gui/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.gui;
  22
  23 import java.util.*;
  24 import java.util.concurrent.ConcurrentHashMap;
  25
  26 import java.awt.*;
  27 import java.awt.event.*;
  28 import java.awt.image.*;
  29 import java.beans.PropertyChangeListener;
  30 import java.beans.PropertyChangeSupport;
  31
  32 import javax.swing.*;
  33
  34 import jalview.datamodel.*;
  35 import jalview.schemes.GraduatedColor;
  36 import jalview.util.MessageManager;
  37
  38 /**
  39  * DOCUMENT ME!
  40  *
  41  * @author $author$
  42  * @version $Revision$
  43  */
  44 public class FeatureRenderer implements jalview.api.FeatureRenderer
  45 {
  46   AlignmentPanel ap;
  47
  48   AlignViewport av;
  49
  50   Color resBoxColour;
  51
  52   /**
  53    * global transparency for feature
  54    */
  55   float transparency = 1.0f;
  56
  57   FontMetrics fm;
  58
  59   int charOffset;
  60
  61   Map featureColours = new ConcurrentHashMap();
  62
  63   // A higher level for grouping features of a
  64   // particular type
  65   Map featureGroups = new ConcurrentHashMap();
  66
  67   // This is actually an Integer held in the hashtable,
  68   // Retrieved using the key feature type
  69   Object currentColour;
  70
  71   String[] renderOrder;
  72
  73   PropertyChangeSupport changeSupport = new PropertyChangeSupport(this);
  74
  75   Vector allfeatures;
  76
  77   /**
  78    * Creates a new FeatureRenderer object.
  79    *
  80    * @param av
  81    *          DOCUMENT ME!
  82    */
  83   public FeatureRenderer(AlignmentPanel ap)
  84   {
  85     this.ap = ap;
  86     this.av = ap.av;
  87     if (ap != null && ap.seqPanel != null && ap.seqPanel.seqCanvas != null
  88             && ap.seqPanel.seqCanvas.fr != null)
  89     {
  90       transferSettings(ap.seqPanel.seqCanvas.fr);
  91     }
  92   }
  93
  94   public class FeatureRendererSettings implements Cloneable
  95   {
  96     String[] renderOrder;
  97
  98     Map featureGroups;
  99
 100     Map featureColours;
 101
 102     float transparency;
 103
 104     Map featureOrder;
 105
 106     public FeatureRendererSettings(String[] renderOrder,
 107             Hashtable featureGroups, Hashtable featureColours,
 108             float transparency, Hashtable featureOrder)
 109     {
 110       super();
 111       this.renderOrder = renderOrder;
 112       this.featureGroups = featureGroups;
 113       this.featureColours = featureColours;
 114       this.transparency = transparency;
 115       this.featureOrder = featureOrder;
 116     }
 117
 118     /**
 119      * create an independent instance of the feature renderer settings
 120      *
 121      * @param fr
 122      */
 123     public FeatureRendererSettings(FeatureRenderer fr)
 124     {
 125       renderOrder = null;
 126       featureGroups = new ConcurrentHashMap();
 127       featureColours = new ConcurrentHashMap();
 128       featureOrder = new ConcurrentHashMap();
 129       if (fr.renderOrder != null)
 130       {
 131         this.renderOrder = new String[fr.renderOrder.length];
 132         System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
 133                 fr.renderOrder.length);
 134       }
 135       if (fr.featureGroups != null)
 136       {
 137         this.featureGroups = new ConcurrentHashMap(fr.featureGroups);
 138       }
 139       if (fr.featureColours != null)
 140       {
 141         this.featureColours = new ConcurrentHashMap(fr.featureColours);
 142       }
 143       Iterator en = fr.featureColours.keySet().iterator();
 144       while (en.hasNext())
 145       {
 146         Object next = en.next();
 147         Object val = featureColours.get(next);
 148         if (val instanceof GraduatedColor)
 149         {
 150           featureColours
 151                   .put(next, new GraduatedColor((GraduatedColor) val));
 152         }
 153       }
 154       this.transparency = fr.transparency;
 155       if (fr.featureOrder != null)
 156       {
 157         this.featureOrder = new ConcurrentHashMap(fr.featureOrder);
 158       }
 159     }
 160   }
 161
 162   public FeatureRendererSettings getSettings()
 163   {
 164     return new FeatureRendererSettings(this);
 165   }
 166
 167   public void transferSettings(FeatureRendererSettings fr)
 168   {
 169     this.renderOrder = fr.renderOrder;
 170     this.featureGroups = fr.featureGroups;
 171     this.featureColours = fr.featureColours;
 172     this.transparency = fr.transparency;
 173     this.featureOrder = fr.featureOrder;
 174   }
 175
 176   /**
 177    * update from another feature renderer
 178    *
 179    * @param fr
 180    *          settings to copy
 181    */
 182   public void transferSettings(FeatureRenderer fr)
 183   {
 184     FeatureRendererSettings frs = new FeatureRendererSettings(fr);
 185     this.renderOrder = frs.renderOrder;
 186     this.featureGroups = frs.featureGroups;
 187     this.featureColours = frs.featureColours;
 188     this.transparency = frs.transparency;
 189     this.featureOrder = frs.featureOrder;
 190     if (av != null && av != fr.av)
 191     {
 192       // copy over the displayed feature settings
 193       if (fr.av != null)
 194       {
 195         if (fr.av.featuresDisplayed != null)
 196         {
 197           // update display settings
 198           if (av.featuresDisplayed == null)
 199           {
 200             av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed);
 201           }
 202           else
 203           {
 204             av.featuresDisplayed.clear();
 205             Enumeration en = fr.av.featuresDisplayed.keys();
 206             while (en.hasMoreElements())
 207             {
 208               av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
 209             }
 210
 211           }
 212         }
 213       }
 214     }
 215   }
 216
 217   BufferedImage offscreenImage;
 218
 219   boolean offscreenRender = false;
 220
 221   public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
 222   {
 223     return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
 224   }
 225
 226   /**
 227    * This is used by the Molecule Viewer and Overview to get the accurate
 228    * colourof the rendered sequence
 229    */
 230   public synchronized int findFeatureColour(int initialCol, SequenceI seq,
 231           int column)
 232   {
 233     if (!av.showSequenceFeatures)
 234     {
 235       return initialCol;
 236     }
 237
 238     if (seq != lastSeq)
 239     {
 240       lastSeq = seq;
 241       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
 242       if (sequenceFeatures != null)
 243       {
 244         sfSize = sequenceFeatures.length;
 245       }
 246     }
 247
 248     if (sequenceFeatures != lastSeq.getDatasetSequence()
 249             .getSequenceFeatures())
 250     {
 251       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
 252       if (sequenceFeatures != null)
 253       {
 254         sfSize = sequenceFeatures.length;
 255       }
 256     }
 257
 258     if (sequenceFeatures == null || sfSize == 0)
 259     {
 260       return initialCol;
 261     }
 262
 263     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
 264     {
 265       return Color.white.getRGB();
 266     }
 267
 268     // Only bother making an offscreen image if transparency is applied
 269     if (transparency != 1.0f && offscreenImage == null)
 270     {
 271       offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
 272     }
 273
 274     currentColour = null;
 275     // TODO: non-threadsafe - each rendering thread needs its own instance of
 276     // the feature renderer - or this should be synchronized.
 277     offscreenRender = true;
 278
 279     if (offscreenImage != null)
 280     {
 281       offscreenImage.setRGB(0, 0, initialCol);
 282       drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
 283
 284       return offscreenImage.getRGB(0, 0);
 285     }
 286     else
 287     {
 288       drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
 289
 290       if (currentColour == null)
 291       {
 292         return initialCol;
 293       }
 294       else
 295       {
 296         return ((Integer) currentColour).intValue();
 297       }
 298     }
 299
 300   }
 301
 302   /**
 303    * DOCUMENT ME!
 304    *
 305    * @param g
 306    *          DOCUMENT ME!
 307    * @param seq
 308    *          DOCUMENT ME!
 309    * @param sg
 310    *          DOCUMENT ME!
 311    * @param start
 312    *          DOCUMENT ME!
 313    * @param end
 314    *          DOCUMENT ME!
 315    * @param x1
 316    *          DOCUMENT ME!
 317    * @param y1
 318    *          DOCUMENT ME!
 319    * @param width
 320    *          DOCUMENT ME!
 321    * @param height
 322    *          DOCUMENT ME!
 323    */
 324   // String type;
 325   // SequenceFeature sf;
 326   SequenceI lastSeq;
 327
 328   SequenceFeature[] sequenceFeatures;
 329
 330   int sfSize, sfindex, spos, epos;
 331
 332   /**
 333    * show scores as heights
 334    */
 335   protected boolean varyHeight = false;
 336
 337   synchronized public void drawSequence(Graphics g, SequenceI seq,
 338           int start, int end, int y1)
 339   {
 340
 341     if (seq.getDatasetSequence().getSequenceFeatures() == null
 342             || seq.getDatasetSequence().getSequenceFeatures().length == 0)
 343     {
 344       return;
 345     }
 346
 347     if (g != null)
 348     {
 349       fm = g.getFontMetrics();
 350     }
 351
 352     if (av.featuresDisplayed == null || renderOrder == null
 353             || newFeatureAdded)
 354     {
 355       findAllFeatures();
 356       if (av.featuresDisplayed.size() < 1)
 357       {
 358         return;
 359       }
 360
 361       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
 362     }
 363
 364     if (lastSeq == null
 365             || seq != lastSeq
 366             || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures)
 367     {
 368       lastSeq = seq;
 369       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
 370     }
 371
 372     if (transparency != 1 && g != null)
 373     {
 374       Graphics2D g2 = (Graphics2D) g;
 375       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 376               transparency));
 377     }
 378
 379     if (!offscreenRender)
 380     {
 381       spos = lastSeq.findPosition(start);
 382       epos = lastSeq.findPosition(end);
 383     }
 384
 385     sfSize = sequenceFeatures.length;
 386     String type;
 387     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
 388     {
 389       type = renderOrder[renderIndex];
 390
 391       if (type == null || !av.featuresDisplayed.containsKey(type))
 392       {
 393         continue;
 394       }
 395
 396       // loop through all features in sequence to find
 397       // current feature to render
 398       for (sfindex = 0; sfindex < sfSize; sfindex++)
 399       {
 400         if (!sequenceFeatures[sfindex].type.equals(type))
 401         {
 402           continue;
 403         }
 404
 405         if (featureGroups != null
 406                 && sequenceFeatures[sfindex].featureGroup != null
 407                 && sequenceFeatures[sfindex].featureGroup.length() != 0
 408                 && featureGroups
 409                         .containsKey(sequenceFeatures[sfindex].featureGroup)
 410                 && !((Boolean) featureGroups
 411                         .get(sequenceFeatures[sfindex].featureGroup))
 412                         .booleanValue())
 413         {
 414           continue;
 415         }
 416
 417         if (!offscreenRender
 418                 && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
 419                         .getEnd() < spos))
 420         {
 421           continue;
 422         }
 423
 424         if (offscreenRender && offscreenImage == null)
 425         {
 426           if (sequenceFeatures[sfindex].begin <= start
 427                   && sequenceFeatures[sfindex].end >= start)
 428           {
 429             // this is passed out to the overview and other sequence renderers
 430             // (e.g. molecule viewer) to get displayed colour for rendered
 431             // sequence
 432             currentColour = new Integer(
 433                     getColour(sequenceFeatures[sfindex]).getRGB());
 434             // used to be retreived from av.featuresDisplayed
 435             // currentColour = av.featuresDisplayed
 436             // .get(sequenceFeatures[sfindex].type);
 437
 438           }
 439         }
 440         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
 441         {
 442
 443           renderFeature(g, seq,
 444                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 445                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 446                   getColour(sequenceFeatures[sfindex])
 447                   // new Color(((Integer) av.featuresDisplayed
 448                   // .get(sequenceFeatures[sfindex].type)).intValue())
 449                   , start, end, y1);
 450           renderFeature(g, seq,
 451                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 452                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 453                   getColour(sequenceFeatures[sfindex])
 454                   // new Color(((Integer) av.featuresDisplayed
 455                   // .get(sequenceFeatures[sfindex].type)).intValue())
 456                   , start, end, y1);
 457
 458         }
 459         else if (showFeature(sequenceFeatures[sfindex]))
 460         {
 461           if (av.showSeqFeaturesHeight
 462                   && sequenceFeatures[sfindex].score != Float.NaN)
 463           {
 464             renderScoreFeature(g, seq,
 465                     seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 466                     seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 467                     getColour(sequenceFeatures[sfindex]), start, end, y1,
 468                     normaliseScore(sequenceFeatures[sfindex]));
 469           }
 470           else
 471           {
 472             renderFeature(g, seq,
 473                     seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 474                     seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 475                     getColour(sequenceFeatures[sfindex]), start, end, y1);
 476           }
 477         }
 478
 479       }
 480
 481     }
 482
 483     if (transparency != 1.0f && g != null)
 484     {
 485       Graphics2D g2 = (Graphics2D) g;
 486       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 487               1.0f));
 488     }
 489   }
 490
 491   Hashtable minmax = new Hashtable();
 492
 493   /**
 494    * normalise a score against the max/min bounds for the feature type.
 495    *
 496    * @param sequenceFeature
 497    * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
 498    *         (0-255) value.
 499    */
 500   private final byte[] normaliseScore(SequenceFeature sequenceFeature)
 501   {
 502     float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
 503     final byte[] r = new byte[]
 504     { 0, (byte) 255 };
 505     if (mm != null)
 506     {
 507       if (r[0] != 0 || mm[0] < 0.0)
 508       {
 509         r[0] = 1;
 510         r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
 511       }
 512       else
 513       {
 514         r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
 515       }
 516     }
 517     return r;
 518   }
 519
 520   char s;
 521
 522   int i;
 523
 524   void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
 525           Color featureColour, int start, int end, int y1)
 526   {
 527
 528     if (((fstart <= end) && (fend >= start)))
 529     {
 530       if (fstart < start)
 531       { // fix for if the feature we have starts before the sequence start,
 532         fstart = start; // but the feature end is still valid!!
 533       }
 534
 535       if (fend >= end)
 536       {
 537         fend = end;
 538       }
 539       int pady = (y1 + av.charHeight) - av.charHeight / 5;
 540       for (i = fstart; i <= fend; i++)
 541       {
 542         s = seq.getCharAt(i);
 543
 544         if (jalview.util.Comparison.isGap(s))
 545         {
 546           continue;
 547         }
 548
 549         g.setColor(featureColour);
 550
 551         g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
 552                 av.charHeight);
 553
 554         if (offscreenRender || !av.validCharWidth)
 555         {
 556           continue;
 557         }
 558
 559         g.setColor(Color.white);
 560         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 561         g.drawString(String.valueOf(s), charOffset
 562                 + (av.charWidth * (i - start)), pady);
 563
 564       }
 565     }
 566   }
 567
 568   void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
 569           Color featureColour, int start, int end, int y1, byte[] bs)
 570   {
 571
 572     if (((fstart <= end) && (fend >= start)))
 573     {
 574       if (fstart < start)
 575       { // fix for if the feature we have starts before the sequence start,
 576         fstart = start; // but the feature end is still valid!!
 577       }
 578
 579       if (fend >= end)
 580       {
 581         fend = end;
 582       }
 583       int pady = (y1 + av.charHeight) - av.charHeight / 5;
 584       int ystrt = 0, yend = av.charHeight;
 585       if (bs[0] != 0)
 586       {
 587         // signed - zero is always middle of residue line.
 588         if (bs[1] < 128)
 589         {
 590           yend = av.charHeight * (128 - bs[1]) / 512;
 591           ystrt = av.charHeight - yend / 2;
 592         }
 593         else
 594         {
 595           ystrt = av.charHeight / 2;
 596           yend = av.charHeight * (bs[1] - 128) / 512;
 597         }
 598       }
 599       else
 600       {
 601         yend = av.charHeight * bs[1] / 255;
 602         ystrt = av.charHeight - yend;
 603
 604       }
 605       for (i = fstart; i <= fend; i++)
 606       {
 607         s = seq.getCharAt(i);
 608
 609         if (jalview.util.Comparison.isGap(s))
 610         {
 611           continue;
 612         }
 613
 614         g.setColor(featureColour);
 615         int x = (i - start) * av.charWidth;
 616         g.drawRect(x, y1, av.charWidth, av.charHeight);
 617         g.fillRect(x, y1 + ystrt, av.charWidth, yend);
 618
 619         if (offscreenRender || !av.validCharWidth)
 620         {
 621           continue;
 622         }
 623
 624         g.setColor(Color.black);
 625         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 626         g.drawString(String.valueOf(s), charOffset
 627                 + (av.charWidth * (i - start)), pady);
 628
 629       }
 630     }
 631   }
 632
 633   boolean newFeatureAdded = false;
 634
 635   /**
 636    * Called when alignment in associated view has new/modified features to
 637    * discover and display.
 638    *
 639    */
 640   public void featuresAdded()
 641   {
 642     lastSeq = null;
 643     findAllFeatures();
 644   }
 645
 646   boolean findingFeatures = false;
 647
 648   /**
 649    * search the alignment for all new features, give them a colour and display
 650    * them. Then fires a PropertyChangeEvent on the changeSupport object.
 651    *
 652    */
 653   void findAllFeatures()
 654   {
 655     synchronized (firing)
 656     {
 657       if (firing.equals(Boolean.FALSE))
 658       {
 659         firing = Boolean.TRUE;
 660         findAllFeatures(true); // add all new features as visible
 661         changeSupport.firePropertyChange("changeSupport", null, null);
 662         firing = Boolean.FALSE;
 663       }
 664     }
 665   }
 666
 667   /**
 668    * Searches alignment for all features and updates colours
 669    *
 670    * @param newMadeVisible
 671    *          if true newly added feature types will be rendered immediatly
 672    */
 673   synchronized void findAllFeatures(boolean newMadeVisible)
 674   {
 675     newFeatureAdded = false;
 676
 677     if (findingFeatures)
 678     {
 679       newFeatureAdded = true;
 680       return;
 681     }
 682
 683     findingFeatures = true;
 684
 685     if (av.featuresDisplayed == null)
 686     {
 687       av.featuresDisplayed = new Hashtable();
 688     }
 689
 690     allfeatures = new Vector();
 691     Vector oldfeatures = new Vector();
 692     if (renderOrder != null)
 693     {
 694       for (int i = 0; i < renderOrder.length; i++)
 695       {
 696         if (renderOrder[i] != null)
 697         {
 698           oldfeatures.addElement(renderOrder[i]);
 699         }
 700       }
 701     }
 702     if (minmax == null)
 703     {
 704       minmax = new Hashtable();
 705     }
 706     AlignmentI alignment = av.getAlignment();
 707     for (int i = 0; i < alignment.getHeight(); i++)
 708     {
 709       SequenceFeature[] features = alignment.getSequenceAt(i)
 710               .getDatasetSequence().getSequenceFeatures();
 711
 712       if (features == null)
 713       {
 714         continue;
 715       }
 716
 717       int index = 0;
 718       while (index < features.length)
 719       {
 720         if (!av.featuresDisplayed.containsKey(features[index].getType()))
 721         {
 722
 723           if (featureGroups.containsKey(features[index].getType()))
 724           {
 725             boolean visible = ((Boolean) featureGroups
 726                     .get(features[index].featureGroup)).booleanValue();
 727
 728             if (!visible)
 729             {
 730               index++;
 731               continue;
 732             }
 733           }
 734
 735           if (!(features[index].begin == 0 && features[index].end == 0))
 736           {
 737             // If beginning and end are 0, the feature is for the whole sequence
 738             // and we don't want to render the feature in the normal way
 739
 740             if (newMadeVisible
 741                     && !oldfeatures.contains(features[index].getType()))
 742             {
 743               // this is a new feature type on the alignment. Mark it for
 744               // display.
 745               av.featuresDisplayed.put(features[index].getType(),
 746                       new Integer(getColour(features[index].getType())
 747                               .getRGB()));
 748               setOrder(features[index].getType(), 0);
 749             }
 750           }
 751         }
 752         if (!allfeatures.contains(features[index].getType()))
 753         {
 754           allfeatures.addElement(features[index].getType());
 755         }
 756         if (features[index].score != Float.NaN)
 757         {
 758           int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
 759           float[][] mm = (float[][]) minmax.get(features[index].getType());
 760           if (mm == null)
 761           {
 762             mm = new float[][]
 763             { null, null };
 764             minmax.put(features[index].getType(), mm);
 765           }
 766           if (mm[nonpos] == null)
 767           {
 768             mm[nonpos] = new float[]
 769             { features[index].score, features[index].score };
 770
 771           }
 772           else
 773           {
 774             if (mm[nonpos][0] > features[index].score)
 775             {
 776               mm[nonpos][0] = features[index].score;
 777             }
 778             if (mm[nonpos][1] < features[index].score)
 779             {
 780               mm[nonpos][1] = features[index].score;
 781             }
 782           }
 783         }
 784         index++;
 785       }
 786     }
 787     updateRenderOrder(allfeatures);
 788     findingFeatures = false;
 789   }
 790
 791   protected Boolean firing = Boolean.FALSE;
 792
 793   /**
 794    * replaces the current renderOrder with the unordered features in
 795    * allfeatures. The ordering of any types in both renderOrder and allfeatures
 796    * is preserved, and all new feature types are rendered on top of the existing
 797    * types, in the order given by getOrder or the order given in allFeatures.
 798    * Note. this operates directly on the featureOrder hash for efficiency. TODO:
 799    * eliminate the float storage for computing/recalling the persistent ordering
 800    * New Cability: updates min/max for colourscheme range if its dynamic
 801    *
 802    * @param allFeatures
 803    */
 804   private void updateRenderOrder(Vector allFeatures)
 805   {
 806     Vector allfeatures = new Vector(allFeatures);
 807     String[] oldRender = renderOrder;
 808     renderOrder = new String[allfeatures.size()];
 809     Object mmrange, fc = null;
 810     boolean initOrders = (featureOrder == null);
 811     int opos = 0;
 812     if (oldRender != null && oldRender.length > 0)
 813     {
 814       for (int j = 0; j < oldRender.length; j++)
 815       {
 816         if (oldRender[j] != null)
 817         {
 818           if (initOrders)
 819           {
 820             setOrder(oldRender[j], (1 - (1 + (float) j)
 821                     / (float) oldRender.length));
 822           }
 823           if (allfeatures.contains(oldRender[j]))
 824           {
 825             renderOrder[opos++] = oldRender[j]; // existing features always
 826             // appear below new features
 827             allfeatures.removeElement(oldRender[j]);
 828             if (minmax != null)
 829             {
 830               mmrange = minmax.get(oldRender[j]);
 831               if (mmrange != null)
 832               {
 833                 fc = featureColours.get(oldRender[j]);
 834                 if (fc != null && fc instanceof GraduatedColor
 835                         && ((GraduatedColor) fc).isAutoScale())
 836                 {
 837                   ((GraduatedColor) fc).updateBounds(
 838                           ((float[][]) mmrange)[0][0],
 839                           ((float[][]) mmrange)[0][1]);
 840                 }
 841               }
 842             }
 843           }
 844         }
 845       }
 846     }
 847     if (allfeatures.size() == 0)
 848     {
 849       // no new features - leave order unchanged.
 850       return;
 851     }
 852     int i = allfeatures.size() - 1;
 853     int iSize = i;
 854     boolean sort = false;
 855     String[] newf = new String[allfeatures.size()];
 856     float[] sortOrder = new float[allfeatures.size()];
 857     Enumeration en = allfeatures.elements();
 858     // sort remaining elements
 859     while (en.hasMoreElements())
 860     {
 861       newf[i] = en.nextElement().toString();
 862       if (minmax != null)
 863       {
 864         // update from new features minmax if necessary
 865         mmrange = minmax.get(newf[i]);
 866         if (mmrange != null)
 867         {
 868           fc = featureColours.get(newf[i]);
 869           if (fc != null && fc instanceof GraduatedColor
 870                   && ((GraduatedColor) fc).isAutoScale())
 871           {
 872             ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
 873                     ((float[][]) mmrange)[0][1]);
 874           }
 875         }
 876       }
 877       if (initOrders || !featureOrder.containsKey(newf[i]))
 878       {
 879         int denom = initOrders ? allfeatures.size() : featureOrder.size();
 880         // new unordered feature - compute persistent ordering at head of
 881         // existing features.
 882         setOrder(newf[i], i / (float) denom);
 883       }
 884       // set order from newly found feature from persisted ordering.
 885       sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
 886       if (i < iSize)
 887       {
 888         // only sort if we need to
 889         sort = sort || sortOrder[i] > sortOrder[i + 1];
 890       }
 891       i--;
 892     }
 893     if (iSize > 1 && sort)
 894     {
 895       jalview.util.QuickSort.sort(sortOrder, newf);
 896     }
 897     sortOrder = null;
 898     System.arraycopy(newf, 0, renderOrder, opos, newf.length);
 899   }
 900
 901   /**
 902    * get a feature style object for the given type string. Creates a
 903    * java.awt.Color for a featureType with no existing colourscheme. TODO:
 904    * replace return type with object implementing standard abstract colour/style
 905    * interface
 906    *
 907    * @param featureType
 908    * @return java.awt.Color or GraduatedColor
 909    */
 910   public Object getFeatureStyle(String featureType)
 911   {
 912     Object fc = featureColours.get(featureType);
 913     if (fc == null)
 914     {
 915       jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
 916       Color col = ucs.createColourFromName(featureType);
 917       featureColours.put(featureType, fc = col);
 918     }
 919     return fc;
 920   }
 921
 922   /**
 923    * return a nominal colour for this feature
 924    *
 925    * @param featureType
 926    * @return standard color, or maximum colour for graduated colourscheme
 927    */
 928   public Color getColour(String featureType)
 929   {
 930     Object fc = getFeatureStyle(featureType);
 931
 932     if (fc instanceof Color)
 933     {
 934       return (Color) fc;
 935     }
 936     else
 937     {
 938       if (fc instanceof GraduatedColor)
 939       {
 940         return ((GraduatedColor) fc).getMaxColor();
 941       }
 942     }
 943     throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),featureType}));
 944   }
 945
 946   /**
 947    * calculate the render colour for a specific feature using current feature
 948    * settings.
 949    *
 950    * @param feature
 951    * @return render colour for the given feature
 952    */
 953   public Color getColour(SequenceFeature feature)
 954   {
 955     Object fc = getFeatureStyle(feature.getType());
 956     if (fc instanceof Color)
 957     {
 958       return (Color) fc;
 959     }
 960     else
 961     {
 962       if (fc instanceof GraduatedColor)
 963       {
 964         return ((GraduatedColor) fc).findColor(feature);
 965       }
 966     }
 967     throw new Error(MessageManager.formatMessage("error.implementation_error_unrecognised_render_object_for_features_type", new String[]{fc.getClass().toString(),feature.getType()}));
 968   }
 969
 970   private boolean showFeature(SequenceFeature sequenceFeature)
 971   {
 972     Object fc = getFeatureStyle(sequenceFeature.type);
 973     if (fc instanceof GraduatedColor)
 974     {
 975       return ((GraduatedColor) fc).isColored(sequenceFeature);
 976     }
 977     else
 978     {
 979       return true;
 980     }
 981   }
 982
 983   // // /////////////
 984   // // Feature Editing Dialog
 985   // // Will be refactored in next release.
 986
 987   static String lastFeatureAdded;
 988
 989   static String lastFeatureGroupAdded;
 990
 991   static String lastDescriptionAdded;
 992
 993   Object oldcol, fcol;
 994
 995   int featureIndex = 0;
 996
 997   boolean amendFeatures(final SequenceI[] sequences,
 998           final SequenceFeature[] features, boolean newFeatures,
 999           final AlignmentPanel ap)
1000   {
1001
1002     featureIndex = 0;
1003
1004     final JPanel bigPanel = new JPanel(new BorderLayout());
1005     final JComboBox overlaps;
1006     final JTextField name = new JTextField(25);
1007     final JTextField source = new JTextField(25);
1008     final JTextArea description = new JTextArea(3, 25);
1009     final JSpinner start = new JSpinner();
1010     final JSpinner end = new JSpinner();
1011     start.setPreferredSize(new Dimension(80, 20));
1012     end.setPreferredSize(new Dimension(80, 20));
1013     final FeatureRenderer me = this;
1014     final JLabel colour = new JLabel();
1015     colour.setOpaque(true);
1016     // colour.setBorder(BorderFactory.createEtchedBorder());
1017     colour.setMaximumSize(new Dimension(30, 16));
1018     colour.addMouseListener(new MouseAdapter()
1019     {
1020       FeatureColourChooser fcc = null;
1021
1022       public void mousePressed(MouseEvent evt)
1023       {
1024         if (fcol instanceof Color)
1025         {
1026           Color col = JColorChooser.showDialog(Desktop.desktop,
1027                   MessageManager.getString("label.select_feature_colour"), ((Color) fcol));
1028           if (col != null)
1029           {
1030             fcol = col;
1031             updateColourButton(bigPanel, colour, col);
1032           }
1033         }
1034         else
1035         {
1036
1037           if (fcc == null)
1038           {
1039             final String type = features[featureIndex].getType();
1040             fcc = new FeatureColourChooser(me, type);
1041             fcc.setRequestFocusEnabled(true);
1042             fcc.requestFocus();
1043
1044             fcc.addActionListener(new ActionListener()
1045             {
1046
1047               public void actionPerformed(ActionEvent e)
1048               {
1049                 fcol = fcc.getLastColour();
1050                 fcc = null;
1051                 setColour(type, fcol);
1052                 updateColourButton(bigPanel, colour, fcol);
1053               }
1054             });
1055
1056           }
1057         }
1058       }
1059     });
1060     JPanel tmp = new JPanel();
1061     JPanel panel = new JPanel(new GridLayout(3, 1));
1062
1063     // /////////////////////////////////////
1064     // /MULTIPLE FEATURES AT SELECTED RESIDUE
1065     if (!newFeatures && features.length > 1)
1066     {
1067       panel = new JPanel(new GridLayout(4, 1));
1068       tmp = new JPanel();
1069       tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
1070       overlaps = new JComboBox();
1071       for (int i = 0; i < features.length; i++)
1072       {
1073         overlaps.addItem(features[i].getType() + "/"
1074                 + features[i].getBegin() + "-" + features[i].getEnd()
1075                 + " (" + features[i].getFeatureGroup() + ")");
1076       }
1077
1078       tmp.add(overlaps);
1079
1080       overlaps.addItemListener(new ItemListener()
1081       {
1082         public void itemStateChanged(ItemEvent e)
1083         {
1084           int index = overlaps.getSelectedIndex();
1085           if (index != -1)
1086           {
1087             featureIndex = index;
1088             name.setText(features[index].getType());
1089             description.setText(features[index].getDescription());
1090             source.setText(features[index].getFeatureGroup());
1091             start.setValue(new Integer(features[index].getBegin()));
1092             end.setValue(new Integer(features[index].getEnd()));
1093
1094             SearchResults highlight = new SearchResults();
1095             highlight.addResult(sequences[0], features[index].getBegin(),
1096                     features[index].getEnd());
1097
1098             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
1099
1100           }
1101           Object col = getFeatureStyle(name.getText());
1102           if (col == null)
1103           {
1104             col = new jalview.schemes.UserColourScheme()
1105                     .createColourFromName(name.getText());
1106           }
1107           oldcol = fcol = col;
1108           updateColourButton(bigPanel, colour, col);
1109         }
1110       });
1111
1112       panel.add(tmp);
1113     }
1114     // ////////
1115     // ////////////////////////////////////
1116
1117     tmp = new JPanel();
1118     panel.add(tmp);
1119     tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
1120     tmp.add(name);
1121
1122     tmp = new JPanel();
1123     panel.add(tmp);
1124     tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
1125             JLabel.RIGHT));
1126     tmp.add(source);
1127
1128     tmp = new JPanel();
1129     panel.add(tmp);
1130     tmp.add(new JLabel(MessageManager.getString("label.colour"),
1131             JLabel.RIGHT));
1132     tmp.add(colour);
1133     colour.setPreferredSize(new Dimension(150, 15));
1134     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
1135     colour.setForeground(Color.black);
1136     colour.setHorizontalAlignment(SwingConstants.CENTER);
1137     colour.setVerticalAlignment(SwingConstants.CENTER);
1138     colour.setHorizontalTextPosition(SwingConstants.CENTER);
1139     colour.setVerticalTextPosition(SwingConstants.CENTER);
1140     bigPanel.add(panel, BorderLayout.NORTH);
1141
1142     panel = new JPanel();
1143     panel.add(new JLabel(MessageManager.getString("label.description"),
1144             JLabel.RIGHT));
1145     description.setFont(JvSwingUtils.getTextAreaFont());
1146     description.setLineWrap(true);
1147     panel.add(new JScrollPane(description));
1148
1149     if (!newFeatures)
1150     {
1151       bigPanel.add(panel, BorderLayout.SOUTH);
1152
1153       panel = new JPanel();
1154       panel.add(new JLabel(MessageManager.getString("label.start"),
1155               JLabel.RIGHT));
1156       panel.add(start);
1157       panel.add(new JLabel(MessageManager.getString("label.end"),
1158               JLabel.RIGHT));
1159       panel.add(end);
1160       bigPanel.add(panel, BorderLayout.CENTER);
1161     }
1162     else
1163     {
1164       bigPanel.add(panel, BorderLayout.CENTER);
1165     }
1166
1167     if (lastFeatureAdded == null)
1168     {
1169       if (features[0].type != null)
1170       {
1171         lastFeatureAdded = features[0].type;
1172       }
1173       else
1174       {
1175         lastFeatureAdded = "feature_1";
1176       }
1177     }
1178
1179     if (lastFeatureGroupAdded == null)
1180     {
1181       if (features[0].featureGroup != null)
1182       {
1183         lastFeatureGroupAdded = features[0].featureGroup;
1184       }
1185       else
1186       {
1187         lastFeatureGroupAdded = "Jalview";
1188       }
1189     }
1190
1191     if (newFeatures)
1192     {
1193       name.setText(lastFeatureAdded);
1194       source.setText(lastFeatureGroupAdded);
1195     }
1196     else
1197     {
1198       name.setText(features[0].getType());
1199       source.setText(features[0].getFeatureGroup());
1200     }
1201
1202     start.setValue(new Integer(features[0].getBegin()));
1203     end.setValue(new Integer(features[0].getEnd()));
1204     description.setText(features[0].getDescription());
1205     updateColourButton(bigPanel, colour,
1206             (oldcol = fcol = getFeatureStyle(name.getText())));
1207     Object[] options;
1208     if (!newFeatures)
1209     {
1210       options = new Object[]
1211       { "Amend", "Delete", "Cancel" };
1212     }
1213     else
1214     {
1215       options = new Object[]
1216       { "OK", "Cancel" };
1217     }
1218
1219     String title = newFeatures ? MessageManager.getString("label.create_new_sequence_features")
1220             : MessageManager.formatMessage("label.amend_delete_features", new String[]{sequences[0].getName()});
1221
1222     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
1223             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
1224             JOptionPane.QUESTION_MESSAGE, null, options, MessageManager.getString("action.ok"));
1225
1226     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
1227
1228     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
1229     {
1230       // This ensures that the last sequence
1231       // is refreshed and new features are rendered
1232       lastSeq = null;
1233       lastFeatureAdded = name.getText().trim();
1234       lastFeatureGroupAdded = source.getText().trim();
1235       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
1236       // TODO: determine if the null feature group is valid
1237       if (lastFeatureGroupAdded.length() < 1)
1238         lastFeatureGroupAdded = null;
1239     }
1240
1241     if (!newFeatures)
1242     {
1243       SequenceFeature sf = features[featureIndex];
1244
1245       if (reply == JOptionPane.NO_OPTION)
1246       {
1247         sequences[0].getDatasetSequence().deleteFeature(sf);
1248       }
1249       else if (reply == JOptionPane.YES_OPTION)
1250       {
1251         sf.type = lastFeatureAdded;
1252         sf.featureGroup = lastFeatureGroupAdded;
1253         sf.description = lastDescriptionAdded;
1254
1255         setColour(sf.type, fcol);
1256         av.featuresDisplayed.put(sf.type, getColour(sf.type));
1257
1258         try
1259         {
1260           sf.begin = ((Integer) start.getValue()).intValue();
1261           sf.end = ((Integer) end.getValue()).intValue();
1262         } catch (NumberFormatException ex)
1263         {
1264         }
1265
1266         ffile.parseDescriptionHTML(sf, false);
1267       }
1268     }
1269     else
1270     // NEW FEATURES ADDED
1271     {
1272       if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
1273       {
1274         for (int i = 0; i < sequences.length; i++)
1275         {
1276           features[i].type = lastFeatureAdded;
1277           if (lastFeatureGroupAdded != null)
1278             features[i].featureGroup = lastFeatureGroupAdded;
1279           features[i].description = lastDescriptionAdded;
1280           sequences[i].addSequenceFeature(features[i]);
1281           ffile.parseDescriptionHTML(features[i], false);
1282         }
1283
1284         if (av.featuresDisplayed == null)
1285         {
1286           av.featuresDisplayed = new Hashtable();
1287         }
1288
1289         if (lastFeatureGroupAdded != null)
1290         {
1291           if (featureGroups == null)
1292             featureGroups = new Hashtable();
1293           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
1294         }
1295         setColour(lastFeatureAdded, fcol);
1296         av.featuresDisplayed.put(lastFeatureAdded,
1297                 getColour(lastFeatureAdded));
1298
1299         findAllFeatures(false);
1300
1301         ap.paintAlignment(true);
1302
1303         return true;
1304       }
1305       else
1306       {
1307         return false;
1308       }
1309     }
1310
1311     ap.paintAlignment(true);
1312
1313     return true;
1314   }
1315
1316   /**
1317    * update the amend feature button dependent on the given style
1318    *
1319    * @param bigPanel
1320    * @param col
1321    * @param col2
1322    */
1323   protected void updateColourButton(JPanel bigPanel, JLabel colour,
1324           Object col2)
1325   {
1326     colour.removeAll();
1327     colour.setIcon(null);
1328     colour.setToolTipText(null);
1329     colour.setText("");
1330
1331     if (col2 instanceof Color)
1332     {
1333       colour.setBackground((Color) col2);
1334     }
1335     else
1336     {
1337       colour.setBackground(bigPanel.getBackground());
1338       colour.setForeground(Color.black);
1339       FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
1340       // colour.setForeground(colour.getBackground());
1341     }
1342   }
1343
1344   public void setColour(String featureType, Object col)
1345   {
1346     // overwrite
1347     // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
1348     // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
1349     // Object c = featureColours.get(featureType);
1350     // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
1351     // !((GraduatedColor)c).getMaxColor().equals(_col)))
1352     {
1353       featureColours.put(featureType, col);
1354     }
1355   }
1356
1357   public void setTransparency(float value)
1358   {
1359     transparency = value;
1360   }
1361
1362   public float getTransparency()
1363   {
1364     return transparency;
1365   }
1366
1367   /**
1368    * Replace current ordering with new ordering
1369    *
1370    * @param data
1371    *          { String(Type), Colour(Type), Boolean(Displayed) }
1372    */
1373   public void setFeaturePriority(Object[][] data)
1374   {
1375     setFeaturePriority(data, true);
1376   }
1377
1378   /**
1379    *
1380    * @param data
1381    *          { String(Type), Colour(Type), Boolean(Displayed) }
1382    * @param visibleNew
1383    *          when true current featureDisplay list will be cleared
1384    */
1385   public void setFeaturePriority(Object[][] data, boolean visibleNew)
1386   {
1387     if (visibleNew)
1388     {
1389       if (av.featuresDisplayed != null)
1390       {
1391         av.featuresDisplayed.clear();
1392       }
1393       else
1394       {
1395         av.featuresDisplayed = new Hashtable();
1396       }
1397     }
1398     if (data == null)
1399     {
1400       return;
1401     }
1402
1403     // The feature table will display high priority
1404     // features at the top, but theses are the ones
1405     // we need to render last, so invert the data
1406     renderOrder = new String[data.length];
1407
1408     if (data.length > 0)
1409     {
1410       for (int i = 0; i < data.length; i++)
1411       {
1412         String type = data[i][0].toString();
1413         setColour(type, data[i][1]); // todo : typesafety - feature color
1414         // interface object
1415         if (((Boolean) data[i][2]).booleanValue())
1416         {
1417           av.featuresDisplayed.put(type, new Integer(getColour(type)
1418                   .getRGB()));
1419         }
1420
1421         renderOrder[data.length - i - 1] = type;
1422       }
1423     }
1424
1425   }
1426
1427   Map featureOrder = null;
1428
1429   /**
1430    * analogous to colour - store a normalized ordering for all feature types in
1431    * this rendering context.
1432    *
1433    * @param type
1434    *          Feature type string
1435    * @param position
1436    *          normalized priority - 0 means always appears on top, 1 means
1437    *          always last.
1438    */
1439   public float setOrder(String type, float position)
1440   {
1441     if (featureOrder == null)
1442     {
1443       featureOrder = new Hashtable();
1444     }
1445     featureOrder.put(type, new Float(position));
1446     return position;
1447   }
1448
1449   /**
1450    * get the global priority (0 (top) to 1 (bottom))
1451    *
1452    * @param type
1453    * @return [0,1] or -1 for a type without a priority
1454    */
1455   public float getOrder(String type)
1456   {
1457     if (featureOrder != null)
1458     {
1459       if (featureOrder.containsKey(type))
1460       {
1461         return ((Float) featureOrder.get(type)).floatValue();
1462       }
1463     }
1464     return -1;
1465   }
1466
1467   /**
1468    * @param listener
1469    * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
1470    */
1471   public void addPropertyChangeListener(PropertyChangeListener listener)
1472   {
1473     changeSupport.addPropertyChangeListener(listener);
1474   }
1475
1476   /**
1477    * @param listener
1478    * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
1479    */
1480   public void removePropertyChangeListener(PropertyChangeListener listener)
1481   {
1482     changeSupport.removePropertyChangeListener(listener);
1483   }
1484 }