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 HiddenColumns hidden = av.getAlignment().getHiddenColumns();
568 Iterator<int[]> regions = hidden.getBoundedVisRegionIterator(startRes,
570 while (regions.hasNext())
572 int[] region = regions.next();
574 blockStart = region[0];
577 * draw up to just before the next hidden region, or the end of
578 * the visible region, whichever comes first
580 blockEnd = Math.min(region[1], blockStart + screenYMax - screenY);
582 g1.translate(screenY * avcharWidth, 0);
584 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
587 * draw the downline of the hidden column marker (ScalePanel draws the
588 * triangle on top) if we reached it
590 if (av.getShowHiddenMarkers() && blockEnd == region[1])
592 g1.setColor(Color.blue);
593 g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
594 0 + offset, (blockEnd - blockStart + 1) * avcharWidth - 1,
595 (endSeq - startSeq + 1) * avcharHeight + offset);
598 g1.translate(-screenY * avcharWidth, 0);
599 screenY += blockEnd - blockStart + 1;
601 if (screenY > screenYMax)
603 // already rendered last block
607 if (screenY <= screenYMax)
609 // remaining visible region to render
610 blockEnd = blockStart + (endRes - startRes) - screenY;
611 g1.translate(screenY * avcharWidth, 0);
612 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
614 g1.translate(-screenY * avcharWidth, 0);
620 // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
621 // int x1, int x2, int y1, int y2, int startx, int starty,
622 void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
625 g.setFont(av.getFont());
626 sr.prepare(g, av.isRenderGaps());
630 // / First draw the sequences
631 // ///////////////////////////
632 for (int i = startSeq; i <= endSeq; i++)
634 nextSeq = av.getAlignment().getSequenceAt(i);
641 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
642 startRes, endRes, offset + ((i - startSeq) * avcharHeight));
644 if (av.isShowSequenceFeatures())
646 fr.drawSequence(g, nextSeq, startRes, endRes,
647 offset + ((i - startSeq) * avcharHeight), false);
650 // / Highlight search Results once all sequences have been drawn
651 // ////////////////////////////////////////////////////////
652 if (av.hasSearchResults())
654 int[] visibleResults = av.getSearchResults().getResults(nextSeq,
656 if (visibleResults != null)
658 for (int r = 0; r < visibleResults.length; r += 2)
660 sr.drawHighlightedText(nextSeq, visibleResults[r],
661 visibleResults[r + 1],
662 (visibleResults[r] - startRes) * avcharWidth,
663 offset + ((i - startSeq) * avcharHeight));
668 if (av.cursorMode && cursorY == i && cursorX >= startRes
669 && cursorX <= endRes)
671 sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
672 offset + ((i - startSeq) * avcharHeight));
676 if (av.getSelectionGroup() != null
677 || av.getAlignment().getGroups().size() > 0)
679 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
684 private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
685 int startSeq, int endSeq, int offset)
688 // ///////////////////////////////////
689 // Now outline any areas if necessary
690 // ///////////////////////////////////
691 SequenceGroup group = av.getSelectionGroup();
698 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
700 group = av.getAlignment().getGroups().get(0);
710 boolean inGroup = false;
713 int alHeight = av.getAlignment().getHeight() - 1;
715 for (i = startSeq; i <= endSeq; i++)
717 sx = (group.getStartRes() - startRes) * avcharWidth;
718 sy = offset + ((i - startSeq) * avcharHeight);
719 ex = (((group.getEndRes() + 1) - group.getStartRes())
722 if (sx + ex < 0 || sx > imgWidth)
727 if ((sx <= (endRes - startRes) * avcharWidth)
728 && group.getSequences(null)
729 .contains(av.getAlignment().getSequenceAt(i)))
732 && (i >= alHeight || !group.getSequences(null).contains(
733 av.getAlignment().getSequenceAt(i + 1))))
735 bottom = sy + avcharHeight;
740 if (((top == -1) && (i == 0)) || !group.getSequences(null)
741 .contains(av.getAlignment().getSequenceAt(i - 1)))
749 if (group == av.getSelectionGroup())
751 g.setColor(Color.red);
755 g.setColor(group.getOutlineColour());
763 if (sx >= 0 && sx < imgWidth)
765 g.drawLine(sx, oldY, sx, sy);
768 if (sx + ex < imgWidth)
770 g.drawLine(sx + ex, oldY, sx + ex, sy);
779 if (sx + ex > imgWidth)
784 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
786 ex = (endRes - startRes + 1) * avcharWidth;
791 g.drawLine(sx, top, sx + ex, top);
797 g.drawLine(sx, bottom, sx + ex, bottom);
808 sy = offset + ((i - startSeq) * avcharHeight);
809 if (sx >= 0 && sx < imgWidth)
811 g.drawLine(sx, oldY, sx, sy);
814 if (sx + ex < imgWidth)
816 g.drawLine(sx + ex, oldY, sx + ex, sy);
825 if (sx + ex > imgWidth)
829 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
831 ex = (endRes - startRes + 1) * avcharWidth;
836 g.drawLine(sx, top, sx + ex, top);
842 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
851 if (groupIndex >= av.getAlignment().getGroups().size())
856 group = av.getAlignment().getGroups().get(groupIndex);
857 } while (groupIndex < av.getAlignment().getGroups().size());
862 public void highlightSearchResults(SearchResultsI results)
864 av.setSearchResults(results);
869 public void propertyChange(PropertyChangeEvent evt)
871 String eventName = evt.getPropertyName();
873 if (!av.getWrapAlignment())
876 if (eventName.equals(ViewportRanges.STARTRES))
878 // Make sure we're not trying to draw a panel
879 // larger than the visible window
880 ViewportRanges vpRanges = av.getRanges();
881 scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
882 int range = vpRanges.getEndRes() - vpRanges.getStartRes();
887 else if (scrollX < -range)
893 // Both scrolling and resizing change viewport ranges: scrolling changes
894 // both start and end points, but resize only changes end values.
895 // Here we only want to fastpaint on a scroll, with resize using a normal
896 // paint, so scroll events are identified as changes to the horizontal or
897 // vertical start value.
898 if (eventName.equals(ViewportRanges.STARTRES))
900 // scroll - startres and endres both change
901 fastPaint(scrollX, 0);
903 else if (eventName.equals(ViewportRanges.STARTSEQ))
906 fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());