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