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