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,
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 List<Integer> positions = hidden.findHiddenRegionPositions(startRes,
496 for (int pos : positions)
498 res = pos - startRes;
502 { res * avcharWidth - avcharHeight / 4,
503 res * avcharWidth + avcharHeight / 4,
506 { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
507 ypos - (avcharHeight / 2) + 8 },
512 if (g.getClip() == null)
514 g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
517 drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
520 if (av.isShowAnnotation())
522 g.translate(0, cHeight + ypos + 4);
523 if (annotations == null)
525 annotations = new AnnotationPanel(av);
528 annotations.drawComponent(g, startRes, endx + 1);
529 g.translate(0, -cHeight - ypos - 4);
531 g.translate(-LABEL_WEST, 0);
533 ypos += cHeight + getAnnotationHeight() + hgap;
540 AnnotationPanel annotations;
542 int getAnnotationHeight()
544 if (!av.isShowAnnotation())
549 if (annotations == null)
551 annotations = new AnnotationPanel(av);
554 return annotations.adjustPanelHeight();
557 private void drawPanel(Graphics g1, final int startRes, final int endRes,
558 final int startSeq, final int endSeq, final int offset)
561 if (!av.hasHiddenColumns())
563 draw(g1, startRes, endRes, startSeq, endSeq, offset);
568 final int screenYMax = endRes - startRes;
569 int blockStart = startRes;
570 int blockEnd = endRes;
572 if (av.hasHiddenColumns())
574 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
575 for (int[] region : hidden.getHiddenColumnsCopy())
577 int hideStart = region[0];
578 int hideEnd = region[1];
580 if (hideStart <= blockStart)
582 blockStart += (hideEnd - hideStart) + 1;
587 * draw up to just before the next hidden region, or the end of
588 * the visible region, whichever comes first
590 blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
593 g1.translate(screenY * avcharWidth, 0);
595 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
598 * draw the downline of the hidden column marker (ScalePanel draws the
599 * triangle on top) if we reached it
601 if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
603 g1.setColor(Color.blue);
604 g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
606 (blockEnd - blockStart + 1) * avcharWidth - 1,
607 (endSeq - startSeq + 1) * avcharHeight + offset);
610 g1.translate(-screenY * avcharWidth, 0);
611 screenY += blockEnd - blockStart + 1;
612 blockStart = hideEnd + 1;
614 if (screenY > screenYMax)
616 // already rendered last block
621 if (screenY <= screenYMax)
623 // remaining visible region to render
624 blockEnd = blockStart + (endRes - startRes) - screenY;
625 g1.translate(screenY * avcharWidth, 0);
626 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
628 g1.translate(-screenY * avcharWidth, 0);
634 // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
635 // int x1, int x2, int y1, int y2, int startx, int starty,
636 void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
639 g.setFont(av.getFont());
640 sr.prepare(g, av.isRenderGaps());
644 // / First draw the sequences
645 // ///////////////////////////
646 for (int i = startSeq; i <= endSeq; i++)
648 nextSeq = av.getAlignment().getSequenceAt(i);
655 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
656 startRes, endRes, offset + ((i - startSeq) * avcharHeight));
658 if (av.isShowSequenceFeatures())
660 fr.drawSequence(g, nextSeq, startRes, endRes,
661 offset + ((i - startSeq) * avcharHeight), false);
664 // / Highlight search Results once all sequences have been drawn
665 // ////////////////////////////////////////////////////////
666 if (av.hasSearchResults())
668 int[] visibleResults = av.getSearchResults().getResults(nextSeq,
670 if (visibleResults != null)
672 for (int r = 0; r < visibleResults.length; r += 2)
674 sr.drawHighlightedText(nextSeq, visibleResults[r],
675 visibleResults[r + 1],
676 (visibleResults[r] - startRes) * avcharWidth,
677 offset + ((i - startSeq) * avcharHeight));
682 if (av.cursorMode && cursorY == i && cursorX >= startRes
683 && cursorX <= endRes)
685 sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
686 offset + ((i - startSeq) * avcharHeight));
690 if (av.getSelectionGroup() != null
691 || av.getAlignment().getGroups().size() > 0)
693 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
698 private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
699 int startSeq, int endSeq, int offset)
702 // ///////////////////////////////////
703 // Now outline any areas if necessary
704 // ///////////////////////////////////
705 SequenceGroup group = av.getSelectionGroup();
712 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
714 group = av.getAlignment().getGroups().get(0);
724 boolean inGroup = false;
727 int alHeight = av.getAlignment().getHeight() - 1;
729 for (i = startSeq; i <= endSeq; i++)
731 sx = (group.getStartRes() - startRes) * avcharWidth;
732 sy = offset + ((i - startSeq) * avcharHeight);
733 ex = (((group.getEndRes() + 1) - group.getStartRes())
736 if (sx + ex < 0 || sx > imgWidth)
741 if ((sx <= (endRes - startRes) * avcharWidth)
742 && group.getSequences(null)
743 .contains(av.getAlignment().getSequenceAt(i)))
746 && (i >= alHeight || !group.getSequences(null).contains(
747 av.getAlignment().getSequenceAt(i + 1))))
749 bottom = sy + avcharHeight;
754 if (((top == -1) && (i == 0)) || !group.getSequences(null)
755 .contains(av.getAlignment().getSequenceAt(i - 1)))
763 if (group == av.getSelectionGroup())
765 g.setColor(Color.red);
769 g.setColor(group.getOutlineColour());
777 if (sx >= 0 && sx < imgWidth)
779 g.drawLine(sx, oldY, sx, sy);
782 if (sx + ex < imgWidth)
784 g.drawLine(sx + ex, oldY, sx + ex, sy);
793 if (sx + ex > imgWidth)
798 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
800 ex = (endRes - startRes + 1) * avcharWidth;
805 g.drawLine(sx, top, sx + ex, top);
811 g.drawLine(sx, bottom, sx + ex, bottom);
822 sy = offset + ((i - startSeq) * avcharHeight);
823 if (sx >= 0 && sx < imgWidth)
825 g.drawLine(sx, oldY, sx, sy);
828 if (sx + ex < imgWidth)
830 g.drawLine(sx + ex, oldY, sx + ex, sy);
839 if (sx + ex > imgWidth)
843 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
845 ex = (endRes - startRes + 1) * avcharWidth;
850 g.drawLine(sx, top, sx + ex, top);
856 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
865 if (groupIndex >= av.getAlignment().getGroups().size())
870 group = av.getAlignment().getGroups().get(groupIndex);
871 } while (groupIndex < av.getAlignment().getGroups().size());
876 public void highlightSearchResults(SearchResultsI results)
878 av.setSearchResults(results);
883 public void propertyChange(PropertyChangeEvent evt)
885 String eventName = evt.getPropertyName();
887 if (!av.getWrapAlignment())
890 if (eventName.equals(ViewportRanges.STARTRES))
892 // Make sure we're not trying to draw a panel
893 // larger than the visible window
894 ViewportRanges vpRanges = av.getRanges();
895 scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
896 int range = vpRanges.getEndRes() - vpRanges.getStartRes();
901 else if (scrollX < -range)
907 // Both scrolling and resizing change viewport ranges: scrolling changes
908 // both start and end points, but resize only changes end values.
909 // Here we only want to fastpaint on a scroll, with resize using a normal
910 // paint, so scroll events are identified as changes to the horizontal or
911 // vertical start value.
912 if (eventName.equals(ViewportRanges.STARTRES))
914 // scroll - startres and endres both change
915 fastPaint(scrollX, 0);
917 else if (eventName.equals(ViewportRanges.STARTSEQ))
920 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());