src/jalview/gui/AnnotationColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 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.SequenceGroup;
  25 import jalview.schemes.AnnotationColourGradient;
  26 import jalview.schemes.ColourSchemeI;
  27 import jalview.util.MessageManager;
  28
  29 import java.awt.BorderLayout;
  30 import java.awt.Color;
  31 import java.awt.Dimension;
  32 import java.awt.FlowLayout;
  33 import java.awt.event.ActionEvent;
  34 import java.awt.event.ActionListener;
  35 import java.awt.event.MouseAdapter;
  36 import java.awt.event.MouseEvent;
  37 import java.util.Hashtable;
  38
  39 import javax.swing.BorderFactory;
  40 import javax.swing.JButton;
  41 import javax.swing.JColorChooser;
  42 import javax.swing.JComboBox;
  43 import javax.swing.JInternalFrame;
  44 import javax.swing.JLayeredPane;
  45 import javax.swing.JPanel;
  46
  47 import net.miginfocom.swing.MigLayout;
  48
  49 @SuppressWarnings("serial")
  50 public class AnnotationColourChooser extends AnnotationRowFilter
  51 {
  52
  53   ColourSchemeI oldcs;
  54
  55   Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  56
  57   /**
  58    * enabled if the user is dragging the slider - try to keep updates to a
  59    * minimun
  60    */
  61
  62   JComboBox<String> annotations;
  63
  64   JButton defColours = new JButton();
  65
  66
  67   JPanel jPanel1 = new JPanel();
  68
  69   JPanel jPanel2 = new JPanel();
  70
  71   BorderLayout borderLayout1 = new BorderLayout();
  72
  73   private JComboBox<String> threshold = new JComboBox<String>();
  74
  75   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  76   {
  77     super(av, ap);
  78     oldcs = av.getGlobalColourScheme();
  79     if (av.getAlignment().getGroups() != null)
  80     {
  81       oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
  82       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  83       {
  84         if (sg.cs != null)
  85         {
  86           oldgroupColours.put(sg, sg.cs);
  87         }
  88       }
  89     }
  90     frame = new JInternalFrame();
  91     frame.setContentPane(this);
  92     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  93     Desktop.addInternalFrame(frame,
  94             MessageManager.getString("label.colour_by_annotation"), 520,
  95             215);
  96
  97     addSliderChangeListener();
  98     addSliderMouseListeners();
  99
 100     if (av.getAlignment().getAlignmentAnnotation() == null)
 101     {
 102       return;
 103     }
 104
 105     // Always get default shading from preferences.
 106     setDefaultMinMax();
 107
 108     adjusting = true;
 109     if (oldcs instanceof AnnotationColourGradient)
 110     {
 111       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 112       currentColours.setSelected(acg.isPredefinedColours()
 113               || acg.getBaseColour() != null);
 114       if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
 115       {
 116         minColour.setBackground(acg.getMinColour());
 117         maxColour.setBackground(acg.getMaxColour());
 118       }
 119       seqAssociated.setSelected(acg.isSeqAssociated());
 120
 121     }
 122     annotations = new JComboBox<String>(
 123             getAnnotationItems(seqAssociated.isSelected()));
 124
 125     populateThresholdComboBox(threshold);
 126
 127     if (oldcs instanceof AnnotationColourGradient)
 128     {
 129       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 130       annotations.setSelectedItem(acg.getAnnotation());
 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("error.implementation_error_dont_know_about_thereshold_setting"));
 144       }
 145       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 146       thresholdValue.setText("" + acg.getAnnotationThreshold());
 147     }
 148
 149     try
 150     {
 151       jbInit();
 152     } catch (Exception ex)
 153     {
 154     }
 155     adjusting = false;
 156
 157     updateView();
 158     frame.invalidate();
 159     frame.pack();
 160   }
 161
 162   public AnnotationColourChooser()
 163   {
 164     try
 165     {
 166       jbInit();
 167     } catch (Exception ex)
 168     {
 169       ex.printStackTrace();
 170     }
 171   }
 172
 173   private void jbInit() throws Exception
 174   {
 175     minColour.setFont(JvSwingUtils.getLabelFont());
 176     minColour.setBorder(BorderFactory.createEtchedBorder());
 177     minColour.setPreferredSize(new Dimension(40, 20));
 178     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 179     minColour.addMouseListener(new MouseAdapter()
 180     {
 181       @Override
 182       public void mousePressed(MouseEvent e)
 183       {
 184         if (minColour.isEnabled())
 185         {
 186           minColour_actionPerformed();
 187         }
 188       }
 189     });
 190     maxColour.setFont(JvSwingUtils.getLabelFont());
 191     maxColour.setBorder(BorderFactory.createEtchedBorder());
 192     maxColour.setPreferredSize(new Dimension(40, 20));
 193     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 194     maxColour.addMouseListener(new MouseAdapter()
 195     {
 196       @Override
 197       public void mousePressed(MouseEvent e)
 198       {
 199         if (maxColour.isEnabled())
 200         {
 201           maxColour_actionPerformed();
 202         }
 203       }
 204     });
 205     ok.setOpaque(false);
 206     ok.setText(MessageManager.getString("action.ok"));
 207     ok.addActionListener(new ActionListener()
 208     {
 209       @Override
 210       public void actionPerformed(ActionEvent e)
 211       {
 212         ok_actionPerformed(e);
 213       }
 214     });
 215     cancel.setOpaque(false);
 216     cancel.setText(MessageManager.getString("action.cancel"));
 217     cancel.addActionListener(new ActionListener()
 218     {
 219       @Override
 220       public void actionPerformed(ActionEvent e)
 221       {
 222         cancel_actionPerformed(e);
 223       }
 224     });
 225     defColours.setOpaque(false);
 226     defColours.setText(MessageManager.getString("action.set_defaults"));
 227     defColours.setToolTipText(MessageManager
 228             .getString("label.reset_min_max_colours_to_defaults"));
 229     defColours.addActionListener(new ActionListener()
 230     {
 231
 232       @Override
 233       public void actionPerformed(ActionEvent arg0)
 234       {
 235         resetColours_actionPerformed(arg0);
 236       }
 237     });
 238
 239     annotations.addActionListener(new ActionListener()
 240     {
 241       @Override
 242       public void actionPerformed(ActionEvent e)
 243       {
 244         annotations_actionPerformed(e);
 245       }
 246     });
 247     getThreshold().addActionListener(new ActionListener()
 248     {
 249       @Override
 250       public void actionPerformed(ActionEvent e)
 251       {
 252         threshold_actionPerformed(e);
 253       }
 254     });
 255     thresholdValue.addActionListener(new ActionListener()
 256     {
 257       @Override
 258       public void actionPerformed(ActionEvent e)
 259       {
 260         thresholdValue_actionPerformed(e);
 261       }
 262     });
 263     slider.setPaintLabels(false);
 264     slider.setPaintTicks(true);
 265     slider.setBackground(Color.white);
 266     slider.setEnabled(false);
 267     slider.setOpaque(false);
 268     slider.setPreferredSize(new Dimension(100, 32));
 269     thresholdValue.setEnabled(false);
 270     thresholdValue.setColumns(7);
 271     currentColours.setFont(JvSwingUtils.getLabelFont());
 272     currentColours.setOpaque(false);
 273     currentColours.setText(MessageManager
 274             .getString("label.use_original_colours"));
 275     currentColours.addActionListener(new ActionListener()
 276     {
 277       @Override
 278       public void actionPerformed(ActionEvent e)
 279       {
 280         currentColours_actionPerformed(e);
 281       }
 282     });
 283     thresholdIsMin.setBackground(Color.white);
 284     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 285     thresholdIsMin.setText(MessageManager
 286             .getString("label.threshold_minmax"));
 287     thresholdIsMin.addActionListener(new ActionListener()
 288     {
 289       @Override
 290       public void actionPerformed(ActionEvent actionEvent)
 291       {
 292         thresholdIsMin_actionPerformed(actionEvent);
 293       }
 294     });
 295     seqAssociated.setBackground(Color.white);
 296     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 297     seqAssociated.setText(MessageManager
 298             .getString("label.per_sequence_only"));
 299     seqAssociated.addActionListener(new ActionListener()
 300     {
 301
 302       @Override
 303       public void actionPerformed(ActionEvent arg0)
 304       {
 305         seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
 306       }
 307     });
 308
 309     this.setLayout(borderLayout1);
 310     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 311     jPanel1.setBackground(Color.white);
 312     jPanel2.setBackground(Color.white);
 313
 314     jPanel1.add(ok);
 315     jPanel1.add(cancel);
 316     jPanel2.add(annotations, "grow, wrap");
 317     jPanel2.add(seqAssociated);
 318     jPanel2.add(currentColours);
 319     JPanel colpanel = new JPanel(new FlowLayout());
 320     colpanel.setBackground(Color.white);
 321     colpanel.add(minColour);
 322     colpanel.add(maxColour);
 323     jPanel2.add(colpanel, "wrap");
 324     jPanel2.add(getThreshold());
 325     jPanel2.add(defColours, "skip 1, wrap");
 326     jPanel2.add(thresholdIsMin);
 327     jPanel2.add(slider, "grow");
 328     jPanel2.add(thresholdValue, "grow");
 329     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 330     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 331     this.validate();
 332   }
 333
 334   protected void resetColours_actionPerformed(ActionEvent arg0)
 335   {
 336     setDefaultMinMax();
 337     updateView();
 338   }
 339
 340   private void setDefaultMinMax()
 341   {
 342     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 343             Color.orange));
 344     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 345             Color.red));
 346   }
 347
 348   public void minColour_actionPerformed()
 349   {
 350     Color col = JColorChooser.showDialog(this,
 351             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 352     if (col != null)
 353     {
 354       minColour.setBackground(col);
 355     }
 356     minColour.repaint();
 357     updateView();
 358   }
 359
 360   public void maxColour_actionPerformed()
 361   {
 362     Color col = JColorChooser.showDialog(this,
 363             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 364     if (col != null)
 365     {
 366       maxColour.setBackground(col);
 367     }
 368     maxColour.repaint();
 369     updateView();
 370   }
 371
 372   public void reset()
 373   {
 374     av.setGlobalColourScheme(oldcs);
 375     if (av.getAlignment().getGroups() != null)
 376     {
 377
 378       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 379       {
 380         sg.cs = oldgroupColours.get(sg);
 381       }
 382     }
 383   }
 384
 385   public void valueChanged(boolean updateAllAnnotation)
 386   {
 387     if (slider.isEnabled())
 388     {
 389       if (currentColours.isSelected()
 390               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 391       {
 392         updateView();
 393       }
 394       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 395       propagateSeqAssociatedThreshold(updateAllAnnotation,
 396               getCurrentAnnotation());
 397       ap.paintAlignment(false);
 398     }
 399   }
 400
 401   public JComboBox<String> getThreshold()
 402   {
 403     return threshold;
 404   }
 405
 406   public void setThreshold(JComboBox<String> threshold)
 407   {
 408     this.threshold = threshold;
 409   }
 410
 411   public void currentColours_actionPerformed(ActionEvent e)
 412   {
 413     if (currentColours.isSelected())
 414     {
 415       reset();
 416     }
 417     maxColour.setEnabled(!currentColours.isSelected());
 418     minColour.setEnabled(!currentColours.isSelected());
 419     updateView();
 420   }
 421
 422   @Override
 423   public void updateView()
 424   {
 425     // Check if combobox is still adjusting
 426     if (adjusting)
 427     {
 428       return;
 429     }
 430
 431     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 432             .getSelectedIndex()]]);
 433
 434     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 435             .getSelectedIndex());
 436
 437     slider.setEnabled(true);
 438     thresholdValue.setEnabled(true);
 439     thresholdIsMin.setEnabled(true);
 440
 441     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 442     {
 443       slider.setEnabled(false);
 444       thresholdValue.setEnabled(false);
 445       thresholdValue.setText("");
 446       thresholdIsMin.setEnabled(false);
 447     }
 448     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 449             && getCurrentAnnotation().threshold == null)
 450     {
 451       getCurrentAnnotation()
 452               .setThreshold(new jalview.datamodel.GraphLine(
 453                       (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 454                       "Threshold", Color.black));
 455     }
 456
 457     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 458     {
 459       adjusting = true;
 460       float range = getCurrentAnnotation().graphMax * 1000
 461               - getCurrentAnnotation().graphMin * 1000;
 462
 463       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 464       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 465       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 466       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 467       slider.setMajorTickSpacing((int) (range / 10f));
 468       slider.setEnabled(true);
 469       thresholdValue.setEnabled(true);
 470       adjusting = false;
 471     }
 472     colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
 473
 474     ap.alignmentChanged();
 475     // ensure all associated views (overviews, structures, etc) are notified of
 476     // updated colours.
 477     ap.paintAlignment(true);
 478   }
 479
 480 }