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   public FeatureColourChooser(FeatureRenderer frender, String type)
  88   {
  89     this(frender, false, type);
  90   }
  91
  92   public FeatureColourChooser(FeatureRenderer frender, boolean block,
  93           String type)
  94   {
  95     this.fr = frender;
  96     this.type = type;
  97     ap = fr.ap;
  98     String title = MessageManager.formatMessage(
  99             "label.graduated_color_for_params", new String[] { type });
 100     initDialogFrame(this, true, block, title, 480, 185);
 101     // frame.setLayer(JLayeredPane.PALETTE_LAYER);
 102     // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
 103     // 480, 145);
 104
 105     slider.addChangeListener(new ChangeListener()
 106     {
 107       @Override
 108       public void stateChanged(ChangeEvent evt)
 109       {
 110         if (!adjusting)
 111         {
 112           thresholdValue.setText((slider.getValue() / scaleFactor) + "");
 113           valueChanged();
 114         }
 115       }
 116     });
 117     slider.addMouseListener(new MouseAdapter()
 118     {
 119       @Override
 120       public void mouseReleased(MouseEvent evt)
 121       {
 122         if (ap != null)
 123         {
 124           ap.paintAlignment(true);
 125         }
 126         ;
 127       }
 128     });
 129
 130     float mm[] = ((float[][]) fr.getMinMax().get(type))[0];
 131     min = mm[0];
 132     max = mm[1];
 133
 134     /*
 135      * ensure scale factor allows a scaled range with
 136      * 10 integer divisions ('ticks'); if we have got here,
 137      * we should expect that max != min
 138      */
 139     scaleFactor = (max == min) ? 1f : 100f / (max - min);
 140
 141     oldcs = fr.getFeatureColours().get(type);
 142     if (oldcs instanceof GraduatedColor)
 143     {
 144       if (((GraduatedColor) oldcs).isAutoScale())
 145       {
 146         // update the scale
 147         cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
 148       }
 149       else
 150       {
 151         cs = new GraduatedColor((GraduatedColor) oldcs);
 152       }
 153     }
 154     else
 155     {
 156       // promote original color to a graduated color
 157       Color bl = Color.black;
 158       if (oldcs instanceof Color)
 159       {
 160         bl = (Color) oldcs;
 161       }
 162       // original colour becomes the maximum colour
 163       cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
 164       cs.setColourByLabel(false);
 165     }
 166     minColour.setBackground(oldminColour = cs.getMinColor());
 167     maxColour.setBackground(oldmaxColour = cs.getMaxColor());
 168     adjusting = true;
 169
 170     try
 171     {
 172       jbInit();
 173     } catch (Exception ex)
 174     {
 175     }
 176     // update the gui from threshold state
 177     thresholdIsMin.setSelected(!cs.isAutoScale());
 178     colourByLabel.setSelected(cs.isColourByLabel());
 179     if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 180     {
 181       // initialise threshold slider and selector
 182       threshold
 183               .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
 184                       : 2);
 185       slider.setEnabled(true);
 186       thresholdValue.setEnabled(true);
 187       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 188               "Threshold", Color.black);
 189
 190     }
 191
 192     adjusting = false;
 193
 194     changeColour();
 195     waitForInput();
 196   }
 197
 198   private void jbInit() throws Exception
 199   {
 200
 201     minColour.setFont(JvSwingUtils.getLabelFont());
 202     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 203     minColour.setPreferredSize(new Dimension(40, 20));
 204     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 205     minColour.addMouseListener(new MouseAdapter()
 206     {
 207       @Override
 208       public void mousePressed(MouseEvent e)
 209       {
 210         if (minColour.isEnabled())
 211         {
 212           minColour_actionPerformed();
 213         }
 214       }
 215     });
 216     maxColour.setFont(JvSwingUtils.getLabelFont());
 217     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 218     maxColour.setPreferredSize(new Dimension(40, 20));
 219     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 220     maxColour.addMouseListener(new MouseAdapter()
 221     {
 222       @Override
 223       public void mousePressed(MouseEvent e)
 224       {
 225         if (maxColour.isEnabled())
 226         {
 227           maxColour_actionPerformed();
 228         }
 229       }
 230     });
 231     maxColour.setBorder(new LineBorder(Color.black));
 232     minText.setText(MessageManager.getString("label.min"));
 233     minText.setFont(JvSwingUtils.getLabelFont());
 234     maxText.setText(MessageManager.getString("label.max"));
 235     maxText.setFont(JvSwingUtils.getLabelFont());
 236     this.setLayout(borderLayout1);
 237     jPanel2.setLayout(flowLayout1);
 238     jPanel1.setBackground(Color.white);
 239     jPanel2.setBackground(Color.white);
 240     threshold.addActionListener(new ActionListener()
 241     {
 242       @Override
 243       public void actionPerformed(ActionEvent e)
 244       {
 245         threshold_actionPerformed(e);
 246       }
 247     });
 248     threshold.setToolTipText(MessageManager
 249             .getString("label.threshold_feature_display_by_score"));
 250     threshold.addItem(MessageManager
 251             .getString("label.threshold_feature_no_thereshold")); // index 0
 252     threshold.addItem(MessageManager
 253             .getString("label.threshold_feature_above_thereshold")); // index 1
 254     threshold.addItem(MessageManager
 255             .getString("label.threshold_feature_below_thereshold")); // index 2
 256     jPanel3.setLayout(flowLayout2);
 257     thresholdValue.addActionListener(new ActionListener()
 258     {
 259       @Override
 260       public void actionPerformed(ActionEvent e)
 261       {
 262         thresholdValue_actionPerformed(e);
 263       }
 264     });
 265     slider.setPaintLabels(false);
 266     slider.setPaintTicks(true);
 267     slider.setBackground(Color.white);
 268     slider.setEnabled(false);
 269     slider.setOpaque(false);
 270     slider.setPreferredSize(new Dimension(100, 32));
 271     slider.setToolTipText(MessageManager
 272             .getString("label.adjust_thereshold"));
 273     thresholdValue.setEnabled(false);
 274     thresholdValue.setColumns(7);
 275     jPanel3.setBackground(Color.white);
 276     thresholdIsMin.setBackground(Color.white);
 277     thresholdIsMin.setText(MessageManager
 278             .getString("label.threshold_minmax"));
 279     thresholdIsMin.setToolTipText(MessageManager
 280             .getString("label.toggle_absolute_relative_display_threshold"));
 281     thresholdIsMin.addActionListener(new ActionListener()
 282     {
 283       @Override
 284       public void actionPerformed(ActionEvent actionEvent)
 285       {
 286         thresholdIsMin_actionPerformed(actionEvent);
 287       }
 288     });
 289     colourByLabel.setBackground(Color.white);
 290     colourByLabel
 291             .setText(MessageManager.getString("label.colour_by_label"));
 292     colourByLabel
 293             .setToolTipText(MessageManager
 294                     .getString("label.display_features_same_type_different_label_using_different_colour"));
 295     colourByLabel.addActionListener(new ActionListener()
 296     {
 297       @Override
 298       public void actionPerformed(ActionEvent actionEvent)
 299       {
 300         colourByLabel_actionPerformed(actionEvent);
 301       }
 302     });
 303     colourPanel.setBackground(Color.white);
 304     jPanel1.add(ok);
 305     jPanel1.add(cancel);
 306     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 307     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 308     colourPanel.add(minText);
 309     colourPanel.add(minColour);
 310     colourPanel.add(maxText);
 311     colourPanel.add(maxColour);
 312     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 313     jPanel3.add(threshold);
 314     jPanel3.add(slider);
 315     jPanel3.add(thresholdValue);
 316     jPanel3.add(thresholdIsMin);
 317     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 318     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 319   }
 320
 321   JLabel minText = new JLabel();
 322
 323   JLabel maxText = new JLabel();
 324
 325   JPanel minColour = new JPanel();
 326
 327   JPanel maxColour = new JPanel();
 328
 329   JPanel colourPanel = new JPanel();
 330
 331   JPanel jPanel1 = new JPanel();
 332
 333   JPanel jPanel2 = new JPanel();
 334
 335   BorderLayout borderLayout1 = new BorderLayout();
 336
 337   JComboBox threshold = new JComboBox();
 338
 339   FlowLayout flowLayout1 = new FlowLayout();
 340
 341   JPanel jPanel3 = new JPanel();
 342
 343   FlowLayout flowLayout2 = new FlowLayout();
 344
 345   JSlider slider = new JSlider();
 346
 347   JTextField thresholdValue = new JTextField(20);
 348
 349   // TODO implement GUI for tolower flag
 350   // JCheckBox toLower = new JCheckBox();
 351
 352   JCheckBox thresholdIsMin = new JCheckBox();
 353
 354   JCheckBox colourByLabel = new JCheckBox();
 355
 356   private GraphLine threshline;
 357
 358   private Color oldmaxColour;
 359
 360   private Color oldminColour;
 361
 362   public void minColour_actionPerformed()
 363   {
 364     Color col = JColorChooser.showDialog(this,
 365             MessageManager.getString("label.select_colour_minimum_value"),
 366             minColour.getBackground());
 367     if (col != null)
 368     {
 369       minColour.setBackground(col);
 370       minColour.setForeground(col);
 371     }
 372     minColour.repaint();
 373     changeColour();
 374   }
 375
 376   public void maxColour_actionPerformed()
 377   {
 378     Color col = JColorChooser.showDialog(this,
 379             MessageManager.getString("label.select_colour_maximum_value"),
 380             maxColour.getBackground());
 381     if (col != null)
 382     {
 383       maxColour.setBackground(col);
 384       maxColour.setForeground(col);
 385     }
 386     maxColour.repaint();
 387     changeColour();
 388   }
 389
 390   void changeColour()
 391   {
 392     // Check if combobox is still adjusting
 393     if (adjusting)
 394     {
 395       return;
 396     }
 397
 398     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
 399     if (threshold.getSelectedIndex() == 1)
 400     {
 401       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 402     }
 403     else if (threshold.getSelectedIndex() == 2)
 404     {
 405       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 406     }
 407
 408     slider.setEnabled(true);
 409     thresholdValue.setEnabled(true);
 410
 411     GraduatedColor acg;
 412     if (cs.isColourByLabel())
 413     {
 414       acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
 415     }
 416     else
 417     {
 418       acg = new GraduatedColor(oldminColour = minColour.getBackground(),
 419               oldmaxColour = maxColour.getBackground(), min, max);
 420
 421     }
 422
 423     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 424     {
 425       slider.setEnabled(false);
 426       thresholdValue.setEnabled(false);
 427       thresholdValue.setText("");
 428       thresholdIsMin.setEnabled(false);
 429     }
 430     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 431             && threshline == null)
 432     {
 433       // todo visual indication of feature threshold
 434       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 435               "Threshold", Color.black);
 436     }
 437
 438     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 439     {
 440       adjusting = true;
 441       acg.setThresh(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.setThreshType(aboveThreshold);
 457     if (thresholdIsMin.isSelected()
 458             && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 459     {
 460       acg.setAutoScaled(false);
 461       if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
 462       {
 463         acg = new GraduatedColor(acg, threshline.value, max);
 464       }
 465       else
 466       {
 467         acg = new GraduatedColor(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.setThresh(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 }