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> oldThresholds;
  67
  68   private JCheckBox useOriginalColours = new JCheckBox();
  69
  70   private JPanel minColour = new JPanel();
  71
  72   private JPanel maxColour = new JPanel();
  73
  74   private JCheckBox thresholdIsMin = new JCheckBox();
  75
  76   protected static final int MIN_WIDTH = 500;
  77
  78   protected static final int MIN_HEIGHT = 240;
  79
  80   /**
  81    * Constructor
  82    *
  83    * @param av
  84    * @param ap
  85    */
  86   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  87   {
  88     super(av, ap);
  89
  90     saveInitialState();
  91
  92     frame = new JInternalFrame();
  93     frame.setContentPane(this);
  94     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  95     Desktop.addInternalFrame(frame,
  96             MessageManager.getString("label.colour_by_annotation"), 520,
  97             215);
  98     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
  99     addSliderChangeListener();
 100     addSliderMouseListeners();
 101
 102     if (av.getAlignment().getAlignmentAnnotation() == null)
 103     {
 104       return;
 105     }
 106
 107     // Always get default shading from preferences.
 108     setDefaultMinMax();
 109
 110     adjusting = true;
 111     if (oldcs instanceof AnnotationColourGradient)
 112     {
 113       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 114       useOriginalColours.setSelected(
 115               acg.isPredefinedColours() || acg.getBaseColour() != null);
 116       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 117       {
 118         minColour.setBackground(acg.getMinColour());
 119         maxColour.setBackground(acg.getMaxColour());
 120       }
 121       seqAssociated.setSelected(acg.isSeqAssociated());
 122
 123     }
 124     Vector<String> annotItems = getAnnotationItems(
 125             seqAssociated.isSelected());
 126     annotations = new JComboBox<>(annotItems);
 127
 128     populateThresholdComboBox(threshold);
 129
 130     if (oldcs instanceof AnnotationColourGradient)
 131     {
 132       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 133       String label = getAnnotationMenuLabel(acg.getAnnotation());
 134       annotations.setSelectedItem(label);
 135       switch (acg.getAboveThreshold())
 136       {
 137       case AnnotationColourGradient.NO_THRESHOLD:
 138         getThreshold().setSelectedIndex(0);
 139         break;
 140       case AnnotationColourGradient.ABOVE_THRESHOLD:
 141         getThreshold().setSelectedIndex(1);
 142         break;
 143       case AnnotationColourGradient.BELOW_THRESHOLD:
 144         getThreshold().setSelectedIndex(2);
 145         break;
 146       default:
 147         throw new Error(MessageManager.getString(
 148                 "error.implementation_error_dont_know_about_threshold_setting"));
 149       }
 150       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 151       thresholdValue.setText("" + acg.getAnnotationThreshold());
 152     }
 153
 154     jbInit();
 155     adjusting = false;
 156
 157     updateView();
 158     frame.invalidate();
 159     frame.pack();
 160   }
 161
 162   /**
 163    * Saves the global and group colour schemes as they are when the dialog is
 164    * opened, so they can be restored on Cancel. Note we also save the threshold
 165    * value for each annotation, in case this gets modified.
 166    */
 167   void saveInitialState()
 168   {
 169     oldcs = av.getGlobalColourScheme();
 170     if (av.getAlignment().getGroups() != null)
 171     {
 172       oldgroupColours = new HashMap<>();
 173       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 174       {
 175         if (sg.getColourScheme() != null)
 176         {
 177           oldgroupColours.put(sg, sg.getColourScheme());
 178         }
 179       }
 180     }
 181
 182     /*
 183      * save any existing annotation threshold settings; note we make a copy
 184      * of each in case the current threshold value gets amended
 185      */
 186     oldThresholds = new HashMap<>();
 187     AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
 188     if (anns != null)
 189     {
 190       for (AlignmentAnnotation ann : anns)
 191       {
 192         GraphLine thresh = ann.getThreshold();
 193         oldThresholds.put(ann,
 194                 thresh == null ? null : new GraphLine(thresh));
 195       }
 196     }
 197   }
 198
 199   @Override
 200   protected void jbInit()
 201   {
 202     super.jbInit();
 203
 204     minColour.setFont(JvSwingUtils.getLabelFont());
 205     minColour.setBorder(BorderFactory.createEtchedBorder());
 206     minColour.setPreferredSize(new Dimension(40, 20));
 207     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 208     minColour.addMouseListener(new MouseAdapter()
 209     {
 210       @Override
 211       public void mousePressed(MouseEvent e)
 212       {
 213         if (minColour.isEnabled())
 214         {
 215           minColour_actionPerformed();
 216         }
 217       }
 218     });
 219     maxColour.setFont(JvSwingUtils.getLabelFont());
 220     maxColour.setBorder(BorderFactory.createEtchedBorder());
 221     maxColour.setPreferredSize(new Dimension(40, 20));
 222     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 223     maxColour.addMouseListener(new MouseAdapter()
 224     {
 225       @Override
 226       public void mousePressed(MouseEvent e)
 227       {
 228         if (maxColour.isEnabled())
 229         {
 230           maxColour_actionPerformed();
 231         }
 232       }
 233     });
 234
 235     defColours = new JButton();
 236     defColours.setOpaque(false);
 237     defColours.setText(MessageManager.getString("action.set_defaults"));
 238     defColours.setToolTipText(MessageManager
 239             .getString("label.reset_min_max_colours_to_defaults"));
 240     defColours.addActionListener(new ActionListener()
 241     {
 242
 243       @Override
 244       public void actionPerformed(ActionEvent arg0)
 245       {
 246         resetColours_actionPerformed();
 247       }
 248     });
 249
 250     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 251     useOriginalColours.setOpaque(false);
 252     useOriginalColours.setText(
 253             MessageManager.getString("label.use_original_colours"));
 254     useOriginalColours.addActionListener(new ActionListener()
 255     {
 256       @Override
 257       public void actionPerformed(ActionEvent e)
 258       {
 259         originalColours_actionPerformed();
 260       }
 261     });
 262     thresholdIsMin.setBackground(Color.white);
 263     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 264     thresholdIsMin
 265             .setText(MessageManager.getString("label.threshold_minmax"));
 266     thresholdIsMin.addActionListener(new ActionListener()
 267     {
 268       @Override
 269       public void actionPerformed(ActionEvent actionEvent)
 270       {
 271         thresholdIsMin_actionPerformed();
 272       }
 273     });
 274     seqAssociated.setBackground(Color.white);
 275     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 276     seqAssociated
 277             .setText(MessageManager.getString("label.per_sequence_only"));
 278     seqAssociated.addActionListener(new ActionListener()
 279     {
 280
 281       @Override
 282       public void actionPerformed(ActionEvent arg0)
 283       {
 284         seqAssociated_actionPerformed(annotations);
 285       }
 286     });
 287
 288     this.setLayout(new BorderLayout());
 289     JPanel jPanel1 = new JPanel();
 290     JPanel jPanel2 = new JPanel();
 291     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 292     jPanel1.setBackground(Color.white);
 293     jPanel2.setBackground(Color.white);
 294
 295     jPanel1.add(ok);
 296     jPanel1.add(cancel);
 297     jPanel2.add(annotations, "grow, wrap");
 298     jPanel2.add(seqAssociated);
 299     jPanel2.add(useOriginalColours);
 300     JPanel colpanel = new JPanel(new FlowLayout());
 301     colpanel.setBackground(Color.white);
 302     colpanel.add(minColour);
 303     colpanel.add(maxColour);
 304     jPanel2.add(colpanel, "wrap");
 305     jPanel2.add(getThreshold());
 306     jPanel2.add(defColours, "skip 1, wrap");
 307     jPanel2.add(thresholdIsMin);
 308     jPanel2.add(slider, "grow");
 309     jPanel2.add(thresholdValue, "grow");
 310     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 311     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 312     this.validate();
 313   }
 314
 315   protected void resetColours_actionPerformed()
 316   {
 317     setDefaultMinMax();
 318     updateView();
 319   }
 320
 321   private void setDefaultMinMax()
 322   {
 323     minColour.setBackground(
 324             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 325     maxColour.setBackground(
 326             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 327   }
 328
 329   public void minColour_actionPerformed()
 330   {
 331     Color col = JColorChooser.showDialog(this,
 332             MessageManager.getString("label.select_colour_minimum_value"),
 333             minColour.getBackground());
 334     if (col != null)
 335     {
 336       minColour.setBackground(col);
 337     }
 338     minColour.repaint();
 339     updateView();
 340   }
 341
 342   public void maxColour_actionPerformed()
 343   {
 344     Color col = JColorChooser.showDialog(this,
 345             MessageManager.getString("label.select_colour_maximum_value"),
 346             maxColour.getBackground());
 347     if (col != null)
 348     {
 349       maxColour.setBackground(col);
 350     }
 351     maxColour.repaint();
 352     updateView();
 353   }
 354
 355   @Override
 356   public void reset()
 357   {
 358     av.setGlobalColourScheme(oldcs);
 359     if (av.getAlignment().getGroups() != null)
 360     {
 361
 362       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 363       {
 364         sg.setColourScheme(oldgroupColours.get(sg));
 365       }
 366     }
 367     for (Entry<AlignmentAnnotation, GraphLine> entry : oldThresholds
 368             .entrySet())
 369     {
 370       entry.getKey().setThreshold(entry.getValue());
 371     }
 372   }
 373
 374   @Override
 375   public void valueChanged(boolean updateAllAnnotation)
 376   {
 377     if (slider.isEnabled())
 378     {
 379       if (useOriginalColours.isSelected() && !(av
 380               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 381       {
 382         updateView();
 383       }
 384       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 385       propagateSeqAssociatedThreshold(updateAllAnnotation,
 386               getCurrentAnnotation());
 387       ap.paintAlignment(false, false);
 388     }
 389   }
 390
 391   public void originalColours_actionPerformed()
 392   {
 393     boolean selected = useOriginalColours.isSelected();
 394     if (selected)
 395     {
 396       reset();
 397     }
 398     maxColour.setEnabled(!selected);
 399     minColour.setEnabled(!selected);
 400     thresholdIsMin.setEnabled(!selected);
 401     updateView();
 402   }
 403
 404   @Override
 405   public void updateView()
 406   {
 407     // Check if combobox is still adjusting
 408     if (adjusting)
 409     {
 410       return;
 411     }
 412
 413     setCurrentAnnotation(
 414             av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 415                     .getSelectedIndex()]]);
 416
 417     int selectedThresholdItem = getSelectedThresholdItem(
 418             getThreshold().getSelectedIndex());
 419
 420     slider.setEnabled(true);
 421     thresholdValue.setEnabled(true);
 422     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 423
 424     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 425     {
 426       slider.setEnabled(false);
 427       thresholdValue.setEnabled(false);
 428       thresholdValue.setText("");
 429       thresholdIsMin.setEnabled(false);
 430     }
 431     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 432             && getCurrentAnnotation().threshold == null)
 433     {
 434       getCurrentAnnotation().setThreshold(new GraphLine(
 435               (getCurrentAnnotation().graphMax
 436                       - getCurrentAnnotation().graphMin) / 2f,
 437               "Threshold", Color.black));
 438     }
 439
 440     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 441     {
 442       adjusting = true;
 443       float range = getCurrentAnnotation().graphMax * ONETHOUSAND
 444               - getCurrentAnnotation().graphMin * ONETHOUSAND;
 445
 446       slider.setMinimum(
 447               (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
 448       slider.setMaximum(
 449               (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
 450       slider.setValue(
 451               (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
 452       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 453       slider.setMajorTickSpacing((int) (range / 10f));
 454       slider.setEnabled(true);
 455       thresholdValue.setEnabled(true);
 456       adjusting = false;
 457     }
 458     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 459
 460     ap.alignmentChanged();
 461   }
 462
 463   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 464           int selectedThresholdOption)
 465   {
 466
 467     AnnotationColourGradient acg = null;
 468     if (useOriginalColours.isSelected())
 469     {
 470       acg = new AnnotationColourGradient(currentAnn,
 471               av.getGlobalColourScheme(), selectedThresholdOption);
 472     }
 473     else
 474     {
 475       acg = new AnnotationColourGradient(currentAnn,
 476               minColour.getBackground(), maxColour.getBackground(),
 477               selectedThresholdOption);
 478     }
 479     acg.setSeqAssociated(seqAssociated.isSelected());
 480
 481     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 482     {
 483       acg.setPredefinedColours(true);
 484     }
 485
 486     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 487
 488     av.setGlobalColourScheme(acg);
 489
 490     if (av.getAlignment().getGroups() != null)
 491     {
 492
 493       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 494       {
 495         if (sg.cs == null)
 496         {
 497           continue;
 498         }
 499         sg.setColourScheme(
 500                 acg.getInstance(sg, ap.av.getHiddenRepSequences()));
 501       }
 502     }
 503   }
 504
 505   @Override
 506   protected void sliderDragReleased()
 507   {
 508     super.sliderDragReleased();
 509     ap.paintAlignment(true, true);
 510   }
 511
 512 }