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.datamodel.GraphLine;
  24 import jalview.schemes.AnnotationColourGradient;
  25 import jalview.schemes.GraduatedColor;
  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 import java.util.Hashtable;
  37
  38 import javax.swing.BorderFactory;
  39 import javax.swing.JCheckBox;
  40 import javax.swing.JColorChooser;
  41 import javax.swing.JComboBox;
  42 import javax.swing.JLabel;
  43 import javax.swing.JPanel;
  44 import javax.swing.JSlider;
  45 import javax.swing.JTextField;
  46 import javax.swing.border.LineBorder;
  47 import javax.swing.event.ChangeEvent;
  48 import javax.swing.event.ChangeListener;
  49
  50 public class FeatureColourChooser extends JalviewDialog
  51 {
  52   // FeatureSettings fs;
  53   FeatureRenderer fr;
  54
  55   private GraduatedColor cs;
  56
  57   private Object oldcs;
  58
  59   /**
  60    *
  61    * @return the last colour setting selected by user - either oldcs (which may
  62    *         be a java.awt.Color) or the new GraduatedColor
  63    */
  64   public Object getLastColour()
  65   {
  66     if (cs == null)
  67     {
  68       return oldcs;
  69     }
  70     return cs;
  71   }
  72
  73   Hashtable oldgroupColours;
  74
  75   AlignmentPanel ap;
  76
  77   boolean adjusting = false;
  78
  79   final private float min;
  80
  81   final private float max;
  82
  83   final private float scaleFactor;
  84
  85   String type = null;
  86
  87   JPanel minColour = new JPanel();
  88
  89   JPanel maxColour = new JPanel();
  90
  91   JComboBox threshold = new JComboBox();
  92
  93   JSlider slider = new JSlider();
  94
  95   JTextField thresholdValue = new JTextField(20);
  96
  97   // TODO implement GUI for tolower flag
  98   // JCheckBox toLower = new JCheckBox();
  99
 100   JCheckBox thresholdIsMin = new JCheckBox();
 101
 102   JCheckBox colourAlternately = new JCheckBox();
 103
 104   JCheckBox colourByLabel = new JCheckBox();
 105
 106   private GraphLine threshline;
 107
 108   private Color oldmaxColour;
 109
 110   private Color oldminColour;
 111
 112   public FeatureColourChooser(FeatureRenderer frender, String type)
 113   {
 114     this(frender, false, type);
 115   }
 116
 117   public FeatureColourChooser(FeatureRenderer frender, boolean block,
 118           String type)
 119   {
 120     this.fr = frender;
 121     this.type = type;
 122     ap = fr.ap;
 123     String title = MessageManager.formatMessage(
 124             "label.graduated_color_for_params", new String[] { type });
 125     initDialogFrame(this, true, block, title, 480, 185);
 126     // frame.setLayer(JLayeredPane.PALETTE_LAYER);
 127     // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
 128     // 480, 145);
 129
 130     slider.addChangeListener(new ChangeListener()
 131     {
 132       @Override
 133       public void stateChanged(ChangeEvent evt)
 134       {
 135         if (!adjusting)
 136         {
 137           thresholdValue.setText((slider.getValue() / scaleFactor) + "");
 138           valueChanged();
 139         }
 140       }
 141     });
 142     slider.addMouseListener(new MouseAdapter()
 143     {
 144       @Override
 145       public void mouseReleased(MouseEvent evt)
 146       {
 147         if (ap != null)
 148         {
 149           ap.paintAlignment(true);
 150         }
 151         ;
 152       }
 153     });
 154
 155     float mm[] = fr.getMinMax().get(type)[0];
 156     min = mm[0];
 157     max = mm[1];
 158
 159     /*
 160      * ensure scale factor allows a scaled range with
 161      * 10 integer divisions ('ticks'); if we have got here,
 162      * we should expect that max != min
 163      */
 164     scaleFactor = (max == min) ? 1f : 100f / (max - min);
 165
 166     oldcs = fr.getFeatureColours().get(type);
 167     if (oldcs instanceof GraduatedColor)
 168     {
 169       if (((GraduatedColor) oldcs).isAutoScale())
 170       {
 171         // update the scale
 172         cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
 173       }
 174       else
 175       {
 176         cs = new GraduatedColor((GraduatedColor) oldcs);
 177       }
 178     }
 179     else
 180     {
 181       // promote original color to a graduated color
 182       Color bl = Color.black;
 183       if (oldcs instanceof Color)
 184       {
 185         bl = (Color) oldcs;
 186       }
 187       // original colour becomes the maximum colour
 188       cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
 189       cs.setColourByLabel(false);
 190     }
 191     minColour.setBackground(oldminColour = cs.getMinColor());
 192     maxColour.setBackground(oldmaxColour = cs.getMaxColor());
 193     adjusting = true;
 194
 195     try
 196     {
 197       jbInit();
 198     } catch (Exception ex)
 199     {
 200     }
 201     // update the gui from threshold state
 202     thresholdIsMin.setSelected(!cs.isAutoScale());
 203     colourByLabel.setSelected(cs.isColourByLabel());
 204     colourAlternately.setSelected(cs.isColourAlternately());
 205     if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 206     {
 207       // initialise threshold slider and selector
 208       threshold
 209               .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
 210                       : 2);
 211       slider.setEnabled(true);
 212       thresholdValue.setEnabled(true);
 213       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 214               "Threshold", Color.black);
 215
 216     }
 217
 218     adjusting = false;
 219
 220     changeColour();
 221     waitForInput();
 222   }
 223
 224   private void jbInit() throws Exception
 225   {
 226
 227     minColour.setFont(JvSwingUtils.getLabelFont());
 228     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 229     minColour.setPreferredSize(new Dimension(40, 20));
 230     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 231     minColour.addMouseListener(new MouseAdapter()
 232     {
 233       @Override
 234       public void mousePressed(MouseEvent e)
 235       {
 236         if (minColour.isEnabled())
 237         {
 238           minColour_actionPerformed();
 239         }
 240       }
 241     });
 242     maxColour.setFont(JvSwingUtils.getLabelFont());
 243     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 244     maxColour.setPreferredSize(new Dimension(40, 20));
 245     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 246     maxColour.addMouseListener(new MouseAdapter()
 247     {
 248       @Override
 249       public void mousePressed(MouseEvent e)
 250       {
 251         if (maxColour.isEnabled())
 252         {
 253           maxColour_actionPerformed();
 254         }
 255       }
 256     });
 257     maxColour.setBorder(new LineBorder(Color.black));
 258     JLabel minText = new JLabel();
 259     minText.setText(MessageManager.getString("label.min"));
 260     minText.setFont(JvSwingUtils.getLabelFont());
 261     JLabel maxText = new JLabel();
 262     maxText.setText(MessageManager.getString("label.max"));
 263     maxText.setFont(JvSwingUtils.getLabelFont());
 264     this.setLayout(new BorderLayout());
 265     JPanel jPanel1 = new JPanel();
 266     JPanel jPanel2 = new JPanel();
 267     jPanel2.setLayout(new FlowLayout());
 268     jPanel1.setBackground(Color.white);
 269     jPanel2.setBackground(Color.white);
 270     threshold.addActionListener(new ActionListener()
 271     {
 272       @Override
 273       public void actionPerformed(ActionEvent e)
 274       {
 275         threshold_actionPerformed(e);
 276       }
 277     });
 278     threshold.setToolTipText(MessageManager
 279             .getString("label.threshold_feature_display_by_score"));
 280     threshold.addItem(MessageManager
 281             .getString("label.threshold_feature_no_thereshold")); // index 0
 282     threshold.addItem(MessageManager
 283             .getString("label.threshold_feature_above_thereshold")); // index 1
 284     threshold.addItem(MessageManager
 285             .getString("label.threshold_feature_below_thereshold")); // index 2
 286     JPanel jPanel3 = new JPanel();
 287     jPanel3.setLayout(new FlowLayout());
 288     thresholdValue.addActionListener(new ActionListener()
 289     {
 290       @Override
 291       public void actionPerformed(ActionEvent e)
 292       {
 293         thresholdValue_actionPerformed(e);
 294       }
 295     });
 296     slider.setPaintLabels(false);
 297     slider.setPaintTicks(true);
 298     slider.setBackground(Color.white);
 299     slider.setEnabled(false);
 300     slider.setOpaque(false);
 301     slider.setPreferredSize(new Dimension(100, 32));
 302     slider.setToolTipText(MessageManager
 303             .getString("label.adjust_thereshold"));
 304     thresholdValue.setEnabled(false);
 305     thresholdValue.setColumns(7);
 306     jPanel3.setBackground(Color.white);
 307     thresholdIsMin.setBackground(Color.white);
 308     thresholdIsMin.setText(MessageManager
 309             .getString("label.threshold_minmax"));
 310     thresholdIsMin.setToolTipText(MessageManager
 311             .getString("label.toggle_absolute_relative_display_threshold"));
 312     thresholdIsMin.addActionListener(new ActionListener()
 313     {
 314       @Override
 315       public void actionPerformed(ActionEvent actionEvent)
 316       {
 317         thresholdIsMin_actionPerformed(actionEvent);
 318       }
 319     });
 320     colourAlternately.setBackground(Color.white);
 321     colourAlternately.setText(MessageManager
 322             .getString("label.colour_alternately"));
 323     colourAlternately.setToolTipText(MessageManager
 324             .getString("label.colour_alternately_tip"));
 325     colourAlternately.addActionListener(new ActionListener()
 326     {
 327       @Override
 328       public void actionPerformed(ActionEvent actionEvent)
 329       {
 330         colourAlternately_actionPerformed(actionEvent);
 331       }
 332     });
 333     colourByLabel.setBackground(Color.white);
 334     colourByLabel
 335             .setText(MessageManager.getString("label.colour_by_label"));
 336     colourByLabel
 337             .setToolTipText(MessageManager
 338                     .getString("label.display_features_same_type_different_label_using_different_colour"));
 339     colourByLabel.addActionListener(new ActionListener()
 340     {
 341       @Override
 342       public void actionPerformed(ActionEvent actionEvent)
 343       {
 344         colourByLabel_actionPerformed(actionEvent);
 345       }
 346     });
 347
 348     JPanel colourPanel = new JPanel();
 349     colourPanel.setBackground(Color.white);
 350     jPanel1.add(ok);
 351     jPanel1.add(cancel);
 352     jPanel2.add(colourAlternately, java.awt.BorderLayout.WEST);
 353     jPanel2.add(colourByLabel, java.awt.BorderLayout.CENTER);
 354     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 355     colourPanel.add(minText);
 356     colourPanel.add(minColour);
 357     colourPanel.add(maxText);
 358     colourPanel.add(maxColour);
 359     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 360     jPanel3.add(threshold);
 361     jPanel3.add(slider);
 362     jPanel3.add(thresholdValue);
 363     jPanel3.add(thresholdIsMin);
 364     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 365     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 366   }
 367
 368   protected void colourAlternately_actionPerformed(ActionEvent actionEvent)
 369   {
 370     changeColour();
 371   }
 372
 373   public void minColour_actionPerformed()
 374   {
 375     Color col = JColorChooser.showDialog(this,
 376             MessageManager.getString("label.select_colour_minimum_value"),
 377             minColour.getBackground());
 378     if (col != null)
 379     {
 380       minColour.setBackground(col);
 381       minColour.setForeground(col);
 382     }
 383     minColour.repaint();
 384     changeColour();
 385   }
 386
 387   public void maxColour_actionPerformed()
 388   {
 389     Color col = JColorChooser.showDialog(this,
 390             MessageManager.getString("label.select_colour_maximum_value"),
 391             maxColour.getBackground());
 392     if (col != null)
 393     {
 394       maxColour.setBackground(col);
 395       maxColour.setForeground(col);
 396     }
 397     maxColour.repaint();
 398     changeColour();
 399   }
 400
 401   void changeColour()
 402   {
 403     // Check if combobox is still adjusting
 404     if (adjusting)
 405     {
 406       return;
 407     }
 408
 409     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
 410     if (threshold.getSelectedIndex() == 1)
 411     {
 412       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 413     }
 414     else if (threshold.getSelectedIndex() == 2)
 415     {
 416       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 417     }
 418
 419     slider.setEnabled(true);
 420     thresholdValue.setEnabled(true);
 421
 422     GraduatedColor acg;
 423     if (cs.isColourByLabel())
 424     {
 425       acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
 426     }
 427     else
 428     {
 429       acg = new GraduatedColor(oldminColour = minColour.getBackground(),
 430               oldmaxColour = maxColour.getBackground(), min, max);
 431
 432     }
 433
 434     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 435     {
 436       slider.setEnabled(false);
 437       thresholdValue.setEnabled(false);
 438       thresholdValue.setText("");
 439       thresholdIsMin.setEnabled(false);
 440     }
 441     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 442             && threshline == null)
 443     {
 444       // todo visual indication of feature threshold
 445       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 446               "Threshold", Color.black);
 447     }
 448
 449     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 450     {
 451       adjusting = true;
 452       acg.setThresh(threshline.value);
 453
 454       float range = (max - min) * scaleFactor;
 455
 456       slider.setMinimum((int) (min * scaleFactor));
 457       slider.setMaximum((int) (max * scaleFactor));
 458       slider.setValue((int) (threshline.value * scaleFactor));
 459       thresholdValue.setText(threshline.value + "");
 460       slider.setMajorTickSpacing((int) (range / 10f));
 461       slider.setEnabled(true);
 462       thresholdValue.setEnabled(true);
 463       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 464       adjusting = false;
 465     }
 466
 467     acg.setThreshType(aboveThreshold);
 468     if (thresholdIsMin.isSelected()
 469             && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 470     {
 471       acg.setAutoScaled(false);
 472       if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
 473       {
 474         acg = new GraduatedColor(acg, threshline.value, max);
 475       }
 476       else
 477       {
 478         acg = new GraduatedColor(acg, min, threshline.value);
 479       }
 480     }
 481     else
 482     {
 483       acg.setAutoScaled(true);
 484     }
 485     acg.setColourByLabel(colourByLabel.isSelected());
 486     acg.setColourAlternately(colourAlternately.isSelected());
 487     colourByLabel.setEnabled(!colourAlternately.isSelected());
 488     colourAlternately.setEnabled(!colourByLabel.isSelected());
 489     if (!fr.isOrdinal(type))
 490     {
 491       // don't allow colour alternately if no feature numbering on features
 492       colourAlternately.setEnabled(false);
 493     }
 494     if (acg.isColourByLabel())
 495     {
 496       maxColour.setEnabled(false);
 497       minColour.setEnabled(false);
 498       maxColour.setBackground(this.getBackground());
 499       maxColour.setForeground(this.getBackground());
 500       minColour.setBackground(this.getBackground());
 501       minColour.setForeground(this.getBackground());
 502
 503     }
 504     else
 505     {
 506       maxColour.setEnabled(true);
 507       minColour.setEnabled(true);
 508       maxColour.setBackground(oldmaxColour);
 509       minColour.setBackground(oldminColour);
 510       maxColour.setForeground(oldmaxColour);
 511       minColour.setForeground(oldminColour);
 512     }
 513     fr.setColour(type, acg);
 514     cs = acg;
 515     ap.paintAlignment(false);
 516   }
 517
 518   @Override
 519   protected void raiseClosed()
 520   {
 521     if (this.colourEditor != null)
 522     {
 523       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 524     }
 525   }
 526
 527   @Override
 528   public void okPressed()
 529   {
 530     changeColour();
 531   }
 532
 533   @Override
 534   public void cancelPressed()
 535   {
 536     reset();
 537   }
 538
 539   void reset()
 540   {
 541     fr.setColour(type, oldcs);
 542     ap.paintAlignment(false);
 543     cs = null;
 544   }
 545
 546   public void thresholdCheck_actionPerformed(ActionEvent e)
 547   {
 548     changeColour();
 549   }
 550
 551   public void annotations_actionPerformed(ActionEvent e)
 552   {
 553     changeColour();
 554   }
 555
 556   public void threshold_actionPerformed(ActionEvent e)
 557   {
 558     changeColour();
 559   }
 560
 561   public void thresholdValue_actionPerformed(ActionEvent e)
 562   {
 563     try
 564     {
 565       float f = Float.parseFloat(thresholdValue.getText());
 566       slider.setValue((int) (f * scaleFactor));
 567       threshline.value = f;
 568     } catch (NumberFormatException ex)
 569     {
 570     }
 571   }
 572
 573   public void valueChanged()
 574   {
 575     threshline.value = slider.getValue() / scaleFactor;
 576     cs.setThresh(threshline.value);
 577     changeColour();
 578     ap.paintAlignment(false);
 579   }
 580
 581   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 582   {
 583     changeColour();
 584   }
 585
 586   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 587   {
 588     changeColour();
 589   }
 590
 591   ActionListener colourEditor = null;
 592
 593   public void addActionListener(ActionListener graduatedColorEditor)
 594   {
 595     if (colourEditor != null)
 596     {
 597       System.err
 598               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 599     }
 600     colourEditor = graduatedColorEditor;
 601   }
 602
 603 }