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