src/jalview/gui/FeatureColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 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 java.util.*;
  24
  25 import java.awt.*;
  26 import java.awt.event.*;
  27 import javax.swing.*;
  28 import javax.swing.border.LineBorder;
  29 import javax.swing.event.*;
  30
  31 import jalview.datamodel.*;
  32 import jalview.schemes.*;
  33 import jalview.util.MessageManager;
  34
  35 import java.awt.Dimension;
  36
  37 public class FeatureColourChooser extends JalviewDialog
  38 {
  39   // FeatureSettings fs;
  40   FeatureRenderer fr;
  41
  42   private GraduatedColor cs;
  43
  44   private Object oldcs;
  45
  46   /**
  47    *
  48    * @return the last colour setting selected by user - either oldcs (which may
  49    *         be a java.awt.Color) or the new GraduatedColor
  50    */
  51   public Object getLastColour()
  52   {
  53     if (cs == null)
  54     {
  55       return oldcs;
  56     }
  57     return cs;
  58   }
  59
  60   Hashtable oldgroupColours;
  61
  62   AlignmentPanel ap;
  63
  64   boolean adjusting = false;
  65
  66   private float min;
  67
  68   private float max;
  69
  70   String type = null;
  71
  72   public FeatureColourChooser(FeatureRenderer frender, String type)
  73   {
  74     this(frender, false, type);
  75   }
  76
  77   public FeatureColourChooser(FeatureRenderer frender, boolean block,
  78           String type)
  79   {
  80     this.fr = frender;
  81     this.type = type;
  82     ap = fr.ap;
  83     initDialogFrame(this, true, block, "Graduated Feature Colour for "
  84             + type, 480, 185);
  85     // frame.setLayer(JLayeredPane.PALETTE_LAYER);
  86     // Desktop.addInternalFrame(frame, "Graduated Feature Colour for "+type,
  87     // 480, 145);
  88
  89     slider.addChangeListener(new ChangeListener()
  90     {
  91       public void stateChanged(ChangeEvent evt)
  92       {
  93         if (!adjusting)
  94         {
  95           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  96           valueChanged();
  97         }
  98       }
  99     });
 100     slider.addMouseListener(new MouseAdapter()
 101     {
 102       public void mouseReleased(MouseEvent evt)
 103       {
 104         if (ap != null)
 105         {
 106           ap.paintAlignment(true);
 107         }
 108         ;
 109       }
 110     });
 111
 112     float mm[] = ((float[][]) fr.minmax.get(type))[0];
 113     min = mm[0];
 114     max = mm[1];
 115     oldcs = fr.featureColours.get(type);
 116     if (oldcs instanceof GraduatedColor)
 117     {
 118       if (((GraduatedColor) oldcs).isAutoScale())
 119       {
 120         // update the scale
 121         cs = new GraduatedColor((GraduatedColor) oldcs, min, max);
 122       }
 123       else
 124       {
 125         cs = new GraduatedColor((GraduatedColor) oldcs);
 126       }
 127     }
 128     else
 129     {
 130       // promote original color to a graduated color
 131       Color bl = Color.black;
 132       if (oldcs instanceof Color)
 133       {
 134         bl = (Color) oldcs;
 135       }
 136       // original colour becomes the maximum colour
 137       cs = new GraduatedColor(Color.white, bl, mm[0], mm[1]);
 138       cs.setColourByLabel(false);
 139     }
 140     minColour.setBackground(oldminColour = cs.getMinColor());
 141     maxColour.setBackground(oldmaxColour = cs.getMaxColor());
 142     adjusting = true;
 143
 144     try
 145     {
 146       jbInit();
 147     } catch (Exception ex)
 148     {
 149     }
 150     // update the gui from threshold state
 151     thresholdIsMin.setSelected(!cs.isAutoScale());
 152     colourByLabel.setSelected(cs.isColourByLabel());
 153     if (cs.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 154     {
 155       // initialise threshold slider and selector
 156       threshold
 157               .setSelectedIndex(cs.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD ? 1
 158                       : 2);
 159       slider.setEnabled(true);
 160       thresholdValue.setEnabled(true);
 161       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 162               "Threshold", Color.black);
 163
 164     }
 165
 166     adjusting = false;
 167
 168     changeColour();
 169     waitForInput();
 170   }
 171
 172   public FeatureColourChooser()
 173   {
 174     try
 175     {
 176       jbInit();
 177     } catch (Exception ex)
 178     {
 179       ex.printStackTrace();
 180     }
 181   }
 182
 183   private void jbInit() throws Exception
 184   {
 185
 186     minColour.setFont(JvSwingUtils.getLabelFont());
 187     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 188     minColour.setPreferredSize(new Dimension(40, 20));
 189     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 190     minColour.addMouseListener(new MouseAdapter()
 191     {
 192       public void mousePressed(MouseEvent e)
 193       {
 194         if (minColour.isEnabled())
 195         {
 196           minColour_actionPerformed();
 197         }
 198       }
 199     });
 200     maxColour.setFont(JvSwingUtils.getLabelFont());
 201     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 202     maxColour.setPreferredSize(new Dimension(40, 20));
 203     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 204     maxColour.addMouseListener(new MouseAdapter()
 205     {
 206       public void mousePressed(MouseEvent e)
 207       {
 208         if (maxColour.isEnabled())
 209         {
 210           maxColour_actionPerformed();
 211         }
 212       }
 213     });
 214     maxColour.setBorder(new LineBorder(Color.black));
 215     minText.setText(MessageManager.getString("label.min"));
 216     minText.setFont(JvSwingUtils.getLabelFont());
 217     maxText.setText(MessageManager.getString("label.max"));
 218     maxText.setFont(JvSwingUtils.getLabelFont());
 219     this.setLayout(borderLayout1);
 220     jPanel2.setLayout(flowLayout1);
 221     jPanel1.setBackground(Color.white);
 222     jPanel2.setBackground(Color.white);
 223     threshold.addActionListener(new ActionListener()
 224     {
 225       public void actionPerformed(ActionEvent e)
 226       {
 227         threshold_actionPerformed(e);
 228       }
 229     });
 230     threshold.setToolTipText(MessageManager
 231             .getString("label.threshold_feature_display_by_score"));
 232     threshold.addItem(MessageManager
 233             .getString("label.threshold_feature_no_thereshold")); // index 0
 234     threshold.addItem(MessageManager
 235             .getString("label.threshold_feature_above_thereshold")); // index 1
 236     threshold.addItem(MessageManager
 237             .getString("label.threshold_feature_below_thereshold")); // index 2
 238     jPanel3.setLayout(flowLayout2);
 239     thresholdValue.addActionListener(new ActionListener()
 240     {
 241       public void actionPerformed(ActionEvent e)
 242       {
 243         thresholdValue_actionPerformed(e);
 244       }
 245     });
 246     slider.setPaintLabels(false);
 247     slider.setPaintTicks(true);
 248     slider.setBackground(Color.white);
 249     slider.setEnabled(false);
 250     slider.setOpaque(false);
 251     slider.setPreferredSize(new Dimension(100, 32));
 252     slider.setToolTipText(MessageManager
 253             .getString("label.adjust_thereshold"));
 254     thresholdValue.setEnabled(false);
 255     thresholdValue.setColumns(7);
 256     jPanel3.setBackground(Color.white);
 257     thresholdIsMin.setBackground(Color.white);
 258     thresholdIsMin.setText(MessageManager
 259             .getString("label.threshold_minmax"));
 260     thresholdIsMin.setToolTipText(MessageManager
 261             .getString("label.toggle_absolute_relative_display_threshold"));
 262     thresholdIsMin.addActionListener(new ActionListener()
 263     {
 264       public void actionPerformed(ActionEvent actionEvent)
 265       {
 266         thresholdIsMin_actionPerformed(actionEvent);
 267       }
 268     });
 269     colourByLabel.setBackground(Color.white);
 270     colourByLabel
 271             .setText(MessageManager.getString("label.colour_by_label"));
 272     colourByLabel
 273             .setToolTipText(MessageManager
 274                     .getString("label.display_features_same_type_different_label_using_different_colour"));
 275     colourByLabel.addActionListener(new ActionListener()
 276     {
 277       public void actionPerformed(ActionEvent actionEvent)
 278       {
 279         colourByLabel_actionPerformed(actionEvent);
 280       }
 281     });
 282     colourPanel.setBackground(Color.white);
 283     jPanel1.add(ok);
 284     jPanel1.add(cancel);
 285     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 286     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 287     colourPanel.add(minText);
 288     colourPanel.add(minColour);
 289     colourPanel.add(maxText);
 290     colourPanel.add(maxColour);
 291     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 292     jPanel3.add(threshold);
 293     jPanel3.add(slider);
 294     jPanel3.add(thresholdValue);
 295     jPanel3.add(thresholdIsMin);
 296     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 297     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 298   }
 299
 300   JLabel minText = new JLabel();
 301
 302   JLabel maxText = new JLabel();
 303
 304   JPanel minColour = new JPanel();
 305
 306   JPanel maxColour = new JPanel();
 307
 308   JPanel colourPanel = new JPanel();
 309
 310   JPanel jPanel1 = new JPanel();
 311
 312   JPanel jPanel2 = new JPanel();
 313
 314   BorderLayout borderLayout1 = new BorderLayout();
 315
 316   JComboBox threshold = new JComboBox();
 317
 318   FlowLayout flowLayout1 = new FlowLayout();
 319
 320   JPanel jPanel3 = new JPanel();
 321
 322   FlowLayout flowLayout2 = new FlowLayout();
 323
 324   JSlider slider = new JSlider();
 325
 326   JTextField thresholdValue = new JTextField(20);
 327
 328   // TODO implement GUI for tolower flag
 329   // JCheckBox toLower = new JCheckBox();
 330
 331   JCheckBox thresholdIsMin = new JCheckBox();
 332
 333   JCheckBox colourByLabel = new JCheckBox();
 334
 335   private GraphLine threshline;
 336
 337   private Color oldmaxColour;
 338
 339   private Color oldminColour;
 340
 341   public void minColour_actionPerformed()
 342   {
 343     Color col = JColorChooser.showDialog(this,
 344             MessageManager.getString("label.select_colour_minimum_value"),
 345             minColour.getBackground());
 346     if (col != null)
 347     {
 348       minColour.setBackground(col);
 349       minColour.setForeground(col);
 350     }
 351     minColour.repaint();
 352     changeColour();
 353   }
 354
 355   public void maxColour_actionPerformed()
 356   {
 357     Color col = JColorChooser.showDialog(this,
 358             MessageManager.getString("label.select_colour_maximum_value"),
 359             maxColour.getBackground());
 360     if (col != null)
 361     {
 362       maxColour.setBackground(col);
 363       maxColour.setForeground(col);
 364     }
 365     maxColour.repaint();
 366     changeColour();
 367   }
 368
 369   void changeColour()
 370   {
 371     // Check if combobox is still adjusting
 372     if (adjusting)
 373     {
 374       return;
 375     }
 376
 377     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
 378     if (threshold.getSelectedIndex() == 1)
 379     {
 380       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 381     }
 382     else if (threshold.getSelectedIndex() == 2)
 383     {
 384       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 385     }
 386
 387     slider.setEnabled(true);
 388     thresholdValue.setEnabled(true);
 389
 390     GraduatedColor acg;
 391     if (cs.isColourByLabel())
 392     {
 393       acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
 394     }
 395     else
 396     {
 397       acg = new GraduatedColor(oldminColour = minColour.getBackground(),
 398               oldmaxColour = maxColour.getBackground(), min, max);
 399
 400     }
 401
 402     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 403     {
 404       slider.setEnabled(false);
 405       thresholdValue.setEnabled(false);
 406       thresholdValue.setText("");
 407       thresholdIsMin.setEnabled(false);
 408     }
 409     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 410             && threshline == null)
 411     {
 412       // todo visual indication of feature threshold
 413       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 414               "Threshold", Color.black);
 415     }
 416
 417     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 418     {
 419       adjusting = true;
 420       acg.setThresh(threshline.value);
 421
 422       float range = max * 1000f - min * 1000f;
 423
 424       slider.setMinimum((int) (min * 1000));
 425       slider.setMaximum((int) (max * 1000));
 426       slider.setValue((int) (threshline.value * 1000));
 427       thresholdValue.setText(threshline.value + "");
 428       slider.setMajorTickSpacing((int) (range / 10f));
 429       slider.setEnabled(true);
 430       thresholdValue.setEnabled(true);
 431       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 432       adjusting = false;
 433     }
 434
 435     acg.setThreshType(aboveThreshold);
 436     if (thresholdIsMin.isSelected()
 437             && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 438     {
 439       acg.setAutoScaled(false);
 440       if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
 441       {
 442         acg = new GraduatedColor(acg, threshline.value, max);
 443       }
 444       else
 445       {
 446         acg = new GraduatedColor(acg, min, threshline.value);
 447       }
 448     }
 449     else
 450     {
 451       acg.setAutoScaled(true);
 452     }
 453     acg.setColourByLabel(colourByLabel.isSelected());
 454     if (acg.isColourByLabel())
 455     {
 456       maxColour.setEnabled(false);
 457       minColour.setEnabled(false);
 458       maxColour.setBackground(this.getBackground());
 459       maxColour.setForeground(this.getBackground());
 460       minColour.setBackground(this.getBackground());
 461       minColour.setForeground(this.getBackground());
 462
 463     }
 464     else
 465     {
 466       maxColour.setEnabled(true);
 467       minColour.setEnabled(true);
 468       maxColour.setBackground(oldmaxColour);
 469       minColour.setBackground(oldminColour);
 470       maxColour.setForeground(oldmaxColour);
 471       minColour.setForeground(oldminColour);
 472     }
 473     fr.featureColours.put(type, acg);
 474     cs = acg;
 475     ap.paintAlignment(false);
 476   }
 477
 478   protected void raiseClosed()
 479   {
 480     if (this.colourEditor != null)
 481     {
 482       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 483     }
 484   }
 485
 486   public void okPressed()
 487   {
 488     changeColour();
 489   }
 490
 491   public void cancelPressed()
 492   {
 493     reset();
 494   }
 495
 496   void reset()
 497   {
 498     fr.featureColours.put(type, oldcs);
 499     ap.paintAlignment(false);
 500     cs = null;
 501   }
 502
 503   public void thresholdCheck_actionPerformed(ActionEvent e)
 504   {
 505     changeColour();
 506   }
 507
 508   public void annotations_actionPerformed(ActionEvent e)
 509   {
 510     changeColour();
 511   }
 512
 513   public void threshold_actionPerformed(ActionEvent e)
 514   {
 515     changeColour();
 516   }
 517
 518   public void thresholdValue_actionPerformed(ActionEvent e)
 519   {
 520     try
 521     {
 522       float f = Float.parseFloat(thresholdValue.getText());
 523       slider.setValue((int) (f * 1000));
 524       threshline.value = f;
 525     } catch (NumberFormatException ex)
 526     {
 527     }
 528   }
 529
 530   public void valueChanged()
 531   {
 532     threshline.value = (float) slider.getValue() / 1000f;
 533     cs.setThresh(threshline.value);
 534     changeColour();
 535     ap.paintAlignment(false);
 536   }
 537
 538   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 539   {
 540     changeColour();
 541   }
 542
 543   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 544   {
 545     changeColour();
 546   }
 547
 548   ActionListener colourEditor = null;
 549
 550   public void addActionListener(ActionListener graduatedColorEditor)
 551   {
 552     if (colourEditor != null)
 553     {
 554       System.err
 555               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 556     }
 557     colourEditor = graduatedColorEditor;
 558   }
 559
 560 }