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   private float min;
  80
  81   private float max;
  82
  83   String type = null;
  84
  85   public FeatureColourChooser(FeatureRenderer frender, String type)
  86   {
  87     this(frender, false, type);
  88   }
  89
  90   public FeatureColourChooser(FeatureRenderer frender, boolean block,
  91           String type)
  92   {
  93     this.fr = frender;
  94     this.type = type;
  95     ap = fr.ap;
  96     String title = MessageManager.formatMessage(
  97             "label.graduated_color_for_params", new String[] { type });
  98     initDialogFrame(this, true, block, title, 480, 185);
  99     // frame.setLayer(JLayeredPane.PALETTE_LAYER);
 100     // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
 101     // 480, 145);
 102
 103     slider.addChangeListener(new ChangeListener()
 104     {
 105       @Override
 106       public void stateChanged(ChangeEvent evt)
 107       {
 108         if (!adjusting)
 109         {
 110           thresholdValue.setText((slider.getValue() / 1000f) + "");
 111           valueChanged();
 112         }
 113       }
 114     });
 115     slider.addMouseListener(new MouseAdapter()
 116     {
 117       @Override
 118       public void mouseReleased(MouseEvent evt)
 119       {
 120         if (ap != null)
 121         {
 122           ap.paintAlignment(true);
 123         }
 124         ;
 125       }
 126     });
 127
 128     float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
 129     min = mm[0];
 130     max = mm[1];
 131     oldcs = fr.getFeatureColours().get(type);
 132     if (oldcs instanceof GraduatedColor)
 133     {
 134       if (((GraduatedColor) oldcs).isAutoScale())
 135       {
 136         // update the scale
 137         cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
 138       }
 139       else
 140       {
 141         cs = new GraduatedColor((GraduatedColor) oldcs);
 142       }
 143     }
 144     else
 145     {
 146       // promote original color to a graduated color
 147       Color bl = Color.black;
 148       if (oldcs instanceof Color)
 149       {
 150         bl = (Color) oldcs;
 151       }
 152       // original colour becomes the maximum colour
 153       cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
 154       cs.setColourByLabel(false);
 155     }
 156     minColour.setBackground(oldminColour = cs.getMinColor());
 157     maxColour.setBackground(oldmaxColour = cs.getMaxColor());
 158     adjusting = true;
 159
 160     try
 161     {
 162       jbInit();
 163     } catch (Exception ex)
 164     {
 165     }
 166     // update the gui from threshold state
 167     thresholdIsMin.setSelected(!cs.isAutoScale());
 168     colourByLabel.setSelected(cs.isColourByLabel());
 169     if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 170     {
 171       // initialise threshold slider and selector
 172       threshold
 173               .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
 174                       : 2);
 175       slider.setEnabled(true);
 176       thresholdValue.setEnabled(true);
 177       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 178               "Threshold", Color.black);
 179
 180     }
 181
 182     adjusting = false;
 183
 184     changeColour();
 185     waitForInput();
 186   }
 187
 188   public FeatureColourChooser()
 189   {
 190     try
 191     {
 192       jbInit();
 193     } catch (Exception ex)
 194     {
 195       ex.printStackTrace();
 196     }
 197   }
 198
 199   private void jbInit() throws Exception
 200   {
 201
 202     minColour.setFont(JvSwingUtils.getLabelFont());
 203     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 204     minColour.setPreferredSize(new Dimension(40, 20));
 205     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 206     minColour.addMouseListener(new MouseAdapter()
 207     {
 208       @Override
 209       public void mousePressed(MouseEvent e)
 210       {
 211         if (minColour.isEnabled())
 212         {
 213           minColour_actionPerformed();
 214         }
 215       }
 216     });
 217     maxColour.setFont(JvSwingUtils.getLabelFont());
 218     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 219     maxColour.setPreferredSize(new Dimension(40, 20));
 220     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 221     maxColour.addMouseListener(new MouseAdapter()
 222     {
 223       @Override
 224       public void mousePressed(MouseEvent e)
 225       {
 226         if (maxColour.isEnabled())
 227         {
 228           maxColour_actionPerformed();
 229         }
 230       }
 231     });
 232     maxColour.setBorder(new LineBorder(Color.black));
 233     minText.setText(MessageManager.getString("label.min"));
 234     minText.setFont(JvSwingUtils.getLabelFont());
 235     maxText.setText(MessageManager.getString("label.max"));
 236     maxText.setFont(JvSwingUtils.getLabelFont());
 237     this.setLayout(borderLayout1);
 238     jPanel2.setLayout(flowLayout1);
 239     jPanel1.setBackground(Color.white);
 240     jPanel2.setBackground(Color.white);
 241     threshold.addActionListener(new ActionListener()
 242     {
 243       @Override
 244       public void actionPerformed(ActionEvent e)
 245       {
 246         threshold_actionPerformed(e);
 247       }
 248     });
 249     threshold.setToolTipText(MessageManager
 250             .getString("label.threshold_feature_display_by_score"));
 251     threshold.addItem(MessageManager
 252             .getString("label.threshold_feature_no_thereshold")); // index 0
 253     threshold.addItem(MessageManager
 254             .getString("label.threshold_feature_above_thereshold")); // index 1
 255     threshold.addItem(MessageManager
 256             .getString("label.threshold_feature_below_thereshold")); // index 2
 257     jPanel3.setLayout(flowLayout2);
 258     thresholdValue.addActionListener(new ActionListener()
 259     {
 260       @Override
 261       public void actionPerformed(ActionEvent e)
 262       {
 263         thresholdValue_actionPerformed(e);
 264       }
 265     });
 266     slider.setPaintLabels(false);
 267     slider.setPaintTicks(true);
 268     slider.setBackground(Color.white);
 269     slider.setEnabled(false);
 270     slider.setOpaque(false);
 271     slider.setPreferredSize(new Dimension(100, 32));
 272     slider.setToolTipText(MessageManager
 273             .getString("label.adjust_thereshold"));
 274     thresholdValue.setEnabled(false);
 275     thresholdValue.setColumns(7);
 276     jPanel3.setBackground(Color.white);
 277     thresholdIsMin.setBackground(Color.white);
 278     thresholdIsMin.setText(MessageManager
 279             .getString("label.threshold_minmax"));
 280     thresholdIsMin.setToolTipText(MessageManager
 281             .getString("label.toggle_absolute_relative_display_threshold"));
 282     thresholdIsMin.addActionListener(new ActionListener()
 283     {
 284       @Override
 285       public void actionPerformed(ActionEvent actionEvent)
 286       {
 287         thresholdIsMin_actionPerformed(actionEvent);
 288       }
 289     });
 290     colourByLabel.setBackground(Color.white);
 291     colourByLabel
 292             .setText(MessageManager.getString("label.colour_by_label"));
 293     colourByLabel
 294             .setToolTipText(MessageManager
 295                     .getString("label.display_features_same_type_different_label_using_different_colour"));
 296     colourByLabel.addActionListener(new ActionListener()
 297     {
 298       @Override
 299       public void actionPerformed(ActionEvent actionEvent)
 300       {
 301         colourByLabel_actionPerformed(actionEvent);
 302       }
 303     });
 304     colourPanel.setBackground(Color.white);
 305     jPanel1.add(ok);
 306     jPanel1.add(cancel);
 307     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 308     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 309     colourPanel.add(minText);
 310     colourPanel.add(minColour);
 311     colourPanel.add(maxText);
 312     colourPanel.add(maxColour);
 313     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 314     jPanel3.add(threshold);
 315     jPanel3.add(slider);
 316     jPanel3.add(thresholdValue);
 317     jPanel3.add(thresholdIsMin);
 318     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 319     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 320   }
 321
 322   JLabel minText = new JLabel();
 323
 324   JLabel maxText = new JLabel();
 325
 326   JPanel minColour = new JPanel();
 327
 328   JPanel maxColour = new JPanel();
 329
 330   JPanel colourPanel = new JPanel();
 331
 332   JPanel jPanel1 = new JPanel();
 333
 334   JPanel jPanel2 = new JPanel();
 335
 336   BorderLayout borderLayout1 = new BorderLayout();
 337
 338   JComboBox threshold = new JComboBox();
 339
 340   FlowLayout flowLayout1 = new FlowLayout();
 341
 342   JPanel jPanel3 = new JPanel();
 343
 344   FlowLayout flowLayout2 = new FlowLayout();
 345
 346   JSlider slider = new JSlider();
 347
 348   JTextField thresholdValue = new JTextField(20);
 349
 350   // TODO implement GUI for tolower flag
 351   // JCheckBox toLower = new JCheckBox();
 352
 353   JCheckBox thresholdIsMin = new JCheckBox();
 354
 355   JCheckBox colourByLabel = new JCheckBox();
 356
 357   private GraphLine threshline;
 358
 359   private Color oldmaxColour;
 360
 361   private Color oldminColour;
 362
 363   public void minColour_actionPerformed()
 364   {
 365     Color col = JColorChooser.showDialog(this,
 366             MessageManager.getString("label.select_colour_minimum_value"),
 367             minColour.getBackground());
 368     if (col != null)
 369     {
 370       minColour.setBackground(col);
 371       minColour.setForeground(col);
 372     }
 373     minColour.repaint();
 374     changeColour();
 375   }
 376
 377   public void maxColour_actionPerformed()
 378   {
 379     Color col = JColorChooser.showDialog(this,
 380             MessageManager.getString("label.select_colour_maximum_value"),
 381             maxColour.getBackground());
 382     if (col != null)
 383     {
 384       maxColour.setBackground(col);
 385       maxColour.setForeground(col);
 386     }
 387     maxColour.repaint();
 388     changeColour();
 389   }
 390
 391   void changeColour()
 392   {
 393     // Check if combobox is still adjusting
 394     if (adjusting)
 395     {
 396       return;
 397     }
 398
 399     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
 400     if (threshold.getSelectedIndex() == 1)
 401     {
 402       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 403     }
 404     else if (threshold.getSelectedIndex() == 2)
 405     {
 406       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 407     }
 408
 409     slider.setEnabled(true);
 410     thresholdValue.setEnabled(true);
 411
 412     GraduatedColor acg;
 413     if (cs.isColourByLabel())
 414     {
 415       acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
 416     }
 417     else
 418     {
 419       acg = new GraduatedColor(oldminColour = minColour.getBackground(),
 420               oldmaxColour = maxColour.getBackground(), min, max);
 421
 422     }
 423
 424     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 425     {
 426       slider.setEnabled(false);
 427       thresholdValue.setEnabled(false);
 428       thresholdValue.setText("");
 429       thresholdIsMin.setEnabled(false);
 430     }
 431     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 432             && threshline == null)
 433     {
 434       // todo visual indication of feature threshold
 435       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 436               "Threshold", Color.black);
 437     }
 438
 439     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 440     {
 441       adjusting = true;
 442       acg.setThresh(threshline.value);
 443
 444       float range = max * 1000f - min * 1000f;
 445
 446       slider.setMinimum((int) (min * 1000));
 447       slider.setMaximum((int) (max * 1000));
 448       slider.setValue((int) (threshline.value * 1000));
 449       thresholdValue.setText(threshline.value + "");
 450       slider.setMajorTickSpacing((int) (range / 10f));
 451       slider.setEnabled(true);
 452       thresholdValue.setEnabled(true);
 453       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 454       adjusting = false;
 455     }
 456
 457     acg.setThreshType(aboveThreshold);
 458     if (thresholdIsMin.isSelected()
 459             && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 460     {
 461       acg.setAutoScaled(false);
 462       if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
 463       {
 464         acg = new GraduatedColor(acg, threshline.value, max);
 465       }
 466       else
 467       {
 468         acg = new GraduatedColor(acg, min, threshline.value);
 469       }
 470     }
 471     else
 472     {
 473       acg.setAutoScaled(true);
 474     }
 475     acg.setColourByLabel(colourByLabel.isSelected());
 476     if (acg.isColourByLabel())
 477     {
 478       maxColour.setEnabled(false);
 479       minColour.setEnabled(false);
 480       maxColour.setBackground(this.getBackground());
 481       maxColour.setForeground(this.getBackground());
 482       minColour.setBackground(this.getBackground());
 483       minColour.setForeground(this.getBackground());
 484
 485     }
 486     else
 487     {
 488       maxColour.setEnabled(true);
 489       minColour.setEnabled(true);
 490       maxColour.setBackground(oldmaxColour);
 491       minColour.setBackground(oldminColour);
 492       maxColour.setForeground(oldmaxColour);
 493       minColour.setForeground(oldminColour);
 494     }
 495     fr.setColour(type, acg);
 496     cs = acg;
 497     ap.paintAlignment(false);
 498   }
 499
 500   @Override
 501   protected void raiseClosed()
 502   {
 503     if (this.colourEditor != null)
 504     {
 505       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 506     }
 507   }
 508
 509   @Override
 510   public void okPressed()
 511   {
 512     changeColour();
 513   }
 514
 515   @Override
 516   public void cancelPressed()
 517   {
 518     reset();
 519   }
 520
 521   void reset()
 522   {
 523     fr.setColour(type, oldcs);
 524     ap.paintAlignment(false);
 525     cs = null;
 526   }
 527
 528   public void thresholdCheck_actionPerformed(ActionEvent e)
 529   {
 530     changeColour();
 531   }
 532
 533   public void annotations_actionPerformed(ActionEvent e)
 534   {
 535     changeColour();
 536   }
 537
 538   public void threshold_actionPerformed(ActionEvent e)
 539   {
 540     changeColour();
 541   }
 542
 543   public void thresholdValue_actionPerformed(ActionEvent e)
 544   {
 545     try
 546     {
 547       float f = Float.parseFloat(thresholdValue.getText());
 548       slider.setValue((int) (f * 1000));
 549       threshline.value = f;
 550     } catch (NumberFormatException ex)
 551     {
 552     }
 553   }
 554
 555   public void valueChanged()
 556   {
 557     threshline.value = slider.getValue() / 1000f;
 558     cs.setThresh(threshline.value);
 559     changeColour();
 560     ap.paintAlignment(false);
 561   }
 562
 563   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 564   {
 565     changeColour();
 566   }
 567
 568   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 569   {
 570     changeColour();
 571   }
 572
 573   ActionListener colourEditor = null;
 574
 575   public void addActionListener(ActionListener graduatedColorEditor)
 576   {
 577     if (colourEditor != null)
 578     {
 579       System.err
 580               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 581     }
 582     colourEditor = graduatedColorEditor;
 583   }
 584
 585 }