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.SequenceFeature;
26 import jalview.datamodel.SequenceI;
27 import jalview.util.Comparison;
28 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
30 import java.awt.AlphaComposite;
31 import java.awt.Color;
32 import java.awt.FontMetrics;
33 import java.awt.Graphics;
34 import java.awt.Graphics2D;
35 import java.util.List;
37 import intervalstore.api.IntervalI;
39 public class FeatureRenderer extends FeatureRendererModel
41 private static final AlphaComposite NO_TRANSPARENCY = AlphaComposite
42 .getInstance(AlphaComposite.SRC_OVER, 1.0f);
45 * Constructor given a viewport
49 public FeatureRenderer(AlignViewportI viewport)
55 * Renders the sequence using the given feature colour between the given start
56 * and end columns. Returns true if at least one column is drawn, else false
57 * (the feature range does not overlap the start and end positions).
63 * @param featureColour
70 boolean renderFeature(Graphics g, SequenceI seq, int featureStart,
71 int featureEnd, Color featureColour, int start, int end, int y1,
74 int charHeight = av.getCharHeight();
75 int charWidth = av.getCharWidth();
76 boolean validCharWidth = av.isValidCharWidth();
78 if (featureStart > end || featureEnd < start)
83 if (featureStart < start)
87 if (featureEnd >= end)
91 int pady = (y1 + charHeight) - charHeight / 5;
93 FontMetrics fm = g.getFontMetrics();
94 for (int i = featureStart; i <= featureEnd; i++)
96 char s = seq.getCharAt(i);
98 if (Comparison.isGap(s))
103 g.setColor(featureColour);
105 g.fillRect((i - start) * charWidth, y1, charWidth, charHeight);
107 if (colourOnly || !validCharWidth)
112 g.setColor(Color.white);
113 int charOffset = (charWidth - fm.charWidth(s)) / 2;
114 g.drawString(String.valueOf(s),
115 charOffset + (charWidth * (i - start)), pady);
121 * Renders the sequence using the given SCORE feature colour between the given
122 * start and end columns. Returns true if at least one column is drawn, else
123 * false (the feature range does not overlap the start and end positions).
129 * @param featureColour
137 boolean renderScoreFeature(Graphics g, SequenceI seq, int fstart,
138 int fend, Color featureColour, int start, int end, int y1,
139 byte[] bs, boolean colourOnly)
141 if (fstart > end || fend < start)
147 { // fix for if the feature we have starts before the sequence start,
148 fstart = start; // but the feature end is still valid!!
155 int charHeight = av.getCharHeight();
156 int pady = (y1 + charHeight) - charHeight / 5;
157 int ystrt = 0, yend = charHeight;
160 // signed - zero is always middle of residue line.
163 yend = charHeight * (128 - bs[1]) / 512;
164 ystrt = charHeight - yend / 2;
168 ystrt = charHeight / 2;
169 yend = charHeight * (bs[1] - 128) / 512;
174 yend = charHeight * bs[1] / 255;
175 ystrt = charHeight - yend;
179 FontMetrics fm = g.getFontMetrics();
180 int charWidth = av.getCharWidth();
182 for (int i = fstart; i <= fend; i++)
184 char s = seq.getCharAt(i);
186 if (Comparison.isGap(s))
191 g.setColor(featureColour);
192 int x = (i - start) * charWidth;
193 g.drawRect(x, y1, charWidth, charHeight);
194 g.fillRect(x, y1 + ystrt, charWidth, yend);
196 if (colourOnly || !av.isValidCharWidth())
201 g.setColor(Color.black);
202 int charOffset = (charWidth - fm.charWidth(s)) / 2;
203 g.drawString(String.valueOf(s),
204 charOffset + (charWidth * (i - start)), pady);
213 public Color findFeatureColour(SequenceI seq, int column, Graphics g)
215 if (!av.isShowSequenceFeatures())
220 // column is 'base 1' but getCharAt is an array index (ie from 0)
221 if (Comparison.isGap(seq.getCharAt(column - 1)))
224 * returning null allows the colour scheme to provide gap colour
225 * - normally white, but can be customised
230 Color renderedColour = null;
231 if (transparency == 1.0f)
234 * simple case - just find the topmost rendered visible feature colour
236 renderedColour = findFeatureColour(seq, column);
241 * transparency case - draw all visible features in render order to
242 * build up a composite colour on the graphics context
244 renderedColour = drawSequence(g, seq, column, column, 0, true);
246 return renderedColour;
250 * Draws the sequence features on the graphics context, or just determines the
251 * colour that would be drawn (if flag colourOnly is true). Returns the last
252 * colour drawn (which may not be the effective colour if transparency
253 * applies), or null if no feature is drawn in the range given.
256 * the graphics context to draw on (may be null if colourOnly==true)
263 * vertical offset at which to draw on the graphics
265 * if true, only do enough to determine the colour for the position,
266 * do not draw the character
269 public synchronized Color drawSequence(final Graphics g,
270 final SequenceI seq, int start, int end, int y1,
274 * if columns are all gapped, or sequence has no features, nothing to do
276 IntervalI visiblePositions = seq.findPositions(start + 1, end + 1);
277 if (visiblePositions == null || !seq.getFeatures().hasFeatures())
284 if (transparency != 1f && g != null)
286 Graphics2D g2 = (Graphics2D) g;
287 g2.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
291 Color drawnColour = null;
294 * iterate over features in ordering of their rendering (last is on top)
296 for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
298 String type = renderOrder[renderIndex];
299 if (!showFeatureOfType(type))
304 FeatureColourI fc = getFeatureStyle(type);
305 List<SequenceFeature> overlaps = seq.getFeatures().findFeatures(
306 visiblePositions.getBegin(), visiblePositions.getEnd(), type);
308 if (fc.isSimpleColour())
310 filterFeaturesForDisplay(overlaps);
313 for (SequenceFeature sf : overlaps)
315 Color featureColour = getColor(sf, fc);
316 if (featureColour == null)
319 * feature excluded by visibility settings, filters, or colour threshold
325 * if feature starts/ends outside the visible range,
326 * restrict to visible positions (or if a contact feature,
327 * to a single position)
329 int visibleStart = sf.getBegin();
330 if (visibleStart < visiblePositions.getBegin())
332 visibleStart = sf.isContactFeature() ? sf.getEnd()
333 : visiblePositions.getBegin();
335 int visibleEnd = sf.getEnd();
336 if (visibleEnd > visiblePositions.getEnd())
338 visibleEnd = sf.isContactFeature() ? sf.getBegin()
339 : visiblePositions.getEnd();
342 int featureStartCol = seq.findIndex(visibleStart);
343 int featureEndCol = sf.begin == sf.end ? featureStartCol : seq
344 .findIndex(visibleEnd);
346 // Color featureColour = getColour(sequenceFeature);
348 boolean isContactFeature = sf.isContactFeature();
350 if (isContactFeature)
352 boolean drawn = renderFeature(g, seq, featureStartCol - 1,
353 featureStartCol - 1, featureColour, start, end, y1,
355 drawn |= renderFeature(g, seq, featureEndCol - 1,
356 featureEndCol - 1, featureColour, start, end, y1,
360 drawnColour = featureColour;
366 * showing feature score by height of colour
367 * is not implemented as a selectable option
369 if (av.isShowSequenceFeaturesHeight()
370 && !Float.isNaN(sequenceFeature.score))
372 boolean drawn = renderScoreFeature(g, seq,
373 seq.findIndex(sequenceFeature.begin) - 1,
374 seq.findIndex(sequenceFeature.end) - 1, featureColour,
375 start, end, y1, normaliseScore(sequenceFeature),
379 drawnColour = featureColour;
385 boolean drawn = renderFeature(g, seq,
387 featureEndCol - 1, featureColour,
388 start, end, y1, colourOnly);
391 drawnColour = featureColour;
398 if (transparency != 1.0f && g != null)
403 Graphics2D g2 = (Graphics2D) g;
404 g2.setComposite(NO_TRANSPARENCY);
411 * Called when alignment in associated view has new/modified features to
412 * discover and display.
416 public void featuresAdded()
422 * Returns the sequence feature colour rendered at the given column position,
423 * or null if none found. The feature of highest render order (i.e. on top) is
424 * found, subject to both feature type and feature group being visible, and
425 * its colour returned. This method is suitable when no feature transparency
426 * applied (only the topmost visible feature colour is rendered).
428 * Note this method does not check for a gap in the column so would return the
429 * colour for features enclosing a gapped column. Check for gap before calling
430 * if different behaviour is wanted.
437 Color findFeatureColour(SequenceI seq, int column)
440 * check for new feature added while processing
445 * inspect features in reverse renderOrder (the last in the array is
446 * displayed on top) until we find one that is rendered at the position
448 for (int renderIndex = renderOrder.length
449 - 1; renderIndex >= 0; renderIndex--)
451 String type = renderOrder[renderIndex];
452 if (!showFeatureOfType(type))
457 List<SequenceFeature> overlaps = seq.findFeatures(column, column,
459 for (SequenceFeature sequenceFeature : overlaps)
461 if (!featureGroupNotShown(sequenceFeature))
463 Color col = getColour(sequenceFeature);
473 * no displayed feature found at position