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.List;
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, ypos
117 - (avcharHeight / 2));
119 g.drawLine((mpos * avcharWidth) + (avcharWidth / 2), (ypos + 2)
120 - (avcharHeight / 2), (mpos * avcharWidth)
121 + (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, (ypos + (i * avcharHeight))
171 - (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, (ypos + (i * avcharHeight))
211 - (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, imgWidth
241 - horizontal * avcharWidth,
242 imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
243 -vertical * avcharHeight);
245 int sr = ranges.getStartRes(), er = ranges.getEndRes(), ss = ranges
246 .getStartSeq(), es = ranges
247 .getEndSeq(), transX = 0, transY = 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) || (getSize().height != g
311 .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());
423 if (av.getScaleRightWrapped())
425 LABEL_EAST = fm.stringWidth(getMask());
428 if (av.getScaleLeftWrapped())
430 LABEL_WEST = fm.stringWidth(getMask());
433 int hgap = avcharHeight;
434 if (av.getScaleAboveWrapped())
436 hgap += avcharHeight;
439 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
440 int cHeight = av.getAlignment().getHeight() * avcharHeight;
442 av.setWrappedWidth(cWidth);
444 av.getRanges().setEndRes(av.getRanges().getStartRes() + cWidth - 1);
449 int maxwidth = av.getAlignment().getWidth() - 1;
451 if (av.hasHiddenColumns())
453 maxwidth = av.getAlignment().getHiddenColumns()
454 .findColumnPosition(maxwidth) - 1;
457 while ((ypos <= canvasHeight) && (startRes < maxwidth))
459 endx = startRes + cWidth - 1;
466 g.setColor(Color.black);
468 if (av.getScaleLeftWrapped())
470 drawWestScale(g, startRes, endx, ypos);
473 if (av.getScaleRightWrapped())
475 g.translate(canvasWidth - LABEL_EAST, 0);
476 drawEastScale(g, startRes, endx, ypos);
477 g.translate(-(canvasWidth - LABEL_EAST), 0);
480 g.translate(LABEL_WEST, 0);
482 if (av.getScaleAboveWrapped())
484 drawNorthScale(g, startRes, endx, ypos);
486 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
488 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
489 g.setColor(Color.blue);
491 List<Integer> positions = hidden.findHiddenRegionPositions();
492 for (int pos : positions)
494 res = pos - startRes;
496 if (res < 0 || res > endx - startRes)
501 gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
502 res * avcharWidth + avcharHeight / 4, res * avcharWidth },
503 new int[] { ypos - (avcharHeight / 2),
504 ypos - (avcharHeight / 2),
505 ypos - (avcharHeight / 2) + 8 }, 3);
510 if (g.getClip() == null)
512 g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
515 drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
518 if (av.isShowAnnotation())
520 g.translate(0, cHeight + ypos + 4);
521 if (annotations == null)
523 annotations = new AnnotationPanel(av);
526 annotations.drawComponent(g, startRes, endx + 1);
527 g.translate(0, -cHeight - ypos - 4);
529 g.translate(-LABEL_WEST, 0);
531 ypos += cHeight + getAnnotationHeight() + hgap;
538 AnnotationPanel annotations;
540 int getAnnotationHeight()
542 if (!av.isShowAnnotation())
547 if (annotations == null)
549 annotations = new AnnotationPanel(av);
552 return annotations.adjustPanelHeight();
555 private void drawPanel(Graphics g1, int startRes, int endRes,
556 int startSeq, int endSeq, int offset)
559 if (!av.hasHiddenColumns())
561 draw(g1, startRes, endRes, startSeq, endSeq, offset);
567 int blockStart = startRes;
568 int blockEnd = endRes;
570 if (av.hasHiddenColumns())
572 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
573 for (int[] region : hidden.getHiddenColumnsCopy())
575 int hideStart = region[0];
576 int hideEnd = region[1];
578 if (hideStart <= blockStart)
580 blockStart += (hideEnd - hideStart) + 1;
584 blockEnd = hideStart - 1;
586 g1.translate(screenY * avcharWidth, 0);
588 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
590 if (av.getShowHiddenMarkers())
592 g1.setColor(Color.blue);
593 g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
594 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
595 - 1, (endSeq - startSeq + 1) * avcharHeight
599 g1.translate(-screenY * avcharWidth, 0);
600 screenY += blockEnd - blockStart + 1;
601 blockStart = hideEnd + 1;
603 if (screenY > (endRes - startRes))
605 // already rendered last block
610 if (screenY <= (endRes - startRes))
612 // remaining visible region to render
613 blockEnd = blockStart + (endRes - startRes) - screenY;
614 g1.translate(screenY * avcharWidth, 0);
615 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
617 g1.translate(-screenY * avcharWidth, 0);
623 // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
624 // int x1, int x2, int y1, int y2, int startx, int starty,
625 void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
628 g.setFont(av.getFont());
629 sr.prepare(g, av.isRenderGaps());
633 // / First draw the sequences
634 // ///////////////////////////
635 for (int i = startSeq; i <= endSeq; i++)
637 nextSeq = av.getAlignment().getSequenceAt(i);
644 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
645 startRes, endRes, offset + ((i - startSeq) * avcharHeight));
647 if (av.isShowSequenceFeatures())
649 fr.drawSequence(g, nextSeq, startRes, endRes, offset
650 + ((i - startSeq) * avcharHeight), false);
653 // / Highlight search Results once all sequences have been drawn
654 // ////////////////////////////////////////////////////////
655 if (av.hasSearchResults())
657 int[] visibleResults = av.getSearchResults().getResults(nextSeq,
660 if (visibleResults != null)
662 for (int r = 0; r < visibleResults.length; r += 2)
664 sr.drawHighlightedText(nextSeq, visibleResults[r],
665 visibleResults[r + 1], (visibleResults[r] - startRes)
666 * avcharWidth, offset
667 + ((i - startSeq) * avcharHeight));
672 if (av.cursorMode && cursorY == i && cursorX >= startRes
673 && cursorX <= endRes)
675 sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
676 offset + ((i - startSeq) * avcharHeight));
680 if (av.getSelectionGroup() != null
681 || av.getAlignment().getGroups().size() > 0)
683 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
688 private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
689 int startSeq, int endSeq, int offset)
692 // ///////////////////////////////////
693 // Now outline any areas if necessary
694 // ///////////////////////////////////
695 SequenceGroup group = av.getSelectionGroup();
702 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
704 group = av.getAlignment().getGroups().get(0);
714 boolean inGroup = false;
717 int alHeight = av.getAlignment().getHeight() - 1;
719 for (i = startSeq; i <= endSeq; i++)
721 sx = (group.getStartRes() - startRes) * avcharWidth;
722 sy = offset + ((i - startSeq) * avcharHeight);
723 ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;
725 if (sx + ex < 0 || sx > imgWidth)
730 if ((sx <= (endRes - startRes) * avcharWidth)
731 && group.getSequences(null).contains(
732 av.getAlignment().getSequenceAt(i)))
735 && (i >= alHeight || !group.getSequences(null)
737 av.getAlignment().getSequenceAt(i + 1))))
739 bottom = sy + avcharHeight;
744 if (((top == -1) && (i == 0))
745 || !group.getSequences(null).contains(
746 av.getAlignment().getSequenceAt(i - 1)))
754 if (group == av.getSelectionGroup())
756 g.setColor(Color.red);
760 g.setColor(group.getOutlineColour());
768 if (sx >= 0 && sx < imgWidth)
770 g.drawLine(sx, oldY, sx, sy);
773 if (sx + ex < imgWidth)
775 g.drawLine(sx + ex, oldY, sx + ex, sy);
784 if (sx + ex > imgWidth)
789 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
791 ex = (endRes - startRes + 1) * avcharWidth;
796 g.drawLine(sx, top, sx + ex, top);
802 g.drawLine(sx, bottom, sx + ex, bottom);
813 sy = offset + ((i - startSeq) * avcharHeight);
814 if (sx >= 0 && sx < imgWidth)
816 g.drawLine(sx, oldY, sx, sy);
819 if (sx + ex < imgWidth)
821 g.drawLine(sx + ex, oldY, sx + ex, sy);
830 if (sx + ex > imgWidth)
834 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
836 ex = (endRes - startRes + 1) * avcharWidth;
841 g.drawLine(sx, top, sx + ex, top);
847 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
856 if (groupIndex >= av.getAlignment().getGroups().size())
861 group = av.getAlignment().getGroups().get(groupIndex);
862 } while (groupIndex < av.getAlignment().getGroups().size());
867 public void highlightSearchResults(SearchResultsI results)
869 av.setSearchResults(results);
874 public void propertyChange(PropertyChangeEvent evt)
876 String eventName = evt.getPropertyName();
878 if (!av.getWrapAlignment())
881 if (eventName.equals(ViewportRanges.STARTRES))
883 // Make sure we're not trying to draw a panel
884 // larger than the visible window
885 ViewportRanges vpRanges = av.getRanges();
886 scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
887 int range = vpRanges.getEndRes() - vpRanges.getStartRes();
892 else if (scrollX < -range)
898 // Both scrolling and resizing change viewport ranges: scrolling changes
899 // both start and end points, but resize only changes end values.
900 // Here we only want to fastpaint on a scroll, with resize using a normal
901 // paint, so scroll events are identified as changes to the horizontal or
902 // vertical start value.
903 if (eventName.equals(ViewportRanges.STARTRES))
905 // scroll - startres and endres both change
906 fastPaint(scrollX, 0);
908 else if (eventName.equals(ViewportRanges.STARTSEQ))
911 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());