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.FeatureColour;
  26 import jalview.util.MessageManager;
  27
  28 import java.awt.BorderLayout;
  29 import java.awt.Color;
  30 import java.awt.Dimension;
  31 import java.awt.FlowLayout;
  32 import java.awt.event.ActionEvent;
  33 import java.awt.event.ActionListener;
  34 import java.awt.event.MouseAdapter;
  35 import java.awt.event.MouseEvent;
  36
  37 import javax.swing.BorderFactory;
  38 import javax.swing.JCheckBox;
  39 import javax.swing.JColorChooser;
  40 import javax.swing.JComboBox;
  41 import javax.swing.JLabel;
  42 import javax.swing.JPanel;
  43 import javax.swing.JSlider;
  44 import javax.swing.JTextField;
  45 import javax.swing.border.LineBorder;
  46 import javax.swing.event.ChangeEvent;
  47 import javax.swing.event.ChangeListener;
  48
  49 public class FeatureColourChooser extends JalviewDialog
  50 {
  51   // FeatureSettings fs;
  52   FeatureRenderer fr;
  53
  54   private FeatureColourI cs;
  55
  56   private FeatureColourI oldcs;
  57
  58   /**
  59    *
  60    * @return the last colour setting selected by user - either oldcs (which may
  61    *         be a java.awt.Color) or the new GraduatedColor
  62    */
  63   public FeatureColourI getLastColour()
  64   {
  65     if (cs == null)
  66     {
  67       return oldcs;
  68     }
  69     return cs;
  70   }
  71
  72   AlignmentPanel ap;
  73
  74   boolean adjusting = false;
  75
  76   final private float min;
  77
  78   final private float max;
  79
  80   final private float scaleFactor;
  81
  82   String type = null;
  83
  84   public FeatureColourChooser(FeatureRenderer frender, String type)
  85   {
  86     this(frender, false, type);
  87   }
  88
  89   public FeatureColourChooser(FeatureRenderer frender, boolean block,
  90           String type)
  91   {
  92     this.fr = frender;
  93     this.type = type;
  94     ap = fr.ap;
  95     String title = MessageManager.formatMessage(
  96             "label.graduated_color_for_params", new String[] { type });
  97     initDialogFrame(this, true, block, title, 480, 185);
  98     // frame.setLayer(JLayeredPane.PALETTE_LAYER);
  99     // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
 100     // 480, 145);
 101
 102     slider.addChangeListener(new ChangeListener()
 103     {
 104       @Override
 105       public void stateChanged(ChangeEvent evt)
 106       {
 107         if (!adjusting)
 108         {
 109           thresholdValue.setText((slider.getValue() / scaleFactor) + "");
 110           valueChanged();
 111         }
 112       }
 113     });
 114     slider.addMouseListener(new MouseAdapter()
 115     {
 116       @Override
 117       public void mouseReleased(MouseEvent evt)
 118       {
 119         if (ap != null)
 120         {
 121           ap.paintAlignment(true);
 122         }
 123         ;
 124       }
 125     });
 126
 127     float mm[] = fr.getMinMax().get(type)[0];
 128     min = mm[0];
 129     max = mm[1];
 130
 131     /*
 132      * ensure scale factor allows a scaled range with
 133      * 10 integer divisions ('ticks'); if we have got here,
 134      * we should expect that max != min
 135      */
 136     scaleFactor = (max == min) ? 1f : 100f / (max - min);
 137
 138     oldcs = fr.getFeatureColours().get(type);
 139     if (!oldcs.isSimpleColour())
 140     {
 141       if (oldcs.isAutoScaled())
 142       {
 143         // update the scale
 144         cs = new FeatureColour((FeatureColour) oldcs, min, max);
 145       }
 146       else
 147       {
 148         cs = new FeatureColour((FeatureColour) oldcs);
 149       }
 150     }
 151     else
 152     {
 153       // promote original color to a graduated color
 154       Color bl = oldcs.getColour();
 155       if (bl == null)
 156       {
 157         bl = Color.BLACK;
 158       }
 159       // original colour becomes the maximum colour
 160       cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
 161       cs.setColourByLabel(false);
 162     }
 163     minColour.setBackground(oldminColour = cs.getMinColour());
 164     maxColour.setBackground(oldmaxColour = cs.getMaxColour());
 165     adjusting = true;
 166
 167     try
 168     {
 169       jbInit();
 170     } catch (Exception ex)
 171     {
 172     }
 173     // update the gui from threshold state
 174     thresholdIsMin.setSelected(!cs.isAutoScaled());
 175     colourByLabel.setSelected(cs.isColourByLabel());
 176     if (cs.hasThreshold())
 177     {
 178       // initialise threshold slider and selector
 179       threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2);
 180       slider.setEnabled(true);
 181       slider.setValue((int) (cs.getThreshold() * scaleFactor));
 182       thresholdValue.setEnabled(true);
 183       threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
 184       threshline.value = cs.getThreshold();
 185     }
 186
 187     adjusting = false;
 188
 189     changeColour();
 190     waitForInput();
 191   }
 192
 193   private void jbInit() throws Exception
 194   {
 195
 196     minColour.setFont(JvSwingUtils.getLabelFont());
 197     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 198     minColour.setPreferredSize(new Dimension(40, 20));
 199     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 200     minColour.addMouseListener(new MouseAdapter()
 201     {
 202       @Override
 203       public void mousePressed(MouseEvent e)
 204       {
 205         if (minColour.isEnabled())
 206         {
 207           minColour_actionPerformed();
 208         }
 209       }
 210     });
 211     maxColour.setFont(JvSwingUtils.getLabelFont());
 212     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 213     maxColour.setPreferredSize(new Dimension(40, 20));
 214     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 215     maxColour.addMouseListener(new MouseAdapter()
 216     {
 217       @Override
 218       public void mousePressed(MouseEvent e)
 219       {
 220         if (maxColour.isEnabled())
 221         {
 222           maxColour_actionPerformed();
 223         }
 224       }
 225     });
 226     maxColour.setBorder(new LineBorder(Color.black));
 227     minText.setText(MessageManager.getString("label.min"));
 228     minText.setFont(JvSwingUtils.getLabelFont());
 229     maxText.setText(MessageManager.getString("label.max"));
 230     maxText.setFont(JvSwingUtils.getLabelFont());
 231     this.setLayout(borderLayout1);
 232     jPanel2.setLayout(flowLayout1);
 233     jPanel1.setBackground(Color.white);
 234     jPanel2.setBackground(Color.white);
 235     threshold.addActionListener(new ActionListener()
 236     {
 237       @Override
 238       public void actionPerformed(ActionEvent e)
 239       {
 240         threshold_actionPerformed(e);
 241       }
 242     });
 243     threshold.setToolTipText(MessageManager
 244             .getString("label.threshold_feature_display_by_score"));
 245     threshold.addItem(MessageManager
 246             .getString("label.threshold_feature_no_threshold")); // index 0
 247     threshold.addItem(MessageManager
 248             .getString("label.threshold_feature_above_threshold")); // index 1
 249     threshold.addItem(MessageManager
 250             .getString("label.threshold_feature_below_threshold")); // index 2
 251     jPanel3.setLayout(flowLayout2);
 252     thresholdValue.addActionListener(new ActionListener()
 253     {
 254       @Override
 255       public void actionPerformed(ActionEvent e)
 256       {
 257         thresholdValue_actionPerformed(e);
 258       }
 259     });
 260     slider.setPaintLabels(false);
 261     slider.setPaintTicks(true);
 262     slider.setBackground(Color.white);
 263     slider.setEnabled(false);
 264     slider.setOpaque(false);
 265     slider.setPreferredSize(new Dimension(100, 32));
 266     slider.setToolTipText(MessageManager
 267             .getString("label.adjust_threshold"));
 268     thresholdValue.setEnabled(false);
 269     thresholdValue.setColumns(7);
 270     jPanel3.setBackground(Color.white);
 271     thresholdIsMin.setBackground(Color.white);
 272     thresholdIsMin.setText(MessageManager
 273             .getString("label.threshold_minmax"));
 274     thresholdIsMin.setToolTipText(MessageManager
 275             .getString("label.toggle_absolute_relative_display_threshold"));
 276     thresholdIsMin.addActionListener(new ActionListener()
 277     {
 278       @Override
 279       public void actionPerformed(ActionEvent actionEvent)
 280       {
 281         thresholdIsMin_actionPerformed(actionEvent);
 282       }
 283     });
 284     colourByLabel.setBackground(Color.white);
 285     colourByLabel
 286             .setText(MessageManager.getString("label.colour_by_label"));
 287     colourByLabel
 288             .setToolTipText(MessageManager
 289                     .getString("label.display_features_same_type_different_label_using_different_colour"));
 290     colourByLabel.addActionListener(new ActionListener()
 291     {
 292       @Override
 293       public void actionPerformed(ActionEvent actionEvent)
 294       {
 295         colourByLabel_actionPerformed(actionEvent);
 296       }
 297     });
 298     colourPanel.setBackground(Color.white);
 299     jPanel1.add(ok);
 300     jPanel1.add(cancel);
 301     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 302     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 303     colourPanel.add(minText);
 304     colourPanel.add(minColour);
 305     colourPanel.add(maxText);
 306     colourPanel.add(maxColour);
 307     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 308     jPanel3.add(threshold);
 309     jPanel3.add(slider);
 310     jPanel3.add(thresholdValue);
 311     jPanel3.add(thresholdIsMin);
 312     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 313     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 314   }
 315
 316   JLabel minText = new JLabel();
 317
 318   JLabel maxText = new JLabel();
 319
 320   JPanel minColour = new JPanel();
 321
 322   JPanel maxColour = new JPanel();
 323
 324   JPanel colourPanel = new JPanel();
 325
 326   JPanel jPanel1 = new JPanel();
 327
 328   JPanel jPanel2 = new JPanel();
 329
 330   BorderLayout borderLayout1 = new BorderLayout();
 331
 332   JComboBox threshold = new JComboBox();
 333
 334   FlowLayout flowLayout1 = new FlowLayout();
 335
 336   JPanel jPanel3 = new JPanel();
 337
 338   FlowLayout flowLayout2 = new FlowLayout();
 339
 340   JSlider slider = new JSlider();
 341
 342   JTextField thresholdValue = new JTextField(20);
 343
 344   // TODO implement GUI for tolower flag
 345   // JCheckBox toLower = new JCheckBox();
 346
 347   JCheckBox thresholdIsMin = new JCheckBox();
 348
 349   JCheckBox colourByLabel = new JCheckBox();
 350
 351   private GraphLine threshline;
 352
 353   private Color oldmaxColour;
 354
 355   private Color oldminColour;
 356
 357   public void minColour_actionPerformed()
 358   {
 359     Color col = JColorChooser.showDialog(this,
 360             MessageManager.getString("label.select_colour_minimum_value"),
 361             minColour.getBackground());
 362     if (col != null)
 363     {
 364       minColour.setBackground(col);
 365       minColour.setForeground(col);
 366     }
 367     minColour.repaint();
 368     changeColour();
 369   }
 370
 371   public void maxColour_actionPerformed()
 372   {
 373     Color col = JColorChooser.showDialog(this,
 374             MessageManager.getString("label.select_colour_maximum_value"),
 375             maxColour.getBackground());
 376     if (col != null)
 377     {
 378       maxColour.setBackground(col);
 379       maxColour.setForeground(col);
 380     }
 381     maxColour.repaint();
 382     changeColour();
 383   }
 384
 385   void changeColour()
 386   {
 387     // Check if combobox is still adjusting
 388     if (adjusting)
 389     {
 390       return;
 391     }
 392
 393     boolean aboveThreshold = false;
 394     boolean belowThreshold = false;
 395     if (threshold.getSelectedIndex() == 1)
 396     {
 397       aboveThreshold = true;
 398     }
 399     else if (threshold.getSelectedIndex() == 2)
 400     {
 401       belowThreshold = true;
 402     }
 403     boolean hasThreshold = aboveThreshold || belowThreshold;
 404
 405     slider.setEnabled(true);
 406     thresholdValue.setEnabled(true);
 407
 408     FeatureColourI acg;
 409     if (cs.isColourByLabel())
 410     {
 411       acg = new FeatureColour(oldminColour, oldmaxColour, min, max);
 412     }
 413     else
 414     {
 415       acg = new FeatureColour(oldminColour = minColour.getBackground(),
 416               oldmaxColour = maxColour.getBackground(), min, max);
 417
 418     }
 419
 420     if (!hasThreshold)
 421     {
 422       slider.setEnabled(false);
 423       thresholdValue.setEnabled(false);
 424       thresholdValue.setText("");
 425       thresholdIsMin.setEnabled(false);
 426     }
 427     else if (threshline == null)
 428     {
 429       // todo visual indication of feature threshold
 430       threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
 431     }
 432
 433     if (hasThreshold)
 434     {
 435       adjusting = true;
 436       acg.setThreshold(threshline.value);
 437
 438       float range = (max - min) * scaleFactor;
 439
 440       slider.setMinimum((int) (min * scaleFactor));
 441       slider.setMaximum((int) (max * scaleFactor));
 442       slider.setValue((int) (threshline.value * scaleFactor));
 443       thresholdValue.setText(threshline.value + "");
 444       slider.setMajorTickSpacing((int) (range / 10f));
 445       slider.setEnabled(true);
 446       thresholdValue.setEnabled(true);
 447       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 448       adjusting = false;
 449     }
 450
 451     acg.setAboveThreshold(aboveThreshold);
 452     acg.setBelowThreshold(belowThreshold);
 453     if (thresholdIsMin.isSelected() && hasThreshold)
 454     {
 455       acg.setAutoScaled(false);
 456       if (aboveThreshold)
 457       {
 458         acg = new FeatureColour((FeatureColour) acg, threshline.value, max);
 459       }
 460       else
 461       {
 462         acg = new FeatureColour((FeatureColour) acg, min, threshline.value);
 463       }
 464     }
 465     else
 466     {
 467       acg.setAutoScaled(true);
 468     }
 469     acg.setColourByLabel(colourByLabel.isSelected());
 470     if (acg.isColourByLabel())
 471     {
 472       maxColour.setEnabled(false);
 473       minColour.setEnabled(false);
 474       maxColour.setBackground(this.getBackground());
 475       maxColour.setForeground(this.getBackground());
 476       minColour.setBackground(this.getBackground());
 477       minColour.setForeground(this.getBackground());
 478
 479     }
 480     else
 481     {
 482       maxColour.setEnabled(true);
 483       minColour.setEnabled(true);
 484       maxColour.setBackground(oldmaxColour);
 485       minColour.setBackground(oldminColour);
 486       maxColour.setForeground(oldmaxColour);
 487       minColour.setForeground(oldminColour);
 488     }
 489     fr.setColour(type, acg);
 490     cs = acg;
 491     ap.paintAlignment(false);
 492   }
 493
 494   @Override
 495   protected void raiseClosed()
 496   {
 497     if (this.colourEditor != null)
 498     {
 499       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 500     }
 501   }
 502
 503   @Override
 504   public void okPressed()
 505   {
 506     changeColour();
 507   }
 508
 509   @Override
 510   public void cancelPressed()
 511   {
 512     reset();
 513   }
 514
 515   void reset()
 516   {
 517     fr.setColour(type, oldcs);
 518     ap.paintAlignment(false);
 519     cs = null;
 520   }
 521
 522   public void thresholdCheck_actionPerformed(ActionEvent e)
 523   {
 524     changeColour();
 525   }
 526
 527   public void annotations_actionPerformed(ActionEvent e)
 528   {
 529     changeColour();
 530   }
 531
 532   public void threshold_actionPerformed(ActionEvent e)
 533   {
 534     changeColour();
 535   }
 536
 537   public void thresholdValue_actionPerformed(ActionEvent e)
 538   {
 539     try
 540     {
 541       float f = Float.parseFloat(thresholdValue.getText());
 542       slider.setValue((int) (f * scaleFactor));
 543       threshline.value = f;
 544     } catch (NumberFormatException ex)
 545     {
 546     }
 547   }
 548
 549   public void valueChanged()
 550   {
 551     threshline.value = slider.getValue() / scaleFactor;
 552     cs.setThreshold(threshline.value);
 553     changeColour();
 554     ap.paintAlignment(false);
 555   }
 556
 557   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 558   {
 559     changeColour();
 560   }
 561
 562   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 563   {
 564     changeColour();
 565   }
 566
 567   ActionListener colourEditor = null;
 568
 569   public void addActionListener(ActionListener graduatedColorEditor)
 570   {
 571     if (colourEditor != null)
 572     {
 573       System.err
 574               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 575     }
 576     colourEditor = graduatedColorEditor;
 577   }
 578
 579 }