appletgui/FeatureRenderer.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.appletgui;
  22
  23 import java.util.*;
  24
  25 import java.awt.*;
  26
  27 import java.awt.event.*;
  28
  29 import jalview.datamodel.*;
  30 import jalview.schemes.AnnotationColourGradient;
  31 import jalview.schemes.GraduatedColor;
  32 import jalview.util.MessageManager;
  33
  34 /**
  35  * DOCUMENT ME!
  36  *
  37  * @author $author$
  38  * @version $Revision$
  39  */
  40 public class FeatureRenderer implements jalview.api.FeatureRenderer
  41 {
  42   AlignViewport av;
  43
  44   Hashtable featureColours = new Hashtable();
  45
  46   // A higher level for grouping features of a
  47   // particular type
  48   Hashtable featureGroups = null;
  49
  50   // Holds web links for feature groups and feature types
  51   // in the form label|link
  52   Hashtable featureLinks = null;
  53
  54   // This is actually an Integer held in the hashtable,
  55   // Retrieved using the key feature type
  56   Object currentColour;
  57
  58   String[] renderOrder;
  59
  60   FontMetrics fm;
  61
  62   int charOffset;
  63
  64   float transparency = 1f;
  65
  66   TransparencySetter transparencySetter = null;
  67
  68   /**
  69    * Creates a new FeatureRenderer object.
  70    *
  71    * @param av
  72    *          DOCUMENT ME!
  73    */
  74   public FeatureRenderer(AlignViewport av)
  75   {
  76     this.av = av;
  77
  78     if (!System.getProperty("java.version").startsWith("1.1"))
  79     {
  80       transparencySetter = new TransparencySetter();
  81     }
  82   }
  83
  84   public void transferSettings(FeatureRenderer fr)
  85   {
  86     renderOrder = fr.renderOrder;
  87     featureGroups = fr.featureGroups;
  88     featureColours = fr.featureColours;
  89     transparency = fr.transparency;
  90     if (av != null && fr.av != null && fr.av != av)
  91     {
  92       if (fr.av.featuresDisplayed != null)
  93       {
  94         if (av.featuresDisplayed == null)
  95         {
  96           av.featuresDisplayed = new Hashtable();
  97         }
  98         else
  99         {
 100           av.featuresDisplayed.clear();
 101         }
 102         Enumeration en = fr.av.featuresDisplayed.keys();
 103         while (en.hasMoreElements())
 104         {
 105           av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
 106         }
 107       }
 108     }
 109   }
 110
 111   static String lastFeatureAdded;
 112
 113   static String lastFeatureGroupAdded;
 114
 115   static String lastDescriptionAdded;
 116
 117   int featureIndex = 0;
 118
 119   boolean deleteFeature = false;
 120
 121   FeatureColourPanel colourPanel;
 122
 123   class FeatureColourPanel extends Panel
 124   {
 125     String label = "";
 126
 127     private Color maxCol;
 128
 129     private boolean isColourByLabel, isGcol;
 130
 131     /**
 132      * render a feature style in the amend feature dialog box
 133      */
 134     public void updateColor(Object newcol)
 135     {
 136
 137       Color bg, col = null;
 138       GraduatedColor gcol = null;
 139       String vlabel = "";
 140       if (newcol instanceof Color)
 141       {
 142         isGcol = false;
 143         col = (Color) newcol;
 144         gcol = null;
 145       }
 146       else if (newcol instanceof GraduatedColor)
 147       {
 148         isGcol = true;
 149         gcol = (GraduatedColor) newcol;
 150         col = null;
 151       }
 152       else
 153       {
 154         throw new Error(MessageManager.getString("error.invalid_colour_for_mycheckbox"));
 155       }
 156       if (col != null)
 157       {
 158         setBackground(bg = col);
 159       }
 160       else
 161       {
 162         if (gcol.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
 163         {
 164           vlabel += " "
 165                   + ((gcol.getThreshType() == AnnotationColourGradient.ABOVE_THRESHOLD) ? "(>)"
 166                           : "(<)");
 167         }
 168         if (isColourByLabel = gcol.isColourByLabel())
 169         {
 170           setBackground(bg = Color.white);
 171           vlabel += " (by Label)";
 172         }
 173         else
 174         {
 175           setBackground(bg = gcol.getMinColor());
 176           maxCol = gcol.getMaxColor();
 177         }
 178       }
 179       label = vlabel;
 180       setBackground(bg);
 181       repaint();
 182     }
 183
 184     FeatureColourPanel()
 185     {
 186       super(null);
 187     }
 188
 189     public void paint(Graphics g)
 190     {
 191       Dimension d = getSize();
 192       if (isGcol)
 193       {
 194         if (isColourByLabel)
 195         {
 196           g.setColor(Color.white);
 197           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 198           g.setColor(Color.black);
 199           Font f = new Font("Verdana", Font.PLAIN, 10);
 200           g.setFont(f);
 201           g.drawString(MessageManager.getString("label.label"), 0, 0);
 202         }
 203         else
 204         {
 205           g.setColor(maxCol);
 206           g.fillRect(d.width / 2, 0, d.width / 2, d.height);
 207
 208         }
 209       }
 210     }
 211
 212   }
 213
 214   boolean amendFeatures(final SequenceI[] sequences,
 215           final SequenceFeature[] features, boolean newFeatures,
 216           final AlignmentPanel ap)
 217   {
 218     Panel bigPanel = new Panel(new BorderLayout());
 219     final TextField name = new TextField(16);
 220     final TextField source = new TextField(16);
 221     final TextArea description = new TextArea(3, 35);
 222     final TextField start = new TextField(8);
 223     final TextField end = new TextField(8);
 224     final Choice overlaps;
 225     Button deleteButton = new Button("Delete");
 226     deleteFeature = false;
 227
 228     colourPanel = new FeatureColourPanel();
 229     colourPanel.setSize(110, 15);
 230     final FeatureRenderer fr = this;
 231
 232     Panel panel = new Panel(new GridLayout(3, 1));
 233
 234     featureIndex = 0; // feature to be amended.
 235     Panel tmp;
 236
 237     // /////////////////////////////////////
 238     // /MULTIPLE FEATURES AT SELECTED RESIDUE
 239     if (!newFeatures && features.length > 1)
 240     {
 241       panel = new Panel(new GridLayout(4, 1));
 242       tmp = new Panel();
 243       tmp.add(new Label("Select Feature: "));
 244       overlaps = new Choice();
 245       for (int i = 0; i < features.length; i++)
 246       {
 247         String item = features[i].getType() + "/" + features[i].getBegin()
 248                 + "-" + features[i].getEnd();
 249
 250         if (features[i].getFeatureGroup() != null)
 251           item += " (" + features[i].getFeatureGroup() + ")";
 252
 253         overlaps.addItem(item);
 254       }
 255
 256       tmp.add(overlaps);
 257
 258       overlaps.addItemListener(new java.awt.event.ItemListener()
 259       {
 260         public void itemStateChanged(java.awt.event.ItemEvent e)
 261         {
 262           int index = overlaps.getSelectedIndex();
 263           if (index != -1)
 264           {
 265             featureIndex = index;
 266             name.setText(features[index].getType());
 267             description.setText(features[index].getDescription());
 268             source.setText(features[index].getFeatureGroup());
 269             start.setText(features[index].getBegin() + "");
 270             end.setText(features[index].getEnd() + "");
 271
 272             SearchResults highlight = new SearchResults();
 273             highlight.addResult(sequences[0], features[index].getBegin(),
 274                     features[index].getEnd());
 275
 276             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
 277
 278           }
 279           Object col = getFeatureStyle(name.getText());
 280           if (col == null)
 281           {
 282             col = new jalview.schemes.UserColourScheme()
 283                     .createColourFromName(name.getText());
 284           }
 285
 286           colourPanel.updateColor(col);
 287         }
 288       });
 289
 290       panel.add(tmp);
 291     }
 292     // ////////
 293     // ////////////////////////////////////
 294
 295     tmp = new Panel();
 296     panel.add(tmp);
 297     tmp.add(new Label("Name: ", Label.RIGHT));
 298     tmp.add(name);
 299
 300     tmp = new Panel();
 301     panel.add(tmp);
 302     tmp.add(new Label("Group: ", Label.RIGHT));
 303     tmp.add(source);
 304
 305     tmp = new Panel();
 306     panel.add(tmp);
 307     tmp.add(new Label("Colour: ", Label.RIGHT));
 308     tmp.add(colourPanel);
 309
 310     bigPanel.add(panel, BorderLayout.NORTH);
 311
 312     panel = new Panel();
 313     panel.add(new Label("Description: ", Label.RIGHT));
 314     panel.add(new ScrollPane().add(description));
 315
 316     if (!newFeatures)
 317     {
 318       bigPanel.add(panel, BorderLayout.SOUTH);
 319
 320       panel = new Panel();
 321       panel.add(new Label(" Start:", Label.RIGHT));
 322       panel.add(start);
 323       panel.add(new Label("  End:", Label.RIGHT));
 324       panel.add(end);
 325       bigPanel.add(panel, BorderLayout.CENTER);
 326     }
 327     else
 328     {
 329       bigPanel.add(panel, BorderLayout.CENTER);
 330     }
 331
 332     if (lastFeatureAdded == null)
 333     {
 334       if (features[0].type != null)
 335       {
 336         lastFeatureAdded = features[0].type;
 337       }
 338       else
 339       {
 340         lastFeatureAdded = "feature_1";
 341       }
 342     }
 343
 344     if (lastFeatureGroupAdded == null)
 345     {
 346       if (features[0].featureGroup != null)
 347       {
 348         lastFeatureGroupAdded = features[0].featureGroup;
 349       }
 350       else
 351       {
 352         lastFeatureAdded = "Jalview";
 353       }
 354     }
 355
 356     String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
 357             : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
 358
 359     final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
 360             240);
 361
 362     dialog.setMainPanel(bigPanel);
 363
 364     if (newFeatures)
 365     {
 366       name.setText(lastFeatureAdded);
 367       source.setText(lastFeatureGroupAdded);
 368     }
 369     else
 370     {
 371       dialog.ok.setLabel(MessageManager.getString("label.amend"));
 372       dialog.buttonPanel.add(deleteButton, 1);
 373       deleteButton.addActionListener(new ActionListener()
 374       {
 375         public void actionPerformed(ActionEvent evt)
 376         {
 377           deleteFeature = true;
 378           dialog.setVisible(false);
 379         }
 380       });
 381       name.setText(features[0].getType());
 382       source.setText(features[0].getFeatureGroup());
 383     }
 384
 385     start.setText(features[0].getBegin() + "");
 386     end.setText(features[0].getEnd() + "");
 387     description.setText(features[0].getDescription());
 388     Color col = getColour(name.getText());
 389     if (col == null)
 390     {
 391       col = new jalview.schemes.UserColourScheme()
 392               .createColourFromName(name.getText());
 393     }
 394     Object fcol = getFeatureStyle(name.getText());
 395     // simply display the feature color in a box
 396     colourPanel.updateColor(fcol);
 397     dialog.setResizable(true);
 398     // TODO: render the graduated color in the box.
 399     colourPanel.addMouseListener(new java.awt.event.MouseAdapter()
 400     {
 401       public void mousePressed(java.awt.event.MouseEvent evt)
 402       {
 403         if (!colourPanel.isGcol)
 404         {
 405           new UserDefinedColours(fr, ap.alignFrame);
 406         }
 407         else
 408         {
 409           FeatureColourChooser fcc = new FeatureColourChooser(
 410                   ap.alignFrame, name.getText());
 411           dialog.transferFocus();
 412         }
 413       }
 414     });
 415     dialog.setVisible(true);
 416
 417     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
 418
 419     if (dialog.accept)
 420     {
 421       // This ensures that the last sequence
 422       // is refreshed and new features are rendered
 423       lastSeq = null;
 424       lastFeatureAdded = name.getText().trim();
 425       lastFeatureGroupAdded = source.getText().trim();
 426       lastDescriptionAdded = description.getText().replace('\n', ' ');
 427     }
 428
 429     if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
 430       lastFeatureGroupAdded = null;
 431
 432     if (!newFeatures)
 433     {
 434
 435       SequenceFeature sf = features[featureIndex];
 436       if (dialog.accept)
 437       {
 438         sf.type = lastFeatureAdded;
 439         sf.featureGroup = lastFeatureGroupAdded;
 440         sf.description = lastDescriptionAdded;
 441         if (!colourPanel.isGcol)
 442         {
 443           // update colour - otherwise its already done.
 444           setColour(sf.type, colourPanel.getBackground());
 445         }
 446         try
 447         {
 448           sf.begin = Integer.parseInt(start.getText());
 449           sf.end = Integer.parseInt(end.getText());
 450         } catch (NumberFormatException ex)
 451         {
 452         }
 453
 454         ffile.parseDescriptionHTML(sf, false);
 455       }
 456       if (deleteFeature)
 457       {
 458         sequences[0].deleteFeature(sf);
 459       }
 460
 461     }
 462     else
 463     {
 464       if (dialog.accept && name.getText().length() > 0)
 465       {
 466         for (int i = 0; i < sequences.length; i++)
 467         {
 468           features[i].type = lastFeatureAdded;
 469           features[i].featureGroup = lastFeatureGroupAdded;
 470           features[i].description = lastDescriptionAdded;
 471           sequences[i].addSequenceFeature(features[i]);
 472           ffile.parseDescriptionHTML(features[i], false);
 473         }
 474
 475         if (av.featuresDisplayed == null)
 476         {
 477           av.featuresDisplayed = new Hashtable();
 478         }
 479
 480         if (featureGroups == null)
 481         {
 482           featureGroups = new Hashtable();
 483         }
 484
 485         col = colourPanel.getBackground();
 486         // setColour(lastFeatureAdded, fcol);
 487
 488         if (lastFeatureGroupAdded != null)
 489         {
 490           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
 491         }
 492         if (fcol instanceof Color)
 493         {
 494           setColour(lastFeatureAdded, fcol);
 495         }
 496         av.featuresDisplayed.put(lastFeatureAdded,
 497                 getFeatureStyle(lastFeatureAdded));
 498
 499         findAllFeatures();
 500
 501         String[] tro = new String[renderOrder.length];
 502         tro[0] = renderOrder[renderOrder.length - 1];
 503         System.arraycopy(renderOrder, 0, tro, 1, renderOrder.length - 1);
 504         renderOrder = tro;
 505       }
 506       else
 507       {
 508         // no update to the alignment
 509         return false;
 510       }
 511     }
 512     // refresh the alignment and the feature settings dialog
 513     if (av.featureSettings != null)
 514     {
 515       av.featureSettings.refreshTable();
 516     }
 517     // findAllFeatures();
 518
 519     ap.paintAlignment(true);
 520
 521     return true;
 522   }
 523
 524   public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
 525   {
 526     overview = true;
 527     if (!av.showSequenceFeatures)
 528     {
 529       return initialCol;
 530     }
 531
 532     lastSeq = seq;
 533     sequenceFeatures = lastSeq.getSequenceFeatures();
 534     if (sequenceFeatures == null)
 535     {
 536       return initialCol;
 537     }
 538
 539     sfSize = sequenceFeatures.length;
 540
 541     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))
 542     {
 543       return Color.white;
 544     }
 545
 546     currentColour = null;
 547
 548     drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);
 549
 550     if (currentColour == null)
 551     {
 552       return initialCol;
 553     }
 554
 555     return new Color(((Integer) currentColour).intValue());
 556   }
 557
 558   /**
 559    * This is used by the Molecule Viewer to get the accurate colour of the
 560    * rendered sequence
 561    */
 562   boolean overview = false;
 563
 564   /**
 565    * DOCUMENT ME!
 566    *
 567    * @param g
 568    *          DOCUMENT ME!
 569    * @param seq
 570    *          DOCUMENT ME!
 571    * @param sg
 572    *          DOCUMENT ME!
 573    * @param start
 574    *          DOCUMENT ME!
 575    * @param end
 576    *          DOCUMENT ME!
 577    * @param x1
 578    *          DOCUMENT ME!
 579    * @param y1
 580    *          DOCUMENT ME!
 581    * @param width
 582    *          DOCUMENT ME!
 583    * @param height
 584    *          DOCUMENT ME!
 585    */
 586   // String type;
 587   // SequenceFeature sf;
 588   SequenceI lastSeq;
 589
 590   SequenceFeature[] sequenceFeatures;
 591
 592   int sfSize, sfindex, spos, epos;
 593
 594   synchronized public void drawSequence(Graphics g, SequenceI seq,
 595           int start, int end, int y1)
 596   {
 597     if (seq.getSequenceFeatures() == null
 598             || seq.getSequenceFeatures().length == 0)
 599     {
 600       return;
 601     }
 602
 603     if (transparencySetter != null && g != null)
 604     {
 605       transparencySetter.setTransparency(g, transparency);
 606     }
 607
 608     if (lastSeq == null || seq != lastSeq
 609             || sequenceFeatures != seq.getSequenceFeatures())
 610     {
 611       lastSeq = seq;
 612       sequenceFeatures = seq.getSequenceFeatures();
 613       sfSize = sequenceFeatures.length;
 614     }
 615
 616     if (av.featuresDisplayed == null || renderOrder == null)
 617     {
 618       findAllFeatures();
 619       if (av.featuresDisplayed.size() < 1)
 620       {
 621         return;
 622       }
 623
 624       sequenceFeatures = seq.getSequenceFeatures();
 625       sfSize = sequenceFeatures.length;
 626     }
 627     if (!overview)
 628     {
 629       spos = lastSeq.findPosition(start);
 630       epos = lastSeq.findPosition(end);
 631       if (g != null)
 632       {
 633         fm = g.getFontMetrics();
 634       }
 635     }
 636     String type;
 637     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
 638     {
 639       type = renderOrder[renderIndex];
 640       if (!av.featuresDisplayed.containsKey(type))
 641       {
 642         continue;
 643       }
 644
 645       // loop through all features in sequence to find
 646       // current feature to render
 647       for (sfindex = 0; sfindex < sfSize; sfindex++)
 648       {
 649         if (!sequenceFeatures[sfindex].type.equals(type))
 650         {
 651           continue;
 652         }
 653
 654         if (featureGroups != null
 655                 && sequenceFeatures[sfindex].featureGroup != null
 656                 && featureGroups
 657                         .containsKey(sequenceFeatures[sfindex].featureGroup)
 658                 && !((Boolean) featureGroups
 659                         .get(sequenceFeatures[sfindex].featureGroup))
 660                         .booleanValue())
 661         {
 662           continue;
 663         }
 664
 665         if (!overview
 666                 && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
 667                         .getEnd() < spos))
 668         {
 669           continue;
 670         }
 671
 672         if (overview)
 673         {
 674           if (sequenceFeatures[sfindex].begin <= start
 675                   && sequenceFeatures[sfindex].end >= start)
 676           {
 677             currentColour = new Integer(
 678                     getColour(sequenceFeatures[sfindex]).getRGB());// av.featuresDisplayed
 679             // .get(sequenceFeatures[sfindex].type);
 680           }
 681
 682         }
 683         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
 684         {
 685
 686           renderFeature(g, seq,
 687                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 688                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 689                   getColour(sequenceFeatures[sfindex])
 690                   // new Color(((Integer) av.featuresDisplayed
 691                   // .get(sequenceFeatures[sfindex].type)).intValue())
 692                   , start, end, y1);
 693           renderFeature(g, seq,
 694                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 695                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 696                   getColour(sequenceFeatures[sfindex])
 697                   // new Color(((Integer) av.featuresDisplayed
 698                   // .get(sequenceFeatures[sfindex].type)).intValue())
 699                   , start, end, y1);
 700
 701         }
 702         else
 703         {
 704           if (showFeature(sequenceFeatures[sfindex]))
 705           {
 706             renderFeature(g, seq,
 707                     seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 708                     seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 709                     getColour(sequenceFeatures[sfindex]), start, end, y1);
 710           }
 711         }
 712
 713       }
 714     }
 715
 716     if (transparencySetter != null && g != null)
 717     {
 718       transparencySetter.setTransparency(g, 1.0f);
 719     }
 720   }
 721
 722   char s;
 723
 724   int i;
 725
 726   void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
 727           Color featureColour, int start, int end, int y1)
 728   {
 729
 730     if (((fstart <= end) && (fend >= start)))
 731     {
 732       if (fstart < start)
 733       { // fix for if the feature we have starts before the sequence start,
 734         fstart = start; // but the feature end is still valid!!
 735       }
 736
 737       if (fend >= end)
 738       {
 739         fend = end;
 740       }
 741
 742       for (i = fstart; i <= fend; i++)
 743       {
 744         s = seq.getCharAt(i);
 745
 746         if (jalview.util.Comparison.isGap(s))
 747         {
 748           continue;
 749         }
 750
 751         g.setColor(featureColour);
 752
 753         g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
 754                 av.charHeight);
 755
 756         if (!av.validCharWidth)
 757         {
 758           continue;
 759         }
 760
 761         g.setColor(Color.white);
 762         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 763         g.drawString(String.valueOf(s), charOffset
 764                 + (av.charWidth * (i - start)), (y1 + av.charHeight)
 765                 - av.charHeight / 5); // pady = height / 5;
 766
 767       }
 768     }
 769   }
 770
 771   Hashtable minmax = null;
 772
 773   /**
 774    * Called when alignment in associated view has new/modified features to
 775    * discover and display.
 776    *
 777    */
 778   public void featuresAdded()
 779   {
 780     lastSeq = null;
 781     findAllFeatures();
 782   }
 783
 784   /**
 785    * find all features on the alignment
 786    */
 787   void findAllFeatures()
 788   {
 789     jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
 790
 791     av.featuresDisplayed = new Hashtable();
 792     Vector allfeatures = new Vector();
 793     minmax = new Hashtable();
 794     AlignmentI alignment = av.getAlignment();
 795     for (int i = 0; i < alignment.getHeight(); i++)
 796     {
 797       SequenceFeature[] features = alignment.getSequenceAt(i)
 798               .getSequenceFeatures();
 799
 800       if (features == null)
 801       {
 802         continue;
 803       }
 804
 805       int index = 0;
 806       while (index < features.length)
 807       {
 808         if (features[index].begin == 0 && features[index].end == 0)
 809         {
 810           index++;
 811           continue;
 812         }
 813         if (!av.featuresDisplayed.containsKey(features[index].getType()))
 814         {
 815           if (getColour(features[index].getType()) == null)
 816           {
 817             featureColours.put(features[index].getType(),
 818                     ucs.createColourFromName(features[index].getType()));
 819           }
 820
 821           av.featuresDisplayed.put(features[index].getType(), new Integer(
 822                   getColour(features[index].getType()).getRGB()));
 823           allfeatures.addElement(features[index].getType());
 824         }
 825         if (features[index].score != Float.NaN)
 826         {
 827           int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
 828           float[][] mm = (float[][]) minmax.get(features[index].getType());
 829           if (mm == null)
 830           {
 831             mm = new float[][]
 832             { null, null };
 833             minmax.put(features[index].getType(), mm);
 834           }
 835           if (mm[nonpos] == null)
 836           {
 837             mm[nonpos] = new float[]
 838             { features[index].score, features[index].score };
 839
 840           }
 841           else
 842           {
 843             if (mm[nonpos][0] > features[index].score)
 844             {
 845               mm[nonpos][0] = features[index].score;
 846             }
 847             if (mm[nonpos][1] < features[index].score)
 848             {
 849               mm[nonpos][1] = features[index].score;
 850             }
 851           }
 852         }
 853
 854         index++;
 855       }
 856     }
 857
 858     renderOrder = new String[allfeatures.size()];
 859     Enumeration en = allfeatures.elements();
 860     int i = allfeatures.size() - 1;
 861     while (en.hasMoreElements())
 862     {
 863       renderOrder[i] = en.nextElement().toString();
 864       i--;
 865     }
 866   }
 867
 868   /**
 869    * get a feature style object for the given type string. Creates a
 870    * java.awt.Color for a featureType with no existing colourscheme. TODO:
 871    * replace return type with object implementing standard abstract colour/style
 872    * interface
 873    *
 874    * @param featureType
 875    * @return java.awt.Color or GraduatedColor
 876    */
 877   public Object getFeatureStyle(String featureType)
 878   {
 879     Object fc = featureColours.get(featureType);
 880     if (fc == null)
 881     {
 882       jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
 883       Color col = ucs.createColourFromName(featureType);
 884       featureColours.put(featureType, fc = col);
 885     }
 886     return fc;
 887   }
 888
 889   public Color getColour(String featureType)
 890   {
 891     Object fc = getFeatureStyle(featureType);
 892
 893     if (fc instanceof Color)
 894     {
 895       return (Color) fc;
 896     }
 897     else
 898     {
 899       if (fc instanceof GraduatedColor)
 900       {
 901         return ((GraduatedColor) fc).getMaxColor();
 902       }
 903     }
 904     throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().getCanonicalName(),featureType}));
 905   }
 906
 907   /**
 908    *
 909    * @param sequenceFeature
 910    * @return true if feature is visible.
 911    */
 912   private boolean showFeature(SequenceFeature sequenceFeature)
 913   {
 914     Object fc = getFeatureStyle(sequenceFeature.type);
 915     if (fc instanceof GraduatedColor)
 916     {
 917       return ((GraduatedColor) fc).isColored(sequenceFeature);
 918     }
 919     else
 920     {
 921       return true;
 922     }
 923   }
 924
 925   /**
 926    * implement graduated colouring for features with scores
 927    *
 928    * @param feature
 929    * @return render colour for the given feature
 930    */
 931   public Color getColour(SequenceFeature feature)
 932   {
 933     Object fc = getFeatureStyle(feature.getType());
 934     if (fc instanceof Color)
 935     {
 936       return (Color) fc;
 937     }
 938     else
 939     {
 940       if (fc instanceof GraduatedColor)
 941       {
 942         return ((GraduatedColor) fc).findColor(feature);
 943       }
 944     }
 945     throw new Error("Implementation Error: Unrecognised render object "
 946             + fc.getClass() + " for features of type " + feature.getType());
 947   }
 948
 949   public void setColour(String featureType, Object col)
 950   {
 951     // overwrite
 952     // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
 953     // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
 954     // Object c = featureColours.get(featureType);
 955     // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
 956     // !((GraduatedColor)c).getMaxColor().equals(_col)))
 957     {
 958       featureColours.put(featureType, col);
 959     }
 960   }
 961
 962   public void setFeaturePriority(Object[][] data)
 963   {
 964     // The feature table will display high priority
 965     // features at the top, but theses are the ones
 966     // we need to render last, so invert the data
 967     if (av.featuresDisplayed != null)
 968     {
 969       av.featuresDisplayed.clear();
 970     }
 971
 972     /*
 973      * if (visibleNew) { if (av.featuresDisplayed != null) {
 974      * av.featuresDisplayed.clear(); } else { av.featuresDisplayed = new
 975      * Hashtable(); } } if (data == null) { return; }
 976      */
 977
 978     renderOrder = new String[data.length];
 979
 980     if (data.length > 0)
 981     {
 982       for (int i = 0; i < data.length; i++)
 983       {
 984         String type = data[i][0].toString();
 985         setColour(type, data[i][1]);
 986         if (((Boolean) data[i][2]).booleanValue())
 987         {
 988           av.featuresDisplayed.put(type, new Integer(getColour(type)
 989                   .getRGB()));
 990         }
 991
 992         renderOrder[data.length - i - 1] = type;
 993       }
 994     }
 995   }
 996
 997   /**
 998    * @return a simple list of feature group names or null
 999    */
1000   public String[] getGroups()
1001   {
1002     buildGroupHash();
1003     if (featureGroups != null)
1004     {
1005       String[] gps = new String[featureGroups.size()];
1006       Enumeration gn = featureGroups.keys();
1007       int i = 0;
1008       while (gn.hasMoreElements())
1009       {
1010         gps[i++] = (String) gn.nextElement();
1011       }
1012       return gps;
1013     }
1014     return null;
1015   }
1016
1017   /**
1018    * get visible or invisible groups
1019    *
1020    * @param visible
1021    *          true to return visible groups, false to return hidden ones.
1022    * @return list of groups
1023    */
1024   public String[] getGroups(boolean visible)
1025   {
1026     buildGroupHash();
1027     if (featureGroups != null)
1028     {
1029       Vector gp = new Vector();
1030
1031       Enumeration gn = featureGroups.keys();
1032       while (gn.hasMoreElements())
1033       {
1034         String nm = (String) gn.nextElement();
1035         Boolean state = (Boolean) featureGroups.get(nm);
1036         if (state.booleanValue() == visible)
1037         {
1038           gp.addElement(nm);
1039         }
1040       }
1041       String[] gps = new String[gp.size()];
1042       gp.copyInto(gps);
1043
1044       int i = 0;
1045       while (gn.hasMoreElements())
1046       {
1047         gps[i++] = (String) gn.nextElement();
1048       }
1049       return gps;
1050     }
1051     return null;
1052   }
1053
1054   /**
1055    * set all feature groups in toset to be visible or invisible
1056    *
1057    * @param toset
1058    *          group names
1059    * @param visible
1060    *          the state of the named groups to set
1061    */
1062   public void setGroupState(String[] toset, boolean visible)
1063   {
1064     buildGroupHash();
1065     if (toset != null && toset.length > 0 && featureGroups != null)
1066     {
1067       boolean rdrw = false;
1068       for (int i = 0; i < toset.length; i++)
1069       {
1070         Object st = featureGroups.get(toset[i]);
1071         featureGroups.put(toset[i], new Boolean(visible));
1072         if (st != null)
1073         {
1074           rdrw = rdrw || (visible != ((Boolean) st).booleanValue());
1075         }
1076       }
1077       if (rdrw)
1078       {
1079         if (this.av != null)
1080           if (this.av.featureSettings != null)
1081           {
1082             av.featureSettings.rebuildGroups();
1083             this.av.featureSettings.resetTable(true);
1084           }
1085           else
1086           {
1087             buildFeatureHash();
1088           }
1089         if (av != null)
1090         {
1091           av.alignmentChanged(null);
1092         }
1093       }
1094     }
1095   }
1096
1097   ArrayList<String> hiddenGroups = new ArrayList<String>();
1098
1099   /**
1100    * analyse alignment for groups and hash tables (used to be embedded in
1101    * FeatureSettings.setTableData)
1102    *
1103    * @return true if features are on the alignment
1104    */
1105   public boolean buildGroupHash()
1106   {
1107     boolean alignmentHasFeatures = false;
1108     if (featureGroups == null)
1109     {
1110       featureGroups = new Hashtable();
1111     }
1112     hiddenGroups = new ArrayList<String>();
1113     hiddenGroups.addAll(featureGroups.keySet());
1114     ArrayList allFeatures = new ArrayList();
1115     ArrayList allGroups = new ArrayList();
1116     SequenceFeature[] tmpfeatures;
1117     String group;
1118     AlignmentI alignment = av.getAlignment();
1119     for (int i = 0; i < alignment.getHeight(); i++)
1120     {
1121       if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
1122       {
1123         continue;
1124       }
1125
1126       alignmentHasFeatures = true;
1127
1128       tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
1129       int index = 0;
1130       while (index < tmpfeatures.length)
1131       {
1132         if (tmpfeatures[index].getFeatureGroup() != null)
1133         {
1134           group = tmpfeatures[index].featureGroup;
1135           // Remove group from the hiddenGroup list
1136           hiddenGroups.remove(group);
1137           if (!allGroups.contains(group))
1138           {
1139             allGroups.add(group);
1140
1141             boolean visible = true;
1142             if (featureGroups.containsKey(group))
1143             {
1144               visible = ((Boolean) featureGroups.get(group)).booleanValue();
1145             }
1146             else
1147             {
1148               featureGroups.put(group, new Boolean(visible));
1149             }
1150           }
1151         }
1152
1153         if (!allFeatures.contains(tmpfeatures[index].getType()))
1154         {
1155           allFeatures.add(tmpfeatures[index].getType());
1156         }
1157         index++;
1158       }
1159     }
1160
1161     return alignmentHasFeatures;
1162   }
1163
1164   /**
1165    * rebuild the featuresDisplayed and renderorder list based on the
1166    * featureGroups hash and any existing display state and force a repaint if
1167    * necessary
1168    *
1169    * @return true if alignment has visible features
1170    */
1171   public boolean buildFeatureHash()
1172   {
1173     boolean alignmentHasFeatures = false;
1174     if (featureGroups == null)
1175     {
1176       alignmentHasFeatures = buildGroupHash();
1177     }
1178     if (!alignmentHasFeatures)
1179       return false;
1180     Hashtable fdisp = av.featuresDisplayed;
1181     Vector allFeatures = new Vector();
1182     SequenceFeature[] tmpfeatures;
1183     String group;
1184     AlignmentI alignment = av.getAlignment();
1185     for (int i = 0; i < alignment.getHeight(); i++)
1186     {
1187       if (alignment.getSequenceAt(i).getSequenceFeatures() == null)
1188       {
1189         continue;
1190       }
1191
1192       alignmentHasFeatures = true;
1193
1194       tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures();
1195       int index = 0;
1196       while (index < tmpfeatures.length)
1197       {
1198         boolean visible = true;
1199         if (tmpfeatures[index].getFeatureGroup() != null)
1200         {
1201           group = tmpfeatures[index].featureGroup;
1202           if (featureGroups.containsKey(group))
1203           {
1204             visible = ((Boolean) featureGroups.get(group)).booleanValue();
1205           }
1206         }
1207
1208         if (visible && !allFeatures.contains(tmpfeatures[index].getType()))
1209         {
1210           allFeatures.addElement(tmpfeatures[index].getType());
1211         }
1212         index++;
1213       }
1214     }
1215     if (allFeatures.size() > 0)
1216     {
1217       String[] neworder = new String[allFeatures.size()];
1218       int p = neworder.length - 1;
1219       for (int i = renderOrder.length - 1; i >= 0; i--)
1220       {
1221         if (allFeatures.contains(renderOrder[i]))
1222         {
1223           neworder[p--] = renderOrder[i];
1224           allFeatures.removeElement(renderOrder[i]);
1225         }
1226         else
1227         {
1228           av.featuresDisplayed.remove(renderOrder[i]);
1229         }
1230       }
1231       for (int i = allFeatures.size() - 1; i > 0; i++)
1232       {
1233         Object e = allFeatures.elementAt(i);
1234         if (e != null)
1235         {
1236           neworder[p--] = (String) e;
1237           av.featuresDisplayed.put(e, getColour((String) e));
1238         }
1239       }
1240       renderOrder = neworder;
1241       return true;
1242     }
1243
1244     return alignmentHasFeatures;
1245   }
1246
1247   /**
1248    *
1249    * @return the displayed feature type as an array of strings
1250    */
1251   protected String[] getDisplayedFeatureTypes()
1252   {
1253     String[] typ = null;
1254     synchronized (renderOrder)
1255     {
1256       typ = new String[renderOrder.length];
1257       System.arraycopy(renderOrder, 0, typ, 0, typ.length);
1258       for (int i = 0; i < typ.length; i++)
1259       {
1260         if (av.featuresDisplayed.get(typ[i]) == null)
1261         {
1262           typ[i] = null;
1263         }
1264       }
1265     }
1266     return typ;
1267   }
1268 }
1269
1270 class TransparencySetter
1271 {
1272   void setTransparency(Graphics g, float value)
1273   {
1274     Graphics2D g2 = (Graphics2D) g;
1275     g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
1276             value));
1277   }
1278 }