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.appletgui;
23 import jalview.datamodel.AlignmentI;
24 import jalview.datamodel.HiddenColumns;
25 import jalview.datamodel.SearchResultsI;
26 import jalview.datamodel.SequenceGroup;
27 import jalview.datamodel.SequenceI;
28 import jalview.renderer.ScaleRenderer;
29 import jalview.renderer.ScaleRenderer.ScaleMark;
30 import jalview.viewmodel.AlignmentViewport;
31 import jalview.viewmodel.ViewportListenerI;
32 import jalview.viewmodel.ViewportRanges;
34 import java.awt.Color;
35 import java.awt.FontMetrics;
36 import java.awt.Graphics;
37 import java.awt.Image;
38 import java.awt.Panel;
39 import java.beans.PropertyChangeEvent;
40 import java.util.Iterator;
42 public class SeqCanvas extends Panel implements ViewportListenerI
58 boolean fastPaint = false;
64 public SeqCanvas(AlignViewport av)
67 fr = new FeatureRenderer(av);
68 sr = new SequenceRenderer(av);
69 PaintRefresher.Register(this, av.getSequenceSetId());
72 av.getRanges().addPropertyChangeListener(this);
75 int avcharHeight = 0, avcharWidth = 0;
77 private void updateViewport()
79 avcharHeight = av.getCharHeight();
80 avcharWidth = av.getCharWidth();
83 public AlignmentViewport getViewport()
88 public FeatureRenderer getFeatureRenderer()
93 public SequenceRenderer getSequenceRenderer()
98 private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
101 g.setColor(Color.black);
102 for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
105 int mpos = mark.column; // (i - startx - 1)
110 String mstring = mark.text;
116 g.drawString(mstring, mpos * avcharWidth,
117 ypos - (avcharHeight / 2));
119 g.drawLine((mpos * avcharWidth) + (avcharWidth / 2),
120 (ypos + 2) - (avcharHeight / 2),
121 (mpos * avcharWidth) + (avcharWidth / 2), ypos - 2);
126 private void drawWestScale(Graphics g, int startx, int endx, int ypos)
128 FontMetrics fm = getFontMetrics(av.getFont());
129 ypos += avcharHeight;
130 if (av.hasHiddenColumns())
132 startx = av.getAlignment().getHiddenColumns()
133 .adjustForHiddenColumns(startx);
134 endx = av.getAlignment().getHiddenColumns()
135 .adjustForHiddenColumns(endx);
138 int maxwidth = av.getAlignment().getWidth();
139 if (av.hasHiddenColumns())
141 maxwidth = av.getAlignment().getHiddenColumns()
142 .findColumnPosition(maxwidth) - 1;
146 for (int i = 0; i < av.getAlignment().getHeight(); i++)
148 SequenceI seq = av.getAlignment().getSequenceAt(i);
154 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
161 value = av.getAlignment().getSequenceAt(i).findPosition(index);
168 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
170 g.drawString(value + "", x,
171 (ypos + (i * avcharHeight)) - (avcharHeight / 5));
176 private void drawEastScale(Graphics g, int startx, int endx, int ypos)
178 ypos += avcharHeight;
180 if (av.hasHiddenColumns())
182 endx = av.getAlignment().getHiddenColumns()
183 .adjustForHiddenColumns(endx);
188 for (int i = 0; i < av.getAlignment().getHeight(); i++)
190 seq = av.getAlignment().getSequenceAt(i);
194 while (index > startx)
196 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
203 value = seq.findPosition(index);
210 g.drawString(String.valueOf(value), 0,
211 (ypos + (i * avcharHeight)) - (avcharHeight / 5));
218 void fastPaint(int horizontal, int vertical)
220 if (fastPaint || gg == null)
225 ViewportRanges ranges = av.getRanges();
229 // Its possible on certain browsers that the call to fastpaint
230 // is faster than it can paint, so this check here catches
232 if (lastsr + horizontal != ranges.getStartRes())
234 horizontal = ranges.getStartRes() - lastsr;
237 lastsr = ranges.getStartRes();
240 gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight,
241 imgWidth - horizontal * avcharWidth,
242 imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
243 -vertical * avcharHeight);
245 int sr = ranges.getStartRes(), er = ranges.getEndRes(),
246 ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transX = 0,
249 if (horizontal > 0) // scrollbar pulled right, image to the left
251 transX = (er - sr - horizontal) * avcharWidth;
252 sr = er - horizontal;
254 else if (horizontal < 0)
256 er = sr - horizontal;
259 else if (vertical > 0) // scroll down
262 if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
266 ss = ranges.getStartSeq();
270 transY = imgHeight - ((vertical + 1) * avcharHeight);
273 else if (vertical < 0)
276 if (es > ranges.getEndSeq())
278 es = ranges.getEndSeq();
282 gg.translate(transX, transY);
284 drawPanel(gg, sr, er, ss, es, 0);
285 gg.translate(-transX, -transY);
292 * Definitions of startx and endx (hopefully): SMJS This is what I'm working
293 * towards! startx is the first residue (starting at 0) to display. endx is
294 * the last residue to display (starting at 0). starty is the first sequence
295 * to display (starting at 0). endy is the last sequence to display (starting
296 * at 0). NOTE 1: The av limits are set in setFont in this class and in the
297 * adjustment listener in SeqPanel when the scrollbars move.
300 public void update(Graphics g)
306 public void paint(Graphics g)
310 && (fastPaint || (getSize().width != g.getClipBounds().width)
311 || (getSize().height != g.getClipBounds().height)))
313 g.drawImage(img, 0, 0, this);
320 g.drawImage(img, 0, 0, this);
326 // this draws the whole of the alignment
327 imgWidth = this.getSize().width;
328 imgHeight = this.getSize().height;
330 imgWidth -= imgWidth % avcharWidth;
331 imgHeight -= imgHeight % avcharHeight;
333 if (imgWidth < 1 || imgHeight < 1)
338 if (img == null || imgWidth != img.getWidth(this)
339 || imgHeight != img.getHeight(this))
341 img = createImage(imgWidth, imgHeight);
342 gg = img.getGraphics();
343 gg.setFont(av.getFont());
346 gg.setColor(Color.white);
347 gg.fillRect(0, 0, imgWidth, imgHeight);
349 ViewportRanges ranges = av.getRanges();
351 if (av.getWrapAlignment())
353 drawWrappedPanel(gg, imgWidth, imgHeight, ranges.getStartRes());
357 drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
358 ranges.getStartSeq(), ranges.getEndSeq(), 0);
361 g.drawImage(img, 0, 0, this);
365 int LABEL_WEST, LABEL_EAST;
367 public int getWrappedCanvasWidth(int cwidth)
369 cwidth -= cwidth % av.getCharWidth();
371 FontMetrics fm = getFontMetrics(av.getFont());
376 if (av.getScaleRightWrapped())
378 LABEL_EAST = fm.stringWidth(getMask());
381 if (av.getScaleLeftWrapped())
383 LABEL_WEST = fm.stringWidth(getMask());
386 return (cwidth - LABEL_EAST - LABEL_WEST) / av.getCharWidth();
390 * Generates a string of zeroes.
399 AlignmentI alignment = av.getAlignment();
400 for (int i = 0; i < alignment.getHeight(); i++)
402 tmp = alignment.getSequenceAt(i).getEnd();
409 for (int i = maxWidth; i > 0; i /= 10)
416 private void drawWrappedPanel(Graphics g, int canvasWidth,
417 int canvasHeight, int startRes)
419 AlignmentI al = av.getAlignment();
421 FontMetrics fm = getFontMetrics(av.getFont());
426 if (av.getScaleRightWrapped())
428 LABEL_EAST = fm.stringWidth(getMask());
431 if (av.getScaleLeftWrapped())
433 LABEL_WEST = fm.stringWidth(getMask());
436 int hgap = avcharHeight;
437 if (av.getScaleAboveWrapped())
439 hgap += avcharHeight;
442 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
443 int cHeight = av.getAlignment().getHeight() * avcharHeight;
445 av.setWrappedWidth(cWidth);
447 av.getRanges().setViewportStartAndWidth(startRes, cWidth);
452 int maxwidth = av.getAlignment().getWidth();
454 if (av.hasHiddenColumns())
456 maxwidth = av.getAlignment().getHiddenColumns()
457 .findColumnPosition(maxwidth);
460 while ((ypos <= canvasHeight) && (startRes < maxwidth))
462 endx = startRes + cWidth - 1;
469 g.setColor(Color.black);
471 if (av.getScaleLeftWrapped())
473 drawWestScale(g, startRes, endx, ypos);
476 if (av.getScaleRightWrapped())
478 g.translate(canvasWidth - LABEL_EAST, 0);
479 drawEastScale(g, startRes, endx, ypos);
480 g.translate(-(canvasWidth - LABEL_EAST), 0);
483 g.translate(LABEL_WEST, 0);
485 if (av.getScaleAboveWrapped())
487 drawNorthScale(g, startRes, endx, ypos);
489 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
491 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
492 g.setColor(Color.blue);
494 Iterator<Integer> it = hidden.getBoundedStartIterator(startRes,
498 res = it.next() - startRes;
501 { res * avcharWidth - avcharHeight / 4, res * avcharWidth + avcharHeight / 4, res * avcharWidth },
503 { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2), ypos - (avcharHeight / 2) + 8 }, 3);
507 if (g.getClip() == null)
509 g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
512 drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
515 if (av.isShowAnnotation())
517 g.translate(0, cHeight + ypos + 4);
518 if (annotations == null)
520 annotations = new AnnotationPanel(av);
523 annotations.drawComponent(g, startRes, endx + 1);
524 g.translate(0, -cHeight - ypos - 4);
526 g.translate(-LABEL_WEST, 0);
528 ypos += cHeight + getAnnotationHeight() + hgap;
535 AnnotationPanel annotations;
537 int getAnnotationHeight()
539 if (!av.isShowAnnotation())
544 if (annotations == null)
546 annotations = new AnnotationPanel(av);
549 return annotations.adjustPanelHeight();
552 private void drawPanel(Graphics g1, final int startRes, final int endRes,
553 final int startSeq, final int endSeq, final int offset)
556 if (!av.hasHiddenColumns())
558 draw(g1, startRes, endRes, startSeq, endSeq, offset);
563 final int screenYMax = endRes - startRes;
564 int blockStart = startRes;
565 int blockEnd = endRes;
567 if (av.hasHiddenColumns())
569 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
570 for (int[] region : hidden.getHiddenColumnsCopy())
572 int hideStart = region[0];
573 int hideEnd = region[1];
575 if (hideStart <= blockStart)
577 blockStart += (hideEnd - hideStart) + 1;
582 * draw up to just before the next hidden region, or the end of
583 * the visible region, whichever comes first
585 blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
588 g1.translate(screenY * avcharWidth, 0);
590 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
593 * draw the downline of the hidden column marker (ScalePanel draws the
594 * triangle on top) if we reached it
596 if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
598 g1.setColor(Color.blue);
599 g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
601 (blockEnd - blockStart + 1) * avcharWidth - 1,
602 (endSeq - startSeq + 1) * avcharHeight + offset);
605 g1.translate(-screenY * avcharWidth, 0);
606 screenY += blockEnd - blockStart + 1;
607 blockStart = hideEnd + 1;
609 if (screenY > screenYMax)
611 // already rendered last block
616 if (screenY <= screenYMax)
618 // remaining visible region to render
619 blockEnd = blockStart + (endRes - startRes) - screenY;
620 g1.translate(screenY * avcharWidth, 0);
621 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
623 g1.translate(-screenY * avcharWidth, 0);
629 // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
630 // int x1, int x2, int y1, int y2, int startx, int starty,
631 void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
634 g.setFont(av.getFont());
635 sr.prepare(g, av.isRenderGaps());
639 // / First draw the sequences
640 // ///////////////////////////
641 for (int i = startSeq; i <= endSeq; i++)
643 nextSeq = av.getAlignment().getSequenceAt(i);
650 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
651 startRes, endRes, offset + ((i - startSeq) * avcharHeight));
653 if (av.isShowSequenceFeatures())
655 fr.drawSequence(g, nextSeq, startRes, endRes,
656 offset + ((i - startSeq) * avcharHeight), false);
659 // / Highlight search Results once all sequences have been drawn
660 // ////////////////////////////////////////////////////////
661 if (av.hasSearchResults())
663 int[] visibleResults = av.getSearchResults().getResults(nextSeq,
665 if (visibleResults != null)
667 for (int r = 0; r < visibleResults.length; r += 2)
669 sr.drawHighlightedText(nextSeq, visibleResults[r],
670 visibleResults[r + 1],
671 (visibleResults[r] - startRes) * avcharWidth,
672 offset + ((i - startSeq) * avcharHeight));
677 if (av.cursorMode && cursorY == i && cursorX >= startRes
678 && cursorX <= endRes)
680 sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
681 offset + ((i - startSeq) * avcharHeight));
685 if (av.getSelectionGroup() != null
686 || av.getAlignment().getGroups().size() > 0)
688 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
693 private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
694 int startSeq, int endSeq, int offset)
697 // ///////////////////////////////////
698 // Now outline any areas if necessary
699 // ///////////////////////////////////
700 SequenceGroup group = av.getSelectionGroup();
707 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
709 group = av.getAlignment().getGroups().get(0);
719 boolean inGroup = false;
722 int alHeight = av.getAlignment().getHeight() - 1;
724 for (i = startSeq; i <= endSeq; i++)
726 sx = (group.getStartRes() - startRes) * avcharWidth;
727 sy = offset + ((i - startSeq) * avcharHeight);
728 ex = (((group.getEndRes() + 1) - group.getStartRes())
731 if (sx + ex < 0 || sx > imgWidth)
736 if ((sx <= (endRes - startRes) * avcharWidth)
737 && group.getSequences(null)
738 .contains(av.getAlignment().getSequenceAt(i)))
741 && (i >= alHeight || !group.getSequences(null).contains(
742 av.getAlignment().getSequenceAt(i + 1))))
744 bottom = sy + avcharHeight;
749 if (((top == -1) && (i == 0)) || !group.getSequences(null)
750 .contains(av.getAlignment().getSequenceAt(i - 1)))
758 if (group == av.getSelectionGroup())
760 g.setColor(Color.red);
764 g.setColor(group.getOutlineColour());
772 if (sx >= 0 && sx < imgWidth)
774 g.drawLine(sx, oldY, sx, sy);
777 if (sx + ex < imgWidth)
779 g.drawLine(sx + ex, oldY, sx + ex, sy);
788 if (sx + ex > imgWidth)
793 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
795 ex = (endRes - startRes + 1) * avcharWidth;
800 g.drawLine(sx, top, sx + ex, top);
806 g.drawLine(sx, bottom, sx + ex, bottom);
817 sy = offset + ((i - startSeq) * avcharHeight);
818 if (sx >= 0 && sx < imgWidth)
820 g.drawLine(sx, oldY, sx, sy);
823 if (sx + ex < imgWidth)
825 g.drawLine(sx + ex, oldY, sx + ex, sy);
834 if (sx + ex > imgWidth)
838 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
840 ex = (endRes - startRes + 1) * avcharWidth;
845 g.drawLine(sx, top, sx + ex, top);
851 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
860 if (groupIndex >= av.getAlignment().getGroups().size())
865 group = av.getAlignment().getGroups().get(groupIndex);
866 } while (groupIndex < av.getAlignment().getGroups().size());
871 public void highlightSearchResults(SearchResultsI results)
873 av.setSearchResults(results);
878 public void propertyChange(PropertyChangeEvent evt)
880 String eventName = evt.getPropertyName();
882 if (!av.getWrapAlignment())
885 if (eventName.equals(ViewportRanges.STARTRES))
887 // Make sure we're not trying to draw a panel
888 // larger than the visible window
889 ViewportRanges vpRanges = av.getRanges();
890 scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
891 int range = vpRanges.getEndRes() - vpRanges.getStartRes();
896 else if (scrollX < -range)
902 // Both scrolling and resizing change viewport ranges: scrolling changes
903 // both start and end points, but resize only changes end values.
904 // Here we only want to fastpaint on a scroll, with resize using a normal
905 // paint, so scroll events are identified as changes to the horizontal or
906 // vertical start value.
907 if (eventName.equals(ViewportRanges.STARTRES))
909 // scroll - startres and endres both change
910 fastPaint(scrollX, 0);
912 else if (eventName.equals(ViewportRanges.STARTSEQ))
915 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());