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.schemes.AnnotationColourGradient;
  28 import jalview.schemes.ColourSchemeI;
  29 import jalview.util.MessageManager;
  30
  31 import java.awt.BorderLayout;
  32 import java.awt.Color;
  33 import java.awt.Dimension;
  34 import java.awt.FlowLayout;
  35 import java.awt.event.ActionEvent;
  36 import java.awt.event.ActionListener;
  37 import java.awt.event.MouseAdapter;
  38 import java.awt.event.MouseEvent;
  39 import java.util.HashMap;
  40 import java.util.Map;
  41 import java.util.Map.Entry;
  42 import java.util.Vector;
  43
  44 import javax.swing.BorderFactory;
  45 import javax.swing.JButton;
  46 import javax.swing.JCheckBox;
  47 import javax.swing.JColorChooser;
  48 import javax.swing.JComboBox;
  49 import javax.swing.JInternalFrame;
  50 import javax.swing.JLayeredPane;
  51 import javax.swing.JPanel;
  52
  53 import net.miginfocom.swing.MigLayout;
  54
  55 @SuppressWarnings("serial")
  56 public class AnnotationColourChooser extends AnnotationRowFilter
  57 {
  58   private static final int ONETHOUSAND = 1000;
  59
  60   private ColourSchemeI oldcs;
  61
  62   private JButton defColours;
  63
  64   private Map<SequenceGroup, ColourSchemeI> oldgroupColours;
  65
  66   private Map<AlignmentAnnotation, GraphLine> oldGraphLines;
  67
  68   private Map<GraphLine, Float> oldThresholds;
  69
  70   private JCheckBox useOriginalColours = new JCheckBox();
  71
  72   private JPanel minColour = new JPanel();
  73
  74   private JPanel maxColour = new JPanel();
  75
  76   private JCheckBox thresholdIsMin = new JCheckBox();
  77
  78   protected static final int MIN_WIDTH = 500;
  79
  80   protected static final int MIN_HEIGHT = 240;
  81
  82   /**
  83    * Constructor
  84    *
  85    * @param av
  86    * @param ap
  87    */
  88   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  89   {
  90     super(av, ap);
  91
  92     saveInitialState();
  93
  94     frame = new JInternalFrame();
  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)
 114     {
 115       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 116       useOriginalColours.setSelected(
 117               acg.isPredefinedColours() || acg.getBaseColour() != null);
 118       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 119       {
 120         minColour.setBackground(acg.getMinColour());
 121         maxColour.setBackground(acg.getMaxColour());
 122       }
 123       seqAssociated.setSelected(acg.isSeqAssociated());
 124
 125     }
 126     Vector<String> annotItems = getAnnotationItems(
 127             seqAssociated.isSelected());
 128     annotations = new JComboBox<>(annotItems);
 129
 130     populateThresholdComboBox(threshold);
 131
 132     if (oldcs instanceof AnnotationColourGradient)
 133     {
 134       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 135       String label = getAnnotationMenuLabel(acg.getAnnotation());
 136       annotations.setSelectedItem(label);
 137       switch (acg.getAboveThreshold())
 138       {
 139       case AnnotationColourGradient.NO_THRESHOLD:
 140         getThreshold().setSelectedIndex(0);
 141         break;
 142       case AnnotationColourGradient.ABOVE_THRESHOLD:
 143         getThreshold().setSelectedIndex(1);
 144         break;
 145       case AnnotationColourGradient.BELOW_THRESHOLD:
 146         getThreshold().setSelectedIndex(2);
 147         break;
 148       default:
 149         throw new Error(MessageManager.getString(
 150                 "error.implementation_error_dont_know_about_threshold_setting"));
 151       }
 152       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 153       thresholdValue.setText("" + acg.getAnnotationThreshold());
 154     }
 155
 156     jbInit();
 157     adjusting = false;
 158
 159     updateView();
 160     frame.invalidate();
 161     frame.pack();
 162   }
 163
 164   /**
 165    * Saves the global and group colour schemes as they are when the dialog is
 166    * opened, so they can be restored on Cancel. Note we also save the threshold
 167    * value for each annotation, in case this gets modified.
 168    */
 169   void saveInitialState()
 170   {
 171     oldcs = av.getGlobalColourScheme();
 172     if (av.getAlignment().getGroups() != null)
 173     {
 174       oldgroupColours = new HashMap<>();
 175       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 176       {
 177         if (sg.getColourScheme() != null)
 178         {
 179           oldgroupColours.put(sg, sg.getColourScheme());
 180         }
 181       }
 182     }
 183
 184     /*
 185      * save any existing annotation threshold settings; note we make a copy
 186      * of each in case the current threshold value gets amended
 187      */
 188     oldGraphLines = new HashMap<>();
 189     oldThresholds = new HashMap<>();
 190     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 191     if (anns != null)
 192     {
 193       for (AlignmentAnnotation ann : anns)
 194       {
 195         GraphLine thresh = ann.getThreshold();
 196         oldGraphLines.put(ann, thresh);
 197         if (thresh != null)
 198         {
 199           oldThresholds.put(thresh, thresh.value);
 200         }
 201       }
 202     }
 203   }
 204
 205   @Override
 206   protected void jbInit()
 207   {
 208     super.jbInit();
 209
 210     minColour.setFont(JvSwingUtils.getLabelFont());
 211     minColour.setBorder(BorderFactory.createEtchedBorder());
 212     minColour.setPreferredSize(new Dimension(40, 20));
 213     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 214     minColour.addMouseListener(new MouseAdapter()
 215     {
 216       @Override
 217       public void mousePressed(MouseEvent e)
 218       {
 219         if (minColour.isEnabled())
 220         {
 221           minColour_actionPerformed();
 222         }
 223       }
 224     });
 225     maxColour.setFont(JvSwingUtils.getLabelFont());
 226     maxColour.setBorder(BorderFactory.createEtchedBorder());
 227     maxColour.setPreferredSize(new Dimension(40, 20));
 228     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 229     maxColour.addMouseListener(new MouseAdapter()
 230     {
 231       @Override
 232       public void mousePressed(MouseEvent e)
 233       {
 234         if (maxColour.isEnabled())
 235         {
 236           maxColour_actionPerformed();
 237         }
 238       }
 239     });
 240
 241     defColours = new JButton();
 242     defColours.setOpaque(false);
 243     defColours.setText(MessageManager.getString("action.set_defaults"));
 244     defColours.setToolTipText(MessageManager
 245             .getString("label.reset_min_max_colours_to_defaults"));
 246     defColours.addActionListener(new ActionListener()
 247     {
 248
 249       @Override
 250       public void actionPerformed(ActionEvent arg0)
 251       {
 252         resetColours_actionPerformed();
 253       }
 254     });
 255
 256     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 257     useOriginalColours.setOpaque(false);
 258     useOriginalColours.setText(
 259             MessageManager.getString("label.use_original_colours"));
 260     useOriginalColours.addActionListener(new ActionListener()
 261     {
 262       @Override
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         originalColours_actionPerformed();
 266       }
 267     });
 268     thresholdIsMin.setBackground(Color.white);
 269     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 270     thresholdIsMin
 271             .setText(MessageManager.getString("label.threshold_minmax"));
 272     thresholdIsMin.addActionListener(new ActionListener()
 273     {
 274       @Override
 275       public void actionPerformed(ActionEvent actionEvent)
 276       {
 277         thresholdIsMin_actionPerformed();
 278       }
 279     });
 280     seqAssociated.setBackground(Color.white);
 281     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 282     seqAssociated
 283             .setText(MessageManager.getString("label.per_sequence_only"));
 284     seqAssociated.addActionListener(new ActionListener()
 285     {
 286
 287       @Override
 288       public void actionPerformed(ActionEvent arg0)
 289       {
 290         seqAssociated_actionPerformed(annotations);
 291       }
 292     });
 293
 294     this.setLayout(new BorderLayout());
 295     JPanel jPanel1 = new JPanel();
 296     JPanel jPanel2 = new JPanel();
 297     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 298     jPanel1.setBackground(Color.white);
 299     jPanel2.setBackground(Color.white);
 300
 301     jPanel1.add(ok);
 302     jPanel1.add(cancel);
 303     jPanel2.add(annotations, "grow, wrap");
 304     jPanel2.add(seqAssociated);
 305     jPanel2.add(useOriginalColours);
 306     JPanel colpanel = new JPanel(new FlowLayout());
 307     colpanel.setBackground(Color.white);
 308     colpanel.add(minColour);
 309     colpanel.add(maxColour);
 310     jPanel2.add(colpanel, "wrap");
 311     jPanel2.add(getThreshold());
 312     jPanel2.add(defColours, "skip 1, wrap");
 313     jPanel2.add(thresholdIsMin);
 314     jPanel2.add(slider, "grow");
 315     jPanel2.add(thresholdValue, "grow");
 316     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 317     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 318     this.validate();
 319   }
 320
 321   protected void resetColours_actionPerformed()
 322   {
 323     setDefaultMinMax();
 324     updateView();
 325   }
 326
 327   private void setDefaultMinMax()
 328   {
 329     minColour.setBackground(
 330             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 331     maxColour.setBackground(
 332             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 333   }
 334
 335   public void minColour_actionPerformed()
 336   {
 337     Color col = JColorChooser.showDialog(this,
 338             MessageManager.getString("label.select_colour_minimum_value"),
 339             minColour.getBackground());
 340     if (col != null)
 341     {
 342       minColour.setBackground(col);
 343     }
 344     minColour.repaint();
 345     updateView();
 346   }
 347
 348   public void maxColour_actionPerformed()
 349   {
 350     Color col = JColorChooser.showDialog(this,
 351             MessageManager.getString("label.select_colour_maximum_value"),
 352             maxColour.getBackground());
 353     if (col != null)
 354     {
 355       maxColour.setBackground(col);
 356     }
 357     maxColour.repaint();
 358     updateView();
 359   }
 360
 361   @Override
 362   public void reset()
 363   {
 364     av.setGlobalColourScheme(oldcs);
 365     if (av.getAlignment().getGroups() != null)
 366     {
 367
 368       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 369       {
 370         sg.setColourScheme(oldgroupColours.get(sg));
 371       }
 372     }
 373     for (Entry<AlignmentAnnotation, GraphLine> entry : oldGraphLines
 374             .entrySet())
 375     {
 376       GraphLine graphLine = entry.getValue();
 377       entry.getKey().setThreshold(graphLine);
 378       if (graphLine != null)
 379       {
 380         graphLine.value = oldThresholds.get(graphLine).floatValue();
 381       }
 382     }
 383   }
 384
 385   @Override
 386   public void valueChanged(boolean updateAllAnnotation)
 387   {
 388     if (slider.isEnabled())
 389     {
 390       if (useOriginalColours.isSelected() && !(av
 391               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 392       {
 393         updateView();
 394       }
 395       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 396       propagateSeqAssociatedThreshold(updateAllAnnotation,
 397               getCurrentAnnotation());
 398       ap.paintAlignment(false, false);
 399     }
 400   }
 401
 402   public void originalColours_actionPerformed()
 403   {
 404     boolean selected = useOriginalColours.isSelected();
 405     if (selected)
 406     {
 407       reset();
 408     }
 409     maxColour.setEnabled(!selected);
 410     minColour.setEnabled(!selected);
 411     thresholdIsMin.setEnabled(!selected);
 412     updateView();
 413   }
 414
 415   @Override
 416   public void updateView()
 417   {
 418     // Check if combobox is still adjusting
 419     if (adjusting)
 420     {
 421       return;
 422     }
 423
 424     setCurrentAnnotation(
 425             av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 426                     .getSelectedIndex()]]);
 427
 428     int selectedThresholdItem = getSelectedThresholdItem(
 429             getThreshold().getSelectedIndex());
 430
 431     slider.setEnabled(true);
 432     thresholdValue.setEnabled(true);
 433     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 434
 435     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 436     {
 437       slider.setEnabled(false);
 438       thresholdValue.setEnabled(false);
 439       thresholdValue.setText("");
 440       thresholdIsMin.setEnabled(false);
 441     }
 442     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 443             && getCurrentAnnotation().threshold == null)
 444     {
 445       getCurrentAnnotation().setThreshold(new GraphLine(
 446               (getCurrentAnnotation().graphMax
 447                       - getCurrentAnnotation().graphMin) / 2f,
 448               "Threshold", Color.black));
 449     }
 450
 451     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 452     {
 453       adjusting = true;
 454       float range = getCurrentAnnotation().graphMax * ONETHOUSAND
 455               - getCurrentAnnotation().graphMin * ONETHOUSAND;
 456
 457       slider.setMinimum(
 458               (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
 459       slider.setMaximum(
 460               (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
 461       slider.setValue(
 462               (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
 463       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 464       slider.setMajorTickSpacing((int) (range / 10f));
 465       slider.setEnabled(true);
 466       thresholdValue.setEnabled(true);
 467       adjusting = false;
 468     }
 469     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 470
 471     ap.alignmentChanged();
 472   }
 473
 474   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 475           int selectedThresholdOption)
 476   {
 477
 478     AnnotationColourGradient acg = null;
 479     if (useOriginalColours.isSelected())
 480     {
 481       acg = new AnnotationColourGradient(currentAnn,
 482               av.getGlobalColourScheme(), selectedThresholdOption);
 483     }
 484     else
 485     {
 486       acg = new AnnotationColourGradient(currentAnn,
 487               minColour.getBackground(), maxColour.getBackground(),
 488               selectedThresholdOption);
 489     }
 490     acg.setSeqAssociated(seqAssociated.isSelected());
 491
 492     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 493     {
 494       acg.setPredefinedColours(true);
 495     }
 496
 497     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 498
 499     av.setGlobalColourScheme(acg);
 500
 501     if (av.getAlignment().getGroups() != null)
 502     {
 503
 504       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 505       {
 506         if (sg.cs == null)
 507         {
 508           continue;
 509         }
 510         sg.setColourScheme(
 511                 acg.getInstance(sg, ap.av.getHiddenRepSequences()));
 512       }
 513     }
 514   }
 515
 516   @Override
 517   protected void sliderDragReleased()
 518   {
 519     super.sliderDragReleased();
 520     ap.paintAlignment(true, true);
 521   }
 522
 523 }