src/jalview/gui/FeatureColourChooser.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   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.getString("label.threshold_feature_display_by_score"));
 231     threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold")); // index 0
 232     threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold")); // index 1
 233     threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold")); // index 2
 234     jPanel3.setLayout(flowLayout2);
 235     thresholdValue.addActionListener(new ActionListener()
 236     {
 237       public void actionPerformed(ActionEvent e)
 238       {
 239         thresholdValue_actionPerformed(e);
 240       }
 241     });
 242     slider.setPaintLabels(false);
 243     slider.setPaintTicks(true);
 244     slider.setBackground(Color.white);
 245     slider.setEnabled(false);
 246     slider.setOpaque(false);
 247     slider.setPreferredSize(new Dimension(100, 32));
 248     slider.setToolTipText(MessageManager.getString("label.adjust_thereshold"));
 249     thresholdValue.setEnabled(false);
 250     thresholdValue.setColumns(7);
 251     jPanel3.setBackground(Color.white);
 252     thresholdIsMin.setBackground(Color.white);
 253     thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
 254     thresholdIsMin
 255             .setToolTipText(MessageManager.getString("label.toggle_absolute_relative_display_threshold"));
 256     thresholdIsMin.addActionListener(new ActionListener()
 257     {
 258       public void actionPerformed(ActionEvent actionEvent)
 259       {
 260         thresholdIsMin_actionPerformed(actionEvent);
 261       }
 262     });
 263     colourByLabel.setBackground(Color.white);
 264     colourByLabel.setText(MessageManager.getString("label.colour_by_label"));
 265     colourByLabel
 266             .setToolTipText(MessageManager.getString("label.display_features_same_type_different_label_using_different_colour"));
 267     colourByLabel.addActionListener(new ActionListener()
 268     {
 269       public void actionPerformed(ActionEvent actionEvent)
 270       {
 271         colourByLabel_actionPerformed(actionEvent);
 272       }
 273     });
 274     colourPanel.setBackground(Color.white);
 275     jPanel1.add(ok);
 276     jPanel1.add(cancel);
 277     jPanel2.add(colourByLabel, java.awt.BorderLayout.WEST);
 278     jPanel2.add(colourPanel, java.awt.BorderLayout.EAST);
 279     colourPanel.add(minText);
 280     colourPanel.add(minColour);
 281     colourPanel.add(maxText);
 282     colourPanel.add(maxColour);
 283     this.add(jPanel3, java.awt.BorderLayout.CENTER);
 284     jPanel3.add(threshold);
 285     jPanel3.add(slider);
 286     jPanel3.add(thresholdValue);
 287     jPanel3.add(thresholdIsMin);
 288     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 289     this.add(jPanel2, java.awt.BorderLayout.NORTH);
 290   }
 291
 292   JLabel minText = new JLabel();
 293
 294   JLabel maxText = new JLabel();
 295
 296   JPanel minColour = new JPanel();
 297
 298   JPanel maxColour = new JPanel();
 299
 300   JPanel colourPanel = new JPanel();
 301
 302   JPanel jPanel1 = new JPanel();
 303
 304   JPanel jPanel2 = new JPanel();
 305
 306   BorderLayout borderLayout1 = new BorderLayout();
 307
 308   JComboBox threshold = new JComboBox();
 309
 310   FlowLayout flowLayout1 = new FlowLayout();
 311
 312   JPanel jPanel3 = new JPanel();
 313
 314   FlowLayout flowLayout2 = new FlowLayout();
 315
 316   JSlider slider = new JSlider();
 317
 318   JTextField thresholdValue = new JTextField(20);
 319
 320   // TODO implement GUI for tolower flag
 321   // JCheckBox toLower = new JCheckBox();
 322
 323   JCheckBox thresholdIsMin = new JCheckBox();
 324
 325   JCheckBox colourByLabel = new JCheckBox();
 326
 327   private GraphLine threshline;
 328
 329   private Color oldmaxColour;
 330
 331   private Color oldminColour;
 332
 333   public void minColour_actionPerformed()
 334   {
 335     Color col = JColorChooser.showDialog(this,
 336             MessageManager.getString("label.select_colour_minimum_value"), minColour.getBackground());
 337     if (col != null)
 338     {
 339       minColour.setBackground(col);
 340       minColour.setForeground(col);
 341     }
 342     minColour.repaint();
 343     changeColour();
 344   }
 345
 346   public void maxColour_actionPerformed()
 347   {
 348     Color col = JColorChooser.showDialog(this,
 349             MessageManager.getString("label.select_colour_maximum_value"), maxColour.getBackground());
 350     if (col != null)
 351     {
 352       maxColour.setBackground(col);
 353       maxColour.setForeground(col);
 354     }
 355     maxColour.repaint();
 356     changeColour();
 357   }
 358
 359   void changeColour()
 360   {
 361     // Check if combobox is still adjusting
 362     if (adjusting)
 363     {
 364       return;
 365     }
 366
 367     int aboveThreshold = AnnotationColourGradient.NO_THRESHOLD;
 368     if (threshold.getSelectedIndex()==1)
 369     {
 370       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 371     }
 372     else if (threshold.getSelectedIndex()==2)
 373     {
 374       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 375     }
 376
 377     slider.setEnabled(true);
 378     thresholdValue.setEnabled(true);
 379
 380     GraduatedColor acg;
 381     if (cs.isColourByLabel())
 382     {
 383       acg = new GraduatedColor(oldminColour, oldmaxColour, min, max);
 384     }
 385     else
 386     {
 387       acg = new GraduatedColor(oldminColour = minColour.getBackground(),
 388               oldmaxColour = maxColour.getBackground(), min, max);
 389
 390     }
 391
 392     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 393     {
 394       slider.setEnabled(false);
 395       thresholdValue.setEnabled(false);
 396       thresholdValue.setText("");
 397       thresholdIsMin.setEnabled(false);
 398     }
 399     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 400             && threshline == null)
 401     {
 402       // todo visual indication of feature threshold
 403       threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
 404               "Threshold", Color.black);
 405     }
 406
 407     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 408     {
 409       adjusting = true;
 410       acg.setThresh(threshline.value);
 411
 412       float range = max * 1000f - min * 1000f;
 413
 414       slider.setMinimum((int) (min * 1000));
 415       slider.setMaximum((int) (max * 1000));
 416       slider.setValue((int) (threshline.value * 1000));
 417       thresholdValue.setText(threshline.value + "");
 418       slider.setMajorTickSpacing((int) (range / 10f));
 419       slider.setEnabled(true);
 420       thresholdValue.setEnabled(true);
 421       thresholdIsMin.setEnabled(!colourByLabel.isSelected());
 422       adjusting = false;
 423     }
 424
 425     acg.setThreshType(aboveThreshold);
 426     if (thresholdIsMin.isSelected()
 427             && aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 428     {
 429       acg.setAutoScaled(false);
 430       if (aboveThreshold == AnnotationColourGradient.ABOVE_THRESHOLD)
 431       {
 432         acg = new GraduatedColor(acg, threshline.value, max);
 433       }
 434       else
 435       {
 436         acg = new GraduatedColor(acg, min, threshline.value);
 437       }
 438     }
 439     else
 440     {
 441       acg.setAutoScaled(true);
 442     }
 443     acg.setColourByLabel(colourByLabel.isSelected());
 444     if (acg.isColourByLabel())
 445     {
 446       maxColour.setEnabled(false);
 447       minColour.setEnabled(false);
 448       maxColour.setBackground(this.getBackground());
 449       maxColour.setForeground(this.getBackground());
 450       minColour.setBackground(this.getBackground());
 451       minColour.setForeground(this.getBackground());
 452
 453     }
 454     else
 455     {
 456       maxColour.setEnabled(true);
 457       minColour.setEnabled(true);
 458       maxColour.setBackground(oldmaxColour);
 459       minColour.setBackground(oldminColour);
 460       maxColour.setForeground(oldmaxColour);
 461       minColour.setForeground(oldminColour);
 462     }
 463     fr.featureColours.put(type, acg);
 464     cs = acg;
 465     ap.paintAlignment(false);
 466   }
 467
 468   protected void raiseClosed()
 469   {
 470     if (this.colourEditor != null)
 471     {
 472       colourEditor.actionPerformed(new ActionEvent(this, 0, "CLOSED"));
 473     }
 474   }
 475
 476   public void okPressed()
 477   {
 478     changeColour();
 479   }
 480
 481   public void cancelPressed()
 482   {
 483     reset();
 484   }
 485
 486   void reset()
 487   {
 488     fr.featureColours.put(type, oldcs);
 489     ap.paintAlignment(false);
 490     cs = null;
 491   }
 492
 493   public void thresholdCheck_actionPerformed(ActionEvent e)
 494   {
 495     changeColour();
 496   }
 497
 498   public void annotations_actionPerformed(ActionEvent e)
 499   {
 500     changeColour();
 501   }
 502
 503   public void threshold_actionPerformed(ActionEvent e)
 504   {
 505     changeColour();
 506   }
 507
 508   public void thresholdValue_actionPerformed(ActionEvent e)
 509   {
 510     try
 511     {
 512       float f = Float.parseFloat(thresholdValue.getText());
 513       slider.setValue((int) (f * 1000));
 514       threshline.value = f;
 515     } catch (NumberFormatException ex)
 516     {
 517     }
 518   }
 519
 520   public void valueChanged()
 521   {
 522     threshline.value = (float) slider.getValue() / 1000f;
 523     cs.setThresh(threshline.value);
 524     changeColour();
 525     ap.paintAlignment(false);
 526   }
 527
 528   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 529   {
 530     changeColour();
 531   }
 532
 533   public void colourByLabel_actionPerformed(ActionEvent actionEvent)
 534   {
 535     changeColour();
 536   }
 537
 538   ActionListener colourEditor = null;
 539
 540   public void addActionListener(ActionListener graduatedColorEditor)
 541   {
 542     if (colourEditor != null)
 543     {
 544       System.err
 545               .println("IMPLEMENTATION ISSUE: overwriting action listener for FeatureColourChooser");
 546     }
 547     colourEditor = graduatedColorEditor;
 548   }
 549
 550 }