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.GraphLine;
  25 import jalview.datamodel.SequenceGroup;
  26 import jalview.schemes.AnnotationColourGradient;
  27 import jalview.schemes.ColourSchemeI;
  28 import jalview.util.MessageManager;
  29
  30 import java.awt.BorderLayout;
  31 import java.awt.Color;
  32 import java.awt.Dimension;
  33 import java.awt.FlowLayout;
  34 import java.awt.event.ActionEvent;
  35 import java.awt.event.ActionListener;
  36 import java.awt.event.MouseAdapter;
  37 import java.awt.event.MouseEvent;
  38 import java.util.Hashtable;
  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
  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     annotations = new JComboBox<String>(
 124             getAnnotationItems(seqAssociated.isSelected()));
 125
 126     populateThresholdComboBox(threshold);
 127
 128     if (oldcs instanceof AnnotationColourGradient)
 129     {
 130       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 131       annotations.setSelectedItem(acg.getAnnotation());
 132       switch (acg.getAboveThreshold())
 133       {
 134       case AnnotationColourGradient.NO_THRESHOLD:
 135         getThreshold().setSelectedIndex(0);
 136         break;
 137       case AnnotationColourGradient.ABOVE_THRESHOLD:
 138         getThreshold().setSelectedIndex(1);
 139         break;
 140       case AnnotationColourGradient.BELOW_THRESHOLD:
 141         getThreshold().setSelectedIndex(2);
 142         break;
 143       default:
 144         throw new Error(MessageManager.getString("error.implementation_error_dont_know_about_thereshold_setting"));
 145       }
 146       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 147       thresholdValue.setText("" + acg.getAnnotationThreshold());
 148     }
 149
 150     try
 151     {
 152       jbInit();
 153     } catch (Exception ex)
 154     {
 155     }
 156     adjusting = false;
 157
 158     updateView();
 159     frame.invalidate();
 160     frame.pack();
 161   }
 162
 163   public AnnotationColourChooser()
 164   {
 165     try
 166     {
 167       jbInit();
 168     } catch (Exception ex)
 169     {
 170       ex.printStackTrace();
 171     }
 172   }
 173
 174   private void jbInit() throws Exception
 175   {
 176     minColour.setFont(JvSwingUtils.getLabelFont());
 177     minColour.setBorder(BorderFactory.createEtchedBorder());
 178     minColour.setPreferredSize(new Dimension(40, 20));
 179     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 180     minColour.addMouseListener(new MouseAdapter()
 181     {
 182       @Override
 183       public void mousePressed(MouseEvent e)
 184       {
 185         if (minColour.isEnabled())
 186         {
 187           minColour_actionPerformed();
 188         }
 189       }
 190     });
 191     maxColour.setFont(JvSwingUtils.getLabelFont());
 192     maxColour.setBorder(BorderFactory.createEtchedBorder());
 193     maxColour.setPreferredSize(new Dimension(40, 20));
 194     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 195     maxColour.addMouseListener(new MouseAdapter()
 196     {
 197       @Override
 198       public void mousePressed(MouseEvent e)
 199       {
 200         if (maxColour.isEnabled())
 201         {
 202           maxColour_actionPerformed();
 203         }
 204       }
 205     });
 206     ok.setOpaque(false);
 207     ok.setText(MessageManager.getString("action.ok"));
 208     ok.addActionListener(new ActionListener()
 209     {
 210       @Override
 211       public void actionPerformed(ActionEvent e)
 212       {
 213         ok_actionPerformed(e);
 214       }
 215     });
 216     cancel.setOpaque(false);
 217     cancel.setText(MessageManager.getString("action.cancel"));
 218     cancel.addActionListener(new ActionListener()
 219     {
 220       @Override
 221       public void actionPerformed(ActionEvent e)
 222       {
 223         cancel_actionPerformed(e);
 224       }
 225     });
 226     defColours.setOpaque(false);
 227     defColours.setText(MessageManager.getString("action.set_defaults"));
 228     defColours.setToolTipText(MessageManager
 229             .getString("label.reset_min_max_colours_to_defaults"));
 230     defColours.addActionListener(new ActionListener()
 231     {
 232
 233       @Override
 234       public void actionPerformed(ActionEvent arg0)
 235       {
 236         resetColours_actionPerformed(arg0);
 237       }
 238     });
 239
 240     annotations.addActionListener(new ActionListener()
 241     {
 242       @Override
 243       public void actionPerformed(ActionEvent e)
 244       {
 245         annotations_actionPerformed(e);
 246       }
 247     });
 248     getThreshold().addActionListener(new ActionListener()
 249     {
 250       @Override
 251       public void actionPerformed(ActionEvent e)
 252       {
 253         threshold_actionPerformed(e);
 254       }
 255     });
 256     thresholdValue.addActionListener(new ActionListener()
 257     {
 258       @Override
 259       public void actionPerformed(ActionEvent e)
 260       {
 261         thresholdValue_actionPerformed(e);
 262       }
 263     });
 264     slider.setPaintLabels(false);
 265     slider.setPaintTicks(true);
 266     slider.setBackground(Color.white);
 267     slider.setEnabled(false);
 268     slider.setOpaque(false);
 269     slider.setPreferredSize(new Dimension(100, 32));
 270     thresholdValue.setEnabled(false);
 271     thresholdValue.setColumns(7);
 272     currentColours.setFont(JvSwingUtils.getLabelFont());
 273     currentColours.setOpaque(false);
 274     currentColours.setText(MessageManager
 275             .getString("label.use_original_colours"));
 276     currentColours.addActionListener(new ActionListener()
 277     {
 278       @Override
 279       public void actionPerformed(ActionEvent e)
 280       {
 281         currentColours_actionPerformed(e);
 282       }
 283     });
 284     thresholdIsMin.setBackground(Color.white);
 285     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 286     thresholdIsMin.setText(MessageManager
 287             .getString("label.threshold_minmax"));
 288     thresholdIsMin.addActionListener(new ActionListener()
 289     {
 290       @Override
 291       public void actionPerformed(ActionEvent actionEvent)
 292       {
 293         thresholdIsMin_actionPerformed(actionEvent);
 294       }
 295     });
 296     seqAssociated.setBackground(Color.white);
 297     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 298     seqAssociated.setText(MessageManager
 299             .getString("label.per_sequence_only"));
 300     seqAssociated.addActionListener(new ActionListener()
 301     {
 302
 303       @Override
 304       public void actionPerformed(ActionEvent arg0)
 305       {
 306         seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
 307       }
 308     });
 309
 310     this.setLayout(borderLayout1);
 311     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 312     jPanel1.setBackground(Color.white);
 313     jPanel2.setBackground(Color.white);
 314
 315     jPanel1.add(ok);
 316     jPanel1.add(cancel);
 317     jPanel2.add(annotations, "grow, wrap");
 318     jPanel2.add(seqAssociated);
 319     jPanel2.add(currentColours);
 320     JPanel colpanel = new JPanel(new FlowLayout());
 321     colpanel.setBackground(Color.white);
 322     colpanel.add(minColour);
 323     colpanel.add(maxColour);
 324     jPanel2.add(colpanel, "wrap");
 325     jPanel2.add(getThreshold());
 326     jPanel2.add(defColours, "skip 1, wrap");
 327     jPanel2.add(thresholdIsMin);
 328     jPanel2.add(slider, "grow");
 329     jPanel2.add(thresholdValue, "grow");
 330     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 331     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 332     this.validate();
 333   }
 334
 335   protected void resetColours_actionPerformed(ActionEvent arg0)
 336   {
 337     setDefaultMinMax();
 338     updateView();
 339   }
 340
 341   private void setDefaultMinMax()
 342   {
 343     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 344             Color.orange));
 345     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 346             Color.red));
 347   }
 348
 349   public void minColour_actionPerformed()
 350   {
 351     Color col = JColorChooser.showDialog(this,
 352             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 353     if (col != null)
 354     {
 355       minColour.setBackground(col);
 356     }
 357     minColour.repaint();
 358     updateView();
 359   }
 360
 361   public void maxColour_actionPerformed()
 362   {
 363     Color col = JColorChooser.showDialog(this,
 364             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 365     if (col != null)
 366     {
 367       maxColour.setBackground(col);
 368     }
 369     maxColour.repaint();
 370     updateView();
 371   }
 372
 373   public void reset()
 374   {
 375     av.setGlobalColourScheme(oldcs);
 376     if (av.getAlignment().getGroups() != null)
 377     {
 378
 379       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 380       {
 381         sg.cs = oldgroupColours.get(sg);
 382       }
 383     }
 384   }
 385
 386   public void valueChanged(boolean updateAllAnnotation)
 387   {
 388     if (slider.isEnabled())
 389     {
 390       if (currentColours.isSelected()
 391               && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 392       {
 393         updateView();
 394       }
 395       getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
 396       propagateSeqAssociatedThreshold(updateAllAnnotation,
 397               getCurrentAnnotation());
 398       ap.paintAlignment(false);
 399     }
 400   }
 401
 402   public JComboBox<String> getThreshold()
 403   {
 404     return threshold;
 405   }
 406
 407   public void setThreshold(JComboBox<String> threshold)
 408   {
 409     this.threshold = threshold;
 410   }
 411
 412   public void currentColours_actionPerformed(ActionEvent e)
 413   {
 414     if (currentColours.isSelected())
 415     {
 416       reset();
 417     }
 418     maxColour.setEnabled(!currentColours.isSelected());
 419     minColour.setEnabled(!currentColours.isSelected());
 420     updateView();
 421   }
 422
 423   @Override
 424   public void updateView()
 425   {
 426     // Check if combobox is still adjusting
 427     if (adjusting)
 428     {
 429       return;
 430     }
 431
 432     setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 433             .getSelectedIndex()]]);
 434
 435     int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
 436             .getSelectedIndex());
 437
 438     slider.setEnabled(true);
 439     thresholdValue.setEnabled(true);
 440     thresholdIsMin.setEnabled(true);
 441
 442     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
 443     {
 444       slider.setEnabled(false);
 445       thresholdValue.setEnabled(false);
 446       thresholdValue.setText("");
 447       thresholdIsMin.setEnabled(false);
 448     }
 449     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
 450             && getCurrentAnnotation().threshold == null)
 451     {
 452       getCurrentAnnotation()
 453               .setThreshold(
 454                       new GraphLine(
 455                       (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
 456                       "Threshold", Color.black));
 457     }
 458
 459     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
 460     {
 461       adjusting = true;
 462       float range = getCurrentAnnotation().graphMax * 1000
 463               - getCurrentAnnotation().graphMin * 1000;
 464
 465       slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
 466       slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
 467       slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
 468       thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
 469       slider.setMajorTickSpacing((int) (range / 10f));
 470       slider.setEnabled(true);
 471       thresholdValue.setEnabled(true);
 472       adjusting = false;
 473     }
 474     colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
 475
 476     ap.alignmentChanged();
 477     // ensure all associated views (overviews, structures, etc) are notified of
 478     // updated colours.
 479     ap.paintAlignment(true);
 480   }
 481
 482 }