src/jalview/gui/FeatureColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
   3  * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  */
  18 package jalview.gui;
  19
  20 import java.util.*;
  21
  22 import java.awt.*;
  23 import java.awt.event.*;
  24 import javax.swing.*;
  25 import javax.swing.border.LineBorder;
  26 import javax.swing.event.*;
  27
  28 import jalview.datamodel.*;
  29 import jalview.schemes.*;
  30 import jalview.util.MessageManager;
  31
  32 import java.awt.Dimension;
  33
  34 public class FeatureColourChooser extends JalviewDialog
  35 {
  36   // FeatureSettings fs;
  37   FeatureRenderer fr;
  38
  39   private GraduatedColor cs;
  40
  41   private Object oldcs;
  42
  43   /**
  44    *
  45    * @return the last colour setting selected by user - either oldcs (which may
  46    *         be a java.awt.Color) or the new GraduatedColor
  47    */
  48   public Object getLastColour()
  49   {
  50     if (cs == null)
  51     {
  52       return oldcs;
  53     }
  54     return cs;
  55   }
  56
  57   Hashtable oldgroupColours;
  58
  59   AlignmentPanel ap;
  60
  61   boolean adjusting = false;
  62
  63   private float min;
  64
  65   private float max;
  66
  67   String type = null;
  68
  69   public FeatureColourChooser(FeatureRenderer frender, String type)
  70   {
  71     this(frender, false, type);
  72   }
  73
  74   public FeatureColourChooser(FeatureRenderer frender, boolean block,
  75           String type)
  76   {
  77     this.fr = frender;
  78     this.type = type;
  79     ap = fr.ap;
  80     initDialogFrame(this, true, block, "Graduated Feature Colour for "
  81             + type, 480, 185);
  82     // frame.setLayer(JLayeredPane.PALETTE_LAYER);
  83     // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
  84     // 480, 145);
  85
  86     slider.addChangeListener(new ChangeListener()
  87     {
  88       public void stateChanged(ChangeEvent evt)
  89       {
  90         if (!adjusting)
  91         {
  92           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  93           valueChanged();
  94         }
  95       }
  96     });
  97     slider.addMouseListener(new MouseAdapter()
  98     {
  99       public void mouseReleased(MouseEvent evt)
 100       {
 101         if (ap != null)
 102         {
 103           ap.paintAlignment(true);
 104         }
 105         ;
 106       }
 107     });
 108
 109     float mm[] = ((float[][]) fr.minmax.get(type))[0];
 110     min = mm[0];
 111     max = mm[1];
 112     oldcs = fr.featureColours.get(type);
 113     if (oldcs instanceof GraduatedColor)
 114     {
 115       if (((GraduatedColor) oldcs).isAutoScale())
 116       {
 117         // update the scale
 118         cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
 119       }
 120       else
 121       {
 122         cs = new GraduatedColor((GraduatedColor) oldcs);
 123       }
 124     }
 125     else
 126     {
 127       // promote original color to a graduated color
 128       Color bl = Color.black;
 129       if (oldcs instanceof Color)
 130       {
 131         bl = (Color) oldcs;
 132       }
 133       // original colour becomes the maximum colour
 134       cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
 135       cs.setColourByLabel(false);
 136     }
 137     minColour.setBackground(oldminColour = cs.getMinColor());
 138     maxColour.setBackground(oldmaxColour = cs.getMaxColor());
 139     adjusting = true;
 140
 141     try
 142     {
 143       jbInit();
 144     } catch (Exception ex)
 145     {
 146     }
 147     // update the gui from threshold state
 148     thresholdIsMin.setSelected(!cs.isAutoScale());
 149     colourByLabel.setSelected(cs.isColourByLabel());
 150     if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 151     {
 152       // initialise threshold slider and selector
 153       threshold
 154               .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
 155                       : 2);
 156       slider.setEnabled(true);
 157       thresholdValue.setEnabled(true);
 158       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 159               "Threshold", Color.black);
 160
 161     }
 162
 163     adjusting = false;
 164
 165     changeColour();
 166     waitForInput();
 167   }
 168
 169   public FeatureColourChooser()
 170   {
 171     try
 172     {
 173       jbInit();
 174     } catch (Exception ex)
 175     {
 176       ex.printStackTrace();
 177     }
 178   }
 179
 180   private void jbInit() throws Exception
 181   {
 182
 183     minColour.setFont(JvSwingUtils.getLabelFont());
 184     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 185     minColour.setPreferredSize(new Dimension(40, 20));
 186     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 187     minColour.addMouseListener(new MouseAdapter()
 188     {
 189       public void mousePressed(MouseEvent e)
 190       {
 191         if (minColour.isEnabled())
 192         {
 193           minColour_actionPerformed();
 194         }
 195       }
 196     });
 197     maxColour.setFont(JvSwingUtils.getLabelFont());
 198     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 199     maxColour.setPreferredSize(new Dimension(40, 20));
 200     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 201     maxColour.addMouseListener(new MouseAdapter()
 202     {
 203       public void mousePressed(MouseEvent e)
 204       {
 205         if (maxColour.isEnabled())
 206         {
 207           maxColour_actionPerformed();
 208         }
 209       }
 210     });
 211     maxColour.setBorder(new LineBorder(Color.black));
 212     minText.setText(MessageManager.getString("label.min"));
 213     minText.setFont(JvSwingUtils.getLabelFont());
 214     maxText.setText(MessageManager.getString("label.max"));
 215     maxText.setFont(JvSwingUtils.getLabelFont());
 216     this.setLayout(borderLayout1);
 217     jPanel2.setLayout(flowLayout1);
 218     jPanel1.setBackground(Color.white);
 219     jPanel2.setBackground(Color.white);
 220     threshold.addActionListener(new ActionListener()
 221     {
 222       public void actionPerformed(ActionEvent e)
 223       {
 224         threshold_actionPerformed(e);
 225       }
 226     });
 227     threshold.setToolTipText(MessageManager.getString("label.threshold_feature_display_by_score"));
 228     threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold")); // index 0
 229     threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold")); // index 1
 230     threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold")); // index 2
 231     jPanel3.setLayout(flowLayout2);
 232     thresholdValue.addActionListener(new ActionListener()
 233     {
 234       public void actionPerformed(ActionEvent e)
 235       {
 236         thresholdValue_actionPerformed(e);
 237       }
 238     });
 239     slider.setPaintLabels(false);
 240     slider.setPaintTicks(true);
 241     slider.setBackground(Color.white);
 242     slider.setEnabled(false);
 243     slider.setOpaque(false);
 244     slider.setPreferredSize(new Dimension(100, 32));
 245     slider.setToolTipText(MessageManager.getString("label.adjust_thereshold"));
 246     thresholdValue.setEnabled(false);
 247     thresholdValue.setColumns(7);
 248     jPanel3.setBackground(Color.white);
 249     thresholdIsMin.setBackground(Color.white);
 250     thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
 251     thresholdIsMin
 252             .setToolTipText(MessageManager.getString("label.toggle_absolute_relative_display_threshold"));
 253     thresholdIsMin.addActionListener(new ActionListener()
 254     {
 255       public void actionPerformed(ActionEvent actionEvent)
 256       {
 257         thresholdIsMin_actionPerformed(actionEvent);
 258       }
 259     });
 260     colourByLabel.setBackground(Color.white);
 261     colourByLabel.setText(MessageManager.getString("label.colour_by_label"));
 262     colourByLabel
 263             .setToolTipText(MessageManager.getString("label.display_features_same_type_different_label_using_different_colour"));
 264     colourByLabel.addActionListener(new ActionListener()
 265     {
 266       public void actionPerformed(ActionEvent actionEvent)
 267       {
 268         colourByLabel_actionPerformed(actionEvent);
 269       }
 270     });
 271     colourPanel.setBackground(Color.white);
 272     jPanel1.add(ok);
 273     jPanel1.add(cancel);
 274     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 275     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 276     colourPanel.add(minText);
 277     colourPanel.add(minColour);
 278     colourPanel.add(maxText);
 279     colourPanel.add(maxColour);
 280     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 281     jPanel3.add(threshold);
 282     jPanel3.add(slider);
 283     jPanel3.add(thresholdValue);
 284     jPanel3.add(thresholdIsMin);
 285     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 286     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 287   }
 288
 289   JLabel minText = new JLabel();
 290
 291   JLabel maxText = new JLabel();
 292
 293   JPanel minColour = new JPanel();
 294
 295   JPanel maxColour = new JPanel();
 296
 297   JPanel colourPanel = new JPanel();
 298
 299   JPanel jPanel1 = new JPanel();
 300
 301   JPanel jPanel2 = new JPanel();
 302
 303   BorderLayout borderLayout1 = new BorderLayout();
 304
 305   JComboBox threshold = new JComboBox();
 306
 307   FlowLayout flowLayout1 = new FlowLayout();
 308
 309   JPanel jPanel3 = new JPanel();
 310
 311   FlowLayout flowLayout2 = new FlowLayout();
 312
 313   JSlider slider = new JSlider();
 314
 315   JTextField thresholdValue = new JTextField(20);
 316
 317   // TODO implement GUI for tolower flag
 318   // JCheckBox toLower = new JCheckBox();
 319
 320   JCheckBox thresholdIsMin = new JCheckBox();
 321
 322   JCheckBox colourByLabel = new JCheckBox();
 323
 324   private GraphLine threshline;
 325
 326   private Color oldmaxColour;
 327
 328   private Color oldminColour;
 329
 330   public void minColour_actionPerformed()
 331   {
 332     Color col = JColorChooser.showDialog(this,
 333             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 334     if (col != null)
 335     {
 336       minColour.setBackground(col);
 337       minColour.setForeground(col);
 338     }
 339     minColour.repaint();
 340     changeColour();
 341   }
 342
 343   public void maxColour_actionPerformed()
 344   {
 345     Color col = JColorChooser.showDialog(this,
 346             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 347     if (col != null)
 348     {
 349       maxColour.setBackground(col);
 350       maxColour.setForeground(col);
 351     }
 352     maxColour.repaint();
 353     changeColour();
 354   }
 355
 356   void changeColour()
 357   {
 358     // Check if combobox is still adjusting
 359     if (adjusting)
 360     {
 361       return;
 362     }
 363
 364     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
 365     if (threshold.getSelectedIndex()==1)
 366     {
 367       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 368     }
 369     else if (threshold.getSelectedIndex()==2)
 370     {
 371       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 372     }
 373
 374     slider.setEnabled(true);
 375     thresholdValue.setEnabled(true);
 376
 377     GraduatedColor acg;
 378     if (cs.isColourByLabel())
 379     {
 380       acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
 381     }
 382     else
 383     {
 384       acg = new GraduatedColor(oldminColour = minColour.getBackground(),
 385               oldmaxColour = maxColour.getBackground(), min, max);
 386
 387     }
 388
 389     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 390     {
 391       slider.setEnabled(false);
 392       thresholdValue.setEnabled(false);
 393       thresholdValue.setText("");
 394       thresholdIsMin.setEnabled(false);
 395     }
 396     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 397             && threshline == null)
 398     {
 399       // todo visual indication of feature threshold
 400       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 401               "Threshold", Color.black);
 402     }
 403
 404     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 405     {
 406       adjusting = true;
 407       acg.setThresh(threshline.value);
 408
 409       float range = max * 1000f - min * 1000f;
 410
 411       slider.setMinimum((int) (min * 1000));
 412       slider.setMaximum((int) (max * 1000));
 413       slider.setValue((int) (threshline.value * 1000));
 414       thresholdValue.setText(threshline.value + "");
 415       slider.setMajorTickSpacing((int) (range / 10f));
 416       slider.setEnabled(true);
 417       thresholdValue.setEnabled(true);
 418       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 419       adjusting = false;
 420     }
 421
 422     acg.setThreshType(aboveThreshold);
 423     if (thresholdIsMin.isSelected()
 424             && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 425     {
 426       acg.setAutoScaled(false);
 427       if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
 428       {
 429         acg = new GraduatedColor(acg, threshline.value, max);
 430       }
 431       else
 432       {
 433         acg = new GraduatedColor(acg, min, threshline.value);
 434       }
 435     }
 436     else
 437     {
 438       acg.setAutoScaled(true);
 439     }
 440     acg.setColourByLabel(colourByLabel.isSelected());
 441     if (acg.isColourByLabel())
 442     {
 443       maxColour.setEnabled(false);
 444       minColour.setEnabled(false);
 445       maxColour.setBackground(this.getBackground());
 446       maxColour.setForeground(this.getBackground());
 447       minColour.setBackground(this.getBackground());
 448       minColour.setForeground(this.getBackground());
 449
 450     }
 451     else
 452     {
 453       maxColour.setEnabled(true);
 454       minColour.setEnabled(true);
 455       maxColour.setBackground(oldmaxColour);
 456       minColour.setBackground(oldminColour);
 457       maxColour.setForeground(oldmaxColour);
 458       minColour.setForeground(oldminColour);
 459     }
 460     fr.featureColours.put(type, acg);
 461     cs = acg;
 462     ap.paintAlignment(false);
 463   }
 464
 465   protected void raiseClosed()
 466   {
 467     if (this.colourEditor != null)
 468     {
 469       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 470     }
 471   }
 472
 473   public void okPressed()
 474   {
 475     changeColour();
 476   }
 477
 478   public void cancelPressed()
 479   {
 480     reset();
 481   }
 482
 483   void reset()
 484   {
 485     fr.featureColours.put(type, oldcs);
 486     ap.paintAlignment(false);
 487     cs = null;
 488   }
 489
 490   public void thresholdCheck_actionPerformed(ActionEvent e)
 491   {
 492     changeColour();
 493   }
 494
 495   public void annotations_actionPerformed(ActionEvent e)
 496   {
 497     changeColour();
 498   }
 499
 500   public void threshold_actionPerformed(ActionEvent e)
 501   {
 502     changeColour();
 503   }
 504
 505   public void thresholdValue_actionPerformed(ActionEvent e)
 506   {
 507     try
 508     {
 509       float f = Float.parseFloat(thresholdValue.getText());
 510       slider.setValue((int) (f * 1000));
 511       threshline.value = f;
 512     } catch (NumberFormatException ex)
 513     {
 514     }
 515   }
 516
 517   public void valueChanged()
 518   {
 519     threshline.value = (float) slider.getValue() / 1000f;
 520     cs.setThresh(threshline.value);
 521     changeColour();
 522     ap.paintAlignment(false);
 523   }
 524
 525   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 526   {
 527     changeColour();
 528   }
 529
 530   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 531   {
 532     changeColour();
 533   }
 534
 535   ActionListener colourEditor = null;
 536
 537   public void addActionListener(ActionListener graduatedColorEditor)
 538   {
 539     if (colourEditor != null)
 540     {
 541       System.err
 542               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 543     }
 544     colourEditor = graduatedColorEditor;
 545   }
 546
 547 }