2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.renderer.seqfeatures;
23 import jalview.api.AlignViewportI;
24 import jalview.api.FeatureColourI;
25 import jalview.datamodel.ContiguousI;
26 import jalview.datamodel.SequenceFeature;
27 import jalview.datamodel.SequenceI;
28 import jalview.util.Comparison;
29 import jalview.util.Platform;
30 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
32 import java.awt.AlphaComposite;
33 import java.awt.Color;
34 import java.awt.FontMetrics;
35 import java.awt.Graphics;
36 import java.awt.Graphics2D;
37 import java.util.ArrayList;
38 import java.util.List;
40 public class FeatureRenderer extends FeatureRendererModel
42 private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
43 .getInstance(AlphaComposite.SRC_OVER, 1.0f);
46 * persistent list used by JalviewJS; not threadsafe for Java
48 private List<SequenceFeature> overlaps = (Platform.isJS()
53 * Constructor given a viewport
57 public FeatureRenderer(AlignViewportI viewport)
63 * Renders the sequence using the given feature colour between the given start
64 * and end columns. Returns true if at least one column is drawn, else false
65 * (the feature range does not overlap the start and end positions).
71 * @param featureColour
78 boolean renderFeature(Graphics g, SequenceI seq, int featureStart,
79 int featureEnd, Color featureColour, int start, int end, int y1,
82 int charHeight = av.getCharHeight();
83 int charWidth = av.getCharWidth();
84 boolean validCharWidth = av.isValidCharWidth();
86 if (featureStart > end || featureEnd < start)
91 if (featureStart < start)
95 if (featureEnd >= end)
99 int pady = (y1 + charHeight) - charHeight / 5;
101 FontMetrics fm = g.getFontMetrics();
103 for (int i = featureStart; i <= featureEnd; i++)
105 if (!colourOnly && Comparison.isGap(s = seq.getCharAt(i)))
110 g.setColor(featureColour);
112 g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
124 g.setColor(Color.white);
125 int charOffset = (charWidth - fm.charWidth(s)) / 2;
126 g.drawString(String.valueOf(s),
127 charOffset + (charWidth * (i - start)), pady);
134 * BH - this method is never called?
136 * Renders the sequence using the given SCORE feature colour between the given
137 * start and end columns. Returns true if at least one column is drawn, else
138 * false (the feature range does not overlap the start and end positions).
144 * @param featureColour
152 boolean renderScoreFeature(Graphics g, SequenceI seq, int fstart,
153 int fend, Color featureColour, int start, int end, int y1,
154 byte[] bs, boolean colourOnly)
156 if (fstart > end || fend < start)
162 { // fix for if the feature we have starts before the sequence start,
163 fstart = start; // but the feature end is still valid!!
170 int charHeight = av.getCharHeight();
171 int pady = (y1 + charHeight) - charHeight / 5;
172 int ystrt = 0, yend = charHeight;
175 // signed - zero is always middle of residue line.
178 yend = charHeight * (128 - bs[1]) / 512;
179 ystrt = charHeight - yend / 2;
183 ystrt = charHeight / 2;
184 yend = charHeight * (bs[1] - 128) / 512;
189 yend = charHeight * bs[1] / 255;
190 ystrt = charHeight - yend;
194 FontMetrics fm = g.getFontMetrics();
195 int charWidth = av.getCharWidth();
197 for (int i = fstart; i <= fend; i++)
199 char s = seq.getCharAt(i);
201 if (Comparison.isGap(s))
206 g.setColor(featureColour);
207 int x = (i - start) * charWidth;
208 g.drawRect(x, y1, charWidth, charHeight);
209 g.fillRect(x, y1 + ystrt, charWidth, yend);
211 if (colourOnly || !av.isValidCharWidth())
216 g.setColor(Color.black);
217 int charOffset = (charWidth - fm.charWidth(s)) / 2;
218 g.drawString(String.valueOf(s),
219 charOffset + (charWidth * (i - start)), pady);
228 public Color findFeatureColour(SequenceI seq, int column, Graphics g)
230 // column is 'base 1' but getCharAt is an array index (ie from 0)
231 if (Comparison.isGap(seq.getCharAt(column - 1)))
234 * returning null allows the colour scheme to provide gap colour
235 * - normally white, but can be customised
240 Color renderedColour = null;
241 if (transparency == 1.0f)
244 * simple case - just find the topmost rendered visible feature colour
246 renderedColour = findFeatureColour(seq, column);
251 * transparency case - draw all visible features in render order to
252 * build up a composite colour on the graphics context
254 renderedColour = drawSequence(g, seq, column, column, 0, true);
256 return renderedColour;
260 * Draws the sequence features on the graphics context, or just determines the
261 * colour that would be drawn (if flag colourOnly is true). Returns the last
262 * colour drawn (which may not be the effective colour if transparency
263 * applies), or null if no feature is drawn in the range given.
266 * the graphics context to draw on (null if no transparency applies)
273 * vertical offset at which to draw on the graphics
275 * if true, only do enough to determine the colour for the position,
276 * do not draw the character
279 public synchronized Color drawSequence(final Graphics g,
280 final SequenceI seq, int start, int end, int y1,
284 * if columns are all gapped, or sequence has no features, nothing to do
286 ContiguousI visiblePositions;
287 if (!seq.getFeatures().hasFeatures() || (visiblePositions = seq
288 .findPositions(start + 1, end + 1)) == null)
293 int vp0 = visiblePositions.getBegin();
294 int vp1 = visiblePositions.getEnd();
298 if (transparency != 1f)
300 Graphics2D g2 = (Graphics2D) g;
301 g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
305 Color drawnColour = null;
308 * iterate over features in ordering of their rendering (last is on top)
310 for (int renderIndex = 0, n = renderOrder.length; renderIndex < n; renderIndex++)
312 String type = renderOrder[renderIndex];
313 if (!seq.hasFeatures(type) || !showFeatureOfType(type))
318 FeatureColourI fc = getFeatureStyle(type);
319 List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(vp0,
322 // colourOnly (i.e. Overview) can only be here if translucent, so
323 // there is no need to check for filtering
324 if (!colourOnly && fc.isSimpleColour())
326 filterFeaturesForDisplay(overlaps);
329 for (int i = 0, j = overlaps.size(); i < j; i++)
331 SequenceFeature sf = overlaps.get(i);
332 Color featureColour = getColor(sf, fc);
333 if (featureColour == null)
336 * feature excluded by visibility settings, filters, or colour threshold
342 * if feature starts/ends outside the visible range,
343 * restrict to visible positions (or if a contact feature,
344 * to a single position)
346 int sf0 = sf.getBegin();
347 int sf1 = sf.getEnd();
348 int visibleStart = sf0;
349 if (visibleStart < vp0)
351 visibleStart = sf.isContactFeature() ? sf1 : vp0;
353 int visibleEnd = sf1;
354 if (visibleEnd > vp1)
356 visibleEnd = sf.isContactFeature() ? sf0 : vp1;
359 int featureStartCol = seq.findIndex(visibleStart);
360 int featureEndCol = (sf.begin == sf.end ? featureStartCol
361 : seq.findIndex(visibleEnd));
363 // Color featureColour = getColour(sequenceFeature);
365 boolean isContactFeature = sf.isContactFeature();
367 if (isContactFeature)
369 boolean drawn = renderFeature(g, seq, featureStartCol - 1,
370 featureStartCol - 1, featureColour, start, end, y1,
372 drawn |= renderFeature(g, seq, featureEndCol - 1,
373 featureEndCol - 1, featureColour, start, end, y1,
377 drawnColour = featureColour;
383 * showing feature score by height of colour
384 * is not implemented as a selectable option
386 if (av.isShowSequenceFeaturesHeight()
387 && !Float.isNaN(sequenceFeature.score))
389 boolean drawn = renderScoreFeature(g, seq,
390 seq.findIndex(sequenceFeature.begin) - 1,
391 seq.findIndex(sequenceFeature.end) - 1, featureColour,
392 start, end, y1, normaliseScore(sequenceFeature),
396 drawnColour = featureColour;
402 boolean drawn = renderFeature(g, seq, featureStartCol - 1,
403 featureEndCol - 1, featureColour, start, end, y1,
407 drawnColour = featureColour;
414 if (transparency != 1.0f)
419 ((Graphics2D) g).setComposite(NO_TRANSPARENCY);
426 * Called when alignment in associated view has new/modified features to
427 * discover and display.
431 public void featuresAdded()
437 * Returns the sequence feature colour rendered at the given column position,
438 * or null if none found. The feature of highest render order (i.e. on top) is
439 * found, subject to both feature type and feature group being visible, and
440 * its colour returned. This method is suitable when no feature transparency
441 * applied (only the topmost visible feature colour is rendered).
443 * Note this method does not check for a gap in the column so would return the
444 * colour for features enclosing a gapped column. Check for gap before calling
445 * if different behaviour is wanted.
452 private Color findFeatureColour(SequenceI seq, int column)
455 * check for new feature added while processing
460 * inspect features in reverse renderOrder (the last in the array is
461 * displayed on top) until we find one that is rendered at the position
463 for (int renderIndex = renderOrder.length; --renderIndex >= 0;)
465 String type = renderOrder[renderIndex];
466 if (!seq.hasFeatures(type) || !showFeatureOfType(type))
472 * field overlaps is used by JalviewJS to avoid object creation;
473 * not thread-safe for Java (Javascript is single-threaded)
475 if (overlaps != null)
479 List<SequenceFeature> list = seq.findFeatures(column, type, overlaps);
482 for (int i = 0, n = list.size(); i < n; i++)
484 SequenceFeature sf = list.get(i);
485 if (featureGroupNotShown(sf))
489 Color col = getColour(sf);
499 * no displayed feature found at position