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