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 jalview.bin.Cache;
  35 import jalview.datamodel.SequenceGroup;
  36 import jalview.schemes.AnnotationColourGradient;
  37 import jalview.schemes.ColourSchemeI;
  38 import jalview.util.MessageManager;
  39
  40 import javax.swing.BorderFactory;
  41 import javax.swing.JButton;
  42 import javax.swing.JColorChooser;
  43 import javax.swing.JComboBox;
  44 import javax.swing.JInternalFrame;
  45 import javax.swing.JLayeredPane;
  46 import javax.swing.JPanel;
  47
  48 import net.miginfocom.swing.MigLayout;
  49
  50 @SuppressWarnings("serial")
  51 public class AnnotationColourChooser extends AnnotationRowFilter
  52 {
  53
  54   ColourSchemeI oldcs;
  55
  56   Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  57
  58   /**
  59    * enabled if the user is dragging the slider - try to keep updates to a
  60    * minimun
  61    */
  62
  63   JComboBox<String> annotations;
  64
  65   JButton defColours = new JButton();
  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     Vector<String> annotItems = getAnnotationItems(seqAssociated
 123             .isSelected());
 124     annotations = new JComboBox<String>(annotItems);
 125
 126     populateThresholdComboBox(threshold);
 127
 128     if (oldcs instanceof AnnotationColourGradient)
 129     {
 130       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 131       String label = getAnnotationMenuLabel(acg.getAnnotation());
 132       annotations.setSelectedItem(label);
 133       switch (acg.getAboveThreshold())
 134       {
 135       case AnnotationColourGradient.NO_THRESHOLD:
 136         getThreshold().setSelectedIndex(0);
 137         break;
 138       case AnnotationColourGradient.ABOVE_THRESHOLD:
 139         getThreshold().setSelectedIndex(1);
 140         break;
 141       case AnnotationColourGradient.BELOW_THRESHOLD:
 142         getThreshold().setSelectedIndex(2);
 143         break;
 144       default:
 145         throw new Error(
 146                 MessageManager
 147                         .getString("error.implementation_error_dont_know_about_threshold_setting"));
 148       }
 149       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 150       thresholdValue.setText("" + acg.getAnnotationThreshold());
 151     }
 152
 153     try
 154     {
 155       jbInit();
 156     } catch (Exception ex)
 157     {
 158     }
 159     adjusting = false;
 160
 161     updateView();
 162     frame.invalidate();
 163     frame.pack();
 164   }
 165
 166   public AnnotationColourChooser()
 167   {
 168     try
 169     {
 170       jbInit();
 171     } catch (Exception ex)
 172     {
 173       ex.printStackTrace();
 174     }
 175   }
 176
 177   private void jbInit() throws Exception
 178   {
 179     minColour.setFont(JvSwingUtils.getLabelFont());
 180     minColour.setBorder(BorderFactory.createEtchedBorder());
 181     minColour.setPreferredSize(new Dimension(40, 20));
 182     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 183     minColour.addMouseListener(new MouseAdapter()
 184     {
 185       @Override
 186       public void mousePressed(MouseEvent e)
 187       {
 188         if (minColour.isEnabled())
 189         {
 190           minColour_actionPerformed();
 191         }
 192       }
 193     });
 194     maxColour.setFont(JvSwingUtils.getLabelFont());
 195     maxColour.setBorder(BorderFactory.createEtchedBorder());
 196     maxColour.setPreferredSize(new Dimension(40, 20));
 197     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 198     maxColour.addMouseListener(new MouseAdapter()
 199     {
 200       @Override
 201       public void mousePressed(MouseEvent e)
 202       {
 203         if (maxColour.isEnabled())
 204         {
 205           maxColour_actionPerformed();
 206         }
 207       }
 208     });
 209     ok.setOpaque(false);
 210     ok.setText(MessageManager.getString("action.ok"));
 211     ok.addActionListener(new ActionListener()
 212     {
 213       @Override
 214       public void actionPerformed(ActionEvent e)
 215       {
 216         ok_actionPerformed();
 217       }
 218     });
 219     cancel.setOpaque(false);
 220     cancel.setText(MessageManager.getString("action.cancel"));
 221     cancel.addActionListener(new ActionListener()
 222     {
 223       @Override
 224       public void actionPerformed(ActionEvent e)
 225       {
 226         cancel_actionPerformed();
 227       }
 228     });
 229     defColours.setOpaque(false);
 230     defColours.setText(MessageManager.getString("action.set_defaults"));
 231     defColours.setToolTipText(MessageManager
 232             .getString("label.reset_min_max_colours_to_defaults"));
 233     defColours.addActionListener(new ActionListener()
 234     {
 235
 236       @Override
 237       public void actionPerformed(ActionEvent arg0)
 238       {
 239         resetColours_actionPerformed();
 240       }
 241     });
 242
 243     annotations.addActionListener(new ActionListener()
 244     {
 245       @Override
 246       public void actionPerformed(ActionEvent e)
 247       {
 248         annotations_actionPerformed();
 249       }
 250     });
 251     getThreshold().addActionListener(new ActionListener()
 252     {
 253       @Override
 254       public void actionPerformed(ActionEvent e)
 255       {
 256         threshold_actionPerformed();
 257       }
 258     });
 259     thresholdValue.addActionListener(new ActionListener()
 260     {
 261       @Override
 262       public void actionPerformed(ActionEvent e)
 263       {
 264         thresholdValue_actionPerformed();
 265       }
 266     });
 267     slider.setPaintLabels(false);
 268     slider.setPaintTicks(true);
 269     slider.setBackground(Color.white);
 270     slider.setEnabled(false);
 271     slider.setOpaque(false);
 272     slider.setPreferredSize(new Dimension(100, 32));
 273     thresholdValue.setEnabled(false);
 274     thresholdValue.setColumns(7);
 275     currentColours.setFont(JvSwingUtils.getLabelFont());
 276     currentColours.setOpaque(false);
 277     currentColours.setText(MessageManager
 278             .getString("label.use_original_colours"));
 279     currentColours.addActionListener(new ActionListener()
 280     {
 281       @Override
 282       public void actionPerformed(ActionEvent e)
 283       {
 284         currentColours_actionPerformed();
 285       }
 286     });
 287     thresholdIsMin.setBackground(Color.white);
 288     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 289     thresholdIsMin.setText(MessageManager
 290             .getString("label.threshold_minmax"));
 291     thresholdIsMin.addActionListener(new ActionListener()
 292     {
 293       @Override
 294       public void actionPerformed(ActionEvent actionEvent)
 295       {
 296         thresholdIsMin_actionPerformed();
 297       }
 298     });
 299     seqAssociated.setBackground(Color.white);
 300     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 301     seqAssociated.setText(MessageManager
 302             .getString("label.per_sequence_only"));
 303     seqAssociated.addActionListener(new ActionListener()
 304     {
 305
 306       @Override
 307       public void actionPerformed(ActionEvent arg0)
 308       {
 309         seqAssociated_actionPerformed(annotations);
 310       }
 311     });
 312
 313     this.setLayout(borderLayout1);
 314     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 315     jPanel1.setBackground(Color.white);
 316     jPanel2.setBackground(Color.white);
 317
 318     jPanel1.add(ok);
 319     jPanel1.add(cancel);
 320     jPanel2.add(annotations, "grow, wrap");
 321     jPanel2.add(seqAssociated);
 322     jPanel2.add(currentColours);
 323     JPanel colpanel = new JPanel(new FlowLayout());
 324     colpanel.setBackground(Color.white);
 325     colpanel.add(minColour);
 326     colpanel.add(maxColour);
 327     jPanel2.add(colpanel, "wrap");
 328     jPanel2.add(getThreshold());
 329     jPanel2.add(defColours, "skip 1, wrap");
 330     jPanel2.add(thresholdIsMin);
 331     jPanel2.add(slider, "grow");
 332     jPanel2.add(thresholdValue, "grow");
 333     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 334     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 335     this.validate();
 336   }
 337
 338   protected void resetColours_actionPerformed()
 339   {
 340     setDefaultMinMax();
 341     updateView();
 342   }
 343
 344   private void setDefaultMinMax()
 345   {
 346     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 347             Color.orange));
 348     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 349             Color.red));
 350   }
 351
 352   public void minColour_actionPerformed()
 353   {
 354     Color col = JColorChooser.showDialog(this,
 355             MessageManager.getString("label.select_colour_minimum_value"),
 356             minColour.getBackground());
 357     if (col != null)
 358     {
 359       minColour.setBackground(col);
 360     }
 361     minColour.repaint();
 362     updateView();
 363   }
 364
 365   public void maxColour_actionPerformed()
 366   {
 367     Color col = JColorChooser.showDialog(this,
 368             MessageManager.getString("label.select_colour_maximum_value"),
 369             maxColour.getBackground());
 370     if (col != null)
 371     {
 372       maxColour.setBackground(col);
 373     }
 374     maxColour.repaint();
 375     updateView();
 376   }
 377
 378   @Override
 379   public void reset()
 380   {
 381     av.setGlobalColourScheme(oldcs);
 382     if (av.getAlignment().getGroups() != null)
 383     {
 384
 385       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 386       {
 387         sg.cs = oldgroupColours.get(sg);
 388       }
 389     }
 390   }
 391
 392   @Override
 393   public void valueChanged(boolean updateAllAnnotation)
 394   {
 395     if (slider.isEnabled())
 396     {
 397       if (currentColours.isSelected()
 398               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 399       {
 400         updateView();
 401       }
 402       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 403       propagateSeqAssociatedThreshold(updateAllAnnotation,
 404               getCurrentAnnotation());
 405       ap.paintAlignment(false);
 406     }
 407   }
 408
 409   public JComboBox<String> getThreshold()
 410   {
 411     return threshold;
 412   }
 413
 414   public void setThreshold(JComboBox<String> threshold)
 415   {
 416     this.threshold = threshold;
 417   }
 418
 419   public void currentColours_actionPerformed()
 420   {
 421     if (currentColours.isSelected())
 422     {
 423       reset();
 424     }
 425     maxColour.setEnabled(!currentColours.isSelected());
 426     minColour.setEnabled(!currentColours.isSelected());
 427     updateView();
 428   }
 429
 430   @Override
 431   public void updateView()
 432   {
 433     // Check if combobox is still adjusting
 434     if (adjusting)
 435     {
 436       return;
 437     }
 438
 439     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 440             .getSelectedIndex()]]);
 441
 442     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 443             .getSelectedIndex());
 444
 445     slider.setEnabled(true);
 446     thresholdValue.setEnabled(true);
 447     thresholdIsMin.setEnabled(true);
 448
 449     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 450     {
 451       slider.setEnabled(false);
 452       thresholdValue.setEnabled(false);
 453       thresholdValue.setText("");
 454       thresholdIsMin.setEnabled(false);
 455     }
 456     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 457             && getCurrentAnnotation().threshold == null)
 458     {
 459       getCurrentAnnotation()
 460               .setThreshold(
 461                       new jalview.datamodel.GraphLine(
 462                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 463                               "Threshold", Color.black));
 464     }
 465
 466     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 467     {
 468       adjusting = true;
 469       float range = getCurrentAnnotation().graphMax * 1000
 470               - getCurrentAnnotation().graphMin * 1000;
 471
 472       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 473       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 474       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 475       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 476       slider.setMajorTickSpacing((int) (range / 10f));
 477       slider.setEnabled(true);
 478       thresholdValue.setEnabled(true);
 479       adjusting = false;
 480     }
 481     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 482
 483     ap.alignmentChanged();
 484     // ensure all associated views (overviews, structures, etc) are notified of
 485     // updated colours.
 486     ap.paintAlignment(true);
 487   }
 488
 489 }