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OverviewRenderer | 42 | 116 | 32 |
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; | |
22 | ||
23 | import jalview.api.AlignmentColsCollectionI; | |
24 | import jalview.api.AlignmentRowsCollectionI; | |
25 | import jalview.api.RendererListenerI; | |
26 | import jalview.datamodel.AlignmentAnnotation; | |
27 | import jalview.datamodel.AlignmentI; | |
28 | import jalview.datamodel.Annotation; | |
29 | import jalview.datamodel.SequenceGroup; | |
30 | import jalview.datamodel.SequenceI; | |
31 | import jalview.renderer.seqfeatures.FeatureColourFinder; | |
32 | import jalview.renderer.seqfeatures.FeatureRenderer; | |
33 | import jalview.viewmodel.OverviewDimensions; | |
34 | ||
35 | import java.awt.AlphaComposite; | |
36 | import java.awt.Color; | |
37 | import java.awt.Graphics; | |
38 | import java.awt.Graphics2D; | |
39 | import java.awt.image.BufferedImage; | |
40 | import java.beans.PropertyChangeSupport; | |
41 | ||
42 | public class OverviewRenderer | |
43 | { | |
44 | // transparency of hidden cols/seqs overlay | |
45 | private final float TRANSPARENCY = 0.5f; | |
46 | ||
47 | public static final String UPDATE = "OverviewUpdate"; | |
48 | ||
49 | private static final int MAX_PROGRESS = 100; | |
50 | ||
51 | private PropertyChangeSupport changeSupport = new PropertyChangeSupport( | |
52 | this); | |
53 | ||
54 | private FeatureColourFinder finder; | |
55 | ||
56 | // image to render on | |
57 | private BufferedImage miniMe; | |
58 | ||
59 | // raw number of pixels to allocate to each column | |
60 | private float pixelsPerCol; | |
61 | ||
62 | // raw number of pixels to allocate to each row | |
63 | private float pixelsPerSeq; | |
64 | ||
65 | // height in pixels of graph | |
66 | private int graphHeight; | |
67 | ||
68 | // flag to indicate whether to halt drawing | |
69 | private volatile boolean redraw = false; | |
70 | ||
71 | // reference to alignment, needed to get sequence groups | |
72 | private AlignmentI al; | |
73 | ||
74 | private ResidueShaderI shader; | |
75 | ||
76 | private OverviewResColourFinder resColFinder; | |
77 | ||
78 | 306 | public OverviewRenderer(FeatureRenderer fr, OverviewDimensions od, |
79 | AlignmentI alignment, ResidueShaderI resshader, | |
80 | OverviewResColourFinder colFinder) | |
81 | { | |
82 | 306 | finder = new FeatureColourFinder(fr); |
83 | 306 | resColFinder = colFinder; |
84 | ||
85 | 306 | al = alignment; |
86 | 306 | shader = resshader; |
87 | ||
88 | 306 | pixelsPerCol = od.getPixelsPerCol(); |
89 | 306 | pixelsPerSeq = od.getPixelsPerSeq(); |
90 | 306 | graphHeight = od.getGraphHeight(); |
91 | 306 | miniMe = new BufferedImage(od.getWidth(), od.getHeight(), |
92 | BufferedImage.TYPE_INT_RGB); | |
93 | } | |
94 | ||
95 | /** | |
96 | * Draw alignment rows and columns onto an image | |
97 | * | |
98 | * @param rit | |
99 | * Iterator over rows to be drawn | |
100 | * @param cit | |
101 | * Iterator over columns to be drawn | |
102 | * @return image containing the drawing | |
103 | */ | |
104 | 306 | public BufferedImage draw(AlignmentRowsCollectionI rows, |
105 | AlignmentColsCollectionI cols) | |
106 | { | |
107 | 306 | int rgbcolor = Color.white.getRGB(); |
108 | 306 | int seqIndex = 0; |
109 | 306 | int pixelRow = 0; |
110 | 306 | int alignmentHeight = miniMe.getHeight() - graphHeight; |
111 | 306 | int totalPixels = miniMe.getWidth() * alignmentHeight; |
112 | ||
113 | 306 | int lastRowUpdate = 0; |
114 | 306 | int lastUpdate = 0; |
115 | 306 | changeSupport.firePropertyChange(UPDATE, -1, 0); |
116 | ||
117 | 306 | for (int alignmentRow : rows) |
118 | { | |
119 | 2710 | if (redraw) |
120 | { | |
121 | 130 | break; |
122 | } | |
123 | ||
124 | // get details of this alignment row | |
125 | 2580 | SequenceI seq = rows.getSequence(alignmentRow); |
126 | ||
127 | // rate limiting step when rendering overview for lots of groups | |
128 | 2580 | SequenceGroup[] allGroups = al.findAllGroups(seq); |
129 | ||
130 | // calculate where this row extends to in pixels | |
131 | 2580 | int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1, |
132 | miniMe.getHeight() - 1); | |
133 | ||
134 | 2580 | int colIndex = 0; |
135 | 2580 | int pixelCol = 0; |
136 | 2580 | for (int alignmentCol : cols) |
137 | { | |
138 | 381095 | if (redraw) |
139 | { | |
140 | 110 | break; |
141 | } | |
142 | ||
143 | // calculate where this column extends to in pixels | |
144 | 380983 | int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, |
145 | miniMe.getWidth() - 1); | |
146 | ||
147 | // don't do expensive colour determination if we're not going to use it | |
148 | // NB this is important to avoid performance issues in the overview | |
149 | // panel | |
150 | 380951 | if (pixelCol <= endCol) |
151 | { | |
152 | 380942 | rgbcolor = getColumnColourFromSequence(allGroups, seq, |
153 | alignmentCol); | |
154 | ||
155 | // fill in the appropriate number of pixels | |
156 | 1342642 | for (int row = pixelRow; row <= endRow; ++row) |
157 | { | |
158 | 3216982 | for (int col = pixelCol; col <= endCol; ++col) |
159 | { | |
160 | 2254836 | miniMe.setRGB(col, row, rgbcolor); |
161 | } | |
162 | } | |
163 | ||
164 | // store last update value | |
165 | 380772 | lastUpdate = sendProgressUpdate( |
166 | (pixelCol + 1) * (endRow - pixelRow), totalPixels, | |
167 | lastRowUpdate, lastUpdate); | |
168 | ||
169 | 380779 | pixelCol = endCol + 1; |
170 | } | |
171 | 380835 | colIndex++; |
172 | } | |
173 | ||
174 | 2580 | if (pixelRow != endRow + 1) |
175 | { | |
176 | // store row offset and last update value | |
177 | 2580 | lastRowUpdate = sendProgressUpdate(endRow + 1, alignmentHeight, 0, |
178 | lastUpdate); | |
179 | 2580 | lastUpdate = lastRowUpdate; |
180 | 2580 | pixelRow = endRow + 1; |
181 | } | |
182 | 2580 | seqIndex++; |
183 | } | |
184 | ||
185 | 306 | overlayHiddenRegions(rows, cols); |
186 | // final update to progress bar if present | |
187 | 306 | if (redraw) |
188 | { | |
189 | 147 | sendProgressUpdate(pixelRow - 1, alignmentHeight, 0, 0); |
190 | } | |
191 | else | |
192 | { | |
193 | 159 | sendProgressUpdate(alignmentHeight, miniMe.getHeight(), 0, 0); |
194 | } | |
195 | 306 | return miniMe; |
196 | } | |
197 | ||
198 | /* | |
199 | * Calculate progress update value and fire event | |
200 | * @param rowOffset number of rows to offset calculation by | |
201 | * @return new rowOffset - return value only to be used when at end of a row | |
202 | */ | |
203 | 383560 | private int sendProgressUpdate(int position, int maximum, int rowOffset, |
204 | int lastUpdate) | |
205 | { | |
206 | 383643 | int newUpdate = rowOffset |
207 | + Math.round(MAX_PROGRESS * ((float) position / maximum)); | |
208 | 383776 | if (newUpdate > lastUpdate) |
209 | { | |
210 | 12751 | changeSupport.firePropertyChange(UPDATE, rowOffset, newUpdate); |
211 | 12751 | return newUpdate; |
212 | } | |
213 | 371054 | return newUpdate; |
214 | } | |
215 | ||
216 | /* | |
217 | * Find the RGB value of the colour of a sequence at a specified column position | |
218 | * | |
219 | * @param seq | |
220 | * sequence to get colour for | |
221 | * @param lastcol | |
222 | * column position to get colour for | |
223 | * @return colour of sequence at this position, as RGB | |
224 | */ | |
225 | 380923 | int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq, |
226 | int lastcol) | |
227 | { | |
228 | 380938 | Color color = resColFinder.gapColour; |
229 | ||
230 | 380896 | if ((seq != null) && (seq.getLength() > lastcol)) |
231 | { | |
232 | 378715 | color = resColFinder.getResidueColour(true, shader, allGroups, seq, |
233 | lastcol, finder); | |
234 | } | |
235 | ||
236 | 380889 | return color.getRGB(); |
237 | } | |
238 | ||
239 | /** | |
240 | * Overlay the hidden regions on the overview image | |
241 | * | |
242 | * @param rows | |
243 | * collection of rows the overview is built over | |
244 | * @param cols | |
245 | * collection of columns the overview is built over | |
246 | */ | |
247 | 306 | private void overlayHiddenRegions(AlignmentRowsCollectionI rows, |
248 | AlignmentColsCollectionI cols) | |
249 | { | |
250 | 306 | if (cols.hasHidden() || rows.hasHidden()) |
251 | { | |
252 | 0 | BufferedImage mask = buildHiddenImage(rows, cols, miniMe.getWidth(), |
253 | miniMe.getHeight()); | |
254 | ||
255 | 0 | Graphics2D g = (Graphics2D) miniMe.getGraphics(); |
256 | 0 | g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER, |
257 | TRANSPARENCY)); | |
258 | 0 | g.drawImage(mask, 0, 0, miniMe.getWidth(), miniMe.getHeight(), null); |
259 | } | |
260 | } | |
261 | ||
262 | /** | |
263 | * Build a masking image of hidden columns and rows to be applied on top of | |
264 | * the main overview image. | |
265 | * | |
266 | * @param rows | |
267 | * collection of rows the overview is built over | |
268 | * @param cols | |
269 | * collection of columns the overview is built over | |
270 | * @param width | |
271 | * width of overview in pixels | |
272 | * @param height | |
273 | * height of overview in pixels | |
274 | * @return BufferedImage containing mask of hidden regions | |
275 | */ | |
276 | 0 | private BufferedImage buildHiddenImage(AlignmentRowsCollectionI rows, |
277 | AlignmentColsCollectionI cols, int width, int height) | |
278 | { | |
279 | // new masking image | |
280 | 0 | BufferedImage hiddenImage = new BufferedImage(width, height, |
281 | BufferedImage.TYPE_INT_ARGB); | |
282 | ||
283 | 0 | int colIndex = 0; |
284 | 0 | int pixelCol = 0; |
285 | ||
286 | 0 | Color hidden = resColFinder.getHiddenColour(); |
287 | ||
288 | 0 | Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics(); |
289 | ||
290 | // set background to transparent | |
291 | // g2d.setComposite(AlphaComposite.Clear); | |
292 | // g2d.fillRect(0, 0, width, height); | |
293 | ||
294 | // set next colour to opaque | |
295 | 0 | g2d.setComposite(AlphaComposite.Src); |
296 | ||
297 | 0 | for (int alignmentCol : cols) |
298 | { | |
299 | 0 | if (redraw) |
300 | { | |
301 | 0 | break; |
302 | } | |
303 | ||
304 | // calculate where this column extends to in pixels | |
305 | 0 | int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, |
306 | hiddenImage.getWidth() - 1); | |
307 | ||
308 | 0 | if (pixelCol <= endCol) |
309 | { | |
310 | // determine the colour based on the sequence and column position | |
311 | 0 | if (cols.isHidden(alignmentCol)) |
312 | { | |
313 | 0 | g2d.setColor(hidden); |
314 | 0 | g2d.fillRect(pixelCol, 0, endCol - pixelCol + 1, height); |
315 | } | |
316 | ||
317 | 0 | pixelCol = endCol + 1; |
318 | } | |
319 | 0 | colIndex++; |
320 | ||
321 | } | |
322 | ||
323 | 0 | int seqIndex = 0; |
324 | 0 | int pixelRow = 0; |
325 | 0 | for (int alignmentRow : rows) |
326 | { | |
327 | 0 | if (redraw) |
328 | { | |
329 | 0 | break; |
330 | } | |
331 | ||
332 | // calculate where this row extends to in pixels | |
333 | 0 | int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1, |
334 | miniMe.getHeight() - 1); | |
335 | ||
336 | // get details of this alignment row | |
337 | 0 | if (rows.isHidden(alignmentRow)) |
338 | { | |
339 | 0 | g2d.setColor(hidden); |
340 | 0 | g2d.fillRect(0, pixelRow, width, endRow - pixelRow + 1); |
341 | } | |
342 | 0 | pixelRow = endRow + 1; |
343 | 0 | seqIndex++; |
344 | } | |
345 | ||
346 | 0 | return hiddenImage; |
347 | } | |
348 | ||
349 | /** | |
350 | * Draw the alignment annotation in the overview panel | |
351 | * | |
352 | * @param g | |
353 | * the graphics object to draw on | |
354 | * @param anno | |
355 | * alignment annotation information | |
356 | * @param y | |
357 | * y-position for the annotation graph | |
358 | * @param cols | |
359 | * the collection of columns used in the overview panel | |
360 | */ | |
361 | 295 | public void drawGraph(Graphics g, AlignmentAnnotation anno, int y, |
362 | AlignmentColsCollectionI cols) | |
363 | { | |
364 | 295 | Annotation[] annotations = anno.annotations; |
365 | 295 | g.setColor(Color.white); |
366 | 295 | g.fillRect(0, 0, miniMe.getWidth(), y); |
367 | ||
368 | 295 | int height; |
369 | 295 | int colIndex = 0; |
370 | 295 | int pixelCol = 0; |
371 | 295 | for (int alignmentCol : cols) |
372 | { | |
373 | 22495 | if (redraw) |
374 | { | |
375 | 142 | changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, 0); |
376 | 142 | break; |
377 | } | |
378 | ||
379 | 22352 | if (alignmentCol >= annotations.length) |
380 | { | |
381 | 1 | break; // no more annotations to draw here |
382 | } | |
383 | else | |
384 | { | |
385 | 22352 | int endCol = Math.min(Math.round((colIndex + 1) * pixelsPerCol) - 1, |
386 | miniMe.getWidth() - 1); | |
387 | ||
388 | 22351 | if (annotations[alignmentCol] != null) |
389 | { | |
390 | 22351 | if (annotations[alignmentCol].colour == null) |
391 | { | |
392 | 0 | g.setColor(Color.black); |
393 | } | |
394 | else | |
395 | { | |
396 | 22351 | g.setColor(annotations[alignmentCol].colour); |
397 | } | |
398 | ||
399 | 22350 | height = (int) ((annotations[alignmentCol].value / anno.graphMax) |
400 | * y); | |
401 | 22350 | if (height > y) |
402 | { | |
403 | 0 | height = y; |
404 | } | |
405 | ||
406 | 22351 | g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height); |
407 | } | |
408 | ||
409 | 22350 | pixelCol = endCol + 1; |
410 | 22352 | colIndex++; |
411 | } | |
412 | } | |
413 | 295 | changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, |
414 | MAX_PROGRESS); | |
415 | } | |
416 | ||
417 | /** | |
418 | * Allows redraw flag to be set | |
419 | * | |
420 | * @param b | |
421 | * value to set redraw to: true = redraw is occurring, false = no | |
422 | * redraw | |
423 | */ | |
424 | 269 | public void setRedraw(boolean b) |
425 | { | |
426 | 269 | synchronized (this) |
427 | { | |
428 | 269 | redraw = b; |
429 | } | |
430 | } | |
431 | ||
432 | 306 | public void addPropertyChangeListener(RendererListenerI listener) |
433 | { | |
434 | 306 | changeSupport.addPropertyChangeListener(listener); |
435 | } | |
436 | ||
437 | 293 | public void removePropertyChangeListener(RendererListenerI listener) |
438 | { | |
439 | 293 | changeSupport.removePropertyChangeListener(listener); |
440 | } | |
441 | } |