }
 499     AnnotationColourChooser achooser = new AnnotationColourChooser(av,ap,newCS);
 500   }
 501 }