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.util.Comparison;
  27 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
  28
  29 import java.awt.AlphaComposite;
  30 import java.awt.Color;
  31 import java.awt.FontMetrics;
  32 import java.awt.Graphics;
  33 import java.awt.Graphics2D;
  34
  35 public class FeatureRenderer extends FeatureRendererModel
  36 {
  37   private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
  38           .getInstance(AlphaComposite.SRC_OVER, 1.0f);
  39
  40   protected SequenceI lastSeq;
  41
  42   private volatile SequenceFeature[] lastSequenceFeatures;
  43
  44   int sfSize;
  45
  46   /**
  47    * Constructor given a viewport
  48    *
  49    * @param viewport
  50    */
  51   public FeatureRenderer(AlignViewportI viewport)
  52   {
  53     this.av = viewport;
  54   }
  55
  56   /**
  57    * Renders the sequence using the given feature colour between the given start
  58    * and end columns. Returns true if at least one column is drawn, else false
  59    * (the feature range does not overlap the start and end positions).
  60    *
  61    * @param g
  62    * @param seq
  63    * @param featureStart
  64    * @param featureEnd
  65    * @param featureColour
  66    * @param start
  67    * @param end
  68    * @param y1
  69    * @param colourOnly
  70    * @return
  71    */
  72   boolean renderFeature(Graphics g, SequenceI seq, int featureStart,
  73           int featureEnd, Color featureColour, int start, int end, int y1,
  74           boolean colourOnly)
  75   {
  76     int charHeight = av.getCharHeight();
  77     int charWidth = av.getCharWidth();
  78     boolean validCharWidth = av.isValidCharWidth();
  79
  80     if (featureStart > end || featureEnd < start)
  81     {
  82       return false;
  83     }
  84
  85     if (featureStart < start)
  86     {
  87       featureStart = start;
  88     }
  89     if (featureEnd >= end)
  90     {
  91       featureEnd = end;
  92     }
  93     int pady = (y1 + charHeight) - charHeight / 5;
  94
  95     FontMetrics fm = g.getFontMetrics();
  96     for (int i = featureStart; i <= featureEnd; i++)
  97     {
  98       char s = seq.getCharAt(i);
  99
 100       if (Comparison.isGap(s))
 101       {
 102         continue;
 103       }
 104
 105       g.setColor(featureColour);
 106
 107       g.fillRect((i - start) * charWidth, y1, charWidth,
 108               charHeight);
 109
 110       if (colourOnly || !validCharWidth)
 111       {
 112         continue;
 113       }
 114
 115       g.setColor(Color.white);
 116       int charOffset = (charWidth - fm.charWidth(s)) / 2;
 117       g.drawString(String.valueOf(s), charOffset
 118               + (charWidth * (i - start)), pady);
 119     }
 120     return true;
 121   }
 122
 123   /**
 124    * Renders the sequence using the given SCORE feature colour between the given
 125    * start and end columns. Returns true if at least one column is drawn, else
 126    * false (the feature range does not overlap the start and end positions).
 127    *
 128    * @param g
 129    * @param seq
 130    * @param fstart
 131    * @param fend
 132    * @param featureColour
 133    * @param start
 134    * @param end
 135    * @param y1
 136    * @param bs
 137    * @param colourOnly
 138    * @return
 139    */
 140   boolean renderScoreFeature(Graphics g, SequenceI seq, int fstart,
 141           int fend, Color featureColour, int start, int end, int y1,
 142           byte[] bs, boolean colourOnly)
 143   {
 144     if (fstart > end || fend < start)
 145     {
 146       return false;
 147     }
 148
 149     if (fstart < start)
 150     { // fix for if the feature we have starts before the sequence start,
 151       fstart = start; // but the feature end is still valid!!
 152     }
 153
 154     if (fend >= end)
 155     {
 156       fend = end;
 157     }
 158     int charHeight = av.getCharHeight();
 159     int pady = (y1 + charHeight) - charHeight / 5;
 160     int ystrt = 0, yend = charHeight;
 161     if (bs[0] != 0)
 162     {
 163       // signed - zero is always middle of residue line.
 164       if (bs[1] < 128)
 165       {
 166         yend = charHeight * (128 - bs[1]) / 512;
 167         ystrt = charHeight - yend / 2;
 168       }
 169       else
 170       {
 171         ystrt = charHeight / 2;
 172         yend = charHeight * (bs[1] - 128) / 512;
 173       }
 174     }
 175     else
 176     {
 177       yend = charHeight * bs[1] / 255;
 178       ystrt = charHeight - yend;
 179
 180     }
 181
 182     FontMetrics fm = g.getFontMetrics();
 183     int charWidth = av.getCharWidth();
 184
 185     for (int i = fstart; i <= fend; i++)
 186     {
 187       char s = seq.getCharAt(i);
 188
 189       if (Comparison.isGap(s))
 190       {
 191         continue;
 192       }
 193
 194       g.setColor(featureColour);
 195       int x = (i - start) * charWidth;
 196       g.drawRect(x, y1, charWidth, charHeight);
 197       g.fillRect(x, y1 + ystrt, charWidth, yend);
 198
 199       if (colourOnly || !av.isValidCharWidth())
 200       {
 201         continue;
 202       }
 203
 204       g.setColor(Color.black);
 205       int charOffset = (charWidth - fm.charWidth(s)) / 2;
 206       g.drawString(String.valueOf(s), charOffset
 207               + (charWidth * (i - start)), pady);
 208     }
 209     return true;
 210   }
 211
 212   /**
 213    * {@inheritDoc}
 214    */
 215   @Override
 216   public Color findFeatureColour(SequenceI seq, int column, Graphics g)
 217   {
 218     if (!av.isShowSequenceFeatures())
 219     {
 220       return null;
 221     }
 222
 223     SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
 224     if (seq != lastSeq)
 225     {
 226       lastSeq = seq;
 227       lastSequenceFeatures = sequenceFeatures;
 228       if (lastSequenceFeatures != null)
 229       {
 230         sfSize = lastSequenceFeatures.length;
 231       }
 232     }
 233     else
 234     {
 235       if (lastSequenceFeatures != sequenceFeatures)
 236       {
 237         lastSequenceFeatures = sequenceFeatures;
 238         if (lastSequenceFeatures != null)
 239         {
 240           sfSize = lastSequenceFeatures.length;
 241         }
 242       }
 243     }
 244
 245     if (lastSequenceFeatures == null || sfSize == 0)
 246     {
 247       return null;
 248     }
 249
 250     if (Comparison.isGap(lastSeq.getCharAt(column)))
 251     {
 252       return Color.white;
 253     }
 254
 255     Color renderedColour = null;
 256     if (transparency == 1.0f)
 257     {
 258       renderedColour = findFeatureColour(seq, seq.findPosition(column));
 259     }
 260     else
 261     {
 262       renderedColour = drawSequence(g, lastSeq, column, column, 0, true);
 263     }
 264     return renderedColour;
 265   }
 266
 267   /**
 268    * Draws the sequence features on the graphics context, or just determines the
 269    * colour that would be drawn (if flag colourOnly is true). Returns the last
 270    * colour drawn (which may not be the effective colour if transparency
 271    * applies), or null if no feature is drawn in the range given.
 272    *
 273    * @param g
 274    *          the graphics context to draw on (may be null if colourOnly==true)
 275    * @param seq
 276    * @param start
 277    *          start column
 278    * @param end
 279    *          end column
 280    * @param y1
 281    *          vertical offset at which to draw on the graphics
 282    * @param colourOnly
 283    *          if true, only do enough to determine the colour for the position,
 284    *          do not draw the character
 285    * @return
 286    */
 287   public synchronized Color drawSequence(final Graphics g,
 288           final SequenceI seq, int start, int end, int y1,
 289           boolean colourOnly)
 290   {
 291     SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
 292     if (sequenceFeatures == null || sequenceFeatures.length == 0)
 293     {
 294       return null;
 295     }
 296
 297     updateFeatures();
 298
 299     if (lastSeq == null || seq != lastSeq
 300             || sequenceFeatures != lastSequenceFeatures)
 301     {
 302       lastSeq = seq;
 303       lastSequenceFeatures = sequenceFeatures;
 304     }
 305
 306     if (transparency != 1f && g != null)
 307     {
 308       Graphics2D g2 = (Graphics2D) g;
 309       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 310               transparency));
 311     }
 312
 313     int startPos = lastSeq.findPosition(start);
 314     int endPos = lastSeq.findPosition(end);
 315
 316     sfSize = lastSequenceFeatures.length;
 317     Color drawnColour = null;
 318
 319     /*
 320      * iterate over features in ordering of their rendering (last is on top)
 321      */
 322     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
 323     {
 324       String type = renderOrder[renderIndex];
 325       if (!showFeatureOfType(type))
 326       {
 327         continue;
 328       }
 329
 330       // loop through all features in sequence to find
 331       // current feature to render
 332       for (int sfindex = 0; sfindex < sfSize; sfindex++)
 333       {
 334         final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
 335         if (!sequenceFeature.type.equals(type))
 336         {
 337           continue;
 338         }
 339
 340         /*
 341          * a feature type may be flagged as shown but the group
 342          * an instance of it belongs to may be hidden
 343          */
 344         if (featureGroupNotShown(sequenceFeature))
 345         {
 346           continue;
 347         }
 348
 349         /*
 350          * check feature overlaps the target range
 351          * TODO: efficient retrieval of features overlapping a range
 352          */
 353         if (sequenceFeature.getBegin() > endPos
 354                 || sequenceFeature.getEnd() < startPos)
 355         {
 356           continue;
 357         }
 358
 359         Color featureColour = getColour(sequenceFeature);
 360         boolean isContactFeature = sequenceFeature.isContactFeature();
 361
 362         if (isContactFeature)
 363         {
 364           boolean drawn = renderFeature(g, seq,
 365                   seq.findIndex(sequenceFeature.begin) - 1,
 366                   seq.findIndex(sequenceFeature.begin) - 1, featureColour,
 367                   start, end, y1, colourOnly);
 368           drawn |= renderFeature(g, seq,
 369                   seq.findIndex(sequenceFeature.end) - 1,
 370                   seq.findIndex(sequenceFeature.end) - 1, featureColour,
 371                   start, end, y1, colourOnly);
 372           if (drawn)
 373           {
 374             drawnColour = featureColour;
 375           }
 376         }
 377         else if (showFeature(sequenceFeature))
 378         {
 379           if (av.isShowSequenceFeaturesHeight()
 380                   && !Float.isNaN(sequenceFeature.score))
 381           {
 382             boolean drawn = renderScoreFeature(g, seq,
 383                     seq.findIndex(sequenceFeature.begin) - 1,
 384                     seq.findIndex(sequenceFeature.end) - 1, featureColour,
 385                     start, end, y1, normaliseScore(sequenceFeature),
 386                     colourOnly);
 387             if (drawn)
 388             {
 389               drawnColour = featureColour;
 390             }
 391           }
 392           else
 393           {
 394             boolean drawn = renderFeature(g, seq,
 395                     seq.findIndex(sequenceFeature.begin) - 1,
 396                     seq.findIndex(sequenceFeature.end) - 1, featureColour,
 397                     start, end, y1, colourOnly);
 398             if (drawn)
 399             {
 400               drawnColour = featureColour;
 401             }
 402           }
 403         }
 404       }
 405     }
 406
 407     if (transparency != 1.0f && g != null)
 408     {
 409       /*
 410        * reset transparency
 411        */
 412       Graphics2D g2 = (Graphics2D) g;
 413       g2.setComposite(NO_TRANSPARENCY);
 414     }
 415
 416     return drawnColour;
 417   }
 418
 419   /**
 420    * Answers true if the feature belongs to a feature group which is not
 421    * currently displayed, else false
 422    *
 423    * @param sequenceFeature
 424    * @return
 425    */
 426   protected boolean featureGroupNotShown(
 427           final SequenceFeature sequenceFeature)
 428   {
 429     return featureGroups != null
 430             && sequenceFeature.featureGroup != null
 431             && sequenceFeature.featureGroup.length() != 0
 432             && featureGroups.containsKey(sequenceFeature.featureGroup)
 433             && !featureGroups.get(sequenceFeature.featureGroup)
 434                     .booleanValue();
 435   }
 436
 437   /**
 438    * Called when alignment in associated view has new/modified features to
 439    * discover and display.
 440    *
 441    */
 442   @Override
 443   public void featuresAdded()
 444   {
 445     lastSeq = null;
 446     findAllFeatures();
 447   }
 448
 449   /**
 450    * Returns the sequence feature colour rendered at the given sequence
 451    * position, or null if none found. The feature of highest render order (i.e.
 452    * on top) is found, subject to both feature type and feature group being
 453    * visible, and its colour returned.
 454    *
 455    * @param seq
 456    * @param pos
 457    * @return
 458    */
 459   Color findFeatureColour(SequenceI seq, int pos)
 460   {
 461     SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
 462     if (sequenceFeatures == null || sequenceFeatures.length == 0)
 463     {
 464       return null;
 465     }
 466
 467     // updateFeatures();
 468
 469     /*
 470      * inspect features in reverse renderOrder (the last in the array is
 471      * displayed on top) until we find one that is rendered at the position
 472      */
 473     for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
 474     {
 475       String type = renderOrder[renderIndex];
 476       if (!showFeatureOfType(type))
 477       {
 478         continue;
 479       }
 480
 481       for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
 482       {
 483         SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
 484         if (!sequenceFeature.type.equals(type))
 485         {
 486           continue;
 487         }
 488
 489         if (featureGroupNotShown(sequenceFeature))
 490         {
 491           continue;
 492         }
 493
 494         boolean featureIsAtPosition = sequenceFeature.begin <= pos
 495                 && sequenceFeature.end >= pos;
 496         if (sequenceFeature.isContactFeature())
 497         {
 498           featureIsAtPosition = sequenceFeature.begin == pos
 499                   || sequenceFeature.end == pos;
 500         }
 501         if (featureIsAtPosition)
 502         {
 503           return getColour(sequenceFeature);
 504         }
 505       }
 506     }
 507
 508     /*
 509      * no displayed feature found at position
 510      */
 511     return null;
 512   }
 513 }