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.GraphLine;
  36 import jalview.datamodel.SequenceGroup;
  37 import jalview.schemes.AnnotationColourGradient;
  38 import jalview.schemes.ColourSchemeI;
  39 import jalview.util.MessageManager;
  40
  41 import javax.swing.BorderFactory;
  42 import javax.swing.JButton;
  43 import javax.swing.JColorChooser;
  44 import javax.swing.JComboBox;
  45 import javax.swing.JInternalFrame;
  46 import javax.swing.JLayeredPane;
  47 import javax.swing.JPanel;
  48
  49 import net.miginfocom.swing.MigLayout;
  50
  51 @SuppressWarnings("serial")
  52 public class AnnotationColourChooser extends AnnotationRowFilter
  53 {
  54
  55   ColourSchemeI oldcs;
  56
  57   Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
  58
  59   /**
  60    * enabled if the user is dragging the slider - try to keep updates to a
  61    * minimun
  62    */
  63
  64   JComboBox<String> annotations;
  65
  66   JButton defColours = new JButton();
  67
  68   JPanel jPanel1 = new JPanel();
  69
  70   JPanel jPanel2 = new JPanel();
  71
  72   BorderLayout borderLayout1 = new BorderLayout();
  73
  74   private JComboBox<String> threshold = new JComboBox<String>();
  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<SequenceGroup, ColourSchemeI>();
  83       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  84       {
  85         if (sg.cs != null)
  86         {
  87           oldgroupColours.put(sg, sg.cs);
  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
  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       currentColours.setSelected(acg.isPredefinedColours()
 114               || 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(seqAssociated
 124             .isSelected());
 125     annotations = new JComboBox<String>(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(
 147                 MessageManager
 148                         .getString("error.implementation_error_dont_know_about_threshold_setting"));
 149       }
 150       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
 151       thresholdValue.setText("" + acg.getAnnotationThreshold());
 152     }
 153
 154     try
 155     {
 156       jbInit();
 157     } catch (Exception ex)
 158     {
 159     }
 160     adjusting = false;
 161
 162     updateView();
 163     frame.invalidate();
 164     frame.pack();
 165   }
 166
 167   public AnnotationColourChooser()
 168   {
 169     try
 170     {
 171       jbInit();
 172     } catch (Exception ex)
 173     {
 174       ex.printStackTrace();
 175     }
 176   }
 177
 178   private void jbInit() throws Exception
 179   {
 180     minColour.setFont(JvSwingUtils.getLabelFont());
 181     minColour.setBorder(BorderFactory.createEtchedBorder());
 182     minColour.setPreferredSize(new Dimension(40, 20));
 183     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 184     minColour.addMouseListener(new MouseAdapter()
 185     {
 186       @Override
 187       public void mousePressed(MouseEvent e)
 188       {
 189         if (minColour.isEnabled())
 190         {
 191           minColour_actionPerformed();
 192         }
 193       }
 194     });
 195     maxColour.setFont(JvSwingUtils.getLabelFont());
 196     maxColour.setBorder(BorderFactory.createEtchedBorder());
 197     maxColour.setPreferredSize(new Dimension(40, 20));
 198     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 199     maxColour.addMouseListener(new MouseAdapter()
 200     {
 201       @Override
 202       public void mousePressed(MouseEvent e)
 203       {
 204         if (maxColour.isEnabled())
 205         {
 206           maxColour_actionPerformed();
 207         }
 208       }
 209     });
 210     ok.setOpaque(false);
 211     ok.setText(MessageManager.getString("action.ok"));
 212     ok.addActionListener(new ActionListener()
 213     {
 214       @Override
 215       public void actionPerformed(ActionEvent e)
 216       {
 217         ok_actionPerformed();
 218       }
 219     });
 220     cancel.setOpaque(false);
 221     cancel.setText(MessageManager.getString("action.cancel"));
 222     cancel.addActionListener(new ActionListener()
 223     {
 224       @Override
 225       public void actionPerformed(ActionEvent e)
 226       {
 227         cancel_actionPerformed();
 228       }
 229     });
 230     defColours.setOpaque(false);
 231     defColours.setText(MessageManager.getString("action.set_defaults"));
 232     defColours.setToolTipText(MessageManager
 233             .getString("label.reset_min_max_colours_to_defaults"));
 234     defColours.addActionListener(new ActionListener()
 235     {
 236
 237       @Override
 238       public void actionPerformed(ActionEvent arg0)
 239       {
 240         resetColours_actionPerformed();
 241       }
 242     });
 243
 244     annotations.addActionListener(new ActionListener()
 245     {
 246       @Override
 247       public void actionPerformed(ActionEvent e)
 248       {
 249         annotations_actionPerformed();
 250       }
 251     });
 252     getThreshold().addActionListener(new ActionListener()
 253     {
 254       @Override
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         threshold_actionPerformed();
 258       }
 259     });
 260     thresholdValue.addActionListener(new ActionListener()
 261     {
 262       @Override
 263       public void actionPerformed(ActionEvent e)
 264       {
 265         thresholdValue_actionPerformed();
 266       }
 267     });
 268     slider.setPaintLabels(false);
 269     slider.setPaintTicks(true);
 270     slider.setBackground(Color.white);
 271     slider.setEnabled(false);
 272     slider.setOpaque(false);
 273     slider.setPreferredSize(new Dimension(100, 32));
 274     thresholdValue.setEnabled(false);
 275     thresholdValue.setColumns(7);
 276     currentColours.setFont(JvSwingUtils.getLabelFont());
 277     currentColours.setOpaque(false);
 278     currentColours.setText(MessageManager
 279             .getString("label.use_original_colours"));
 280     currentColours.addActionListener(new ActionListener()
 281     {
 282       @Override
 283       public void actionPerformed(ActionEvent e)
 284       {
 285         currentColours_actionPerformed();
 286       }
 287     });
 288     thresholdIsMin.setBackground(Color.white);
 289     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 290     thresholdIsMin.setText(MessageManager
 291             .getString("label.threshold_minmax"));
 292     thresholdIsMin.addActionListener(new ActionListener()
 293     {
 294       @Override
 295       public void actionPerformed(ActionEvent actionEvent)
 296       {
 297         thresholdIsMin_actionPerformed();
 298       }
 299     });
 300     seqAssociated.setBackground(Color.white);
 301     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 302     seqAssociated.setText(MessageManager
 303             .getString("label.per_sequence_only"));
 304     seqAssociated.addActionListener(new ActionListener()
 305     {
 306
 307       @Override
 308       public void actionPerformed(ActionEvent arg0)
 309       {
 310         seqAssociated_actionPerformed(annotations);
 311       }
 312     });
 313
 314     this.setLayout(borderLayout1);
 315     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 316     jPanel1.setBackground(Color.white);
 317     jPanel2.setBackground(Color.white);
 318
 319     jPanel1.add(ok);
 320     jPanel1.add(cancel);
 321     jPanel2.add(annotations, "grow, wrap");
 322     jPanel2.add(seqAssociated);
 323     jPanel2.add(currentColours);
 324     JPanel colpanel = new JPanel(new FlowLayout());
 325     colpanel.setBackground(Color.white);
 326     colpanel.add(minColour);
 327     colpanel.add(maxColour);
 328     jPanel2.add(colpanel, "wrap");
 329     jPanel2.add(getThreshold());
 330     jPanel2.add(defColours, "skip 1, wrap");
 331     jPanel2.add(thresholdIsMin);
 332     jPanel2.add(slider, "grow");
 333     jPanel2.add(thresholdValue, "grow");
 334     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 335     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 336     this.validate();
 337   }
 338
 339   protected void resetColours_actionPerformed()
 340   {
 341     setDefaultMinMax();
 342     updateView();
 343   }
 344
 345   private void setDefaultMinMax()
 346   {
 347     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 348             Color.orange));
 349     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 350             Color.red));
 351   }
 352
 353   public void minColour_actionPerformed()
 354   {
 355     Color col = JColorChooser.showDialog(this,
 356             MessageManager.getString("label.select_colour_minimum_value"),
 357             minColour.getBackground());
 358     if (col != null)
 359     {
 360       minColour.setBackground(col);
 361     }
 362     minColour.repaint();
 363     updateView();
 364   }
 365
 366   public void maxColour_actionPerformed()
 367   {
 368     Color col = JColorChooser.showDialog(this,
 369             MessageManager.getString("label.select_colour_maximum_value"),
 370             maxColour.getBackground());
 371     if (col != null)
 372     {
 373       maxColour.setBackground(col);
 374     }
 375     maxColour.repaint();
 376     updateView();
 377   }
 378
 379   @Override
 380   public void reset()
 381   {
 382     av.setGlobalColourScheme(oldcs);
 383     if (av.getAlignment().getGroups() != null)
 384     {
 385
 386       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 387       {
 388         sg.cs = oldgroupColours.get(sg);
 389       }
 390     }
 391   }
 392
 393   @Override
 394   public void valueChanged(boolean updateAllAnnotation)
 395   {
 396     if (slider.isEnabled())
 397     {
 398       if (currentColours.isSelected()
 399               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 400       {
 401         updateView();
 402       }
 403       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 404       propagateSeqAssociatedThreshold(updateAllAnnotation,
 405               getCurrentAnnotation());
 406       ap.paintAlignment(false);
 407     }
 408   }
 409
 410   public JComboBox<String> getThreshold()
 411   {
 412     return threshold;
 413   }
 414
 415   public void setThreshold(JComboBox<String> threshold)
 416   {
 417     this.threshold = threshold;
 418   }
 419
 420   public void currentColours_actionPerformed()
 421   {
 422     if (currentColours.isSelected())
 423     {
 424       reset();
 425     }
 426     maxColour.setEnabled(!currentColours.isSelected());
 427     minColour.setEnabled(!currentColours.isSelected());
 428     updateView();
 429   }
 430
 431   @Override
 432   public void updateView()
 433   {
 434     // Check if combobox is still adjusting
 435     if (adjusting)
 436     {
 437       return;
 438     }
 439
 440     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 441             .getSelectedIndex()]]);
 442
 443     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 444             .getSelectedIndex());
 445
 446     slider.setEnabled(true);
 447     thresholdValue.setEnabled(true);
 448     thresholdIsMin.setEnabled(true);
 449
 450     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 451     {
 452       slider.setEnabled(false);
 453       thresholdValue.setEnabled(false);
 454       thresholdValue.setText("");
 455       thresholdIsMin.setEnabled(false);
 456     }
 457     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 458             && getCurrentAnnotation().threshold == null)
 459     {
 460       getCurrentAnnotation()
 461               .setThreshold(
 462                       new GraphLine(
 463                               (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 464                               "Threshold", Color.black));
 465     }
 466
 467     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 468     {
 469       adjusting = true;
 470       float range = getCurrentAnnotation().graphMax * 1000
 471               - getCurrentAnnotation().graphMin * 1000;
 472
 473       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 474       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 475       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 476       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 477       slider.setMajorTickSpacing((int) (range / 10f));
 478       slider.setEnabled(true);
 479       thresholdValue.setEnabled(true);
 480       adjusting = false;
 481     }
 482     colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 483
 484     ap.alignmentChanged();
 485     // ensure all associated views (overviews, structures, etc) are notified of
 486     // updated colours.
 487     ap.paintAlignment(true);
 488   }
 489
 490 }