src/jalview/renderer/seqfeatures/FeatureRenderer.java

   1 package jalview.renderer.seqfeatures;
   2
   3 import jalview.datamodel.SequenceFeature;
   4 import jalview.datamodel.SequenceI;
   5
   6 import java.awt.AlphaComposite;
   7 import java.awt.Color;
   8 import java.awt.FontMetrics;
   9 import java.awt.Graphics;
  10 import java.awt.Graphics2D;
  11 import java.awt.image.BufferedImage;
  12
  13 public class FeatureRenderer extends
  14         jalview.viewmodel.seqfeatures.FeatureRendererModel
  15 {
  16
  17   FontMetrics fm;
  18
  19   int charOffset;
  20
  21   boolean offscreenRender = false;
  22
  23   /**
  24    * DOCUMENT ME!
  25    *
  26    * @param g
  27    *          DOCUMENT ME!
  28    * @param seq
  29    *          DOCUMENT ME!
  30    * @param sg
  31    *          DOCUMENT ME!
  32    * @param start
  33    *          DOCUMENT ME!
  34    * @param end
  35    *          DOCUMENT ME!
  36    * @param x1
  37    *          DOCUMENT ME!
  38    * @param y1
  39    *          DOCUMENT ME!
  40    * @param width
  41    *          DOCUMENT ME!
  42    * @param height
  43    *          DOCUMENT ME!
  44    */
  45   protected SequenceI lastSeq;
  46
  47   char s;
  48
  49   int i;
  50
  51   int av_charHeight, av_charWidth;
  52
  53   boolean av_validCharWidth, av_isShowSeqFeatureHeight;
  54
  55   protected void updateAvConfig()
  56   {
  57     av_charHeight = av.getCharHeight();
  58     av_charWidth = av.getCharWidth();
  59     av_validCharWidth = av.isValidCharWidth();
  60     av_isShowSeqFeatureHeight = av.isShowSequenceFeaturesHeight();
  61   }
  62
  63   void renderFeature(Graphics g, SequenceI seq, int fstart, int fend,
  64           Color featureColour, int start, int end, int y1)
  65   {
  66     updateAvConfig();
  67     if (((fstart <= end) && (fend >= start)))
  68     {
  69       if (fstart < start)
  70       { // fix for if the feature we have starts before the sequence start,
  71         fstart = start; // but the feature end is still valid!!
  72       }
  73
  74       if (fend >= end)
  75       {
  76         fend = end;
  77       }
  78       int pady = (y1 + av_charHeight) - av_charHeight / 5;
  79       for (i = fstart; i <= fend; i++)
  80       {
  81         s = seq.getCharAt(i);
  82
  83         if (jalview.util.Comparison.isGap(s))
  84         {
  85           continue;
  86         }
  87
  88         g.setColor(featureColour);
  89
  90         g.fillRect((i - start) * av_charWidth, y1, av_charWidth,
  91                 av_charHeight);
  92
  93         if (offscreenRender || !av_validCharWidth)
  94         {
  95           continue;
  96         }
  97
  98         g.setColor(Color.white);
  99         charOffset = (av_charWidth - fm.charWidth(s)) / 2;
 100         g.drawString(String.valueOf(s), charOffset
 101                 + (av_charWidth * (i - start)), pady);
 102
 103       }
 104     }
 105   }
 106
 107   void renderScoreFeature(Graphics g, SequenceI seq, int fstart, int fend,
 108           Color featureColour, int start, int end, int y1, byte[] bs)
 109   {
 110     updateAvConfig();
 111     if (((fstart <= end) && (fend >= start)))
 112     {
 113       if (fstart < start)
 114       { // fix for if the feature we have starts before the sequence start,
 115         fstart = start; // but the feature end is still valid!!
 116       }
 117
 118       if (fend >= end)
 119       {
 120         fend = end;
 121       }
 122       int pady = (y1 + av_charHeight) - av_charHeight / 5;
 123       int ystrt = 0, yend = av_charHeight;
 124       if (bs[0] != 0)
 125       {
 126         // signed - zero is always middle of residue line.
 127         if (bs[1] < 128)
 128         {
 129           yend = av_charHeight * (128 - bs[1]) / 512;
 130           ystrt = av_charHeight - yend / 2;
 131         }
 132         else
 133         {
 134           ystrt = av_charHeight / 2;
 135           yend = av_charHeight * (bs[1] - 128) / 512;
 136         }
 137       }
 138       else
 139       {
 140         yend = av_charHeight * bs[1] / 255;
 141         ystrt = av_charHeight - yend;
 142
 143       }
 144       for (i = fstart; i <= fend; i++)
 145       {
 146         s = seq.getCharAt(i);
 147
 148         if (jalview.util.Comparison.isGap(s))
 149         {
 150           continue;
 151         }
 152
 153         g.setColor(featureColour);
 154         int x = (i - start) * av_charWidth;
 155         g.drawRect(x, y1, av_charWidth, av_charHeight);
 156         g.fillRect(x, y1 + ystrt, av_charWidth, yend);
 157
 158         if (offscreenRender || !av_validCharWidth)
 159         {
 160           continue;
 161         }
 162
 163         g.setColor(Color.black);
 164         charOffset = (av_charWidth - fm.charWidth(s)) / 2;
 165         g.drawString(String.valueOf(s), charOffset
 166                 + (av_charWidth * (i - start)), pady);
 167
 168       }
 169     }
 170   }
 171
 172   BufferedImage offscreenImage;
 173
 174   public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
 175   {
 176     return new Color(findFeatureColour(initialCol.getRGB(), seq, res));
 177   }
 178
 179   /**
 180    * This is used by the Molecule Viewer and Overview to get the accurate
 181    * colourof the rendered sequence
 182    */
 183   public synchronized int findFeatureColour(int initialCol, final SequenceI seq,
 184           int column)
 185   {
 186     if (!av.isShowSequenceFeatures())
 187     {
 188       return initialCol;
 189     }
 190
 191     SequenceFeature[] sf = seq.getSequenceFeatures();
 192     if (seq != lastSeq)
 193     {
 194       lastSeq = seq;
 195       sequenceFeatures = sf;
 196       if (sequenceFeatures != null)
 197       {
 198         sfSize = sequenceFeatures.length;
 199       }
 200     }
 201     else
 202     {
 203       if (sequenceFeatures != sf)
 204       {
 205         sequenceFeatures = sf;
 206         if (sequenceFeatures != null)
 207         {
 208           sfSize = sequenceFeatures.length;
 209         }
 210       }
 211     }
 212
 213     if (sequenceFeatures == null || sfSize == 0)
 214     {
 215       return initialCol;
 216     }
 217
 218     if (jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
 219     {
 220       return Color.white.getRGB();
 221     }
 222
 223     // Only bother making an offscreen image if transparency is applied
 224     if (transparency != 1.0f && offscreenImage == null)
 225     {
 226       offscreenImage = new BufferedImage(1, 1, BufferedImage.TYPE_INT_ARGB);
 227     }
 228
 229     currentColour = null;
 230     // TODO: non-threadsafe - each rendering thread needs its own instance of
 231     // the feature renderer - or this should be synchronized.
 232     offscreenRender = true;
 233
 234     if (offscreenImage != null)
 235     {
 236       offscreenImage.setRGB(0, 0, initialCol);
 237       drawSequence(offscreenImage.getGraphics(), lastSeq, column, column, 0);
 238
 239       return offscreenImage.getRGB(0, 0);
 240     }
 241     else
 242     {
 243       drawSequence(null, lastSeq, lastSeq.findPosition(column), -1, -1);
 244
 245       if (currentColour == null)
 246       {
 247         return initialCol;
 248       }
 249       else
 250       {
 251         return ((Integer) currentColour).intValue();
 252       }
 253     }
 254
 255   }
 256
 257   private volatile SequenceFeature[] sequenceFeatures;
 258
 259   int sfSize;
 260
 261   int sfindex;
 262
 263   int spos;
 264
 265   int epos;
 266
 267   public synchronized void drawSequence(Graphics g, final SequenceI seq,
 268           int start, int end, int y1)
 269   {
 270     SequenceFeature[] sf = seq.getSequenceFeatures();
 271     if (sf == null || sf.length == 0)
 272     {
 273       return;
 274     }
 275
 276     if (g != null)
 277     {
 278       fm = g.getFontMetrics();
 279     }
 280
 281     updateFeatures();
 282
 283     if (lastSeq == null || seq != lastSeq
 284  || sf != sequenceFeatures)
 285     {
 286       lastSeq = seq;
 287       sequenceFeatures = sf;
 288     }
 289
 290     if (transparency != 1 && g != null)
 291     {
 292       Graphics2D g2 = (Graphics2D) g;
 293       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 294               transparency));
 295     }
 296
 297     if (!offscreenRender)
 298     {
 299       spos = lastSeq.findPosition(start);
 300       epos = lastSeq.findPosition(end);
 301     }
 302
 303     sfSize = sequenceFeatures.length;
 304     String type;
 305     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
 306     {
 307       type = renderOrder[renderIndex];
 308
 309       if (type == null || !showFeatureOfType(type))
 310       {
 311         continue;
 312       }
 313
 314       // loop through all features in sequence to find
 315       // current feature to render
 316       for (sfindex = 0; sfindex < sfSize; sfindex++)
 317       {
 318         if (!sequenceFeatures[sfindex].type.equals(type))
 319         {
 320           continue;
 321         }
 322
 323         if (featureGroups != null
 324                 && sequenceFeatures[sfindex].featureGroup != null
 325                 && sequenceFeatures[sfindex].featureGroup.length() != 0
 326                 && featureGroups
 327                         .containsKey(sequenceFeatures[sfindex].featureGroup)
 328                 && !featureGroups
 329                         .get(sequenceFeatures[sfindex].featureGroup)
 330                         .booleanValue())
 331         {
 332           continue;
 333         }
 334
 335         if (!offscreenRender
 336                 && (sequenceFeatures[sfindex].getBegin() > epos || sequenceFeatures[sfindex]
 337                         .getEnd() < spos))
 338         {
 339           continue;
 340         }
 341
 342         if (offscreenRender && offscreenImage == null)
 343         {
 344           if (sequenceFeatures[sfindex].begin <= start
 345                   && sequenceFeatures[sfindex].end >= start)
 346           {
 347             // this is passed out to the overview and other sequence renderers
 348             // (e.g. molecule viewer) to get displayed colour for rendered
 349             // sequence
 350             currentColour = new Integer(
 351                     getColour(sequenceFeatures[sfindex]).getRGB());
 352             // used to be retreived from av.featuresDisplayed
 353             // currentColour = av.featuresDisplayed
 354             // .get(sequenceFeatures[sfindex].type);
 355
 356           }
 357         }
 358         else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
 359         {
 360
 361           renderFeature(g, seq,
 362                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 363                   seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 364                   getColour(sequenceFeatures[sfindex])
 365                   // new Color(((Integer) av.featuresDisplayed
 366                   // .get(sequenceFeatures[sfindex].type)).intValue())
 367                   , start, end, y1);
 368           renderFeature(g, seq,
 369                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 370                   seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 371                   getColour(sequenceFeatures[sfindex])
 372                   // new Color(((Integer) av.featuresDisplayed
 373                   // .get(sequenceFeatures[sfindex].type)).intValue())
 374                   , start, end, y1);
 375
 376         }
 377         else if (showFeature(sequenceFeatures[sfindex]))
 378         {
 379           if (av_isShowSeqFeatureHeight
 380                   && sequenceFeatures[sfindex].score != Float.NaN)
 381           {
 382             renderScoreFeature(g, seq,
 383                     seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 384                     seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 385                     getColour(sequenceFeatures[sfindex]), start, end, y1,
 386                     normaliseScore(sequenceFeatures[sfindex]));
 387           }
 388           else
 389           {
 390             renderFeature(g, seq,
 391                     seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
 392                     seq.findIndex(sequenceFeatures[sfindex].end) - 1,
 393                     getColour(sequenceFeatures[sfindex]), start, end, y1);
 394           }
 395         }
 396
 397       }
 398
 399     }
 400
 401     if (transparency != 1.0f && g != null && transparencyAvailable)
 402     {
 403       Graphics2D g2 = (Graphics2D) g;
 404       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 405               1.0f));
 406     }
 407   }
 408
 409   boolean transparencyAvailable = true;
 410
 411   protected void setTransparencyAvailable(boolean isTransparencyAvailable)
 412   {
 413     transparencyAvailable = isTransparencyAvailable;
 414   }
 415
 416   @Override
 417   public boolean isTransparencyAvailable()
 418   {
 419     return transparencyAvailable;
 420   }
 421
 422   /**
 423    * Called when alignment in associated view has new/modified features to
 424    * discover and display.
 425    *
 426    */
 427   public void featuresAdded()
 428   {
 429     lastSeq = null;
 430     findAllFeatures();
 431   }
 432 }