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.api.FeatureColourI;
  24 import jalview.datamodel.GraphLine;
  25 import jalview.schemes.FeatureColour;
  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
  37 import javax.swing.BorderFactory;
  38 import javax.swing.JCheckBox;
  39 import javax.swing.JColorChooser;
  40 import javax.swing.JComboBox;
  41 import javax.swing.JLabel;
  42 import javax.swing.JPanel;
  43 import javax.swing.JSlider;
  44 import javax.swing.JTextField;
  45 import javax.swing.border.LineBorder;
  46 import javax.swing.event.ChangeEvent;
  47 import javax.swing.event.ChangeListener;
  48
  49 public class FeatureColourChooser extends JalviewDialog
  50 {
  51   // FeatureSettings fs;
  52   FeatureRenderer fr;
  53
  54   private FeatureColourI cs;
  55
  56   private FeatureColourI oldcs;
  57
  58   /**
  59    *
  60    * @return the last colour setting selected by user - either oldcs (which may
  61    *         be a java.awt.Color) or the new GraduatedColor
  62    */
  63   public FeatureColourI getLastColour()
  64   {
  65     if (cs == null)
  66     {
  67       return oldcs;
  68     }
  69     return cs;
  70   }
  71
  72   AlignmentPanel ap;
  73
  74   boolean adjusting = false;
  75
  76   final private float min;
  77
  78   final private float max;
  79
  80   final private float scaleFactor;
  81
  82   String type = null;
  83
  84   public FeatureColourChooser(FeatureRenderer frender, String type)
  85   {
  86     this(frender, false, type);
  87   }
  88
  89   public FeatureColourChooser(FeatureRenderer frender, boolean block,
  90           String type)
  91   {
  92     this.fr = frender;
  93     this.type = type;
  94     ap = fr.ap;
  95     String title = MessageManager.formatMessage(
  96             "label.graduated_color_for_params", new String[] { type });
  97     initDialogFrame(this, true, block, title, 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       @Override
 105       public void stateChanged(ChangeEvent evt)
 106       {
 107         if (!adjusting)
 108         {
 109           thresholdValue.setText((slider.getValue() / scaleFactor) + "");
 110           valueChanged();
 111         }
 112       }
 113     });
 114     slider.addMouseListener(new MouseAdapter()
 115     {
 116       @Override
 117       public void mouseReleased(MouseEvent evt)
 118       {
 119         if (ap != null)
 120         {
 121           ap.paintAlignment(true);
 122         }
 123         ;
 124       }
 125     });
 126
 127     float mm[] = fr.getMinMax().get(type)[0];
 128     min = mm[0];
 129     max = mm[1];
 130
 131     /*
 132      * ensure scale factor allows a scaled range with
 133      * 10 integer divisions ('ticks'); if we have got here,
 134      * we should expect that max != min
 135      */
 136     scaleFactor = (max == min) ? 1f : 100f / (max - min);
 137
 138     oldcs = fr.getFeatureColours().get(type);
 139     if (!oldcs.isSimpleColour())
 140     {
 141       if (oldcs.isAutoScaled())
 142       {
 143         // update the scale
 144         cs = new FeatureColour((FeatureColour) oldcs, min, max);
 145       }
 146       else
 147       {
 148         cs = new FeatureColour((FeatureColour) oldcs);
 149       }
 150     }
 151     else
 152     {
 153       // promote original color to a graduated color
 154       Color bl = oldcs.getColour();
 155       if (bl == null)
 156       {
 157         bl = Color.BLACK;
 158       }
 159       // original colour becomes the maximum colour
 160       cs = new FeatureColour(Color.white, bl, mm[0], mm[1]);
 161       cs.setColourByLabel(false);
 162     }
 163     minColour.setBackground(oldminColour = cs.getMinColour());
 164     maxColour.setBackground(oldmaxColour = cs.getMaxColour());
 165     adjusting = true;
 166
 167     try
 168     {
 169       jbInit();
 170     } catch (Exception ex)
 171     {
 172     }
 173     // update the gui from threshold state
 174     thresholdIsMin.setSelected(!cs.isAutoScaled());
 175     colourByLabel.setSelected(cs.isColourByLabel());
 176     if (cs.hasThreshold())
 177     {
 178       // initialise threshold slider and selector
 179       threshold.setSelectedIndex(cs.isAboveThreshold() ? 1 : 2);
 180       slider.setEnabled(true);
 181       thresholdValue.setEnabled(true);
 182       threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
 183
 184     }
 185
 186     adjusting = false;
 187
 188     changeColour();
 189     waitForInput();
 190   }
 191
 192   private void jbInit() throws Exception
 193   {
 194
 195     minColour.setFont(JvSwingUtils.getLabelFont());
 196     minColour.setBorder(BorderFactory.createLineBorder(Color.black));
 197     minColour.setPreferredSize(new Dimension(40, 20));
 198     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 199     minColour.addMouseListener(new MouseAdapter()
 200     {
 201       @Override
 202       public void mousePressed(MouseEvent e)
 203       {
 204         if (minColour.isEnabled())
 205         {
 206           minColour_actionPerformed();
 207         }
 208       }
 209     });
 210     maxColour.setFont(JvSwingUtils.getLabelFont());
 211     maxColour.setBorder(BorderFactory.createLineBorder(Color.black));
 212     maxColour.setPreferredSize(new Dimension(40, 20));
 213     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 214     maxColour.addMouseListener(new MouseAdapter()
 215     {
 216       @Override
 217       public void mousePressed(MouseEvent e)
 218       {
 219         if (maxColour.isEnabled())
 220         {
 221           maxColour_actionPerformed();
 222         }
 223       }
 224     });
 225     maxColour.setBorder(new LineBorder(Color.black));
 226     minText.setText(MessageManager.getString("label.min"));
 227     minText.setFont(JvSwingUtils.getLabelFont());
 228     maxText.setText(MessageManager.getString("label.max"));
 229     maxText.setFont(JvSwingUtils.getLabelFont());
 230     this.setLayout(borderLayout1);
 231     jPanel2.setLayout(flowLayout1);
 232     jPanel1.setBackground(Color.white);
 233     jPanel2.setBackground(Color.white);
 234     threshold.addActionListener(new ActionListener()
 235     {
 236       @Override
 237       public void actionPerformed(ActionEvent e)
 238       {
 239         threshold_actionPerformed(e);
 240       }
 241     });
 242     threshold.setToolTipText(MessageManager
 243             .getString("label.threshold_feature_display_by_score"));
 244     threshold.addItem(MessageManager
 245             .getString("label.threshold_feature_no_threshold")); // index 0
 246     threshold.addItem(MessageManager
 247             .getString("label.threshold_feature_above_threshold")); // index 1
 248     threshold.addItem(MessageManager
 249             .getString("label.threshold_feature_below_threshold")); // index 2
 250     jPanel3.setLayout(flowLayout2);
 251     thresholdValue.addActionListener(new ActionListener()
 252     {
 253       @Override
 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_threshold"));
 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       @Override
 278       public void actionPerformed(ActionEvent actionEvent)
 279       {
 280         thresholdIsMin_actionPerformed(actionEvent);
 281       }
 282     });
 283     colourByLabel.setBackground(Color.white);
 284     colourByLabel
 285             .setText(MessageManager.getString("label.colour_by_label"));
 286     colourByLabel
 287             .setToolTipText(MessageManager
 288                     .getString("label.display_features_same_type_different_label_using_different_colour"));
 289     colourByLabel.addActionListener(new ActionListener()
 290     {
 291       @Override
 292       public void actionPerformed(ActionEvent actionEvent)
 293       {
 294         colourByLabel_actionPerformed(actionEvent);
 295       }
 296     });
 297     colourPanel.setBackground(Color.white);
 298     jPanel1.add(ok);
 299     jPanel1.add(cancel);
 300     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 301     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 302     colourPanel.add(minText);
 303     colourPanel.add(minColour);
 304     colourPanel.add(maxText);
 305     colourPanel.add(maxColour);
 306     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 307     jPanel3.add(threshold);
 308     jPanel3.add(slider);
 309     jPanel3.add(thresholdValue);
 310     jPanel3.add(thresholdIsMin);
 311     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 312     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 313   }
 314
 315   JLabel minText = new JLabel();
 316
 317   JLabel maxText = new JLabel();
 318
 319   JPanel minColour = new JPanel();
 320
 321   JPanel maxColour = new JPanel();
 322
 323   JPanel colourPanel = new JPanel();
 324
 325   JPanel jPanel1 = new JPanel();
 326
 327   JPanel jPanel2 = new JPanel();
 328
 329   BorderLayout borderLayout1 = new BorderLayout();
 330
 331   JComboBox threshold = new JComboBox();
 332
 333   FlowLayout flowLayout1 = new FlowLayout();
 334
 335   JPanel jPanel3 = new JPanel();
 336
 337   FlowLayout flowLayout2 = new FlowLayout();
 338
 339   JSlider slider = new JSlider();
 340
 341   JTextField thresholdValue = new JTextField(20);
 342
 343   // TODO implement GUI for tolower flag
 344   // JCheckBox toLower = new JCheckBox();
 345
 346   JCheckBox thresholdIsMin = new JCheckBox();
 347
 348   JCheckBox colourByLabel = new JCheckBox();
 349
 350   private GraphLine threshline;
 351
 352   private Color oldmaxColour;
 353
 354   private Color oldminColour;
 355
 356   public void minColour_actionPerformed()
 357   {
 358     Color col = JColorChooser.showDialog(this,
 359             MessageManager.getString("label.select_colour_minimum_value"),
 360             minColour.getBackground());
 361     if (col != null)
 362     {
 363       minColour.setBackground(col);
 364       minColour.setForeground(col);
 365     }
 366     minColour.repaint();
 367     changeColour();
 368   }
 369
 370   public void maxColour_actionPerformed()
 371   {
 372     Color col = JColorChooser.showDialog(this,
 373             MessageManager.getString("label.select_colour_maximum_value"),
 374             maxColour.getBackground());
 375     if (col != null)
 376     {
 377       maxColour.setBackground(col);
 378       maxColour.setForeground(col);
 379     }
 380     maxColour.repaint();
 381     changeColour();
 382   }
 383
 384   void changeColour()
 385   {
 386     // Check if combobox is still adjusting
 387     if (adjusting)
 388     {
 389       return;
 390     }
 391
 392     boolean aboveThreshold = false;
 393     boolean belowThreshold = false;
 394     if (threshold.getSelectedIndex() == 1)
 395     {
 396       aboveThreshold = true;
 397     }
 398     else if (threshold.getSelectedIndex() == 2)
 399     {
 400       belowThreshold = true;
 401     }
 402     boolean hasThreshold = aboveThreshold || belowThreshold;
 403
 404     slider.setEnabled(true);
 405     thresholdValue.setEnabled(true);
 406
 407     FeatureColourI acg;
 408     if (cs.isColourByLabel())
 409     {
 410       acg = new FeatureColour(oldminColour, oldmaxColour, min, max);
 411     }
 412     else
 413     {
 414       acg = new FeatureColour(oldminColour = minColour.getBackground(),
 415               oldmaxColour = maxColour.getBackground(), min, max);
 416
 417     }
 418
 419     if (!hasThreshold)
 420     {
 421       slider.setEnabled(false);
 422       thresholdValue.setEnabled(false);
 423       thresholdValue.setText("");
 424       thresholdIsMin.setEnabled(false);
 425     }
 426     else if (threshline == null)
 427     {
 428       // todo visual indication of feature threshold
 429       threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
 430     }
 431
 432     if (hasThreshold)
 433     {
 434       adjusting = true;
 435       acg.setThreshold(threshline.value);
 436
 437       float range = (max - min) * scaleFactor;
 438
 439       slider.setMinimum((int) (min * scaleFactor));
 440       slider.setMaximum((int) (max * scaleFactor));
 441       slider.setValue((int) (threshline.value * scaleFactor));
 442       thresholdValue.setText(threshline.value + "");
 443       slider.setMajorTickSpacing((int) (range / 10f));
 444       slider.setEnabled(true);
 445       thresholdValue.setEnabled(true);
 446       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 447       adjusting = false;
 448     }
 449
 450     acg.setAboveThreshold(aboveThreshold);
 451     acg.setBelowThreshold(belowThreshold);
 452     if (thresholdIsMin.isSelected() && hasThreshold)
 453     {
 454       acg.setAutoScaled(false);
 455       if (aboveThreshold)
 456       {
 457         acg = new FeatureColour((FeatureColour) acg, threshline.value, max);
 458       }
 459       else
 460       {
 461         acg = new FeatureColour((FeatureColour) acg, min, threshline.value);
 462       }
 463     }
 464     else
 465     {
 466       acg.setAutoScaled(true);
 467     }
 468     acg.setColourByLabel(colourByLabel.isSelected());
 469     if (acg.isColourByLabel())
 470     {
 471       maxColour.setEnabled(false);
 472       minColour.setEnabled(false);
 473       maxColour.setBackground(this.getBackground());
 474       maxColour.setForeground(this.getBackground());
 475       minColour.setBackground(this.getBackground());
 476       minColour.setForeground(this.getBackground());
 477
 478     }
 479     else
 480     {
 481       maxColour.setEnabled(true);
 482       minColour.setEnabled(true);
 483       maxColour.setBackground(oldmaxColour);
 484       minColour.setBackground(oldminColour);
 485       maxColour.setForeground(oldmaxColour);
 486       minColour.setForeground(oldminColour);
 487     }
 488     fr.setColour(type, acg);
 489     cs = acg;
 490     ap.paintAlignment(false);
 491   }
 492
 493   @Override
 494   protected void raiseClosed()
 495   {
 496     if (this.colourEditor != null)
 497     {
 498       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 499     }
 500   }
 501
 502   @Override
 503   public void okPressed()
 504   {
 505     changeColour();
 506   }
 507
 508   @Override
 509   public void cancelPressed()
 510   {
 511     reset();
 512   }
 513
 514   void reset()
 515   {
 516     fr.setColour(type, oldcs);
 517     ap.paintAlignment(false);
 518     cs = null;
 519   }
 520
 521   public void thresholdCheck_actionPerformed(ActionEvent e)
 522   {
 523     changeColour();
 524   }
 525
 526   public void annotations_actionPerformed(ActionEvent e)
 527   {
 528     changeColour();
 529   }
 530
 531   public void threshold_actionPerformed(ActionEvent e)
 532   {
 533     changeColour();
 534   }
 535
 536   public void thresholdValue_actionPerformed(ActionEvent e)
 537   {
 538     try
 539     {
 540       float f = Float.parseFloat(thresholdValue.getText());
 541       slider.setValue((int) (f * scaleFactor));
 542       threshline.value = f;
 543     } catch (NumberFormatException ex)
 544     {
 545     }
 546   }
 547
 548   public void valueChanged()
 549   {
 550     threshline.value = slider.getValue() / scaleFactor;
 551     cs.setThreshold(threshline.value);
 552     changeColour();
 553     ap.paintAlignment(false);
 554   }
 555
 556   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 557   {
 558     changeColour();
 559   }
 560
 561   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 562   {
 563     changeColour();
 564   }
 565
 566   ActionListener colourEditor = null;
 567
 568   public void addActionListener(ActionListener graduatedColorEditor)
 569   {
 570     if (colourEditor != null)
 571     {
 572       System.err
 573               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 574     }
 575     colourEditor = graduatedColorEditor;
 576   }
 577
 578 }