src/jalview/gui/FeatureRenderer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 import java.util.concurrent.ConcurrentHashMap;
  22
  23 import java.awt.*;
  24 import java.awt.event.*;
  25 import java.awt.image.*;
  26 import java.beans.PropertyChangeListener;
  27 import java.beans.PropertyChangeSupport;
  28
  29 import javax.swing.*;
  30
  31 import jalview.datamodel.*;
  32 import jalview.schemes.GraduatedColor;
  33
  34 /**
  35  * DOCUMENT ME!
  36  *
  37  * @author $author$
  38  * @version $Revision$
  39  */
  40 public class FeatureRenderer implements jalview.api.FeatureRenderer
  41 {
  42   AlignmentPanel ap;
  43
  44   AlignViewport av;
  45
  46   Color resBoxColour;
  47
  48   /**
  49    * global transparency for feature
  50    */
  51   float transparency = 1.0f;
  52
  53   FontMetrics fm;
  54
  55   int charOffset;
  56
  57   Map featureColours = new ConcurrentHashMap();
  58
  59   // A higher level for grouping features of a
  60   // particular type
  61   Map featureGroups = new ConcurrentHashMap();
  62
  63   // This is actually an Integer held in the hashtable,
  64   // Retrieved using the key feature type
  65   Object currentColour;
  66
  67   String[] renderOrder;
  68
  69   PropertyChangeSupport changeSupport = new PropertyChangeSupport(this);
  70
  71   Vector allfeatures;
  72
  73   /**
  74    * Creates a new FeatureRenderer object.
  75    *
  76    * @param av
  77    *          DOCUMENT ME!
  78    */
  79   public FeatureRenderer(AlignmentPanel ap)
  80   {
  81     this.ap = ap;
  82     this.av = ap.av;
  83   }
  84
  85   public class FeatureRendererSettings implements Cloneable
  86   {
  87     String[] renderOrder;
  88
  89     Map featureGroups;
  90
  91     Map featureColours;
  92
  93     float transparency;
  94
  95     Map featureOrder;
  96
  97     public FeatureRendererSettings(String[] renderOrder,
  98             Hashtable featureGroups, Hashtable featureColours,
  99             float transparency, Hashtable featureOrder)
 100     {
 101       super();
 102       this.renderOrder = renderOrder;
 103       this.featureGroups = featureGroups;
 104       this.featureColours = featureColours;
 105       this.transparency = transparency;
 106       this.featureOrder = featureOrder;
 107     }
 108
 109     /**
 110      * create an independent instance of the feature renderer settings
 111      *
 112      * @param fr
 113      */
 114     public FeatureRendererSettings(FeatureRenderer fr)
 115     {
 116       renderOrder = null;
 117       featureGroups = new ConcurrentHashMap();
 118       featureColours = new ConcurrentHashMap();
 119       featureOrder = new ConcurrentHashMap();
 120       if (fr.renderOrder != null)
 121       {
 122         this.renderOrder = new String[fr.renderOrder.length];
 123         System.arraycopy(fr.renderOrder, 0, renderOrder, 0,
 124                 fr.renderOrder.length);
 125       }
 126       if (fr.featureGroups != null)
 127       {
 128         this.featureGroups = new ConcurrentHashMap(fr.featureGroups);
 129       }
 130       if (fr.featureColours != null)
 131       {
 132         this.featureColours = new ConcurrentHashMap(fr.featureColours);
 133       }
 134       Iterator en = fr.featureColours.keySet().iterator();
 135       while (en.hasNext())
 136       {
 137         Object next = en.next();
 138         Object val = featureColours.get(next);
 139         if (val instanceof GraduatedColor)
 140         {
 141           featureColours
 142                   .put(next, new GraduatedColor((GraduatedColor) val));
 143         }
 144       }
 145       this.transparency = fr.transparency;
 146       if (fr.featureOrder != null)
 147       {
 148         this.featureOrder = new ConcurrentHashMap(fr.featureOrder);
 149       }
 150     }
 151   }
 152
 153   public FeatureRendererSettings getSettings()
 154   {
 155     return new FeatureRendererSettings(this);
 156   }
 157
 158   public void transferSettings(FeatureRendererSettings fr)
 159   {
 160     this.renderOrder = fr.renderOrder;
 161     this.featureGroups = fr.featureGroups;
 162     this.featureColours = fr.featureColours;
 163     this.transparency = fr.transparency;
 164     this.featureOrder = fr.featureOrder;
 165   }
 166
 167   public void transferSettings(FeatureRenderer fr)
 168   {
 169     FeatureRendererSettings frs = new FeatureRendererSettings(fr);
 170     this.renderOrder = frs.renderOrder;
 171     this.featureGroups = frs.featureGroups;
 172     this.featureColours = frs.featureColours;
 173     this.transparency = frs.transparency;
 174     this.featureOrder = frs.featureOrder;
 175     if (av != null && av!=fr.av)
 176     {
 177       // copy over the displayed feature settings
 178       if (fr.av != null)
 179       {
 180         if (fr.av.featuresDisplayed != null)
 181         {
 182           // update display settings
 183           if (av.featuresDisplayed == null)
 184           {
 185             av.featuresDisplayed = new Hashtable(fr.av.featuresDisplayed);
 186           }
 187           else
 188           {
 189             av.featuresDisplayed.clear();
 190             Enumeration en = fr.av.featuresDisplayed.keys();
 191             while (en.hasMoreElements())
 192             {
 193               av.featuresDisplayed.put(en.nextElement(), Boolean.TRUE);
 194             }
 195
 196           }
 197         }
 198       }
 199   }
 200   }
 201
 202   BufferedImage offscreenImage;
 203
 204   boolean offscreenRender = false;
 205
 206   public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
 207   {
 208     return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
 209   }
 210
 211   /**
 212    * This is used by the Molecule Viewer and Overview to get the accurate
 213    * colourof the rendered sequence
 214    */
 215   public synchronized int findFeatureColour(int initialCol, SequenceI seq, int column)
 216   {
 217     if (!av.showSequenceFeatures)
 218     {
 219       return initialCol;
 220     }
 221
 222     if (seq != lastSeq)
 223     {
 224       lastSeq = seq;
 225       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
 226       if (sequenceFeatures != null)
 227       {
 228         sfSize = sequenceFeatures.length;
 229       }
 230     }
 231
 232     if (sequenceFeatures != lastSeq.getDatasetSequence()
 233             .getSequenceFeatures())
 234     {
 235       sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
 236       if (sequenceFeatures != null)
 237       {
 238         sfSize = sequenceFeatures.length;
 239       }
 240     }
 241
 242     if (sequenceFeatures == null || sfSize == 0)
 243     {
 244       return initialCol;
 245     }
 246
 247     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
 248     {
 249       return Color.white.getRGB();
 250     }
 251
 252     // Only bother making an offscreen image if transparency is applied
 253     if (transparency != 1.0f && offscreenImage == null)
 254     {
 255       offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
 256     }
 257
 258     currentColour = null;
 259     // TODO: non-threadsafe - each rendering thread needs its own instance of the feature renderer - or this should be synchronized.
 260     offscreenRender = true;
 261
 262     if (offscreenImage != null)
 263     {
 264       offscreenImage.setRGB(0, 0, initialCol);
 265       drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
 266
 267       return offscreenImage.getRGB(0, 0);
 268     }
 269     else
 270     {
 271       drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
 272
 273       if (currentColour == null)
 274       {
 275         return initialCol;
 276       }
 277       else
 278       {
 279         return ((Integer) currentColour).intValue();
 280       }
 281     }
 282
 283   }
 284
 285   /**
 286    * DOCUMENT ME!
 287    *
 288    * @param g
 289    *          DOCUMENT ME!
 290    * @param seq
 291    *          DOCUMENT ME!
 292    * @param sg
 293    *          DOCUMENT ME!
 294    * @param start
 295    *          DOCUMENT ME!
 296    * @param end
 297    *          DOCUMENT ME!
 298    * @param x1
 299    *          DOCUMENT ME!
 300    * @param y1
 301    *          DOCUMENT ME!
 302    * @param width
 303    *          DOCUMENT ME!
 304    * @param height
 305    *          DOCUMENT ME!
 306    */
 307   // String type;
 308   // SequenceFeature sf;
 309   SequenceI lastSeq;
 310
 311   SequenceFeature[] sequenceFeatures;
 312
 313   int sfSize, sfindex, spos, epos;
 314
 315   /**
 316    * show scores as heights
 317    */
 318   protected boolean varyHeight = false;
 319
 320   synchronized public void drawSequence(Graphics g, SequenceI seq,
 321           int start, int end, int y1)
 322   {
 323
 324     if (seq.getDatasetSequence().getSequenceFeatures() == null
 325             || seq.getDatasetSequence().getSequenceFeatures().length == 0)
 326     {
 327       return;
 328     }
 329
 330     if (g != null)
 331     {
 332       fm = g.getFontMetrics();
 333     }
 334
 335     if (av.featuresDisplayed == null || renderOrder == null
 336             || newFeatureAdded)
 337     {
 338       findAllFeatures();
 339       if (av.featuresDisplayed.size() < 1)
 340       {
 341         return;
 342       }
 343
 344       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
 345     }
 346
 347     if (lastSeq == null
 348             || seq != lastSeq
 349             || seq.getDatasetSequence().getSequenceFeatures() != sequenceFeatures)
 350     {
 351       lastSeq = seq;
 352       sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
 353     }
 354
 355     if (transparency != 1 && g != null)
 356     {
 357       Graphics2D g2 = (Graphics2D) g;
 358       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 359               transparency));
 360     }
 361
 362     if (!offscreenRender)
 363     {
 364       spos = lastSeq.findPosition(start);
 365       epos = lastSeq.findPosition(end);
 366     }
 367
 368     sfSize = sequenceFeatures.length;
 369     String type;
 370     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
 371     {
 372       type = renderOrder[renderIndex];
 373
 374       if (type == null || !av.featuresDisplayed.containsKey(type))
 375       {
 376         continue;
 377       }
 378
 379       // loop through all features in sequence to find
 380       // current feature to render
 381       for (sfindex = 0; sfindex < sfSize; sfindex++)
 382       {
 383         if (!sequenceFeatures[sfindex].type.equals(type))
 384         {
 385           continue;
 386         }
 387
 388         if (featureGroups != null
 389                 && sequenceFeatures[sfindex].featureGroup != null
 390                 && sequenceFeatures[sfindex].featureGroup.length() != 0
 391                 && featureGroups
 392                         .containsKey(sequenceFeatures[sfindex].featureGroup)
 393                 && !((Boolean) featureGroups
 394                         .get(sequenceFeatures[sfindex].featureGroup))
 395                         .booleanValue())
 396         {
 397           continue;
 398         }
 399
 400         if (!offscreenRender
 401                 && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
 402                         .getEnd() < spos))
 403         {
 404           continue;
 405         }
 406
 407         if (offscreenRender && offscreenImage == null)
 408         {
 409           if (sequenceFeatures[sfindex].begin <= start
 410                   && sequenceFeatures[sfindex].end >= start)
 411           {
 412             // this is passed out to the overview and other sequence renderers
 413             // (e.g. molecule viewer) to get displayed colour for rendered
 414             // sequence
 415             currentColour = new Integer(
 416                     getColour(sequenceFeatures[sfindex]).getRGB());
 417             // used to be retreived from av.featuresDisplayed
 418             // currentColour = av.featuresDisplayed
 419             // .get(sequenceFeatures[sfindex].type);
 420
 421           }
 422         }
 423         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
 424         {
 425
 426           renderFeature(g, seq,
 427                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 428                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 429                   getColour(sequenceFeatures[sfindex])
 430                   // new Color(((Integer) av.featuresDisplayed
 431                   // .get(sequenceFeatures[sfindex].type)).intValue())
 432                   , start, end, y1);
 433           renderFeature(g, seq,
 434                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 435                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 436                   getColour(sequenceFeatures[sfindex])
 437                   // new Color(((Integer) av.featuresDisplayed
 438                   // .get(sequenceFeatures[sfindex].type)).intValue())
 439                   , start, end, y1);
 440
 441         }
 442         else if (showFeature(sequenceFeatures[sfindex]))
 443         {
 444           if (av.showSeqFeaturesHeight
 445                   && sequenceFeatures[sfindex].score != Float.NaN)
 446           {
 447             renderScoreFeature(g, seq,
 448                     seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 449                     seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 450                     getColour(sequenceFeatures[sfindex]), start, end, y1,
 451                     normaliseScore(sequenceFeatures[sfindex]));
 452           }
 453           else
 454           {
 455             renderFeature(g, seq,
 456                     seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 457                     seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 458                     getColour(sequenceFeatures[sfindex]), start, end, y1);
 459           }
 460         }
 461
 462       }
 463
 464     }
 465
 466     if (transparency != 1.0f && g != null)
 467     {
 468       Graphics2D g2 = (Graphics2D) g;
 469       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 470               1.0f));
 471     }
 472   }
 473
 474   Hashtable minmax = new Hashtable();
 475
 476   /**
 477    * normalise a score against the max/min bounds for the feature type.
 478    *
 479    * @param sequenceFeature
 480    * @return byte[] { signed, normalised signed (-127 to 127) or unsigned
 481    *         (0-255) value.
 482    */
 483   private final byte[] normaliseScore(SequenceFeature sequenceFeature)
 484   {
 485     float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
 486     final byte[] r = new byte[]
 487     { 0, (byte) 255 };
 488     if (mm != null)
 489     {
 490       if (r[0] != 0 || mm[0] < 0.0)
 491       {
 492         r[0] = 1;
 493         r[1] = (byte) ((int) 128.0 + 127.0 * (sequenceFeature.score / mm[1]));
 494       }
 495       else
 496       {
 497         r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
 498       }
 499     }
 500     return r;
 501   }
 502
 503   char s;
 504
 505   int i;
 506
 507   void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
 508           Color featureColour, int start, int end, int y1)
 509   {
 510
 511     if (((fstart <= end) && (fend >= start)))
 512     {
 513       if (fstart < start)
 514       { // fix for if the feature we have starts before the sequence start,
 515         fstart = start; // but the feature end is still valid!!
 516       }
 517
 518       if (fend >= end)
 519       {
 520         fend = end;
 521       }
 522       int pady = (y1 + av.charHeight) - av.charHeight / 5;
 523       for (i = fstart; i <= fend; i++)
 524       {
 525         s = seq.getCharAt(i);
 526
 527         if (jalview.util.Comparison.isGap(s))
 528         {
 529           continue;
 530         }
 531
 532         g.setColor(featureColour);
 533
 534         g.fillRect((i - start) * av.charWidth, y1, av.charWidth,
 535                 av.charHeight);
 536
 537         if (offscreenRender || !av.validCharWidth)
 538         {
 539           continue;
 540         }
 541
 542         g.setColor(Color.white);
 543         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 544         g.drawString(String.valueOf(s), charOffset
 545                 + (av.charWidth * (i - start)), pady);
 546
 547       }
 548     }
 549   }
 550
 551   void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
 552           Color featureColour, int start, int end, int y1, byte[] bs)
 553   {
 554
 555     if (((fstart <= end) && (fend >= start)))
 556     {
 557       if (fstart < start)
 558       { // fix for if the feature we have starts before the sequence start,
 559         fstart = start; // but the feature end is still valid!!
 560       }
 561
 562       if (fend >= end)
 563       {
 564         fend = end;
 565       }
 566       int pady = (y1 + av.charHeight) - av.charHeight / 5;
 567       int ystrt = 0, yend = av.charHeight;
 568       if (bs[0] != 0)
 569       {
 570         // signed - zero is always middle of residue line.
 571         if (bs[1] < 128)
 572         {
 573           yend = av.charHeight * (128 - bs[1]) / 512;
 574           ystrt = av.charHeight - yend / 2;
 575         }
 576         else
 577         {
 578           ystrt = av.charHeight / 2;
 579           yend = av.charHeight * (bs[1] - 128) / 512;
 580         }
 581       }
 582       else
 583       {
 584         yend = av.charHeight * bs[1] / 255;
 585         ystrt = av.charHeight - yend;
 586
 587       }
 588       for (i = fstart; i <= fend; i++)
 589       {
 590         s = seq.getCharAt(i);
 591
 592         if (jalview.util.Comparison.isGap(s))
 593         {
 594           continue;
 595         }
 596
 597         g.setColor(featureColour);
 598         int x = (i - start) * av.charWidth;
 599         g.drawRect(x, y1, av.charWidth, av.charHeight);
 600         g.fillRect(x, y1 + ystrt, av.charWidth, yend);
 601
 602         if (offscreenRender || !av.validCharWidth)
 603         {
 604           continue;
 605         }
 606
 607         g.setColor(Color.black);
 608         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
 609         g.drawString(String.valueOf(s), charOffset
 610                 + (av.charWidth * (i - start)), pady);
 611
 612       }
 613     }
 614   }
 615
 616   boolean newFeatureAdded = false;
 617
 618   /**
 619    * Called when alignment in associated view has new/modified features to
 620    * discover and display.
 621    *
 622    */
 623   public void featuresAdded()
 624   {
 625     lastSeq = null;
 626     findAllFeatures();
 627   }
 628
 629   boolean findingFeatures = false;
 630
 631   /**
 632    * search the alignment for all new features, give them a colour and display
 633    * them. Then fires a PropertyChangeEvent on the changeSupport object.
 634    *
 635    */
 636   void findAllFeatures()
 637   {
 638     synchronized (firing)
 639     {
 640       if (firing.equals(Boolean.FALSE))
 641       {
 642         firing = Boolean.TRUE;
 643         findAllFeatures(true); // add all new features as visible
 644         changeSupport.firePropertyChange("changeSupport", null, null);
 645         firing = Boolean.FALSE;
 646       }
 647     }
 648   }
 649
 650   /**
 651    * Searches alignment for all features and updates colours
 652    *
 653    * @param newMadeVisible
 654    *          if true newly added feature types will be rendered immediatly
 655    */
 656   synchronized void findAllFeatures(boolean newMadeVisible)
 657   {
 658     newFeatureAdded = false;
 659
 660     if (findingFeatures)
 661     {
 662       newFeatureAdded = true;
 663       return;
 664     }
 665
 666     findingFeatures = true;
 667
 668     if (av.featuresDisplayed == null)
 669     {
 670       av.featuresDisplayed = new Hashtable();
 671     }
 672
 673     allfeatures = new Vector();
 674     Vector oldfeatures = new Vector();
 675     if (renderOrder != null)
 676     {
 677       for (int i = 0; i < renderOrder.length; i++)
 678       {
 679         if (renderOrder[i] != null)
 680         {
 681           oldfeatures.addElement(renderOrder[i]);
 682         }
 683       }
 684     }
 685     if (minmax == null)
 686     {
 687       minmax = new Hashtable();
 688     }
 689     AlignmentI alignment=av.getAlignment();
 690     for (int i = 0; i < alignment.getHeight(); i++)
 691     {
 692       SequenceFeature[] features = alignment.getSequenceAt(i)
 693               .getDatasetSequence().getSequenceFeatures();
 694
 695       if (features == null)
 696       {
 697         continue;
 698       }
 699
 700       int index = 0;
 701       while (index < features.length)
 702       {
 703         if (!av.featuresDisplayed.containsKey(features[index].getType()))
 704         {
 705
 706           if (featureGroups.containsKey(features[index].getType()))
 707           {
 708             boolean visible = ((Boolean) featureGroups
 709                     .get(features[index].featureGroup)).booleanValue();
 710
 711             if (!visible)
 712             {
 713               index++;
 714               continue;
 715             }
 716           }
 717
 718           if (!(features[index].begin == 0 && features[index].end == 0))
 719           {
 720             // If beginning and end are 0, the feature is for the whole sequence
 721             // and we don't want to render the feature in the normal way
 722
 723             if (newMadeVisible
 724                     && !oldfeatures.contains(features[index].getType()))
 725             {
 726               // this is a new feature type on the alignment. Mark it for
 727               // display.
 728               av.featuresDisplayed.put(features[index].getType(),
 729                       new Integer(getColour(features[index].getType())
 730                               .getRGB()));
 731               setOrder(features[index].getType(), 0);
 732             }
 733           }
 734         }
 735         if (!allfeatures.contains(features[index].getType()))
 736         {
 737           allfeatures.addElement(features[index].getType());
 738         }
 739         if (features[index].score != Float.NaN)
 740         {
 741           int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
 742           float[][] mm = (float[][]) minmax.get(features[index].getType());
 743           if (mm == null)
 744           {
 745             mm = new float[][]
 746             { null, null };
 747             minmax.put(features[index].getType(), mm);
 748           }
 749           if (mm[nonpos] == null)
 750           {
 751             mm[nonpos] = new float[]
 752             { features[index].score, features[index].score };
 753
 754           }
 755           else
 756           {
 757             if (mm[nonpos][0] > features[index].score)
 758             {
 759               mm[nonpos][0] = features[index].score;
 760             }
 761             if (mm[nonpos][1] < features[index].score)
 762             {
 763               mm[nonpos][1] = features[index].score;
 764             }
 765           }
 766         }
 767         index++;
 768       }
 769     }
 770     updateRenderOrder(allfeatures);
 771     findingFeatures = false;
 772   }
 773
 774   protected Boolean firing = Boolean.FALSE;
 775
 776   /**
 777    * replaces the current renderOrder with the unordered features in
 778    * allfeatures. The ordering of any types in both renderOrder and allfeatures
 779    * is preserved, and all new feature types are rendered on top of the existing
 780    * types, in the order given by getOrder or the order given in allFeatures.
 781    * Note. this operates directly on the featureOrder hash for efficiency. TODO:
 782    * eliminate the float storage for computing/recalling the persistent ordering
 783    * New Cability: updates min/max for colourscheme range if its dynamic
 784    *
 785    * @param allFeatures
 786    */
 787   private void updateRenderOrder(Vector allFeatures)
 788   {
 789     Vector allfeatures = new Vector(allFeatures);
 790     String[] oldRender = renderOrder;
 791     renderOrder = new String[allfeatures.size()];
 792     Object mmrange, fc = null;
 793     boolean initOrders = (featureOrder == null);
 794     int opos = 0;
 795     if (oldRender != null && oldRender.length > 0)
 796     {
 797       for (int j = 0; j < oldRender.length; j++)
 798       {
 799         if (oldRender[j] != null)
 800         {
 801           if (initOrders)
 802           {
 803             setOrder(oldRender[j], (1 - (1 + (float) j)
 804                     / (float) oldRender.length));
 805           }
 806           if (allfeatures.contains(oldRender[j]))
 807           {
 808             renderOrder[opos++] = oldRender[j]; // existing features always
 809             // appear below new features
 810             allfeatures.removeElement(oldRender[j]);
 811             if (minmax != null)
 812             {
 813               mmrange = minmax.get(oldRender[j]);
 814               if (mmrange != null)
 815               {
 816                 fc = featureColours.get(oldRender[j]);
 817                 if (fc != null && fc instanceof GraduatedColor
 818                         && ((GraduatedColor) fc).isAutoScale())
 819                 {
 820                   ((GraduatedColor) fc).updateBounds(
 821                           ((float[][]) mmrange)[0][0],
 822                           ((float[][]) mmrange)[0][1]);
 823                 }
 824               }
 825             }
 826           }
 827         }
 828       }
 829     }
 830     if (allfeatures.size() == 0)
 831     {
 832       // no new features - leave order unchanged.
 833       return;
 834     }
 835     int i = allfeatures.size() - 1;
 836     int iSize = i;
 837     boolean sort = false;
 838     String[] newf = new String[allfeatures.size()];
 839     float[] sortOrder = new float[allfeatures.size()];
 840     Enumeration en = allfeatures.elements();
 841     // sort remaining elements
 842     while (en.hasMoreElements())
 843     {
 844       newf[i] = en.nextElement().toString();
 845       if (minmax != null)
 846       {
 847         // update from new features minmax if necessary
 848         mmrange = minmax.get(newf[i]);
 849         if (mmrange != null)
 850         {
 851           fc = featureColours.get(newf[i]);
 852           if (fc != null && fc instanceof GraduatedColor
 853                   && ((GraduatedColor) fc).isAutoScale())
 854           {
 855             ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
 856                     ((float[][]) mmrange)[0][1]);
 857           }
 858         }
 859       }
 860       if (initOrders || !featureOrder.containsKey(newf[i]))
 861       {
 862         int denom = initOrders ? allfeatures.size() : featureOrder.size();
 863         // new unordered feature - compute persistent ordering at head of
 864         // existing features.
 865         setOrder(newf[i], i / (float) denom);
 866       }
 867       // set order from newly found feature from persisted ordering.
 868       sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
 869       if (i < iSize)
 870       {
 871         // only sort if we need to
 872         sort = sort || sortOrder[i] > sortOrder[i + 1];
 873       }
 874       i--;
 875     }
 876     if (iSize > 1 && sort)
 877     {
 878       jalview.util.QuickSort.sort(sortOrder, newf);
 879     }
 880     sortOrder = null;
 881     System.arraycopy(newf, 0, renderOrder, opos, newf.length);
 882   }
 883
 884   /**
 885    * get a feature style object for the given type string. Creates a
 886    * java.awt.Color for a featureType with no existing colourscheme. TODO:
 887    * replace return type with object implementing standard abstract colour/style
 888    * interface
 889    *
 890    * @param featureType
 891    * @return java.awt.Color or GraduatedColor
 892    */
 893   public Object getFeatureStyle(String featureType)
 894   {
 895     Object fc = featureColours.get(featureType);
 896     if (fc == null)
 897     {
 898       jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
 899       Color col = ucs.createColourFromName(featureType);
 900       featureColours.put(featureType, fc = col);
 901     }
 902     return fc;
 903   }
 904
 905   /**
 906    * return a nominal colour for this feature
 907    *
 908    * @param featureType
 909    * @return standard color, or maximum colour for graduated colourscheme
 910    */
 911   public Color getColour(String featureType)
 912   {
 913     Object fc = getFeatureStyle(featureType);
 914
 915     if (fc instanceof Color)
 916     {
 917       return (Color) fc;
 918     }
 919     else
 920     {
 921       if (fc instanceof GraduatedColor)
 922       {
 923         return ((GraduatedColor) fc).getMaxColor();
 924       }
 925     }
 926     throw new Error("Implementation Error: Unrecognised render object "
 927             + fc.getClass() + " for features of type " + featureType);
 928   }
 929
 930   /**
 931    * calculate the render colour for a specific feature using current feature
 932    * settings.
 933    *
 934    * @param feature
 935    * @return render colour for the given feature
 936    */
 937   public Color getColour(SequenceFeature feature)
 938   {
 939     Object fc = getFeatureStyle(feature.getType());
 940     if (fc instanceof Color)
 941     {
 942       return (Color) fc;
 943     }
 944     else
 945     {
 946       if (fc instanceof GraduatedColor)
 947       {
 948         return ((GraduatedColor) fc).findColor(feature);
 949       }
 950     }
 951     throw new Error("Implementation Error: Unrecognised render object "
 952             + fc.getClass() + " for features of type " + feature.getType());
 953   }
 954
 955   private boolean showFeature(SequenceFeature sequenceFeature)
 956   {
 957     Object fc = getFeatureStyle(sequenceFeature.type);
 958     if (fc instanceof GraduatedColor)
 959     {
 960       return ((GraduatedColor) fc).isColored(sequenceFeature);
 961     }
 962     else
 963     {
 964       return true;
 965     }
 966   }
 967
 968   // // /////////////
 969   // // Feature Editing Dialog
 970   // // Will be refactored in next release.
 971
 972   static String lastFeatureAdded;
 973
 974   static String lastFeatureGroupAdded;
 975
 976   static String lastDescriptionAdded;
 977
 978   Object oldcol, fcol;
 979
 980   int featureIndex = 0;
 981
 982   boolean amendFeatures(final SequenceI[] sequences,
 983           final SequenceFeature[] features, boolean newFeatures,
 984           final AlignmentPanel ap)
 985   {
 986
 987     featureIndex = 0;
 988
 989     final JPanel bigPanel = new JPanel(new BorderLayout());
 990     final JComboBox overlaps;
 991     final JTextField name = new JTextField(25);
 992     final JTextField source = new JTextField(25);
 993     final JTextArea description = new JTextArea(3, 25);
 994     final JSpinner start = new JSpinner();
 995     final JSpinner end = new JSpinner();
 996     start.setPreferredSize(new Dimension(80, 20));
 997     end.setPreferredSize(new Dimension(80, 20));
 998     final FeatureRenderer me = this;
 999     final JLabel colour = new JLabel();
1000     colour.setOpaque(true);
1001     // colour.setBorder(BorderFactory.createEtchedBorder());
1002     colour.setMaximumSize(new Dimension(30, 16));
1003     colour.addMouseListener(new MouseAdapter()
1004     {
1005       FeatureColourChooser fcc = null;
1006
1007       public void mousePressed(MouseEvent evt)
1008       {
1009         if (fcol instanceof Color)
1010         {
1011           Color col = JColorChooser.showDialog(Desktop.desktop,
1012                   "Select Feature Colour", ((Color) fcol));
1013           if (col != null)
1014           {
1015             fcol = col;
1016             updateColourButton(bigPanel, colour, col);
1017           }
1018         }
1019         else
1020         {
1021
1022           if (fcc == null)
1023           {
1024             final String type = features[featureIndex].getType();
1025             fcc = new FeatureColourChooser(me, type);
1026             fcc.setRequestFocusEnabled(true);
1027             fcc.requestFocus();
1028
1029             fcc.addActionListener(new ActionListener()
1030             {
1031
1032               public void actionPerformed(ActionEvent e)
1033               {
1034                 fcol = fcc.getLastColour();
1035                 fcc = null;
1036                 setColour(type, fcol);
1037                 updateColourButton(bigPanel, colour, fcol);
1038               }
1039             });
1040
1041           }
1042         }
1043       }
1044     });
1045     JPanel tmp = new JPanel();
1046     JPanel panel = new JPanel(new GridLayout(3, 1));
1047
1048     // /////////////////////////////////////
1049     // /MULTIPLE FEATURES AT SELECTED RESIDUE
1050     if (!newFeatures && features.length > 1)
1051     {
1052       panel = new JPanel(new GridLayout(4, 1));
1053       tmp = new JPanel();
1054       tmp.add(new JLabel("Select Feature: "));
1055       overlaps = new JComboBox();
1056       for (int i = 0; i < features.length; i++)
1057       {
1058         overlaps.addItem(features[i].getType() + "/"
1059                 + features[i].getBegin() + "-" + features[i].getEnd()
1060                 + " (" + features[i].getFeatureGroup() + ")");
1061       }
1062
1063       tmp.add(overlaps);
1064
1065       overlaps.addItemListener(new ItemListener()
1066       {
1067         public void itemStateChanged(ItemEvent e)
1068         {
1069           int index = overlaps.getSelectedIndex();
1070           if (index != -1)
1071           {
1072             featureIndex = index;
1073             name.setText(features[index].getType());
1074             description.setText(features[index].getDescription());
1075             source.setText(features[index].getFeatureGroup());
1076             start.setValue(new Integer(features[index].getBegin()));
1077             end.setValue(new Integer(features[index].getEnd()));
1078
1079             SearchResults highlight = new SearchResults();
1080             highlight.addResult(sequences[0], features[index].getBegin(),
1081                     features[index].getEnd());
1082
1083             ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
1084
1085           }
1086           Object col = getFeatureStyle(name.getText());
1087           if (col == null)
1088           {
1089             col = new jalview.schemes.UserColourScheme()
1090                     .createColourFromName(name.getText());
1091           }
1092           oldcol = fcol = col;
1093           updateColourButton(bigPanel, colour, col);
1094         }
1095       });
1096
1097       panel.add(tmp);
1098     }
1099     // ////////
1100     // ////////////////////////////////////
1101
1102     tmp = new JPanel();
1103     panel.add(tmp);
1104     tmp.add(new JLabel("Name: ", JLabel.RIGHT));
1105     tmp.add(name);
1106
1107     tmp = new JPanel();
1108     panel.add(tmp);
1109     tmp.add(new JLabel("Group: ", JLabel.RIGHT));
1110     tmp.add(source);
1111
1112     tmp = new JPanel();
1113     panel.add(tmp);
1114     tmp.add(new JLabel("Colour: ", JLabel.RIGHT));
1115     tmp.add(colour);
1116     colour.setPreferredSize(new Dimension(150, 15));
1117     colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
1118     colour.setForeground(Color.black);
1119     colour.setHorizontalAlignment(SwingConstants.CENTER);
1120     colour.setVerticalAlignment(SwingConstants.CENTER);
1121     colour.setHorizontalTextPosition(SwingConstants.CENTER);
1122     colour.setVerticalTextPosition(SwingConstants.CENTER);
1123     bigPanel.add(panel, BorderLayout.NORTH);
1124
1125     panel = new JPanel();
1126     panel.add(new JLabel("Description: ", JLabel.RIGHT));
1127     description.setFont(JvSwingUtils.getTextAreaFont());
1128     description.setLineWrap(true);
1129     panel.add(new JScrollPane(description));
1130
1131     if (!newFeatures)
1132     {
1133       bigPanel.add(panel, BorderLayout.SOUTH);
1134
1135       panel = new JPanel();
1136       panel.add(new JLabel(" Start:", JLabel.RIGHT));
1137       panel.add(start);
1138       panel.add(new JLabel("  End:", JLabel.RIGHT));
1139       panel.add(end);
1140       bigPanel.add(panel, BorderLayout.CENTER);
1141     }
1142     else
1143     {
1144       bigPanel.add(panel, BorderLayout.CENTER);
1145     }
1146
1147     if (lastFeatureAdded == null)
1148     {
1149       if (features[0].type != null)
1150       {
1151         lastFeatureAdded = features[0].type;
1152       }
1153       else
1154       {
1155         lastFeatureAdded = "feature_1";
1156       }
1157     }
1158
1159     if (lastFeatureGroupAdded == null)
1160     {
1161       if (features[0].featureGroup != null)
1162       {
1163         lastFeatureGroupAdded = features[0].featureGroup;
1164       }
1165       else
1166       {
1167         lastFeatureGroupAdded = "Jalview";
1168       }
1169     }
1170
1171     if (newFeatures)
1172     {
1173       name.setText(lastFeatureAdded);
1174       source.setText(lastFeatureGroupAdded);
1175     }
1176     else
1177     {
1178       name.setText(features[0].getType());
1179       source.setText(features[0].getFeatureGroup());
1180     }
1181
1182     start.setValue(new Integer(features[0].getBegin()));
1183     end.setValue(new Integer(features[0].getEnd()));
1184     description.setText(features[0].getDescription());
1185     updateColourButton(bigPanel, colour,
1186             (oldcol = fcol = getFeatureStyle(name.getText())));
1187     Object[] options;
1188     if (!newFeatures)
1189     {
1190       options = new Object[]
1191       { "Amend", "Delete", "Cancel" };
1192     }
1193     else
1194     {
1195       options = new Object[]
1196       { "OK", "Cancel" };
1197     }
1198
1199     String title = newFeatures ? "Create New Sequence Feature(s)"
1200             : "Amend/Delete Features for " + sequences[0].getName();
1201
1202     int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
1203             bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
1204             JOptionPane.QUESTION_MESSAGE, null, options, "OK");
1205
1206     jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
1207
1208     if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
1209     {
1210       // This ensures that the last sequence
1211       // is refreshed and new features are rendered
1212       lastSeq = null;
1213       lastFeatureAdded = name.getText().trim();
1214       lastFeatureGroupAdded = source.getText().trim();
1215       lastDescriptionAdded = description.getText().replaceAll("\n", " ");
1216       // TODO: determine if the null feature group is valid
1217       if (lastFeatureGroupAdded.length() < 1)
1218         lastFeatureGroupAdded = null;
1219     }
1220
1221     if (!newFeatures)
1222     {
1223       SequenceFeature sf = features[featureIndex];
1224
1225       if (reply == JOptionPane.NO_OPTION)
1226       {
1227         sequences[0].getDatasetSequence().deleteFeature(sf);
1228       }
1229       else if (reply == JOptionPane.YES_OPTION)
1230       {
1231         sf.type = lastFeatureAdded;
1232         sf.featureGroup = lastFeatureGroupAdded;
1233         sf.description = lastDescriptionAdded;
1234
1235         setColour(sf.type, fcol);
1236         av.featuresDisplayed.put(sf.type, getColour(sf.type));
1237
1238         try
1239         {
1240           sf.begin = ((Integer) start.getValue()).intValue();
1241           sf.end = ((Integer) end.getValue()).intValue();
1242         } catch (NumberFormatException ex)
1243         {
1244         }
1245
1246         ffile.parseDescriptionHTML(sf, false);
1247       }
1248     }
1249     else
1250     // NEW FEATURES ADDED
1251     {
1252       if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
1253       {
1254         for (int i = 0; i < sequences.length; i++)
1255         {
1256           features[i].type = lastFeatureAdded;
1257           if (lastFeatureGroupAdded != null)
1258             features[i].featureGroup = lastFeatureGroupAdded;
1259           features[i].description = lastDescriptionAdded;
1260           sequences[i].addSequenceFeature(features[i]);
1261           ffile.parseDescriptionHTML(features[i], false);
1262         }
1263
1264         if (av.featuresDisplayed == null)
1265         {
1266           av.featuresDisplayed = new Hashtable();
1267         }
1268
1269         if (lastFeatureGroupAdded != null)
1270         {
1271           if (featureGroups == null)
1272             featureGroups = new Hashtable();
1273           featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
1274         }
1275         setColour(lastFeatureAdded, fcol);
1276         av.featuresDisplayed.put(lastFeatureAdded,
1277                 getColour(lastFeatureAdded));
1278
1279         findAllFeatures(false);
1280
1281         ap.paintAlignment(true);
1282
1283         return true;
1284       }
1285       else
1286       {
1287         return false;
1288       }
1289     }
1290
1291     ap.paintAlignment(true);
1292
1293     return true;
1294   }
1295
1296   /**
1297    * update the amend feature button dependent on the given style
1298    *
1299    * @param bigPanel
1300    * @param col
1301    * @param col2
1302    */
1303   protected void updateColourButton(JPanel bigPanel, JLabel colour,
1304           Object col2)
1305   {
1306     colour.removeAll();
1307     colour.setIcon(null);
1308     colour.setToolTipText(null);
1309     colour.setText("");
1310
1311     if (col2 instanceof Color)
1312     {
1313       colour.setBackground((Color) col2);
1314     }
1315     else
1316     {
1317       colour.setBackground(bigPanel.getBackground());
1318       colour.setForeground(Color.black);
1319       FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
1320       // colour.setForeground(colour.getBackground());
1321     }
1322   }
1323
1324   public void setColour(String featureType, Object col)
1325   {
1326     // overwrite
1327     // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
1328     // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
1329     // Object c = featureColours.get(featureType);
1330     // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
1331     // !((GraduatedColor)c).getMaxColor().equals(_col)))
1332     {
1333       featureColours.put(featureType, col);
1334     }
1335   }
1336
1337   public void setTransparency(float value)
1338   {
1339     transparency = value;
1340   }
1341
1342   public float getTransparency()
1343   {
1344     return transparency;
1345   }
1346
1347   /**
1348    * Replace current ordering with new ordering
1349    *
1350    * @param data
1351    *          { String(Type), Colour(Type), Boolean(Displayed) }
1352    */
1353   public void setFeaturePriority(Object[][] data)
1354   {
1355     setFeaturePriority(data, true);
1356   }
1357
1358   /**
1359    *
1360    * @param data
1361    *          { String(Type), Colour(Type), Boolean(Displayed) }
1362    * @param visibleNew
1363    *          when true current featureDisplay list will be cleared
1364    */
1365   public void setFeaturePriority(Object[][] data, boolean visibleNew)
1366   {
1367     if (visibleNew)
1368     {
1369       if (av.featuresDisplayed != null)
1370       {
1371         av.featuresDisplayed.clear();
1372       }
1373       else
1374       {
1375         av.featuresDisplayed = new Hashtable();
1376       }
1377     }
1378     if (data == null)
1379     {
1380       return;
1381     }
1382
1383     // The feature table will display high priority
1384     // features at the top, but theses are the ones
1385     // we need to render last, so invert the data
1386     renderOrder = new String[data.length];
1387
1388     if (data.length > 0)
1389     {
1390       for (int i = 0; i < data.length; i++)
1391       {
1392         String type = data[i][0].toString();
1393         setColour(type, data[i][1]); // todo : typesafety - feature color
1394         // interface object
1395         if (((Boolean) data[i][2]).booleanValue())
1396         {
1397           av.featuresDisplayed.put(type, new Integer(getColour(type)
1398                   .getRGB()));
1399         }
1400
1401         renderOrder[data.length - i - 1] = type;
1402       }
1403     }
1404
1405   }
1406
1407   Map featureOrder = null;
1408
1409   /**
1410    * analogous to colour - store a normalized ordering for all feature types in
1411    * this rendering context.
1412    *
1413    * @param type
1414    *          Feature type string
1415    * @param position
1416    *          normalized priority - 0 means always appears on top, 1 means
1417    *          always last.
1418    */
1419   public float setOrder(String type, float position)
1420   {
1421     if (featureOrder == null)
1422     {
1423       featureOrder = new Hashtable();
1424     }
1425     featureOrder.put(type, new Float(position));
1426     return position;
1427   }
1428
1429   /**
1430    * get the global priority (0 (top) to 1 (bottom))
1431    *
1432    * @param type
1433    * @return [0,1] or -1 for a type without a priority
1434    */
1435   public float getOrder(String type)
1436   {
1437     if (featureOrder != null)
1438     {
1439       if (featureOrder.containsKey(type))
1440       {
1441         return ((Float) featureOrder.get(type)).floatValue();
1442       }
1443     }
1444     return -1;
1445   }
1446
1447   /**
1448    * @param listener
1449    * @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
1450    */
1451   public void addPropertyChangeListener(PropertyChangeListener listener)
1452   {
1453     changeSupport.addPropertyChangeListener(listener);
1454   }
1455
1456   /**
1457    * @param listener
1458    * @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
1459    */
1460   public void removePropertyChangeListener(PropertyChangeListener listener)
1461   {
1462     changeSupport.removePropertyChangeListener(listener);
1463   }
1464 }