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