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
  79   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap,
  80           AnnotationColourGradient initSettings)
  81   {
  82     super(av, ap);
  83     oldcs = av.getGlobalColourScheme();
  84     if (av.getAlignment().getGroups() != null)
  85     {
  86       oldgroupColours = new Hashtable<>();
  87       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  88       {
  89         if (sg.getColourScheme() != null)
  90         {
  91           oldgroupColours.put(sg, sg.getColourScheme());
  92         }
  93       }
  94     }
  95     frame = new JInternalFrame();
  96     frame.setFrameIcon(null);
  97     frame.setContentPane(this);
  98     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  99     Desktop.addInternalFrame(frame,
 100             MessageManager.getString("label.colour_by_annotation"), 520,
 101             215);
 102     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 103     addSliderChangeListener();
 104     addSliderMouseListeners();
 105
 106     if (av.getAlignment().getAlignmentAnnotation() == null)
 107     {
 108       return;
 109     }
 110
 111     // Always get default shading from preferences.
 112     setDefaultMinMax();
 113
 114     adjusting = true;
 115     if (oldcs instanceof AnnotationColourGradient && initSettings == null)
 116     {
 117       // init from oldcs
 118       initialiseFrom((AnnotationColourGradient) oldcs);
 119     }
 120     else
 121     {
 122       // use initial colour gradient - if any..
 123       initialiseFrom(initSettings);
 124     }
 125
 126     jbInit();
 127     adjusting = false;
 128
 129     updateView();
 130     frame.invalidate();
 131     frame.pack();
 132   }
 133
 134   private void initialiseFrom(AnnotationColourGradient acg)
 135   {
 136     if (acg != null)
 137     {
 138       useOriginalColours.setSelected(
 139               acg.isPredefinedColours() || acg.getBaseColour() != null);
 140       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 141       {
 142         minColour.setBackground(acg.getMinColour());
 143         maxColour.setBackground(acg.getMaxColour());
 144       }
 145       seqAssociated.setSelected(acg.isSeqAssociated());
 146
 147     }
 148     Vector<String> annotItems = getAnnotationItems(
 149             seqAssociated.isSelected());
 150     annotations = new JComboBox<>(annotItems);
 151
 152     populateThresholdComboBox(threshold);
 153
 154     if (acg != null)
 155     {
 156       String label = getAnnotationMenuLabel(acg.getAnnotation());
 157       // TODO: workaround below shouldn't be necessary - there's a bug in
 158       // getAnnotationMenuLabel!
 159       if (acg.isSeqAssociated())
 160       {
 161         label = acg.getAnnotation().label;
 162       }
 163       annotations.setSelectedItem(label);
 164       switch (acg.getAboveThreshold())
 165       {
 166       case AnnotationColourGradient.NO_THRESHOLD:
 167         getThreshold().setSelectedIndex(0);
 168         break;
 169       case AnnotationColourGradient.ABOVE_THRESHOLD:
 170         getThreshold().setSelectedIndex(1);
 171         break;
 172       case AnnotationColourGradient.BELOW_THRESHOLD:
 173         getThreshold().setSelectedIndex(2);
 174         break;
 175       default:
 176         throw new Error(MessageManager.getString(
 177                 "error.implementation_error_dont_know_about_threshold_setting"));
 178       }
 179       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 180       thresholdValue.setText(String.valueOf(acg.getAnnotationThreshold()));
 181     }
 182   }
 183
 184   @Override
 185   protected void jbInit()
 186   {
 187     super.jbInit();
 188
 189     minColour.setFont(JvSwingUtils.getLabelFont());
 190     minColour.setBorder(BorderFactory.createEtchedBorder());
 191     minColour.setPreferredSize(new Dimension(40, 20));
 192     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 193     minColour.addMouseListener(new MouseAdapter()
 194     {
 195       @Override
 196       public void mousePressed(MouseEvent e)
 197       {
 198         if (minColour.isEnabled())
 199         {
 200           showColourChooser(minColour, "label.select_colour_minimum_value");
 201         }
 202       }
 203     });
 204     maxColour.setFont(JvSwingUtils.getLabelFont());
 205     maxColour.setBorder(BorderFactory.createEtchedBorder());
 206     maxColour.setPreferredSize(new Dimension(40, 20));
 207     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 208     maxColour.addMouseListener(new MouseAdapter()
 209     {
 210       @Override
 211       public void mousePressed(MouseEvent e)
 212       {
 213         if (maxColour.isEnabled())
 214         {
 215           showColourChooser(maxColour, "label.select_colour_maximum_value");
 216         }
 217       }
 218     });
 219
 220     defColours = new JButton();
 221     defColours.setOpaque(false);
 222     defColours.setText(MessageManager.getString("action.set_defaults"));
 223     defColours.setToolTipText(MessageManager
 224             .getString("label.reset_min_max_colours_to_defaults"));
 225     defColours.addActionListener(new ActionListener()
 226     {
 227
 228       @Override
 229       public void actionPerformed(ActionEvent arg0)
 230       {
 231         resetColours_actionPerformed();
 232       }
 233     });
 234
 235     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 236     useOriginalColours.setOpaque(false);
 237     useOriginalColours.setText(
 238             MessageManager.getString("label.use_original_colours"));
 239     useOriginalColours.addActionListener(new ActionListener()
 240     {
 241       @Override
 242       public void actionPerformed(ActionEvent e)
 243       {
 244         originalColours_actionPerformed();
 245       }
 246     });
 247     thresholdIsMin.setBackground(Color.white);
 248     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 249     thresholdIsMin
 250             .setText(MessageManager.getString("label.threshold_minmax"));
 251     thresholdIsMin.addActionListener(new ActionListener()
 252     {
 253       @Override
 254       public void actionPerformed(ActionEvent actionEvent)
 255       {
 256         thresholdIsMin_actionPerformed();
 257       }
 258     });
 259     seqAssociated.setBackground(Color.white);
 260     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 261     seqAssociated
 262             .setText(MessageManager.getString("label.per_sequence_only"));
 263     seqAssociated.addActionListener(new ActionListener()
 264     {
 265
 266       @Override
 267       public void actionPerformed(ActionEvent arg0)
 268       {
 269         seqAssociated_actionPerformed(annotations);
 270       }
 271     });
 272
 273     this.setLayout(new BorderLayout());
 274     JPanel jPanel1 = new JPanel();
 275     JPanel jPanel2 = new JPanel();
 276     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 277     jPanel1.setBackground(Color.white);
 278     jPanel2.setBackground(Color.white);
 279
 280     jPanel1.add(ok);
 281     jPanel1.add(cancel);
 282     jPanel2.add(annotations, "grow, wrap");
 283     jPanel2.add(seqAssociated);
 284     jPanel2.add(useOriginalColours);
 285     JPanel colpanel = new JPanel(new FlowLayout());
 286     colpanel.setBackground(Color.white);
 287     colpanel.add(minColour);
 288     colpanel.add(maxColour);
 289     jPanel2.add(colpanel, "wrap");
 290     jPanel2.add(getThreshold());
 291     jPanel2.add(defColours, "skip 1, wrap");
 292     jPanel2.add(thresholdIsMin);
 293     jPanel2.add(slider, "grow");
 294     jPanel2.add(thresholdValue, "grow");
 295     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 296     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 297     this.validate();
 298   }
 299
 300   protected void resetColours_actionPerformed()
 301   {
 302     setDefaultMinMax();
 303     updateView();
 304   }
 305
 306   private void setDefaultMinMax()
 307   {
 308     minColour.setBackground(
 309             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 310     maxColour.setBackground(
 311             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 312   }
 313
 314   protected void showColourChooser(JPanel colourPanel, String titleKey)
 315   {
 316     String ttl = MessageManager.getString(titleKey);
 317     ColourChooserListener listener = new ColourChooserListener()
 318     {
 319       @Override
 320       public void colourSelected(Color c)
 321       {
 322         colourPanel.setBackground(c);
 323         colourPanel.repaint();
 324         updateView();
 325       }
 326     };
 327     JalviewColourChooser.showColourChooser(Desktop.getDesktop(), ttl,
 328             colourPanel.getBackground(), listener);
 329   }
 330
 331   @Override
 332   public void reset()
 333   {
 334     this.ap.alignFrame.changeColour(oldcs);
 335     if (av.getAlignment().getGroups() != null)
 336     {
 337
 338       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 339       {
 340         sg.setColourScheme(oldgroupColours.get(sg));
 341       }
 342     }
 343   }
 344
 345   @Override
 346   public void valueChanged(boolean updateAllAnnotation)
 347   {
 348     if (slider.isEnabled())
 349     {
 350       if (useOriginalColours.isSelected() && !(av
 351               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 352       {
 353         updateView();
 354       }
 355       getCurrentAnnotation().threshold.value = getSliderValue();
 356       propagateSeqAssociatedThreshold(updateAllAnnotation,
 357               getCurrentAnnotation());
 358       ap.paintAlignment(false, false);
 359     }
 360   }
 361
 362   public void originalColours_actionPerformed()
 363   {
 364     boolean selected = useOriginalColours.isSelected();
 365     if (selected)
 366     {
 367       reset();
 368     }
 369     maxColour.setEnabled(!selected);
 370     minColour.setEnabled(!selected);
 371     thresholdIsMin.setEnabled(!selected);
 372     updateView();
 373   }
 374
 375   @Override
 376   public void updateView()
 377   {
 378     // Check if combobox is still adjusting
 379     if (adjusting)
 380     {
 381       return;
 382     }
 383
 384     int selIndex = annotations.getSelectedIndex();
 385     int annIndex = annmap[selIndex];
 386     setCurrentAnnotation(
 387             av.getAlignment().getAlignmentAnnotation()[annIndex]);
 388
 389     int selectedThresholdItem = getSelectedThresholdItem(
 390             getThreshold().getSelectedIndex());
 391
 392     slider.setEnabled(true);
 393     thresholdValue.setEnabled(true);
 394     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 395
 396     final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
 397     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 398     {
 399       slider.setEnabled(false);
 400       thresholdValue.setEnabled(false);
 401       thresholdValue.setText("");
 402       thresholdIsMin.setEnabled(false);
 403     }
 404     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 405             && currentAnnotation.threshold == null)
 406     {
 407       currentAnnotation.setThreshold(new GraphLine(
 408               (currentAnnotation.graphMax - currentAnnotation.graphMin)
 409                       / 2f,
 410               "Threshold", Color.black));
 411     }
 412
 413     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 414     {
 415       adjusting = true;
 416       setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
 417               currentAnnotation.threshold.value);
 418       slider.setEnabled(true);
 419
 420       setThresholdValueText();
 421       thresholdValue.setEnabled(true);
 422       adjusting = false;
 423     }
 424     colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 425
 426     ap.alignmentChanged();
 427   }
 428
 429   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 430           int selectedThresholdOption)
 431   {
 432
 433     AnnotationColourGradient acg = null;
 434     if (useOriginalColours.isSelected())
 435     {
 436       acg = new AnnotationColourGradient(currentAnn,
 437               av.getGlobalColourScheme(), selectedThresholdOption);
 438     }
 439     else
 440     {
 441       acg = new AnnotationColourGradient(currentAnn,
 442               minColour.getBackground(), maxColour.getBackground(),
 443               selectedThresholdOption);
 444     }
 445     acg.setSeqAssociated(seqAssociated.isSelected());
 446
 447     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 448     {
 449       acg.setPredefinedColours(true);
 450     }
 451
 452     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 453
 454     this.ap.alignFrame.changeColour(acg);
 455
 456     if (av.getAlignment().getGroups() != null)
 457     {
 458
 459       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 460       {
 461         if (sg.cs == null)
 462         {
 463           continue;
 464         }
 465         sg.setColourScheme(acg.getInstance(av, sg));
 466       }
 467     }
 468   }
 469
 470   @Override
 471   protected void sliderDragReleased()
 472   {
 473     super.sliderDragReleased();
 474     ap.paintAlignment(true, true);
 475   }
 476
 477   /**
 478    * construct and display a colourchooser for a given annotation row
 479    *
 480    * @param av
 481    * @param ap
 482    * @param alignmentAnnotation
 483    * @param perseq
 484    *          - when true, enable per-sequence if alignment annotation is per
 485    *          sequence
 486    */
 487   public static void displayFor(AlignViewport av, AlignmentPanel ap,
 488           AlignmentAnnotation alignmentAnnotation, boolean perSeq)
 489   {
 490     ColourSchemeI global = av.getGlobalColourScheme();
 491     AnnotationColourGradient newCS = new AnnotationColourGradient(
 492             alignmentAnnotation, global,
 493             alignmentAnnotation.threshold != null
 494                     ? AnnotationColourGradient.ABOVE_THRESHOLD
 495                     : AnnotationColourGradient.NO_THRESHOLD);
 496     if (alignmentAnnotation.sequenceRef != null)
 497     {
 498       newCS.setSeqAssociated(perSeq);
 499     }
 500     for (int i = 0; i < alignmentAnnotation.annotations.length; i++)
 501     {
 502       Annotation ann = alignmentAnnotation.annotations[i];
 503       if (ann != null && ann.colour != null
 504               && !ann.colour.equals(Color.white))
 505       {
 506         newCS.setPredefinedColours(true);
 507         break;
 508       }
 509     }
 510     AnnotationColourChooser achooser = new AnnotationColourChooser(av, ap,
 511             newCS);
 512   }
 513 }