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.Hashtable;
  40 import java.util.Vector;
  41
  42 import javax.swing.BorderFactory;
  43 import javax.swing.JButton;
  44 import javax.swing.JCheckBox;
  45 import javax.swing.JColorChooser;
  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   private JPanel minColour = new JPanel();
  67
  68   private 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           minColour_actionPerformed();
 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           maxColour_actionPerformed();
 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   public void minColour_actionPerformed()
 292   {
 293     Color col = JColorChooser.showDialog(this,
 294             MessageManager.getString("label.select_colour_minimum_value"),
 295             minColour.getBackground());
 296     if (col != null)
 297     {
 298       minColour.setBackground(col);
 299     }
 300     minColour.repaint();
 301     updateView();
 302   }
 303
 304   public void maxColour_actionPerformed()
 305   {
 306     Color col = JColorChooser.showDialog(this,
 307             MessageManager.getString("label.select_colour_maximum_value"),
 308             maxColour.getBackground());
 309     if (col != null)
 310     {
 311       maxColour.setBackground(col);
 312     }
 313     maxColour.repaint();
 314     updateView();
 315   }
 316
 317   @Override
 318   public void reset()
 319   {
 320     av.setGlobalColourScheme(oldcs);
 321     if (av.getAlignment().getGroups() != null)
 322     {
 323
 324       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 325       {
 326         sg.setColourScheme(oldgroupColours.get(sg));
 327       }
 328     }
 329   }
 330
 331   @Override
 332   public void valueChanged(boolean updateAllAnnotation)
 333   {
 334     if (slider.isEnabled())
 335     {
 336       if (useOriginalColours.isSelected() && !(av
 337               .getGlobalColourScheme() instanceof AnnotationColourGradient))
 338       {
 339         updateView();
 340       }
 341       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 342       propagateSeqAssociatedThreshold(updateAllAnnotation,
 343               getCurrentAnnotation());
 344       ap.paintAlignment(false, false);
 345     }
 346   }
 347
 348   public void originalColours_actionPerformed()
 349   {
 350     boolean selected = useOriginalColours.isSelected();
 351     if (selected)
 352     {
 353       reset();
 354     }
 355     maxColour.setEnabled(!selected);
 356     minColour.setEnabled(!selected);
 357     thresholdIsMin.setEnabled(!selected);
 358     updateView();
 359   }
 360
 361   @Override
 362   public void updateView()
 363   {
 364     // Check if combobox is still adjusting
 365     if (adjusting)
 366     {
 367       return;
 368     }
 369
 370     setCurrentAnnotation(
 371             av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 372                     .getSelectedIndex()]]);
 373
 374     int selectedThresholdItem = getSelectedThresholdItem(
 375             getThreshold().getSelectedIndex());
 376
 377     slider.setEnabled(true);
 378     thresholdValue.setEnabled(true);
 379     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 380
 381     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 382     {
 383       slider.setEnabled(false);
 384       thresholdValue.setEnabled(false);
 385       thresholdValue.setText("");
 386       thresholdIsMin.setEnabled(false);
 387     }
 388     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 389             && getCurrentAnnotation().threshold == null)
 390     {
 391       getCurrentAnnotation().setThreshold(new GraphLine(
 392               (getCurrentAnnotation().graphMax
 393                       - getCurrentAnnotation().graphMin) / 2f,
 394               "Threshold", Color.black));
 395     }
 396
 397     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 398     {
 399       adjusting = true;
 400       float range = getCurrentAnnotation().graphMax * ONETHOUSAND
 401               - getCurrentAnnotation().graphMin * ONETHOUSAND;
 402
 403       slider.setMinimum(
 404               (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
 405       slider.setMaximum(
 406               (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
 407       slider.setValue(
 408               (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
 409       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 410       slider.setMajorTickSpacing((int) (range / 10f));
 411       slider.setEnabled(true);
 412       thresholdValue.setEnabled(true);
 413       adjusting = false;
 414     }
 415     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 416
 417     ap.alignmentChanged();
 418   }
 419
 420   protected void colorAlignmentContaining(AlignmentAnnotation currentAnn,
 421           int selectedThresholdOption)
 422   {
 423
 424     AnnotationColourGradient acg = null;
 425     if (useOriginalColours.isSelected())
 426     {
 427       acg = new AnnotationColourGradient(currentAnn,
 428               av.getGlobalColourScheme(), selectedThresholdOption);
 429     }
 430     else
 431     {
 432       acg = new AnnotationColourGradient(currentAnn,
 433               minColour.getBackground(), maxColour.getBackground(),
 434               selectedThresholdOption);
 435     }
 436     acg.setSeqAssociated(seqAssociated.isSelected());
 437
 438     if (currentAnn.graphMin == 0f && currentAnn.graphMax == 0f)
 439     {
 440       acg.setPredefinedColours(true);
 441     }
 442
 443     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 444
 445     av.setGlobalColourScheme(acg);
 446
 447     if (av.getAlignment().getGroups() != null)
 448     {
 449
 450       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 451       {
 452         if (sg.cs == null)
 453         {
 454           continue;
 455         }
 456         sg.setColourScheme(
 457                 acg.getInstance(sg, ap.av.getHiddenRepSequences()));
 458       }
 459     }
 460   }
 461
 462 }