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, MessageManager.getString("label.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     adjusting = true;
 124     if (oldcs instanceof AnnotationColourGradient)
 125     {
 126       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 127       currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
 128       if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
 129       {
 130         minColour.setBackground(acg.getMinColour());
 131         maxColour.setBackground(acg.getMaxColour());
 132       }
 133       seqAssociated.setSelected(acg.isSeqAssociated());
 134
 135     }
 136     annotations = new JComboBox(
 137             getAnnotationItems(seqAssociated.isSelected()));
 138
 139     threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
 140     threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
 141     threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
 142
 143     if (oldcs instanceof AnnotationColourGradient)
 144     {
 145       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
 146       annotations.setSelectedItem(acg.getAnnotation());
 147       switch (acg.getAboveThreshold())
 148       {
 149       case AnnotationColourGradient.NO_THRESHOLD:
 150         threshold.setSelectedIndex(0);
 151         break;
 152       case AnnotationColourGradient.ABOVE_THRESHOLD:
 153         threshold.setSelectedIndex(1);
 154         break;
 155       case AnnotationColourGradient.BELOW_THRESHOLD:
 156         threshold.setSelectedIndex(2);
 157         break;
 158       default:
 159         throw new Error(
 160                 "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
 161       }
 162       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
 163       thresholdValue.setText("" + acg.getAnnotationThreshold());
 164     }
 165
 166     try
 167     {
 168       jbInit();
 169     } catch (Exception ex)
 170     {
 171     }
 172
 173     adjusting = false;
 174
 175     changeColour();
 176     frame.invalidate();
 177     frame.pack();
 178
 179   }
 180
 181   private Vector<String> getAnnotationItems(boolean isSeqAssociated)
 182   {
 183     Vector<String> list = new Vector<String>();
 184     int index = 1;
 185     int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
 186     boolean enableSeqAss = false;
 187     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 188     {
 189       if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
 190       {
 191         if (isSeqAssociated)
 192         {
 193           continue;
 194         }
 195       }
 196       else
 197       {
 198         enableSeqAss = true;
 199       }
 200       String label = av.getAlignment().getAlignmentAnnotation()[i].label;
 201       if (!list.contains(label))
 202       {
 203         anmap[list.size()] = i;
 204         list.addElement(label);
 205
 206       }
 207       else
 208       {
 209         if (!isSeqAssociated)
 210         {
 211           anmap[list.size()] = i;
 212           list.addElement(label + "_" + (index++));
 213         }
 214       }
 215     }
 216     seqAssociated.setEnabled(enableSeqAss);
 217     annmap = new int[list.size()];
 218     System.arraycopy(anmap, 0, annmap, 0, annmap.length);
 219     return list;
 220   }
 221   private void setDefaultMinMax()
 222   {
 223     minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
 224             Color.orange));
 225     maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
 226             Color.red));
 227   }
 228
 229   public AnnotationColourChooser()
 230   {
 231     try
 232     {
 233       jbInit();
 234     } catch (Exception ex)
 235     {
 236       ex.printStackTrace();
 237     }
 238   }
 239
 240   private void jbInit() throws Exception
 241   {
 242     minColour.setFont(JvSwingUtils.getLabelFont());
 243     minColour.setBorder(BorderFactory.createEtchedBorder());
 244     minColour.setPreferredSize(new Dimension(40, 20));
 245     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
 246     minColour.addMouseListener(new MouseAdapter()
 247     {
 248       public void mousePressed(MouseEvent e)
 249       {
 250         if (minColour.isEnabled())
 251         {
 252           minColour_actionPerformed();
 253         }
 254       }
 255     });
 256     maxColour.setFont(JvSwingUtils.getLabelFont());
 257     maxColour.setBorder(BorderFactory.createEtchedBorder());
 258     maxColour.setPreferredSize(new Dimension(40, 20));
 259     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
 260     maxColour.addMouseListener(new MouseAdapter()
 261     {
 262       public void mousePressed(MouseEvent e)
 263       {
 264         if (maxColour.isEnabled())
 265         {
 266           maxColour_actionPerformed();
 267         }
 268       }
 269     });
 270     ok.setOpaque(false);
 271     ok.setText(MessageManager.getString("action.ok"));
 272     ok.addActionListener(new ActionListener()
 273     {
 274       public void actionPerformed(ActionEvent e)
 275       {
 276         ok_actionPerformed(e);
 277       }
 278     });
 279     cancel.setOpaque(false);
 280     cancel.setText(MessageManager.getString("action.cancel"));
 281     cancel.addActionListener(new ActionListener()
 282     {
 283       public void actionPerformed(ActionEvent e)
 284       {
 285         cancel_actionPerformed(e);
 286       }
 287     });
 288     defColours.setOpaque(false);
 289     defColours.setText(MessageManager.getString("action.set_defaults"));
 290     defColours
 291             .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
 292     defColours.addActionListener(new ActionListener()
 293     {
 294
 295       @Override
 296       public void actionPerformed(ActionEvent arg0)
 297       {
 298         resetColours_actionPerformed(arg0);
 299       }
 300     });
 301
 302     annotations.addActionListener(new ActionListener()
 303     {
 304       public void actionPerformed(ActionEvent e)
 305       {
 306         annotations_actionPerformed(e);
 307       }
 308     });
 309     threshold.addActionListener(new ActionListener()
 310     {
 311       public void actionPerformed(ActionEvent e)
 312       {
 313         threshold_actionPerformed(e);
 314       }
 315     });
 316     thresholdValue.addActionListener(new ActionListener()
 317     {
 318       public void actionPerformed(ActionEvent e)
 319       {
 320         thresholdValue_actionPerformed(e);
 321       }
 322     });
 323     slider.setPaintLabels(false);
 324     slider.setPaintTicks(true);
 325     slider.setBackground(Color.white);
 326     slider.setEnabled(false);
 327     slider.setOpaque(false);
 328     slider.setPreferredSize(new Dimension(100, 32));
 329     thresholdValue.setEnabled(false);
 330     thresholdValue.setColumns(7);
 331     currentColours.setFont(JvSwingUtils.getLabelFont());
 332     currentColours.setOpaque(false);
 333     currentColours.setText(MessageManager.getString("label.use_original_colours"));
 334     currentColours.addActionListener(new ActionListener()
 335     {
 336       public void actionPerformed(ActionEvent e)
 337       {
 338         currentColours_actionPerformed(e);
 339       }
 340     });
 341     thresholdIsMin.setBackground(Color.white);
 342     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
 343     thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
 344     thresholdIsMin.addActionListener(new ActionListener()
 345     {
 346       public void actionPerformed(ActionEvent actionEvent)
 347       {
 348         thresholdIsMin_actionPerformed(actionEvent);
 349       }
 350     });
 351     seqAssociated.setBackground(Color.white);
 352     seqAssociated.setFont(JvSwingUtils.getLabelFont());
 353     seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
 354     seqAssociated.addActionListener(new ActionListener()
 355     {
 356
 357       @Override
 358       public void actionPerformed(ActionEvent arg0)
 359       {
 360         seqAssociated_actionPerformed(arg0);
 361       }
 362     });
 363
 364     this.setLayout(borderLayout1);
 365     jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
 366     jPanel1.setBackground(Color.white);
 367     jPanel2.setBackground(Color.white);
 368
 369     jPanel1.add(ok);
 370     jPanel1.add(cancel);
 371     jPanel2.add(annotations, "grow, wrap");
 372     jPanel2.add(seqAssociated);
 373     jPanel2.add(currentColours);
 374     JPanel colpanel = new JPanel(new FlowLayout());
 375     colpanel.setBackground(Color.white);
 376     colpanel.add(minColour);
 377     colpanel.add(maxColour);
 378     jPanel2.add(colpanel, "wrap");
 379     jPanel2.add(threshold);
 380     jPanel2.add(defColours, "skip 1, wrap");
 381     jPanel2.add(thresholdIsMin);
 382     jPanel2.add(slider, "grow");
 383     jPanel2.add(thresholdValue, "grow");
 384     this.add(jPanel1, java.awt.BorderLayout.SOUTH);
 385     this.add(jPanel2, java.awt.BorderLayout.CENTER);
 386     this.validate();
 387   }
 388
 389   protected void seqAssociated_actionPerformed(ActionEvent arg0)
 390   {
 391     adjusting = true;
 392     String cursel = (String) annotations.getSelectedItem();
 393     boolean isvalid = false, isseqs = seqAssociated.isSelected();
 394     this.annotations.removeAllItems();
 395     for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
 396     {
 397       if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
 398       {
 399         isvalid = true;
 400         cursel = anitem;
 401       }
 402       this.annotations.addItem(anitem);
 403     }
 404     adjusting = false;
 405     if (isvalid)
 406     {
 407       this.annotations.setSelectedItem(cursel);
 408     }
 409     else
 410     {
 411       if (annotations.getItemCount() > 0)
 412       {
 413         annotations.setSelectedIndex(0);
 414       }
 415     }
 416   }
 417
 418   protected void resetColours_actionPerformed(ActionEvent arg0)
 419   {
 420     setDefaultMinMax();
 421     changeColour();
 422   }
 423
 424   JComboBox annotations;
 425
 426   int[] annmap;
 427
 428   JPanel minColour = new JPanel();
 429
 430   JPanel maxColour = new JPanel();
 431
 432   JButton defColours = new JButton();
 433
 434   JButton ok = new JButton();
 435
 436   JButton cancel = new JButton();
 437
 438   JPanel jPanel1 = new JPanel();
 439
 440   JPanel jPanel2 = new JPanel();
 441
 442   BorderLayout borderLayout1 = new BorderLayout();
 443
 444   JComboBox threshold = new JComboBox();
 445
 446   JSlider slider = new JSlider();
 447
 448   JTextField thresholdValue = new JTextField(20);
 449
 450   JCheckBox currentColours = new JCheckBox();
 451
 452   JCheckBox thresholdIsMin = new JCheckBox();
 453
 454   JCheckBox seqAssociated = new JCheckBox();
 455
 456   public void minColour_actionPerformed()
 457   {
 458     Color col = JColorChooser.showDialog(this,
 459             "Select Colour for Minimum Value", minColour.getBackground());
 460     if (col != null)
 461     {
 462       minColour.setBackground(col);
 463     }
 464     minColour.repaint();
 465     changeColour();
 466   }
 467
 468   public void maxColour_actionPerformed()
 469   {
 470     Color col = JColorChooser.showDialog(this,
 471             "Select Colour for Maximum Value", maxColour.getBackground());
 472     if (col != null)
 473     {
 474       maxColour.setBackground(col);
 475     }
 476     maxColour.repaint();
 477     changeColour();
 478   }
 479
 480   void changeColour()
 481   {
 482     // Check if combobox is still adjusting
 483     if (adjusting)
 484     {
 485       return;
 486     }
 487
 488     currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
 489             .getSelectedIndex()]];
 490
 491     int aboveThreshold = -1;
 492     if (threshold.getSelectedIndex()==1)
 493     {
 494       aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
 495     }
 496     else if (threshold.getSelectedIndex()==2)
 497     {
 498       aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
 499     }
 500
 501     slider.setEnabled(true);
 502     thresholdValue.setEnabled(true);
 503     thresholdIsMin.setEnabled(true);
 504
 505     if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
 506     {
 507       slider.setEnabled(false);
 508       thresholdValue.setEnabled(false);
 509       thresholdValue.setText("");
 510       thresholdIsMin.setEnabled(false);
 511     }
 512     else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
 513             && currentAnnotation.threshold == null)
 514     {
 515       currentAnnotation
 516               .setThreshold(new jalview.datamodel.GraphLine(
 517                       (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
 518                       "Threshold", Color.black));
 519     }
 520
 521     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
 522     {
 523       adjusting = true;
 524       float range = currentAnnotation.graphMax * 1000
 525               - currentAnnotation.graphMin * 1000;
 526
 527       slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
 528       slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
 529       slider.setValue((int) (currentAnnotation.threshold.value * 1000));
 530       thresholdValue.setText(currentAnnotation.threshold.value + "");
 531       slider.setMajorTickSpacing((int) (range / 10f));
 532       slider.setEnabled(true);
 533       thresholdValue.setEnabled(true);
 534       adjusting = false;
 535     }
 536
 537     AnnotationColourGradient acg = null;
 538     if (currentColours.isSelected())
 539     {
 540       acg = new AnnotationColourGradient(currentAnnotation,
 541               av.getGlobalColourScheme(), aboveThreshold);
 542     }
 543     else
 544     {
 545       acg = new AnnotationColourGradient(currentAnnotation,
 546               minColour.getBackground(), maxColour.getBackground(),
 547               aboveThreshold);
 548     }
 549     acg.setSeqAssociated(seqAssociated.isSelected());
 550
 551     if (currentAnnotation.graphMin == 0f
 552             && currentAnnotation.graphMax == 0f)
 553     {
 554       acg.setPredefinedColours(true);
 555     }
 556
 557     acg.thresholdIsMinMax = thresholdIsMin.isSelected();
 558
 559     av.setGlobalColourScheme(acg);
 560
 561     if (av.getAlignment().getGroups() != null)
 562     {
 563
 564       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 565       {
 566         if (sg.cs == null)
 567         {
 568           continue;
 569         }
 570
 571         if (currentColours.isSelected())
 572         {
 573           sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
 574                   aboveThreshold);
 575           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 576                   .isSelected());
 577
 578         }
 579         else
 580         {
 581           sg.cs = new AnnotationColourGradient(currentAnnotation,
 582                   minColour.getBackground(), maxColour.getBackground(),
 583                   aboveThreshold);
 584           ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
 585                   .isSelected());
 586         }
 587
 588       }
 589     }
 590     ap.alignmentChanged();
 591     // ensure all associated views (overviews, structures, etc) are notified of
 592     // updated colours.
 593     ap.paintAlignment(true);
 594   }
 595
 596   public void ok_actionPerformed(ActionEvent e)
 597   {
 598     changeColour();
 599     try
 600     {
 601       frame.setClosed(true);
 602     } catch (Exception ex)
 603     {
 604     }
 605   }
 606
 607   public void cancel_actionPerformed(ActionEvent e)
 608   {
 609     reset();
 610     // ensure all original colouring is propagated to listeners.
 611     ap.paintAlignment(true);
 612     try
 613     {
 614       frame.setClosed(true);
 615     } catch (Exception ex)
 616     {
 617     }
 618   }
 619
 620   void reset()
 621   {
 622     av.setGlobalColourScheme(oldcs);
 623     if (av.getAlignment().getGroups() != null)
 624     {
 625
 626       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
 627       {
 628         sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
 629       }
 630     }
 631   }
 632
 633   public void thresholdCheck_actionPerformed(ActionEvent e)
 634   {
 635     changeColour();
 636   }
 637
 638   public void annotations_actionPerformed(ActionEvent e)
 639   {
 640     changeColour();
 641   }
 642
 643   public void threshold_actionPerformed(ActionEvent e)
 644   {
 645     changeColour();
 646   }
 647
 648   public void thresholdValue_actionPerformed(ActionEvent e)
 649   {
 650     try
 651     {
 652       float f = Float.parseFloat(thresholdValue.getText());
 653       slider.setValue((int) (f * 1000));
 654     } catch (NumberFormatException ex)
 655     {
 656     }
 657   }
 658
 659   public void valueChanged(boolean updateAllAnnotation)
 660   {
 661     if (currentColours.isSelected()
 662             && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
 663     {
 664       changeColour();
 665     }
 666     currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
 667     propagateSeqAssociatedThreshold(updateAllAnnotation);
 668     ap.paintAlignment(false);
 669   }
 670
 671   private void propagateSeqAssociatedThreshold(boolean allAnnotation)
 672   {
 673     if (currentAnnotation.sequenceRef == null
 674             || currentAnnotation.threshold == null)
 675     {
 676       return;
 677     }
 678     // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
 679
 680     float thr = currentAnnotation.threshold.value;
 681     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
 682     {
 683       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
 684       if (aa.label.equals(currentAnnotation.label))
 685       {
 686         aa.threshold.value = thr;
 687       }
 688     }
 689   }
 690
 691   public void currentColours_actionPerformed(ActionEvent e)
 692   {
 693     if (currentColours.isSelected())
 694     {
 695       reset();
 696     }
 697
 698     maxColour.setEnabled(!currentColours.isSelected());
 699     minColour.setEnabled(!currentColours.isSelected());
 700
 701     changeColour();
 702   }
 703
 704   public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
 705   {
 706     changeColour();
 707   }
 708
 709 }