src/jalview/gui/AnnotationColourChooser.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
  25 import javax.swing.*;
  26 import javax.swing.event.*;
  27
  28 import net.miginfocom.swing.MigLayout;
  29
  30 import jalview.bin.Cache;
  31 import jalview.datamodel.*;
  32 import jalview.schemes.*;
  33 import jalview.util.MessageManager;
  34
  35 import java.awt.Dimension;
  36
  37 public class AnnotationColourChooser extends JPanel
  38 {
  39   JInternalFrame frame;
  40
  41   AlignViewport av;
  42
  43   AlignmentPanel ap;
  44
  45   ColourSchemeI oldcs;
  46
  47   Hashtable oldgroupColours;
  48
  49   jalview.datamodel.AlignmentAnnotation currentAnnotation;
  50
  51   boolean adjusting = false;
  52   /**
  53    * enabled if the user is dragging the slider - try to keep updates to a minimun
  54    */
  55   boolean sliderDragging = false;
  56
  57   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
  58   {
  59     oldcs = av.getGlobalColourScheme();
  60     if (av.getAlignment().getGroups() != null)
  61     {
  62       oldgroupColours = new Hashtable();
  63       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
  64       {
  65         if (sg.cs != null)
  66         {
  67           oldgroupColours.put(sg, sg.cs);
  68         }
  69       }
  70     }
  71     this.av = av;
  72     this.ap = ap;
  73     frame = new JInternalFrame();
  74     frame.setContentPane(this);
  75     frame.setLayer(JLayeredPane.PALETTE_LAYER);
  76     Desktop.addInternalFrame(frame, "Colour by Annotation", 520, 215);
  77
  78     slider.addChangeListener(new ChangeListener()
  79     {
  80       public void stateChanged(ChangeEvent evt)
  81       {
  82         if (!adjusting)
  83         {
  84           thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
  85           valueChanged(!sliderDragging);
  86         }
  87       }
  88     });
  89     slider.addMouseListener(new MouseAdapter()
  90     {
  91       @Override
  92       public void mousePressed(MouseEvent e)
  93       {
  94         sliderDragging=true;
  95         super.mousePressed(e);
  96       }
  97
  98       @Override
  99       public void mouseDragged(MouseEvent e)
 100       {
 101         sliderDragging=true;
 102         super.mouseDragged(e);
 103       }
 104       public void mouseReleased(MouseEvent evt)
 105       {
 106         if (sliderDragging)
 107         {
 108           sliderDragging=false;
 109           valueChanged(true);
 110         }
 111         ap.paintAlignment(true);
 112       }
 113     });
 114
 115     if (av.getAlignment().getAlignmentAnnotation() == null)
 116     {
 117       return;
 118     }
 119
 120     // Always get default shading from preferences.
 121     setDefaultMinMax();
 122
 123     if (oldcs instanceof AnnotationColourGradient)
 124     {
 125       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 126       currentColours.setSelected(acg.predefinedColours);
 127       if (!acg.predefinedColours)
 128       {
 129         minColour.setBackground(acg.getMinColour());
 130         maxColour.setBackground(acg.getMaxColour());
 131       }
 132       seqAssociated.setSelected(acg.isSeqAssociated());
 133     }
 134     adjusting = true;
 135     annotations = new JComboBox(
 136             getAnnotationItems(seqAssociated.isSelected()));
 137
 138     threshold.addItem("No Threshold");
 139     threshold.addItem("Above Threshold");
 140     threshold.addItem("Below Threshold");
 141
 142     if (oldcs instanceof AnnotationColourGradient)
 143     {
 144       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 145       annotations.setSelectedItem(acg.getAnnotation());
 146       switch (acg.getAboveThreshold())
 147       {
 148       case AnnotationColourGradient.NO_THRESHOLD:
 149         threshold.setSelectedItem("No Threshold");
 150         break;
 151       case AnnotationColourGradient.ABOVE_THRESHOLD:
 152         threshold.setSelectedItem("Above Threshold");
 153         break;
 154       case AnnotationColourGradient.BELOW_THRESHOLD:
 155         threshold.setSelectedItem("Below Threshold");
 156         break;
 157       default:
 158         throw new Error(
 159                 "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 160       }
 161       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 162       thresholdValue.setText("" + acg.getAnnotationThreshold());
 163     }
 164
 165     try
 166     {
 167       jbInit();
 168     } catch (Exception ex)
 169     {
 170     }
 171
 172     adjusting = false;
 173
 174     changeColour();
 175     frame.invalidate();
 176     frame.pack();
 177
 178   }
 179
 180   private Vector<String> getAnnotationItems(boolean isSeqAssociated)
 181   {
 182     Vector<String> list = new Vector<String>();
 183     int index = 1;
 184     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 185     boolean enableSeqAss = false;
 186     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 187     {
 188       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 189       {
 190         if (isSeqAssociated)
 191         {
 192           continue;
 193         }
 194       }
 195       else
 196       {
 197         enableSeqAss = true;
 198       }
 199       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 200       if (!list.contains(label))
 201       {
 202         anmap[list.size()] = i;
 203         list.addElement(label);
 204
 205       }
 206       else
 207       {
 208         if (!isSeqAssociated)
 209         {
 210           anmap[list.size()] = i;
 211           list.addElement(label + "_" + (index++));
 212         }
 213       }
 214     }
 215     seqAssociated.setEnabled(enableSeqAss);
 216     annmap = new int[list.size()];
 217     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
 218     return list;
 219   }
 220   private void setDefaultMinMax()
 221   {
 222     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 223             Color.orange));
 224     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 225             Color.red));
 226   }
 227
 228   public AnnotationColourChooser()
 229   {
 230     try
 231     {
 232       jbInit();
 233     } catch (Exception ex)
 234     {
 235       ex.printStackTrace();
 236     }
 237   }
 238
 239   private void jbInit() throws Exception
 240   {
 241     minColour.setFont(JvSwingUtils.getLabelFont());
 242     minColour.setBorder(BorderFactory.createEtchedBorder());
 243     minColour.setPreferredSize(new Dimension(40, 20));
 244     minColour.setToolTipText("Minimum Colour");
 245     minColour.addMouseListener(new MouseAdapter()
 246     {
 247       public void mousePressed(MouseEvent e)
 248       {
 249         if (minColour.isEnabled())
 250         {
 251           minColour_actionPerformed();
 252         }
 253       }
 254     });
 255     maxColour.setFont(JvSwingUtils.getLabelFont());
 256     maxColour.setBorder(BorderFactory.createEtchedBorder());
 257     maxColour.setPreferredSize(new Dimension(40, 20));
 258     maxColour.setToolTipText("Maximum Colour");
 259     maxColour.addMouseListener(new MouseAdapter()
 260     {
 261       public void mousePressed(MouseEvent e)
 262       {
 263         if (maxColour.isEnabled())
 264         {
 265           maxColour_actionPerformed();
 266         }
 267       }
 268     });
 269     ok.setOpaque(false);
 270     ok.setText(MessageManager.getString("action.ok"));
 271     ok.addActionListener(new ActionListener()
 272     {
 273       public void actionPerformed(ActionEvent e)
 274       {
 275         ok_actionPerformed(e);
 276       }
 277     });
 278     cancel.setOpaque(false);
 279     cancel.setText(MessageManager.getString("action.cancel"));
 280     cancel.addActionListener(new ActionListener()
 281     {
 282       public void actionPerformed(ActionEvent e)
 283       {
 284         cancel_actionPerformed(e);
 285       }
 286     });
 287     defColours.setOpaque(false);
 288     defColours.setText(MessageManager.getString("action.set_defaults"));
 289     defColours
 290             .setToolTipText("Reset min and max colours to defaults from user preferences.");
 291     defColours.addActionListener(new ActionListener()
 292     {
 293
 294       @Override
 295       public void actionPerformed(ActionEvent arg0)
 296       {
 297         resetColours_actionPerformed(arg0);
 298       }
 299     });
 300
 301     annotations.addActionListener(new ActionListener()
 302     {
 303       public void actionPerformed(ActionEvent e)
 304       {
 305         annotations_actionPerformed(e);
 306       }
 307     });
 308     threshold.addActionListener(new ActionListener()
 309     {
 310       public void actionPerformed(ActionEvent e)
 311       {
 312         threshold_actionPerformed(e);
 313       }
 314     });
 315     thresholdValue.addActionListener(new ActionListener()
 316     {
 317       public void actionPerformed(ActionEvent e)
 318       {
 319         thresholdValue_actionPerformed(e);
 320       }
 321     });
 322     slider.setPaintLabels(false);
 323     slider.setPaintTicks(true);
 324     slider.setBackground(Color.white);
 325     slider.setEnabled(false);
 326     slider.setOpaque(false);
 327     slider.setPreferredSize(new Dimension(100, 32));
 328     thresholdValue.setEnabled(false);
 329     thresholdValue.setColumns(7);
 330     currentColours.setFont(JvSwingUtils.getLabelFont());
 331     currentColours.setOpaque(false);
 332     currentColours.setText(MessageManager.getString("label.use_original_colours"));
 333     currentColours.addActionListener(new ActionListener()
 334     {
 335       public void actionPerformed(ActionEvent e)
 336       {
 337         currentColours_actionPerformed(e);
 338       }
 339     });
 340     thresholdIsMin.setBackground(Color.white);
 341     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 342     thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
 343     thresholdIsMin.addActionListener(new ActionListener()
 344     {
 345       public void actionPerformed(ActionEvent actionEvent)
 346       {
 347         thresholdIsMin_actionPerformed(actionEvent);
 348       }
 349     });
 350     seqAssociated.setBackground(Color.white);
 351     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 352     seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
 353     seqAssociated.addActionListener(new ActionListener()
 354     {
 355
 356       @Override
 357       public void actionPerformed(ActionEvent arg0)
 358       {
 359         seqAssociated_actionPerformed(arg0);
 360       }
 361     });
 362
 363     this.setLayout(borderLayout1);
 364     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 365     jPanel1.setBackground(Color.white);
 366     jPanel2.setBackground(Color.white);
 367
 368     jPanel1.add(ok);
 369     jPanel1.add(cancel);
 370     jPanel2.add(annotations, "grow, wrap");
 371     jPanel2.add(seqAssociated);
 372     jPanel2.add(currentColours);
 373     JPanel colpanel = new JPanel(new FlowLayout());
 374     colpanel.setBackground(Color.white);
 375     colpanel.add(minColour);
 376     colpanel.add(maxColour);
 377     jPanel2.add(colpanel, "wrap");
 378     jPanel2.add(threshold);
 379     jPanel2.add(defColours, "skip 1, wrap");
 380     jPanel2.add(thresholdIsMin);
 381     jPanel2.add(slider, "grow");
 382     jPanel2.add(thresholdValue, "grow");
 383     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 384     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 385     this.validate();
 386   }
 387
 388   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 389   {
 390     adjusting = true;
 391     String cursel = (String) annotations.getSelectedItem();
 392     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 393     this.annotations.removeAllItems();
 394     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 395     {
 396       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 397       {
 398         isvalid = true;
 399         cursel = anitem;
 400       }
 401       this.annotations.addItem(anitem);
 402     }
 403     adjusting = false;
 404     if (isvalid)
 405     {
 406       this.annotations.setSelectedItem(cursel);
 407     }
 408     else
 409     {
 410       if (annotations.getItemCount() > 0)
 411       {
 412         annotations.setSelectedIndex(0);
 413       }
 414     }
 415   }
 416
 417   protected void resetColours_actionPerformed(ActionEvent arg0)
 418   {
 419     setDefaultMinMax();
 420     changeColour();
 421   }
 422
 423   JComboBox annotations;
 424
 425   int[] annmap;
 426
 427   JPanel minColour = new JPanel();
 428
 429   JPanel maxColour = new JPanel();
 430
 431   JButton defColours = new JButton();
 432
 433   JButton ok = new JButton();
 434
 435   JButton cancel = new JButton();
 436
 437   JPanel jPanel1 = new JPanel();
 438
 439   JPanel jPanel2 = new JPanel();
 440
 441   BorderLayout borderLayout1 = new BorderLayout();
 442
 443   JComboBox threshold = new JComboBox();
 444
 445   JSlider slider = new JSlider();
 446
 447   JTextField thresholdValue = new JTextField(20);
 448
 449   JCheckBox currentColours = new JCheckBox();
 450
 451   JCheckBox thresholdIsMin = new JCheckBox();
 452
 453   JCheckBox seqAssociated = new JCheckBox();
 454
 455   public void minColour_actionPerformed()
 456   {
 457     Color col = JColorChooser.showDialog(this,
 458             "Select Colour for Minimum Value", minColour.getBackground());
 459     if (col != null)
 460     {
 461       minColour.setBackground(col);
 462     }
 463     minColour.repaint();
 464     changeColour();
 465   }
 466
 467   public void maxColour_actionPerformed()
 468   {
 469     Color col = JColorChooser.showDialog(this,
 470             "Select Colour for Maximum Value", maxColour.getBackground());
 471     if (col != null)
 472     {
 473       maxColour.setBackground(col);
 474     }
 475     maxColour.repaint();
 476     changeColour();
 477   }
 478
 479   void changeColour()
 480   {
 481     // Check if combobox is still adjusting
 482     if (adjusting)
 483     {
 484       return;
 485     }
 486
 487     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 488             .getSelectedIndex()]];
 489
 490     int aboveThreshold = -1;
 491     if (threshold.getSelectedItem().equals("Above Threshold"))
 492     {
 493       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 494     }
 495     else if (threshold.getSelectedItem().equals("Below Threshold"))
 496     {
 497       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 498     }
 499
 500     slider.setEnabled(true);
 501     thresholdValue.setEnabled(true);
 502     thresholdIsMin.setEnabled(true);
 503
 504     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 505     {
 506       slider.setEnabled(false);
 507       thresholdValue.setEnabled(false);
 508       thresholdValue.setText("");
 509       thresholdIsMin.setEnabled(false);
 510     }
 511     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 512             && currentAnnotation.threshold == null)
 513     {
 514       currentAnnotation
 515               .setThreshold(new jalview.datamodel.GraphLine(
 516                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 517                       "Threshold", Color.black));
 518     }
 519
 520     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 521     {
 522       adjusting = true;
 523       float range = currentAnnotation.graphMax * 1000
 524               - currentAnnotation.graphMin * 1000;
 525
 526       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 527       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 528       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 529       thresholdValue.setText(currentAnnotation.threshold.value + "");
 530       slider.setMajorTickSpacing((int) (range / 10f));
 531       slider.setEnabled(true);
 532       thresholdValue.setEnabled(true);
 533       adjusting = false;
 534     }
 535
 536     AnnotationColourGradient acg = null;
 537     if (currentColours.isSelected())
 538     {
 539       acg = new AnnotationColourGradient(currentAnnotation,
 540               av.getGlobalColourScheme(), aboveThreshold);
 541     }
 542     else
 543     {
 544       acg = new AnnotationColourGradient(currentAnnotation,
 545               minColour.getBackground(), maxColour.getBackground(),
 546               aboveThreshold);
 547     }
 548     acg.setSeqAssociated(seqAssociated.isSelected());
 549
 550     if (currentAnnotation.graphMin == 0f
 551             && currentAnnotation.graphMax == 0f)
 552     {
 553       acg.predefinedColours = true;
 554     }
 555
 556     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 557
 558     av.setGlobalColourScheme(acg);
 559
 560     if (av.getAlignment().getGroups() != null)
 561     {
 562
 563       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 564       {
 565         if (sg.cs == null)
 566         {
 567           continue;
 568         }
 569
 570         if (currentColours.isSelected())
 571         {
 572           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 573                   aboveThreshold);
 574           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 575                   .isSelected());
 576
 577         }
 578         else
 579         {
 580           sg.cs = new AnnotationColourGradient(currentAnnotation,
 581                   minColour.getBackground(), maxColour.getBackground(),
 582                   aboveThreshold);
 583           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 584                   .isSelected());
 585         }
 586
 587       }
 588     }
 589     ap.alignmentChanged();
 590     // ensure all associated views (overviews, structures, etc) are notified of
 591     // updated colours.
 592     ap.paintAlignment(true);
 593   }
 594
 595   public void ok_actionPerformed(ActionEvent e)
 596   {
 597     changeColour();
 598     try
 599     {
 600       frame.setClosed(true);
 601     } catch (Exception ex)
 602     {
 603     }
 604   }
 605
 606   public void cancel_actionPerformed(ActionEvent e)
 607   {
 608     reset();
 609     // ensure all original colouring is propagated to listeners.
 610     ap.paintAlignment(true);
 611     try
 612     {
 613       frame.setClosed(true);
 614     } catch (Exception ex)
 615     {
 616     }
 617   }
 618
 619   void reset()
 620   {
 621     av.setGlobalColourScheme(oldcs);
 622     if (av.getAlignment().getGroups() != null)
 623     {
 624
 625       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 626       {
 627         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 628       }
 629     }
 630   }
 631
 632   public void thresholdCheck_actionPerformed(ActionEvent e)
 633   {
 634     changeColour();
 635   }
 636
 637   public void annotations_actionPerformed(ActionEvent e)
 638   {
 639     changeColour();
 640   }
 641
 642   public void threshold_actionPerformed(ActionEvent e)
 643   {
 644     changeColour();
 645   }
 646
 647   public void thresholdValue_actionPerformed(ActionEvent e)
 648   {
 649     try
 650     {
 651       float f = Float.parseFloat(thresholdValue.getText());
 652       slider.setValue((int) (f * 1000));
 653     } catch (NumberFormatException ex)
 654     {
 655     }
 656   }
 657
 658   public void valueChanged(boolean updateAllAnnotation)
 659   {
 660     if (currentColours.isSelected()
 661             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 662     {
 663       changeColour();
 664     }
 665     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 666     propagateSeqAssociatedThreshold(updateAllAnnotation);
 667     ap.paintAlignment(false);
 668   }
 669
 670   private void propagateSeqAssociatedThreshold(boolean allAnnotation)
 671   {
 672     if (currentAnnotation.sequenceRef == null
 673             || currentAnnotation.threshold == null)
 674     {
 675       return;
 676     }
 677     // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
 678
 679     float thr = currentAnnotation.threshold.value;
 680     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 681     {
 682       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 683       if (aa.label.equals(currentAnnotation.label))
 684       {
 685         aa.threshold.value = thr;
 686       }
 687     }
 688   }
 689
 690   public void currentColours_actionPerformed(ActionEvent e)
 691   {
 692     if (currentColours.isSelected())
 693     {
 694       reset();
 695     }
 696
 697     maxColour.setEnabled(!currentColours.isSelected());
 698     minColour.setEnabled(!currentColours.isSelected());
 699
 700     changeColour();
 701   }
 702
 703   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 704   {
 705     changeColour();
 706   }
 707
 708 }