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;
23 import jalview.api.AlignmentColsCollectionI;
24 import jalview.api.AlignmentRowsCollectionI;
25 import jalview.api.AlignmentViewPanel;
26 import jalview.api.RendererListenerI;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.AlignmentI;
29 import jalview.datamodel.Annotation;
30 import jalview.datamodel.SequenceGroup;
31 import jalview.datamodel.SequenceI;
32 import jalview.renderer.seqfeatures.FeatureColourFinder;
33 import jalview.util.Platform;
34 import jalview.viewmodel.OverviewDimensions;
36 import java.awt.AlphaComposite;
37 import java.awt.Color;
38 import java.awt.Graphics;
39 import java.awt.Graphics2D;
40 import java.awt.event.ActionEvent;
41 import java.awt.event.ActionListener;
42 import java.awt.image.BufferedImage;
43 import java.awt.image.DataBufferInt;
44 import java.awt.image.WritableRaster;
45 import java.beans.PropertyChangeSupport;
46 import java.util.BitSet;
47 import java.util.Iterator;
49 import javax.swing.Timer;
51 public class OverviewRenderer
53 public static final String UPDATE = "OverviewUpdate";
55 // transparency of hidden cols/seqs overlay
56 private static final float TRANSPARENCY = 0.5f;
58 private static final int MAX_PROGRESS = 100;
60 private static final int STATE_INIT = 0;
62 private static final int STATE_NEXT = 1;
64 private static final int STATE_DONE = 2;
70 private int delay = (Platform.isJS() ? 1 : 0);
78 private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
81 private FeatureColourFinder finder;
84 private BufferedImage miniMe;
87 * Number of pixelsPerCol;
89 private float pixelsPerCol;
92 * Number of visible columns per pixel.
95 private float colsPerPixel;
98 * raw number of pixels to allocate to each row
100 private float pixelsPerSeq;
103 * true when colsPerPixel > 1
105 private boolean skippingColumns;
108 * pre-calculated list of columns needed for a "dense" overview, where there
109 * are more columns than pixels
112 private int[] columnsToShow;
114 // height in pixels of graph
115 private int graphHeight;
117 // flag to indicate whether to halt drawing
118 private volatile boolean redraw = false;
120 // reference to alignment, needed to get sequence groups
121 private AlignmentI al;
123 private ResidueShaderI shader;
125 private OverviewResColourFinder resColFinder;
127 private boolean showProgress;
129 private AlignmentViewPanel panel;
131 private int ndone = 0;
133 private AlignmentRowsCollectionI rows;
135 private AlignmentColsCollectionI cols;
137 private Iterator<Integer> rowIterator;
139 private int alignmentHeight;
141 private int totalPixels;
143 private int lastRowUpdate;
145 private int lastUpdate;
147 private int[] pixels;
149 private BitSet bscol;
155 public OverviewRenderer(AlignmentViewPanel panel,
156 jalview.api.FeatureRenderer fr, OverviewDimensions od,
157 AlignmentI alignment, ResidueShaderI resshader,
158 OverviewResColourFinder colFinder)
160 this(panel, fr, od, alignment, resshader, colFinder, true);
170 * @param shwoProgress
171 * possibly not, in JavaScript and for testng
173 public OverviewRenderer(AlignmentViewPanel panel,
174 jalview.api.FeatureRenderer fr, OverviewDimensions od,
175 AlignmentI alignment, ResidueShaderI resshader,
176 OverviewResColourFinder colFinder, boolean showProgress)
179 finder = new FeatureColourFinder(fr);
182 resColFinder = colFinder;
183 this.showProgress = showProgress;
187 rows = od.getRows(alignment);
188 cols = od.getColumns(alignment);
189 graphHeight = od.getGraphHeight();
190 alignmentHeight = od.getSequencesHeight();
192 pixelsPerSeq = od.getPixelsPerSeq();
193 pixelsPerCol = od.getPixelsPerCol();
194 colsPerPixel = Math.max(1, 1f / pixelsPerCol);
196 skippingColumns = (pixelsPerCol < 1);
200 * Draw alignment rows and columns onto an image. This method is asynchronous
201 * in JavaScript and interruptible in Java.
203 * Whether hidden rows or columns are drawn depends upon the type of
206 * Updated to skip through high-density sequences, where columns/pixels > 1.
208 * When the process is complete, the image is passed to the AlignmentViewPanel
209 * provided by the constructor.
212 * collection of rows to be drawn
214 * collection of columns to be drawn
215 * @return image containing the drawing
217 * @author Bob Hanson 2019.07.30
219 public void drawMiniMe()
225 protected void mainLoop()
236 if (!rowIterator.hasNext())
252 // Java will continue without a timeout
259 rowIterator = rows.iterator();
264 totalPixels = w * alignmentHeight;
267 changeSupport.firePropertyChange(UPDATE, -1, 0);
270 miniMe = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB);
271 WritableRaster raster = miniMe.getRaster();
272 DataBufferInt db = (DataBufferInt) raster.getDataBuffer();
273 pixels = db.getBankData()[0];
274 bscol = cols.getShownBitSet();
277 columnsToShow = calcColumnsToShow();
280 Platform.timeCheck(null, Platform.TIME_MARK);
283 private void nextRow()
285 row = rowIterator.next();
286 SequenceI seq = rows.getSequence(row);
288 // rate limiting step when rendering overview for lots of groups
289 SequenceGroup[] allGroups = al.findAllGroups(seq);
291 // calculate where this row extends to in pixels
292 int endRow = Math.min(Math.round((++seqIndex) * pixelsPerSeq), h);
293 // this is the key modification -- we use bscol to jump to the next column
294 // when there are more columns than pixels.
296 for (int pixelCol = 0, colNext = 0, pixelEnd = 0, icol = bscol
297 .nextSetBit(0); icol >= 0; icol = getNextCol(icol, colNext))
299 // asynchronous exit flag
306 pixelEnd = getNextPixel(colNext, colNext);
308 if (pixelCol == pixelEnd)
312 else if (pixelCol < pixelEnd)
314 int rgb = getColumnColourFromSequence(allGroups, seq, icol);
315 // fill in the appropriate number of pixels
316 for (int row = pixelRow; row < endRow; ++row)
318 for (int col = pixelCol; col < pixelEnd; ++col)
320 // BH 2019.07.27 was:
322 // miniMe.setRGB(col, row, rgbcolor);
324 // but just directly writing to the int[] pixel buffer
325 // is three times faster by my experimentation
326 pixels[row * w + col] = rgb;
331 // store last update value
334 lastUpdate = sendProgressUpdate(
335 pixelEnd * (endRow - 1 - pixelRow), totalPixels,
336 lastRowUpdate, lastUpdate);
341 if (pixelRow < endRow)
344 // store row offset and last update value
347 // BH 2019.07.29 was (old) endRow + 1 (now endRow), but should be
348 // pixelRow + 1, surely
349 lastRowUpdate = sendProgressUpdate(endRow, alignmentHeight, 0,
351 lastUpdate = lastRowUpdate;
357 * Precalculate the columns that will be used for each pixel in a dense
358 * overview. So we have to skip through the bscol BitSet to pick up one
359 * (representative?) column for each pixel.
361 * Note that there is no easy solution if we want to do color averaging, but
362 * this method might be adapted to do that. Or it could be adapted to pick the
363 * "most representative color" for a group of columns.
365 * @author Bob Hanson 2019.09.03
366 * @return a -1 terminated int[]
368 private int[] calcColumnsToShow()
370 int[] a = new int[w + 1];
372 float offset = bscol.nextSetBit(0);
375 return new int[] { -1 };
378 a[pixel++] = (int) offset;
379 // for example, say we have 10 pixels per column:
380 // ...............xxxxxxxx....xxxxxx.........xxxxxx......
381 // nextSet(i).....^...........^..............^...........
382 // nextClear..............^.........^..............^.....
383 // run lengths....|--n1--|....|-n2-|.........|-n3-|......
384 // 10 pixel/col...|---pixel1---||-----pixel2------|......
385 // pixel..........^0............^1.......................
386 for (int i, iClear = -1; pixel < w
387 && (i = bscol.nextSetBit(iClear + 1)) >= 0;)
389 // find the next clear bit
390 iClear = bscol.nextClearBit(i + 1);
391 // add the run length n1, n2, n3 to grow the column buffer
392 colBuffer += iClear - i; // n1, n2, etc.
393 // add columns if we have accumulated enough pixels
395 while (colBuffer > colsPerPixel && pixel < w)
397 colBuffer -= colsPerPixel;
398 offset += colsPerPixel;
399 a[pixel++] = i + (int) offset;
401 // set back column pointer relative to the next run
410 * The next column is either a precalculated pixel (when there are multiple
411 * pixels per column) or the next set bit for the column that aligns with the
412 * next pixel (when there are more columns than pixels).
414 * When columns are hidden, this value is precalculated; otherwise it is
419 * pixel pointer into columnsToShow
422 private int getNextCol(int icol, int pixel)
424 return (skippingColumns ? columnsToShow[pixel]
425 : bscol.nextSetBit(icol + 1));
429 * Derive the next pixel from either as the given pixel (when we are skipping
430 * columns because this is a dense overview and the pixel known), or from the
431 * current column based on pixels/column. The latter is used for drawing the
432 * hidden-column mask or for overviews that have more pixels across than
439 private int getNextPixel(int icol, int pixel)
441 return Math.min(skippingColumns && pixel > 0 ? pixel
442 : Math.round(icol * pixelsPerCol), w);
445 private boolean loop()
453 timer = new Timer(delay, new ActionListener()
456 public void actionPerformed(ActionEvent e)
461 timer.setRepeats(false);
476 "overviewrender " + ndone + " pixels row:" + row + " redraw:"
481 overlayHiddenRegions();
484 // final update to progress bar if present
488 // BH was pixelRow - 1, but that could go negative
489 sendProgressUpdate(pixelRow, alignmentHeight, 0, 0);
493 // sendProgressUpdate(alignmentHeight, miniMe.getHeight(), 0, 0);
494 sendProgressUpdate(1, 1, 0, 0);
498 panel.overviewDone(miniMe);
502 * Calculate progress update value and fire event
503 * @param rowOffset number of rows to offset calculation by
504 * @return new rowOffset - return value only to be used when at end of a row
506 private int sendProgressUpdate(int position, int maximum, int rowOffset,
509 int newUpdate = rowOffset
510 + Math.round(MAX_PROGRESS * ((float) position / maximum));
511 if (newUpdate > lastUpdate)
513 changeSupport.firePropertyChange(UPDATE, rowOffset, newUpdate);
520 * Find the RGB value of the colour of a sequence at a specified column position
523 * sequence to get colour for
525 * column position to get colour for
526 * @return colour of sequence at this position, as RGB
528 int getColumnColourFromSequence(SequenceGroup[] allGroups, SequenceI seq,
531 return (seq == null || icol >= seq.getLength()
532 ? resColFinder.gapColourInt
533 : resColFinder.getResidueColourInt(true, shader, allGroups, seq,
538 * Overlay the hidden regions on the overview image
541 private void overlayHiddenRegions()
543 if (cols.hasHidden() || rows.hasHidden())
545 BufferedImage mask = buildHiddenImage();
547 Graphics2D g = (Graphics2D) miniMe.getGraphics();
548 g.setComposite(AlphaComposite.getInstance(AlphaComposite.SRC_OVER,
550 g.drawImage(mask, 0, 0, miniMe.getWidth(), miniMe.getHeight(), null);
556 * Build a masking image of hidden columns and rows to be applied on top of
557 * the main overview image.
560 * collection of rows the overview is built over
562 * collection of columns the overview is built over
564 * width of overview in pixels
566 * height of overview in pixels
567 * @return BufferedImage containing mask of hidden regions
569 private BufferedImage buildHiddenImage()
572 BufferedImage hiddenImage = new BufferedImage(w, h,
573 BufferedImage.TYPE_INT_ARGB);
575 Color hidden = resColFinder.getHiddenColour();
577 Graphics2D g2d = (Graphics2D) hiddenImage.getGraphics();
579 g2d.setColor(hidden);
580 // set background to transparent
581 // g2d.setComposite(AlphaComposite.Clear);
582 // g2d.fillRect(0, 0, width, height);
584 // set next colour to opaque
585 g2d.setComposite(AlphaComposite.Src);
587 // System.out.println(cols.getClass().getName());
588 if (cols.hasHidden())
590 // AllColsCollection only
591 BitSet bs = cols.getHiddenBitSet();
592 for (int pixelCol = -1, icol2 = 0, icol = bs
593 .nextSetBit(0); icol >= 0; icol = bs.nextSetBit(icol2))
599 icol2 = bs.nextClearBit(icol + 1);
600 int pixelEnd = getNextPixel(icol2, 0);
601 if (pixelEnd > pixelCol)
603 pixelCol = getNextPixel(icol, 0);
604 g2d.fillRect(pixelCol, 0, Math.max(1, pixelEnd - pixelCol),
610 if (rows.hasHidden())
614 for (int alignmentRow : rows)
621 // calculate where this row extends to in pixels
622 int endRow = Math.min(Math.round((++seqIndex) * pixelsPerSeq),
625 // get details of this alignment row
626 if (rows.isHidden(alignmentRow))
628 // BH 2019.09.24 fixes JAL-3440 Java+JavaScript off by one row in
630 g2d.fillRect(0, pixelRow, w, endRow - pixelRow);
640 * Draw the alignment annotation in the overview panel
643 * alignment annotation information
645 public void drawGraph(AlignmentAnnotation anno)
648 Graphics g = miniMe.getGraphics();
649 g.translate(0, alignmentHeight);
651 Annotation[] annotations = anno.annotations;
652 float max = anno.graphMax;
653 g.setColor(Color.white);
654 g.fillRect(0, 0, w, y);
656 for (int pixelCol = 0, colNext = 0, pixelEnd = 0, len = annotations.length, icol = bscol
657 .nextSetBit(0); icol >= 0
658 && icol < len; icol = getNextCol(icol, colNext))
664 changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1, 0);
670 pixelEnd = getNextPixel(colNext, colNext);
671 Annotation ann = annotations[icol];
674 Color color = ann.colour;
675 g.setColor(color == null ? Color.black : color);
676 int height = Math.min(y, (int) ((ann.value / max) * y));
677 g.fillRect(pixelCol, y - height, Math.max(1, pixelEnd - pixelCol),
683 g.translate(0, -alignmentHeight);
688 changeSupport.firePropertyChange(UPDATE, MAX_PROGRESS - 1,
695 * Allows redraw flag to be set
698 * value to set redraw to: true = redraw is occurring, false = no
701 public void setRedraw(boolean b)
709 public void addPropertyChangeListener(RendererListenerI listener)
711 changeSupport.addPropertyChangeListener(listener);
714 public void removePropertyChangeListener(RendererListenerI listener)
716 changeSupport.removePropertyChangeListener(listener);