src/jalview/renderer/seqfeatures/FeatureRenderer.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.renderer.seqfeatures;
  22
  23 import jalview.datamodel.SequenceFeature;
  24 import jalview.datamodel.SequenceI;
  25
  26 import java.awt.AlphaComposite;
  27 import java.awt.Color;
  28 import java.awt.FontMetrics;
  29 import java.awt.Graphics;
  30 import java.awt.Graphics2D;
  31 import java.awt.image.BufferedImage;
  32
  33 public class FeatureRenderer extends
  34         jalview.viewmodel.seqfeatures.FeatureRendererModel
  35 {
  36
  37   FontMetrics fm;
  38
  39   int charOffset;
  40
  41   boolean offscreenRender = false;
  42
  43   protected SequenceI lastSeq;
  44
  45   char s;
  46
  47   int i;
  48
  49   int av_charHeight, av_charWidth;
  50
  51   boolean av_validCharWidth, av_isShowSeqFeatureHeight;
  52
  53   private Integer currentColour;
  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   BufferedImage offscreenImage;
 172
 173   @Override
 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 colour
 181    * of the rendered sequence
 182    */
 183   public synchronized int findFeatureColour(int initialCol,
 184           final SequenceI seq, int column)
 185   {
 186     if (!av.isShowSequenceFeatures())
 187     {
 188       return initialCol;
 189     }
 190
 191     SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
 192     if (seq != lastSeq)
 193     {
 194       lastSeq = seq;
 195       lastSequenceFeatures = sequenceFeatures;
 196       if (lastSequenceFeatures != null)
 197       {
 198         sfSize = lastSequenceFeatures.length;
 199       }
 200     }
 201     else
 202     {
 203       if (lastSequenceFeatures != sequenceFeatures)
 204       {
 205         lastSequenceFeatures = sequenceFeatures;
 206         if (lastSequenceFeatures != null)
 207         {
 208           sfSize = lastSequenceFeatures.length;
 209         }
 210       }
 211     }
 212
 213     if (lastSequenceFeatures == 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 currentColour.intValue();
 252       }
 253     }
 254
 255   }
 256
 257   private volatile SequenceFeature[] lastSequenceFeatures;
 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[] sequenceFeatures = seq.getSequenceFeatures();
 271     if (sequenceFeatures == null || sequenceFeatures.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             || sequenceFeatures != lastSequenceFeatures)
 285     {
 286       lastSeq = seq;
 287       lastSequenceFeatures = sequenceFeatures;
 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 = lastSequenceFeatures.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         final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
 319         if (!sequenceFeature.type.equals(type))
 320         {
 321           continue;
 322         }
 323
 324         if (featureGroups != null
 325                 && sequenceFeature.featureGroup != null
 326                 && sequenceFeature.featureGroup.length() != 0
 327                 && featureGroups.containsKey(sequenceFeature.featureGroup)
 328                 && !featureGroups.get(sequenceFeature.featureGroup)
 329                         .booleanValue())
 330         {
 331           continue;
 332         }
 333
 334         if (!offscreenRender
 335                 && (sequenceFeature.getBegin() > epos || sequenceFeature
 336                         .getEnd() < spos))
 337         {
 338           continue;
 339         }
 340
 341         if (offscreenRender && offscreenImage == null)
 342         {
 343           if (sequenceFeature.begin <= start
 344                   && sequenceFeature.end >= start)
 345           {
 346             // this is passed out to the overview and other sequence renderers
 347             // (e.g. molecule viewer) to get displayed colour for rendered
 348             // sequence
 349             currentColour = new Integer(getColour(sequenceFeature).getRGB());
 350             // used to be retreived from av.featuresDisplayed
 351             // currentColour = av.featuresDisplayed
 352             // .get(sequenceFeatures[sfindex].type);
 353
 354           }
 355         }
 356         else if (sequenceFeature.type.equals("disulfide bond"))
 357         {
 358           renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
 359                   seq.findIndex(sequenceFeature.begin) - 1,
 360                   getColour(sequenceFeature)
 361                   // new Color(((Integer) av.featuresDisplayed
 362                   // .get(sequenceFeatures[sfindex].type)).intValue())
 363                   , start, end, y1);
 364           renderFeature(g, seq, seq.findIndex(sequenceFeature.end) - 1,
 365                   seq.findIndex(sequenceFeature.end) - 1,
 366                   getColour(sequenceFeature)
 367                   // new Color(((Integer) av.featuresDisplayed
 368                   // .get(sequenceFeatures[sfindex].type)).intValue())
 369                   , start, end, y1);
 370
 371         }
 372         else if (showFeature(sequenceFeature))
 373         {
 374           if (av_isShowSeqFeatureHeight
 375                   && !Float.isNaN(sequenceFeature.score))
 376           {
 377             renderScoreFeature(g, seq,
 378                     seq.findIndex(sequenceFeature.begin) - 1,
 379                     seq.findIndex(sequenceFeature.end) - 1,
 380                     getColour(sequenceFeature), start, end, y1,
 381                     normaliseScore(sequenceFeature));
 382           }
 383           else
 384           {
 385             renderFeature(g, seq, seq.findIndex(sequenceFeature.begin) - 1,
 386                     seq.findIndex(sequenceFeature.end) - 1,
 387                     getColour(sequenceFeature), start, end, y1);
 388           }
 389         }
 390
 391       }
 392
 393     }
 394
 395     if (transparency != 1.0f && g != null && transparencyAvailable)
 396     {
 397       Graphics2D g2 = (Graphics2D) g;
 398       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 399               1.0f));
 400     }
 401   }
 402
 403   boolean transparencyAvailable = true;
 404
 405   protected void setTransparencyAvailable(boolean isTransparencyAvailable)
 406   {
 407     transparencyAvailable = isTransparencyAvailable;
 408   }
 409
 410   @Override
 411   public boolean isTransparencyAvailable()
 412   {
 413     return transparencyAvailable;
 414   }
 415
 416   /**
 417    * Called when alignment in associated view has new/modified features to
 418    * discover and display.
 419    *
 420    */
 421   @Override
 422   public void featuresAdded()
 423   {
 424     lastSeq = null;
 425     findAllFeatures();
 426   }
 427 }