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.gui.JalviewColourChooser.ColourChooserListener;
  28 import jalview.schemes.AnnotationColourGradient;
  29 import jalview.schemes.ColourSchemeI;
  30 import jalview.util.MessageManager;
  31
  32 import java.awt.BorderLayout;
  33 import java.awt.Color;
  34 import java.awt.Dimension;
  35 import java.awt.FlowLayout;
  36 import java.awt.event.ActionEvent;
  37 import java.awt.event.ActionListener;
  38 import java.awt.event.MouseAdapter;
  39 import java.awt.event.MouseEvent;
  40 import java.util.Hashtable;
  41 import java.util.Vector;
  42
  43 import javax.swing.BorderFactory;
  44 import javax.swing.JButton;
  45 import javax.swing.JCheckBox;
  46 import javax.swing.JComboBox;
  47 import javax.swing.JInternalFrame;
  48 import javax.swing.JLayeredPane;
  49 import javax.swing.JPanel;
  50
  51 import net.miginfocom.swing.MigLayout;
  52
  53 @SuppressWarnings("serial")
  54 public class AnnotationColourChooser extends AnnotationRowFilter
  55 {
  56   private static final int ONETHOUSAND = 1000;
  57
  58   private ColourSchemeI oldcs;
  59
  60   private JButton defColours;
  61
  62   private Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  63
  64   private JCheckBox useOriginalColours = new JCheckBox();
  65
  66   JPanel minColour = new JPanel();
  67
  68   JPanel maxColour = new JPanel();
  69
  70   private JCheckBox thresholdIsMin = new JCheckBox();
  71
  72   protected static final int MIN_WIDTH = 500;
  73
  74   protected static final int MIN_HEIGHT = 240;
  75
  76   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  77   {
  78     super(av, ap);
  79     oldcs = av.getGlobalColourScheme();
  80     if (av.getAlignment().getGroups() != null)
  81     {
  82       oldgroupColours = new Hashtable<>();
  83       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  84       {
  85         if (sg.getColourScheme() != null)
  86         {
  87           oldgroupColours.put(sg, sg.getColourScheme());
  88         }
  89       }
  90     }
  91     frame = new JInternalFrame();
  92     frame.setContentPane(this);
  93     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  94     Desktop.addInternalFrame(frame,
  95             MessageManager.getString("label.colour_by_annotation"), 520,
  96             215);
  97     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
  98     addSliderChangeListener();
  99     addSliderMouseListeners();
 100
 101     if (av.getAlignment().getAlignmentAnnotation() == null)
 102     {
 103       return;
 104     }
 105
 106     // Always get default shading from preferences.
 107     setDefaultMinMax();
 108
 109     adjusting = true;
 110     if (oldcs instanceof AnnotationColourGradient)
 111     {
 112       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 113       useOriginalColours.setSelected(
 114               acg.isPredefinedColours() || acg.getBaseColour() != null);
 115       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 116       {
 117         minColour.setBackground(acg.getMinColour());
 118         maxColour.setBackground(acg.getMaxColour());
 119       }
 120       seqAssociated.setSelected(acg.isSeqAssociated());
 121
 122     }
 123     Vector<String> annotItems = getAnnotationItems(
 124             seqAssociated.isSelected());
 125     annotations = new JComboBox<>(annotItems);
 126
 127     populateThresholdComboBox(threshold);
 128
 129     if (oldcs instanceof AnnotationColourGradient)
 130     {
 131       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 132       String label = getAnnotationMenuLabel(acg.getAnnotation());
 133       annotations.setSelectedItem(label);
 134       switch (acg.getAboveThreshold())
 135       {
 136       case AnnotationColourGradient.NO_THRESHOLD:
 137         getThreshold().setSelectedIndex(0);
 138         break;
 139       case AnnotationColourGradient.ABOVE_THRESHOLD:
 140         getThreshold().setSelectedIndex(1);
 141         break;
 142       case AnnotationColourGradient.BELOW_THRESHOLD:
 143         getThreshold().setSelectedIndex(2);
 144         break;
 145       default:
 146         throw new Error(MessageManager.getString(
 147                 "error.implementation_error_dont_know_about_threshold_setting"));
 148       }
 149       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 150       thresholdValue.setText("" + acg.getAnnotationThreshold());
 151     }
 152
 153     jbInit();
 154     adjusting = false;
 155
 156     updateView();
 157     frame.invalidate();
 158     frame.pack();
 159   }
 160
 161   @Override
 162   protected void jbInit()
 163   {
 164     super.jbInit();
 165
 166     minColour.setFont(JvSwingUtils.getLabelFont());
 167     minColour.setBorder(BorderFactory.createEtchedBorder());
 168     minColour.setPreferredSize(new Dimension(40, 20));
 169     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 170     minColour.addMouseListener(new MouseAdapter()
 171     {
 172       @Override
 173       public void mousePressed(MouseEvent e)
 174       {
 175         if (minColour.isEnabled())
 176         {
 177           showColourChooser(minColour, "label.select_colour_minimum_value");
 178         }
 179       }
 180     });
 181     maxColour.setFont(JvSwingUtils.getLabelFont());
 182     maxColour.setBorder(BorderFactory.createEtchedBorder());
 183     maxColour.setPreferredSize(new Dimension(40, 20));
 184     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 185     maxColour.addMouseListener(new MouseAdapter()
 186     {
 187       @Override
 188       public void mousePressed(MouseEvent e)
 189       {
 190         if (maxColour.isEnabled())
 191         {
 192           showColourChooser(maxColour, "label.select_colour_maximum_value");
 193         }
 194       }
 195     });
 196
 197     defColours = new JButton();
 198     defColours.setOpaque(false);
 199     defColours.setText(MessageManager.getString("action.set_defaults"));
 200     defColours.setToolTipText(MessageManager
 201             .getString("label.reset_min_max_colours_to_defaults"));
 202     defColours.addActionListener(new ActionListener()
 203     {
 204
 205       @Override
 206       public void actionPerformed(ActionEvent arg0)
 207       {
 208         resetColours_actionPerformed();
 209       }
 210     });
 211
 212     useOriginalColours.setFont(JvSwingUtils.getLabelFont());
 213     useOriginalColours.setOpaque(false);
 214     useOriginalColours.setText(
 215             MessageManager.getString("label.use_original_colours"));
 216     useOriginalColours.addActionListener(new ActionListener()
 217     {
 218       @Override
 219       public void actionPerformed(ActionEvent e)
 220       {
 221         originalColours_actionPerformed();
 222       }
 223     });
 224     thresholdIsMin.setBackground(Color.white);
 225     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 226     thresholdIsMin
 227             .setText(MessageManager.getString("label.threshold_minmax"));
 228     thresholdIsMin.addActionListener(new ActionListener()
 229     {
 230       @Override
 231       public void actionPerformed(ActionEvent actionEvent)
 232       {
 233         thresholdIsMin_actionPerformed();
 234       }
 235     });
 236     seqAssociated.setBackground(Color.white);
 237     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 238     seqAssociated
 239             .setText(MessageManager.getString("label.per_sequence_only"));
 240     seqAssociated.addActionListener(new ActionListener()
 241     {
 242
 243       @Override
 244       public void actionPerformed(ActionEvent arg0)
 245       {
 246         seqAssociated_actionPerformed(annotations);
 247       }
 248     });
 249
 250     this.setLayout(new BorderLayout());
 251     JPanel jPanel1 = new JPanel();
 252     JPanel jPanel2 = new JPanel();
 253     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 254     jPanel1.setBackground(Color.white);
 255     jPanel2.setBackground(Color.white);
 256
 257     jPanel1.add(ok);
 258     jPanel1.add(cancel);
 259     jPanel2.add(annotations, "grow, wrap");
 260     jPanel2.add(seqAssociated);
 261     jPanel2.add(useOriginalColours);
 262     JPanel colpanel = new JPanel(new FlowLayout());
 263     colpanel.setBackground(Color.white);
 264     colpanel.add(minColour);
 265     colpanel.add(maxColour);
 266     jPanel2.add(colpanel, "wrap");
 267     jPanel2.add(getThreshold());
 268     jPanel2.add(defColours, "skip 1, wrap");
 269     jPanel2.add(thresholdIsMin);
 270     jPanel2.add(slider, "grow");
 271     jPanel2.add(thresholdValue, "grow");
 272     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 273     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 274     this.validate();
 275   }
 276
 277   protected void resetColours_actionPerformed()
 278   {
 279     setDefaultMinMax();
 280     updateView();
 281   }
 282
 283   private void setDefaultMinMax()
 284   {
 285     minColour.setBackground(
 286             Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
 287     maxColour.setBackground(
 288             Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
 289   }
 290
 291   protected void showColourChooser(JPanel colourPanel, String titleKey)
 292   {
 293     String ttl = MessageManager.getString(titleKey);
 294     ColourChooserListener listener = new ColourChooserListener()
 295     {
 296       @Override
 297       public void colourSelected(Color c)
 298       {
 299         colourPanel.setBackground(c);
 300         colourPanel.repaint();
 301         updateView();
 302       }
 303     };
 304     JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(), ttl,
 305             colourPanel.getBackground(), listener);
 306   }
 307
 308   @Override
 309   public void reset()
 310   {
 311     this.ap.alignFrame.changeColour(oldcs);
 312     if (av.getAlignment().getGroups() != null)
 313     {
 314
 315       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 316       {
 317         sg.setColourScheme(oldgroupColours.get(sg));
 318       }
 319     }
 320   }
 321
 322   @Override
 323   public void valueChanged(boolean updateAllAnnotation)
 324   {
 325     if (slider.isEnabled())
 326     {
 327       if (useOriginalColours.isSelected() && !(av
 328               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 329       {
 330         updateView();
 331       }
 332       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 333       propagateSeqAssociatedThreshold(updateAllAnnotation,
 334               getCurrentAnnotation());
 335       ap.paintAlignment(false, false);
 336     }
 337   }
 338
 339   public void originalColours_actionPerformed()
 340   {
 341     boolean selected = useOriginalColours.isSelected();
 342     if (selected)
 343     {
 344       reset();
 345     }
 346     maxColour.setEnabled(!selected);
 347     minColour.setEnabled(!selected);
 348     thresholdIsMin.setEnabled(!selected);
 349     updateView();
 350   }
 351
 352   @Override
 353   public void updateView()
 354   {
 355     // Check if combobox is still adjusting
 356     if (adjusting)
 357     {
 358       return;
 359     }
 360
 361     setCurrentAnnotation(
 362             av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 363                     .getSelectedIndex()]]);
 364
 365     int selectedThresholdItem = getSelectedThresholdItem(
 366             getThreshold().getSelectedIndex());
 367
 368     slider.setEnabled(true);
 369     thresholdValue.setEnabled(true);
 370     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 371
 372     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 373     {
 374       slider.setEnabled(false);
 375       thresholdValue.setEnabled(false);
 376       thresholdValue.setText("");
 377       thresholdIsMin.setEnabled(false);
 378     }
 379     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 380             && getCurrentAnnotation().threshold == null)
 381     {
 382       getCurrentAnnotation().setThreshold(new GraphLine(
 383               (getCurrentAnnotation().graphMax
 384                       - getCurrentAnnotation().graphMin) / 2f,
 385               "Threshold", Color.black));
 386     }
 387
 388     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 389     {
 390       adjusting = true;
 391       float range = getCurrentAnnotation().graphMax * ONETHOUSAND
 392               - getCurrentAnnotation().graphMin * ONETHOUSAND;
 393
 394       slider.setMinimum(
 395               (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
 396       slider.setMaximum(
 397               (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
 398       slider.setValue(
 399               (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
 400       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 401       slider.setMajorTickSpacing((int) (range / 10f));
 402       slider.setEnabled(true);
 403       thresholdValue.setEnabled(true);
 404       adjusting = false;
 405     }
 406     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 407
 408     ap.alignmentChanged();
 409   }
 410
 411   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 412           int selectedThresholdOption)
 413   {
 414
 415     AnnotationColourGradient acg = null;
 416     if (useOriginalColours.isSelected())
 417     {
 418       acg = new AnnotationColourGradient(currentAnn,
 419               av.getGlobalColourScheme(), selectedThresholdOption);
 420     }
 421     else
 422     {
 423       acg = new AnnotationColourGradient(currentAnn,
 424               minColour.getBackground(), maxColour.getBackground(),
 425               selectedThresholdOption);
 426     }
 427     acg.setSeqAssociated(seqAssociated.isSelected());
 428
 429     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 430     {
 431       acg.setPredefinedColours(true);
 432     }
 433
 434     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 435
 436     this.ap.alignFrame.changeColour(acg);
 437
 438     if (av.getAlignment().getGroups() != null)
 439     {
 440
 441       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 442       {
 443         if (sg.cs == null)
 444         {
 445           continue;
 446         }
 447         sg.setColourScheme(
 448                 acg.getInstance(av, sg));
 449       }
 450     }
 451   }
 452
 453   @Override
 454   protected void sliderDragReleased()
 455   {
 456     super.sliderDragReleased();
 457     ap.paintAlignment(true, true);
 458   }
 459 }