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.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     this(av,ap,null);
  77   }
  78   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,AnnotationColourGradient initSettings)
  79   {
  80     super(av, ap);
  81     oldcs = av.getGlobalColourScheme();
  82     if (av.getAlignment().getGroups() != null)
  83     {
  84       oldgroupColours = new Hashtable<>();
  85       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  86       {
  87         if (sg.getColourScheme() != null)
  88         {
  89           oldgroupColours.put(sg, sg.getColourScheme());
  90         }
  91       }
  92     }
  93     frame = new JInternalFrame();
  94     frame.setFrameIcon(null);
  95     frame.setContentPane(this);
  96     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  97     Desktop.addInternalFrame(frame,
  98             MessageManager.getString("label.colour_by_annotation"), 520,
  99             215);
 100     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 101     addSliderChangeListener();
 102     addSliderMouseListeners();
 103
 104     if (av.getAlignment().getAlignmentAnnotation() == null)
 105     {
 106       return;
 107     }
 108
 109     // Always get default shading from preferences.
 110     setDefaultMinMax();
 111
 112     adjusting = true;
 113     if (oldcs instanceof AnnotationColourGradient && initSettings==null)
 114     {
 115       // init from oldcs
 116       initialiseFrom((AnnotationColourGradient) oldcs);
 117     } else {
 118       // use initial colour gradient - if any..
 119       initialiseFrom(initSettings);
 120     }
 121
 122     jbInit();
 123     adjusting = false;
 124
 125     updateView();
 126     frame.invalidate();
 127     frame.pack();
 128   }
 129   private void initialiseFrom(AnnotationColourGradient acg)
 130   {
 131     if (acg!=null)
 132     {
 133       useOriginalColours.setSelected(
 134             acg.isPredefinedColours() || acg.getBaseColour() != null);
 135       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 136       {
 137         minColour.setBackground(acg.getMinColour());
 138         maxColour.setBackground(acg.getMaxColour());
 139       }
 140       seqAssociated.setSelected(acg.isSeqAssociated());
 141
 142     }
 143     Vector<String> annotItems = getAnnotationItems(
 144             seqAssociated.isSelected());
 145     annotations = new JComboBox<>(annotItems);
 146
 147     populateThresholdComboBox(threshold);
 148
 149     if (acg!=null)
 150     {
 151       String label = getAnnotationMenuLabel(acg.getAnnotation());
 152       // TODO: workaround below shouldn't be necessary - there's a bug in getAnnotationMenuLabel!
 153       if (acg.isSeqAssociated())
 154       {
 155         label = acg.getAnnotation().label;
 156       }
 157       annotations.setSelectedItem(label);
 158       switch (acg.getAboveThreshold())
 159       {
 160       case AnnotationColourGradient.NO_THRESHOLD:
 161         getThreshold().setSelectedIndex(0);
 162         break;
 163       case AnnotationColourGradient.ABOVE_THRESHOLD:
 164         getThreshold().setSelectedIndex(1);
 165         break;
 166       case AnnotationColourGradient.BELOW_THRESHOLD:
 167         getThreshold().setSelectedIndex(2);
 168         break;
 169       default:
 170         throw new Error(MessageManager.getString(
 171                 "error.implementation_error_dont_know_about_threshold_setting"));
 172       }
 173       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 174       thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
 175     }
 176   }
 177
 178   @Override
 179   protected void jbInit()
 180   {
 181     super.jbInit();
 182
 183     minColour.setFont(JvSwingUtils.getLabelFont());
 184     minColour.setBorder(BorderFactory.createEtchedBorder());
 185     minColour.setPreferredSize(new Dimension(40, 20));
 186     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 187     minColour.addMouseListener(new MouseAdapter()
 188     {
 189       @Override
 190       public void mousePressed(MouseEvent e)
 191       {
 192         if (minColour.isEnabled())
 193         {
 194           showColourChooser(minColour, "label.select_colour_minimum_value");
 195         }
 196       }
 197     });
 198     maxColour.setFont(JvSwingUtils.getLabelFont());
 199     maxColour.setBorder(BorderFactory.createEtchedBorder());
 200     maxColour.setPreferredSize(new Dimension(40, 20));
 201     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 202     maxColour.addMouseListener(new MouseAdapter()
 203     {
 204       @Override
 205       public void mousePressed(MouseEvent e)
 206       {
 207         if (maxColour.isEnabled())
 208         {
 209           showColourChooser(maxColour, "label.select_colour_maximum_value");
 210         }
 211       }
 212     });
 213
 214     defColours = new JButton();
 215     defColours.setOpaque(false);
 216     defColours.setText(MessageManager.getString("action.set_defaults"));
 217     defColours.setToolTipText(MessageManager
 218             .getString("label.reset_min_max_colours_to_defaults"));
 219     defColours.addActionListener(new ActionListener()
 220     {
 221
 222       @Override
 223       public void actionPerformed(ActionEvent arg0)
 224       {
 225         resetColours_actionPerformed();
 226       }
 227     });
 228
 229     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 230     useOriginalColours.setOpaque(false);
 231     useOriginalColours.setText(
 232             MessageManager.getString("label.use_original_colours"));
 233     useOriginalColours.addActionListener(new ActionListener()
 234     {
 235       @Override
 236       public void actionPerformed(ActionEvent e)
 237       {
 238         originalColours_actionPerformed();
 239       }
 240     });
 241     thresholdIsMin.setBackground(Color.white);
 242     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 243     thresholdIsMin
 244             .setText(MessageManager.getString("label.threshold_minmax"));
 245     thresholdIsMin.addActionListener(new ActionListener()
 246     {
 247       @Override
 248       public void actionPerformed(ActionEvent actionEvent)
 249       {
 250         thresholdIsMin_actionPerformed();
 251       }
 252     });
 253     seqAssociated.setBackground(Color.white);
 254     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 255     seqAssociated
 256             .setText(MessageManager.getString("label.per_sequence_only"));
 257     seqAssociated.addActionListener(new ActionListener()
 258     {
 259
 260       @Override
 261       public void actionPerformed(ActionEvent arg0)
 262       {
 263         seqAssociated_actionPerformed(annotations);
 264       }
 265     });
 266
 267     this.setLayout(new BorderLayout());
 268     JPanel jPanel1 = new JPanel();
 269     JPanel jPanel2 = new JPanel();
 270     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 271     jPanel1.setBackground(Color.white);
 272     jPanel2.setBackground(Color.white);
 273
 274     jPanel1.add(ok);
 275     jPanel1.add(cancel);
 276     jPanel2.add(annotations, "grow, wrap");
 277     jPanel2.add(seqAssociated);
 278     jPanel2.add(useOriginalColours);
 279     JPanel colpanel = new JPanel(new FlowLayout());
 280     colpanel.setBackground(Color.white);
 281     colpanel.add(minColour);
 282     colpanel.add(maxColour);
 283     jPanel2.add(colpanel, "wrap");
 284     jPanel2.add(getThreshold());
 285     jPanel2.add(defColours, "skip 1, wrap");
 286     jPanel2.add(thresholdIsMin);
 287     jPanel2.add(slider, "grow");
 288     jPanel2.add(thresholdValue, "grow");
 289     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 290     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 291     this.validate();
 292   }
 293
 294   protected void resetColours_actionPerformed()
 295   {
 296     setDefaultMinMax();
 297     updateView();
 298   }
 299
 300   private void setDefaultMinMax()
 301   {
 302     minColour.setBackground(
 303             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 304     maxColour.setBackground(
 305             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 306   }
 307
 308   protected void showColourChooser(JPanel colourPanel, String titleKey)
 309   {
 310     String ttl = MessageManager.getString(titleKey);
 311     ColourChooserListener listener = new ColourChooserListener()
 312     {
 313       @Override
 314       public void colourSelected(Color c)
 315       {
 316         colourPanel.setBackground(c);
 317         colourPanel.repaint();
 318         updateView();
 319       }
 320     };
 321     JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
 322             colourPanel.getBackground(), listener);
 323   }
 324
 325   @Override
 326   public void reset()
 327   {
 328     this.ap.alignFrame.changeColour(oldcs);
 329     if (av.getAlignment().getGroups() != null)
 330     {
 331
 332       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 333       {
 334         sg.setColourScheme(oldgroupColours.get(sg));
 335       }
 336     }
 337   }
 338
 339   @Override
 340   public void valueChanged(boolean updateAllAnnotation)
 341   {
 342     if (slider.isEnabled())
 343     {
 344       if (useOriginalColours.isSelected() && !(av
 345               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 346       {
 347         updateView();
 348       }
 349       getCurrentAnnotation().threshold.value = getSliderValue();
 350       propagateSeqAssociatedThreshold(updateAllAnnotation,
 351               getCurrentAnnotation());
 352       ap.paintAlignment(false, false);
 353     }
 354   }
 355
 356   public void originalColours_actionPerformed()
 357   {
 358     boolean selected = useOriginalColours.isSelected();
 359     if (selected)
 360     {
 361       reset();
 362     }
 363     maxColour.setEnabled(!selected);
 364     minColour.setEnabled(!selected);
 365     thresholdIsMin.setEnabled(!selected);
 366     updateView();
 367   }
 368
 369   @Override
 370   public void updateView()
 371   {
 372     // Check if combobox is still adjusting
 373     if (adjusting)
 374     {
 375       return;
 376     }
 377
 378     int selIndex = annotations
 379             .getSelectedIndex();
 380     int annIndex = annmap[selIndex];
 381     setCurrentAnnotation(
 382             av.getAlignment().getAlignmentAnnotation()[annIndex]);
 383
 384     int selectedThresholdItem = getSelectedThresholdItem(
 385             getThreshold().getSelectedIndex());
 386
 387     slider.setEnabled(true);
 388     thresholdValue.setEnabled(true);
 389     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 390
 391     final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
 392     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 393     {
 394       slider.setEnabled(false);
 395       thresholdValue.setEnabled(false);
 396       thresholdValue.setText("");
 397       thresholdIsMin.setEnabled(false);
 398     }
 399     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 400             && currentAnnotation.threshold == null)
 401     {
 402       currentAnnotation.setThreshold(new GraphLine(
 403               (currentAnnotation.graphMax - currentAnnotation.graphMin)
 404                       / 2f,
 405               "Threshold", Color.black));
 406     }
 407
 408     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 409     {
 410       adjusting = true;
 411       setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
 412               currentAnnotation.threshold.value);
 413       slider.setEnabled(true);
 414
 415       setThresholdValueText();
 416       thresholdValue.setEnabled(true);
 417       adjusting = false;
 418     }
 419     colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 420
 421     ap.alignmentChanged();
 422   }
 423
 424   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 425           int selectedThresholdOption)
 426   {
 427
 428     AnnotationColourGradient acg = null;
 429     if (useOriginalColours.isSelected())
 430     {
 431       acg = new AnnotationColourGradient(currentAnn,
 432               av.getGlobalColourScheme(), selectedThresholdOption);
 433     }
 434     else
 435     {
 436       acg = new AnnotationColourGradient(currentAnn,
 437               minColour.getBackground(), maxColour.getBackground(),
 438               selectedThresholdOption);
 439     }
 440     acg.setSeqAssociated(seqAssociated.isSelected());
 441
 442     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 443     {
 444       acg.setPredefinedColours(true);
 445     }
 446
 447     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 448
 449     this.ap.alignFrame.changeColour(acg);
 450
 451     if (av.getAlignment().getGroups() != null)
 452     {
 453
 454       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 455       {
 456         if (sg.cs == null)
 457         {
 458           continue;
 459         }
 460         sg.setColourScheme(acg.getInstance(av, sg));
 461       }
 462     }
 463   }
 464
 465   @Override
 466   protected void sliderDragReleased()
 467   {
 468     super.sliderDragReleased();
 469     ap.paintAlignment(true, true);
 470   }
 471
 472   /**
 473    * construct and display a colourchooser for a given annotation row
 474    *
 475    * @param av
 476    * @param ap
 477    * @param alignmentAnnotation
 478    * @param perseq - when true, enable per-sequence if alignment annotation is per sequence
 479    */
 480   public static void displayFor(AlignViewport av, AlignmentPanel ap,
 481           AlignmentAnnotation alignmentAnnotation, boolean perSeq)
 482   {
 483     ColourSchemeI global = av.getGlobalColourScheme();
 484     AnnotationColourGradient newCS = new AnnotationColourGradient(alignmentAnnotation, global, alignmentAnnotation.threshold!=null ? AnnotationColourGradient.ABOVE_THRESHOLD:AnnotationColourGradient.NO_THRESHOLD);
 485     if (alignmentAnnotation.sequenceRef!=null)
 486     {
 487       newCS.setSeqAssociated(perSeq);
 488     }
 489     for (int i=0;i<alignmentAnnotation.annotations.length;i++)
 490     {
 491       Annotation ann = alignmentAnnotation.annotations[i];
 492       if (ann!=null && ann.colour!=null && !ann.colour.equals(Color.white))
 493       {
 494         newCS.setPredefinedColours(true);
 495         break;
 496       }
 497     }
 498     AnnotationColourChooser achooser = new AnnotationColourChooser(av,ap,newCS);
 499   }
 500 }