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