src/jalview/gui/FeatureColourChooser.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.api.FeatureColourI;
  24 import jalview.datamodel.GraphLine;
  25 import jalview.schemes.Colour;
  26 import jalview.schemes.FeatureColour;
  27 import jalview.util.ColorUtils;
  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
  39 import javax.swing.BorderFactory;
  40 import javax.swing.JCheckBox;
  41 import javax.swing.JColorChooser;
  42 import javax.swing.JComboBox;
  43 import javax.swing.JLabel;
  44 import javax.swing.JPanel;
  45 import javax.swing.JSlider;
  46 import javax.swing.JTextField;
  47 import javax.swing.border.LineBorder;
  48 import javax.swing.event.ChangeEvent;
  49 import javax.swing.event.ChangeListener;
  50
  51 public class FeatureColourChooser extends JalviewDialog
  52 {
  53   // FeatureSettings fs;
  54   FeatureRenderer fr;
  55
  56   private FeatureColourI cs;
  57
  58   private FeatureColourI oldcs;
  59
  60   /**
  61    *
  62    * @return the last colour setting selected by user - either oldcs (which may
  63    *         be a java.awt.Color) or the new GraduatedColor
  64    */
  65   public FeatureColourI getLastColour()
  66   {
  67     if (cs == null)
  68     {
  69       return oldcs;
  70     }
  71     return cs;
  72   }
  73
  74   AlignmentPanel ap;
  75
  76   boolean adjusting = false;
  77
  78   final private float min;
  79
  80   final private float max;
  81
  82   final private float scaleFactor;
  83
  84   String type = null;
  85
  86   public FeatureColourChooser(FeatureRenderer frender, String type)
  87   {
  88     this(frender, false, type);
  89   }
  90
  91   public FeatureColourChooser(FeatureRenderer frender, boolean block,
  92           String type)
  93   {
  94     this.fr = frender;
  95     this.type = type;
  96     ap = fr.ap;
  97     String title = MessageManager.formatMessage(
  98             "label.graduated_color_for_params", new String[] { type });
  99     initDialogFrame(this, true, block, title, 480, 185);
 100     // frame.setLayer(JLayeredPane.PALETTE_LAYER);
 101     // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
 102     // 480, 145);
 103
 104     slider.addChangeListener(new ChangeListener()
 105     {
 106       @Override
 107       public void stateChanged(ChangeEvent evt)
 108       {
 109         if (!adjusting)
 110         {
 111           thresholdValue.setText((slider.getValue() / scaleFactor) + "");
 112           valueChanged();
 113         }
 114       }
 115     });
 116     slider.addMouseListener(new MouseAdapter()
 117     {
 118       @Override
 119       public void mouseReleased(MouseEvent evt)
 120       {
 121         if (ap != null)
 122         {
 123           ap.paintAlignment(true);
 124         }
 125         ;
 126       }
 127     });
 128
 129     float mm[] = fr.getMinMax().get(type)[0];
 130     min = mm[0];
 131     max = mm[1];
 132
 133     /*
 134      * ensure scale factor allows a scaled range with
 135      * 10 integer divisions ('ticks'); if we have got here,
 136      * we should expect that max != min
 137      */
 138     scaleFactor = (max == min) ? 1f : 100f / (max - min);
 139
 140     oldcs = fr.getFeatureColours().get(type);
 141     if (!oldcs.isSimpleColour())
 142     {
 143       if (oldcs.isAutoScaled())
 144       {
 145         // update the scale
 146         cs = new FeatureColour((FeatureColour) oldcs, min, max);
 147       }
 148       else
 149       {
 150         cs = new FeatureColour((FeatureColour) oldcs);
 151       }
 152     }
 153     else
 154     {
 155       // promote original color to a graduated color
 156       Color bl = ColorUtils.getColor(oldcs.getColour());
 157       if (bl == null)
 158       {
 159         bl = Color.BLACK;
 160       }
 161       // original colour becomes the maximum colour
 162       cs = new FeatureColour(new Colour(Color.white), new Colour(bl),
 163               mm[0], mm[1]);
 164       cs.setColourByLabel(false);
 165     }
 166     minColour.setBackground(oldminColour = ColorUtils.getColor(cs
 167             .getMinColour()));
 168     maxColour.setBackground(oldmaxColour = ColorUtils.getColor(cs
 169             .getMaxColour()));
 170     adjusting = true;
 171
 172     try
 173     {
 174       jbInit();
 175     } catch (Exception ex)
 176     {
 177     }
 178     // update the gui from threshold state
 179     thresholdIsMin.setSelected(!cs.isAutoScaled());
 180     colourByLabel.setSelected(cs.isColourByLabel());
 181     if (cs.hasThreshold())
 182     {
 183       // initialise threshold slider and selector
 184       threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2);
 185       slider.setEnabled(true);
 186       thresholdValue.setEnabled(true);
 187       threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
 188
 189     }
 190
 191     adjusting = false;
 192
 193     changeColour();
 194     waitForInput();
 195   }
 196
 197   private void jbInit() throws Exception
 198   {
 199
 200     minColour.setFont(JvSwingUtils.getLabelFont());
 201     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 202     minColour.setPreferredSize(new Dimension(40, 20));
 203     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 204     minColour.addMouseListener(new MouseAdapter()
 205     {
 206       @Override
 207       public void mousePressed(MouseEvent e)
 208       {
 209         if (minColour.isEnabled())
 210         {
 211           minColour_actionPerformed();
 212         }
 213       }
 214     });
 215     maxColour.setFont(JvSwingUtils.getLabelFont());
 216     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 217     maxColour.setPreferredSize(new Dimension(40, 20));
 218     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 219     maxColour.addMouseListener(new MouseAdapter()
 220     {
 221       @Override
 222       public void mousePressed(MouseEvent e)
 223       {
 224         if (maxColour.isEnabled())
 225         {
 226           maxColour_actionPerformed();
 227         }
 228       }
 229     });
 230     maxColour.setBorder(new LineBorder(Color.black));
 231     minText.setText(MessageManager.getString("label.min"));
 232     minText.setFont(JvSwingUtils.getLabelFont());
 233     maxText.setText(MessageManager.getString("label.max"));
 234     maxText.setFont(JvSwingUtils.getLabelFont());
 235     this.setLayout(borderLayout1);
 236     jPanel2.setLayout(flowLayout1);
 237     jPanel1.setBackground(Color.white);
 238     jPanel2.setBackground(Color.white);
 239     threshold.addActionListener(new ActionListener()
 240     {
 241       @Override
 242       public void actionPerformed(ActionEvent e)
 243       {
 244         threshold_actionPerformed(e);
 245       }
 246     });
 247     threshold.setToolTipText(MessageManager
 248             .getString("label.threshold_feature_display_by_score"));
 249     threshold.addItem(MessageManager
 250             .getString("label.threshold_feature_no_threshold")); // index 0
 251     threshold.addItem(MessageManager
 252             .getString("label.threshold_feature_above_threshold")); // index 1
 253     threshold.addItem(MessageManager
 254             .getString("label.threshold_feature_below_threshold")); // index 2
 255     jPanel3.setLayout(flowLayout2);
 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     slider.setToolTipText(MessageManager
 271             .getString("label.adjust_threshold"));
 272     thresholdValue.setEnabled(false);
 273     thresholdValue.setColumns(7);
 274     jPanel3.setBackground(Color.white);
 275     thresholdIsMin.setBackground(Color.white);
 276     thresholdIsMin.setText(MessageManager
 277             .getString("label.threshold_minmax"));
 278     thresholdIsMin.setToolTipText(MessageManager
 279             .getString("label.toggle_absolute_relative_display_threshold"));
 280     thresholdIsMin.addActionListener(new ActionListener()
 281     {
 282       @Override
 283       public void actionPerformed(ActionEvent actionEvent)
 284       {
 285         thresholdIsMin_actionPerformed(actionEvent);
 286       }
 287     });
 288     colourByLabel.setBackground(Color.white);
 289     colourByLabel
 290             .setText(MessageManager.getString("label.colour_by_label"));
 291     colourByLabel
 292             .setToolTipText(MessageManager
 293                     .getString("label.display_features_same_type_different_label_using_different_colour"));
 294     colourByLabel.addActionListener(new ActionListener()
 295     {
 296       @Override
 297       public void actionPerformed(ActionEvent actionEvent)
 298       {
 299         colourByLabel_actionPerformed(actionEvent);
 300       }
 301     });
 302     colourPanel.setBackground(Color.white);
 303     jPanel1.add(ok);
 304     jPanel1.add(cancel);
 305     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 306     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 307     colourPanel.add(minText);
 308     colourPanel.add(minColour);
 309     colourPanel.add(maxText);
 310     colourPanel.add(maxColour);
 311     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 312     jPanel3.add(threshold);
 313     jPanel3.add(slider);
 314     jPanel3.add(thresholdValue);
 315     jPanel3.add(thresholdIsMin);
 316     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 317     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 318   }
 319
 320   JLabel minText = new JLabel();
 321
 322   JLabel maxText = new JLabel();
 323
 324   JPanel minColour = new JPanel();
 325
 326   JPanel maxColour = new JPanel();
 327
 328   JPanel colourPanel = new JPanel();
 329
 330   JPanel jPanel1 = new JPanel();
 331
 332   JPanel jPanel2 = new JPanel();
 333
 334   BorderLayout borderLayout1 = new BorderLayout();
 335
 336   JComboBox threshold = new JComboBox();
 337
 338   FlowLayout flowLayout1 = new FlowLayout();
 339
 340   JPanel jPanel3 = new JPanel();
 341
 342   FlowLayout flowLayout2 = new FlowLayout();
 343
 344   JSlider slider = new JSlider();
 345
 346   JTextField thresholdValue = new JTextField(20);
 347
 348   // TODO implement GUI for tolower flag
 349   // JCheckBox toLower = new JCheckBox();
 350
 351   JCheckBox thresholdIsMin = new JCheckBox();
 352
 353   JCheckBox colourByLabel = new JCheckBox();
 354
 355   private GraphLine threshline;
 356
 357   private Color oldmaxColour;
 358
 359   private Color oldminColour;
 360
 361   public void minColour_actionPerformed()
 362   {
 363     Color col = JColorChooser.showDialog(this,
 364             MessageManager.getString("label.select_colour_minimum_value"),
 365             minColour.getBackground());
 366     if (col != null)
 367     {
 368       minColour.setBackground(col);
 369       minColour.setForeground(col);
 370     }
 371     minColour.repaint();
 372     changeColour();
 373   }
 374
 375   public void maxColour_actionPerformed()
 376   {
 377     Color col = JColorChooser.showDialog(this,
 378             MessageManager.getString("label.select_colour_maximum_value"),
 379             maxColour.getBackground());
 380     if (col != null)
 381     {
 382       maxColour.setBackground(col);
 383       maxColour.setForeground(col);
 384     }
 385     maxColour.repaint();
 386     changeColour();
 387   }
 388
 389   void changeColour()
 390   {
 391     // Check if combobox is still adjusting
 392     if (adjusting)
 393     {
 394       return;
 395     }
 396
 397     boolean aboveThreshold = false;
 398     boolean belowThreshold = false;
 399     if (threshold.getSelectedIndex() == 1)
 400     {
 401       aboveThreshold = true;
 402     }
 403     else if (threshold.getSelectedIndex() == 2)
 404     {
 405       belowThreshold = true;
 406     }
 407     boolean hasThreshold = aboveThreshold || belowThreshold;
 408
 409     slider.setEnabled(true);
 410     thresholdValue.setEnabled(true);
 411
 412     FeatureColourI acg;
 413     if (cs.isColourByLabel())
 414     {
 415       acg = new FeatureColour(new Colour(oldminColour), new Colour(
 416               oldmaxColour), min, max);
 417     }
 418     else
 419     {
 420       acg = new FeatureColour(new Colour(
 421               oldminColour = minColour.getBackground()), new Colour(
 422               oldmaxColour = maxColour.getBackground()), min, max);
 423     }
 424
 425     if (!hasThreshold)
 426     {
 427       slider.setEnabled(false);
 428       thresholdValue.setEnabled(false);
 429       thresholdValue.setText("");
 430       thresholdIsMin.setEnabled(false);
 431     }
 432     else if (threshline == null)
 433     {
 434       // todo visual indication of feature threshold
 435       threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
 436     }
 437
 438     if (hasThreshold)
 439     {
 440       adjusting = true;
 441       acg.setThreshold(threshline.value);
 442
 443       float range = (max - min) * scaleFactor;
 444
 445       slider.setMinimum((int) (min * scaleFactor));
 446       slider.setMaximum((int) (max * scaleFactor));
 447       slider.setValue((int) (threshline.value * scaleFactor));
 448       thresholdValue.setText(threshline.value + "");
 449       slider.setMajorTickSpacing((int) (range / 10f));
 450       slider.setEnabled(true);
 451       thresholdValue.setEnabled(true);
 452       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 453       adjusting = false;
 454     }
 455
 456     acg.setAboveThreshold(aboveThreshold);
 457     acg.setBelowThreshold(belowThreshold);
 458     if (thresholdIsMin.isSelected() && hasThreshold)
 459     {
 460       acg.setAutoScaled(false);
 461       if (aboveThreshold)
 462       {
 463         acg = new FeatureColour((FeatureColour) acg, threshline.value, max);
 464       }
 465       else
 466       {
 467         acg = new FeatureColour((FeatureColour) acg, min, threshline.value);
 468       }
 469     }
 470     else
 471     {
 472       acg.setAutoScaled(true);
 473     }
 474     acg.setColourByLabel(colourByLabel.isSelected());
 475     if (acg.isColourByLabel())
 476     {
 477       maxColour.setEnabled(false);
 478       minColour.setEnabled(false);
 479       maxColour.setBackground(this.getBackground());
 480       maxColour.setForeground(this.getBackground());
 481       minColour.setBackground(this.getBackground());
 482       minColour.setForeground(this.getBackground());
 483
 484     }
 485     else
 486     {
 487       maxColour.setEnabled(true);
 488       minColour.setEnabled(true);
 489       maxColour.setBackground(oldmaxColour);
 490       minColour.setBackground(oldminColour);
 491       maxColour.setForeground(oldmaxColour);
 492       minColour.setForeground(oldminColour);
 493     }
 494     fr.setColour(type, acg);
 495     cs = acg;
 496     ap.paintAlignment(false);
 497   }
 498
 499   @Override
 500   protected void raiseClosed()
 501   {
 502     if (this.colourEditor != null)
 503     {
 504       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 505     }
 506   }
 507
 508   @Override
 509   public void okPressed()
 510   {
 511     changeColour();
 512   }
 513
 514   @Override
 515   public void cancelPressed()
 516   {
 517     reset();
 518   }
 519
 520   void reset()
 521   {
 522     fr.setColour(type, oldcs);
 523     ap.paintAlignment(false);
 524     cs = null;
 525   }
 526
 527   public void thresholdCheck_actionPerformed(ActionEvent e)
 528   {
 529     changeColour();
 530   }
 531
 532   public void annotations_actionPerformed(ActionEvent e)
 533   {
 534     changeColour();
 535   }
 536
 537   public void threshold_actionPerformed(ActionEvent e)
 538   {
 539     changeColour();
 540   }
 541
 542   public void thresholdValue_actionPerformed(ActionEvent e)
 543   {
 544     try
 545     {
 546       float f = Float.parseFloat(thresholdValue.getText());
 547       slider.setValue((int) (f * scaleFactor));
 548       threshline.value = f;
 549     } catch (NumberFormatException ex)
 550     {
 551     }
 552   }
 553
 554   public void valueChanged()
 555   {
 556     threshline.value = slider.getValue() / scaleFactor;
 557     cs.setThreshold(threshline.value);
 558     changeColour();
 559     ap.paintAlignment(false);
 560   }
 561
 562   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 563   {
 564     changeColour();
 565   }
 566
 567   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 568   {
 569     changeColour();
 570   }
 571
 572   ActionListener colourEditor = null;
 573
 574   public void addActionListener(ActionListener graduatedColorEditor)
 575   {
 576     if (colourEditor != null)
 577     {
 578       System.err
 579               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 580     }
 581     colourEditor = graduatedColorEditor;
 582   }
 583
 584 }