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