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    * This is used by Structure Viewers and the Overview Window to get the
 214    * feature colour of the rendered sequence
 215    *
 216    * @param seq
 217    * @param column
 218    * @return
 219    */
 220   @Override
 221   public Color findFeatureColour(SequenceI seq, int column, Graphics g)
 222   {
 223     if (!av.isShowSequenceFeatures())
 224     {
 225       return null;
 226     }
 227
 228     SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
 229     if (seq != lastSeq)
 230     {
 231       lastSeq = seq;
 232       lastSequenceFeatures = sequenceFeatures;
 233       if (lastSequenceFeatures != null)
 234       {
 235         sfSize = lastSequenceFeatures.length;
 236       }
 237     }
 238     else
 239     {
 240       if (lastSequenceFeatures != sequenceFeatures)
 241       {
 242         lastSequenceFeatures = sequenceFeatures;
 243         if (lastSequenceFeatures != null)
 244         {
 245           sfSize = lastSequenceFeatures.length;
 246         }
 247       }
 248     }
 249
 250     if (lastSequenceFeatures == null || sfSize == 0)
 251     {
 252       return null;
 253     }
 254
 255     if (Comparison.isGap(lastSeq.getCharAt(column)))
 256     {
 257       return Color.white;
 258     }
 259
 260     Color renderedColour = null;
 261     if (transparency == 1.0f)
 262     {
 263       renderedColour = findFeatureColour(seq, seq.findPosition(column));
 264     }
 265     else
 266     {
 267       renderedColour = drawSequence(g, lastSeq, column, column, 0, true);
 268     }
 269     return renderedColour;
 270   }
 271
 272   /**
 273    * Draws the sequence features on the graphics context, or just determines the
 274    * colour that would be drawn (if flag offscreenrender is true).
 275    *
 276    * @param g
 277    *          the graphics context to draw on (may be null if colourOnly==true)
 278    * @param seq
 279    * @param start
 280    *          start column (or sequence position in offscreenrender mode)
 281    * @param end
 282    *          end column (not used in offscreenrender mode)
 283    * @param y1
 284    *          vertical offset at which to draw on the graphics
 285    * @param colourOnly
 286    *          if true, only do enough to determine the colour for the position,
 287    *          do not draw the character
 288    * @return
 289    */
 290   public synchronized Color drawSequence(final Graphics g,
 291           final SequenceI seq, int start, int end, int y1,
 292           boolean colourOnly)
 293   {
 294     SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
 295     if (sequenceFeatures == null || sequenceFeatures.length == 0)
 296     {
 297       return null;
 298     }
 299
 300     updateFeatures();
 301
 302     if (lastSeq == null || seq != lastSeq
 303             || sequenceFeatures != lastSequenceFeatures)
 304     {
 305       lastSeq = seq;
 306       lastSequenceFeatures = sequenceFeatures;
 307     }
 308
 309     if (transparency != 1f && g != null)
 310     {
 311       Graphics2D g2 = (Graphics2D) g;
 312       g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
 313               transparency));
 314     }
 315
 316     int startPos = lastSeq.findPosition(start);
 317     int endPos = lastSeq.findPosition(end);
 318
 319     sfSize = lastSequenceFeatures.length;
 320     Color drawnColour = null;
 321
 322     /*
 323      * iterate over features in ordering of their rendering (last is on top)
 324      */
 325     for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
 326     {
 327       String type = renderOrder[renderIndex];
 328       if (!showFeatureOfType(type))
 329       {
 330         continue;
 331       }
 332
 333       // loop through all features in sequence to find
 334       // current feature to render
 335       for (int sfindex = 0; sfindex < sfSize; sfindex++)
 336       {
 337         final SequenceFeature sequenceFeature = lastSequenceFeatures[sfindex];
 338         if (!sequenceFeature.type.equals(type))
 339         {
 340           continue;
 341         }
 342
 343         /*
 344          * a feature type may be flagged as shown but the group
 345          * an instance of it belongs to may be hidden
 346          */
 347         if (featureGroupNotShown(sequenceFeature))
 348         {
 349           continue;
 350         }
 351
 352         /*
 353          * check feature overlaps the target range
 354          * TODO: efficient retrieval of features overlapping a range
 355          */
 356         if (sequenceFeature.getBegin() > endPos
 357                 || sequenceFeature.getEnd() < startPos)
 358         {
 359           continue;
 360         }
 361
 362         Color featureColour = getColour(sequenceFeature);
 363         boolean isContactFeature = sequenceFeature.isContactFeature();
 364
 365         if (isContactFeature)
 366         {
 367           boolean drawn = renderFeature(g, seq,
 368                   seq.findIndex(sequenceFeature.begin) - 1,
 369                   seq.findIndex(sequenceFeature.begin) - 1, featureColour,
 370                   start, end, y1, colourOnly);
 371           drawn |= renderFeature(g, seq,
 372                   seq.findIndex(sequenceFeature.end) - 1,
 373                   seq.findIndex(sequenceFeature.end) - 1, featureColour,
 374                   start, end, y1, colourOnly);
 375           if (drawn)
 376           {
 377             drawnColour = featureColour;
 378           }
 379         }
 380         else if (showFeature(sequenceFeature))
 381         {
 382           if (av.isShowSequenceFeaturesHeight()
 383                   && !Float.isNaN(sequenceFeature.score))
 384           {
 385             boolean drawn = renderScoreFeature(g, seq,
 386                     seq.findIndex(sequenceFeature.begin) - 1,
 387                     seq.findIndex(sequenceFeature.end) - 1, featureColour,
 388                     start, end, y1, normaliseScore(sequenceFeature),
 389                     colourOnly);
 390             if (drawn)
 391             {
 392               drawnColour = featureColour;
 393             }
 394           }
 395           else
 396           {
 397             boolean drawn = renderFeature(g, seq,
 398                     seq.findIndex(sequenceFeature.begin) - 1,
 399                     seq.findIndex(sequenceFeature.end) - 1, featureColour,
 400                     start, end, y1, colourOnly);
 401             if (drawn)
 402             {
 403               drawnColour = featureColour;
 404             }
 405           }
 406         }
 407       }
 408     }
 409
 410     if (transparency != 1.0f && g != null)
 411     {
 412       /*
 413        * reset transparency
 414        */
 415       Graphics2D g2 = (Graphics2D) g;
 416       g2.setComposite(NO_TRANSPARENCY);
 417     }
 418
 419     return drawnColour;
 420   }
 421
 422   /**
 423    * Answers true if the feature belongs to a feature group which is not
 424    * currently displayed, else false
 425    *
 426    * @param sequenceFeature
 427    * @return
 428    */
 429   protected boolean featureGroupNotShown(
 430           final SequenceFeature sequenceFeature)
 431   {
 432     return featureGroups != null
 433             && sequenceFeature.featureGroup != null
 434             && sequenceFeature.featureGroup.length() != 0
 435             && featureGroups.containsKey(sequenceFeature.featureGroup)
 436             && !featureGroups.get(sequenceFeature.featureGroup)
 437                     .booleanValue();
 438   }
 439
 440   /**
 441    * Called when alignment in associated view has new/modified features to
 442    * discover and display.
 443    *
 444    */
 445   @Override
 446   public void featuresAdded()
 447   {
 448     lastSeq = null;
 449     findAllFeatures();
 450   }
 451
 452   /**
 453    * Returns the sequence feature colour rendered at the given sequence
 454    * position, or null if none found. The feature of highest render order (i.e.
 455    * on top) is found, subject to both feature type and feature group being
 456    * visible, and its colour returned.
 457    *
 458    * @param seq
 459    * @param pos
 460    * @return
 461    */
 462   Color findFeatureColour(SequenceI seq, int pos)
 463   {
 464     SequenceFeature[] sequenceFeatures = seq.getSequenceFeatures();
 465     if (sequenceFeatures == null || sequenceFeatures.length == 0)
 466     {
 467       return null;
 468     }
 469
 470     // updateFeatures();
 471
 472     /*
 473      * inspect features in reverse renderOrder (the last in the array is
 474      * displayed on top) until we find one that is rendered at the position
 475      */
 476     for (int renderIndex = renderOrder.length - 1; renderIndex >= 0; renderIndex--)
 477     {
 478       String type = renderOrder[renderIndex];
 479       if (!showFeatureOfType(type))
 480       {
 481         continue;
 482       }
 483
 484       for (int sfindex = 0; sfindex < sequenceFeatures.length; sfindex++)
 485       {
 486         SequenceFeature sequenceFeature = sequenceFeatures[sfindex];
 487         if (!sequenceFeature.type.equals(type))
 488         {
 489           continue;
 490         }
 491
 492         if (featureGroupNotShown(sequenceFeature))
 493         {
 494           continue;
 495         }
 496
 497         boolean featureIsAtPosition = sequenceFeature.begin <= pos
 498                 && sequenceFeature.end >= pos;
 499         if (sequenceFeature.isContactFeature())
 500         {
 501           featureIsAtPosition = sequenceFeature.begin == pos
 502                   || sequenceFeature.end == pos;
 503         }
 504         if (featureIsAtPosition)
 505         {
 506           return getColour(sequenceFeature);
 507         }
 508       }
 509     }
 510
 511     /*
 512      * no displayed feature found at position
 513      */
 514     return null;
 515   }
 516 }