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.SearchResults;
25 import jalview.datamodel.SequenceGroup;
26 import jalview.datamodel.SequenceI;
27 import jalview.util.Comparison;
28 import jalview.viewmodel.AlignmentViewport;
30 import java.awt.Color;
31 import java.awt.FontMetrics;
32 import java.awt.Graphics;
33 import java.awt.Image;
34 import awt2swing.Panel;
36 public class SeqCanvas extends Panel
52 SearchResults searchResults = null;
54 boolean fastPaint = false;
60 public SeqCanvas(AlignViewport av)
63 fr = new FeatureRenderer(av);
64 sr = new SequenceRenderer(av);
65 PaintRefresher.Register(this, av.getSequenceSetId());
69 int avcharHeight = 0, avcharWidth = 0;
71 private void updateViewport()
73 avcharHeight = av.getCharHeight();
74 avcharWidth = av.getCharWidth();
77 public AlignmentViewport getViewport()
82 public FeatureRenderer getFeatureRenderer()
87 public SequenceRenderer getSequenceRenderer()
92 private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
94 int scalestartx = startx - startx % 10 + 10;
96 g.setColor(Color.black);
99 for (int i = scalestartx; i < endx; i += 10)
102 if (av.hasHiddenColumns())
104 value = av.getColumnSelection().adjustForHiddenColumns(value);
107 g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth,
108 ypos - (avcharHeight / 2));
110 g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
111 (ypos + 2) - (avcharHeight / 2),
112 ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
117 private void drawWestScale(Graphics g, int startx, int endx, int ypos)
119 FontMetrics fm = getFontMetrics(av.getFont());
120 ypos += avcharHeight;
121 if (av.hasHiddenColumns())
123 startx = av.getColumnSelection().adjustForHiddenColumns(startx);
124 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
127 int maxwidth = av.getAlignment().getWidth();
128 if (av.hasHiddenColumns())
130 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
134 for (int i = 0; i < av.getAlignment().getHeight(); i++)
136 SequenceI seq = av.getAlignment().getSequenceAt(i);
142 if (Comparison.isGap(seq.getCharAt(index)))
149 value = av.getAlignment().getSequenceAt(i).findPosition(index);
156 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
158 g.drawString(value + "", x, (ypos + (i * avcharHeight))
159 - (avcharHeight / 5));
164 private void drawEastScale(Graphics g, int startx, int endx, int ypos)
166 ypos += avcharHeight;
168 if (av.hasHiddenColumns())
170 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
175 for (int i = 0; i < av.getAlignment().getHeight(); i++)
177 seq = av.getAlignment().getSequenceAt(i);
181 while (index > startx)
183 if (Comparison.isGap(seq.getCharAt(index)))
190 value = seq.findPosition(index);
197 g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight))
198 - (avcharHeight / 5));
205 void fastPaint(int horizontal, int vertical)
207 if (fastPaint || gg == null)
214 // Its possible on certain browsers that the call to fastpaint
215 // is faster than it can paint, so this check here catches
217 if (lastsr + horizontal != av.startRes)
219 horizontal = av.startRes - lastsr;
222 lastsr = av.startRes;
225 gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
226 - horizontal * avcharWidth,
227 imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
228 -vertical * avcharHeight);
230 int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
232 if (horizontal > 0) // scrollbar pulled right, image to the left
234 transX = (er - sr - horizontal) * avcharWidth;
235 sr = er - horizontal;
237 else if (horizontal < 0)
239 er = sr - horizontal;
242 else if (vertical > 0) // scroll down
245 if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
251 transY = imgHeight - vertical * avcharHeight;
254 else if (vertical < 0)
263 gg.translate(transX, transY);
265 drawPanel(gg, sr, er, ss, es, 0);
266 gg.translate(-transX, -transY);
273 * Definitions of startx and endx (hopefully): SMJS This is what I'm working
274 * towards! startx is the first residue (starting at 0) to display. endx is
275 * the last residue to display (starting at 0). starty is the first sequence
276 * to display (starting at 0). endy is the last sequence to display (starting
277 * at 0). NOTE 1: The av limits are set in setFont in this class and in the
278 * adjustment listener in SeqPanel when the scrollbars move.
282 public void paintComponent(Graphics g)
285 && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
286 .getClipBounds().height)))
288 g.drawImage(img, 0, 0, this);
295 g.drawImage(img, 0, 0, this);
301 // this draws the whole of the alignment
302 imgWidth = this.getSize().width;
303 imgHeight = this.getSize().height;
305 imgWidth -= imgWidth % avcharWidth;
306 imgHeight -= imgHeight % avcharHeight;
308 if (imgWidth < 1 || imgHeight < 1)
313 if (img == null || imgWidth != img.getWidth(this)
314 || imgHeight != img.getHeight(this))
316 img = createImage(imgWidth, imgHeight);
317 gg = img.getGraphics();
318 gg.setFont(av.getFont());
321 gg.setColor(Color.white);
322 gg.fillRect(0, 0, imgWidth, imgHeight);
324 if (av.getWrapAlignment())
326 drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
330 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
333 g.drawImage(img, 0, 0, this);
337 int LABEL_WEST, LABEL_EAST;
339 public int getWrappedCanvasWidth(int cwidth)
341 cwidth -= cwidth % av.getCharWidth();
343 FontMetrics fm = getFontMetrics(av.getFont());
348 if (av.getScaleRightWrapped())
350 LABEL_EAST = fm.stringWidth(getMask());
353 if (av.getScaleLeftWrapped())
355 LABEL_WEST = fm.stringWidth(getMask());
358 return (cwidth - LABEL_EAST - LABEL_WEST) / av.getCharWidth();
362 * Generates a string of zeroes.
371 AlignmentI alignment = av.getAlignment();
372 for (int i = 0; i < alignment.getHeight(); i++)
374 tmp = alignment.getSequenceAt(i).getEnd();
381 for (int i = maxWidth; i > 0; i /= 10)
388 private void drawWrappedPanel(Graphics g, int canvasWidth,
389 int canvasHeight, int startRes)
391 AlignmentI al = av.getAlignment();
393 FontMetrics fm = getFontMetrics(av.getFont());
395 if (av.getScaleRightWrapped())
397 LABEL_EAST = fm.stringWidth(getMask());
400 if (av.getScaleLeftWrapped())
402 LABEL_WEST = fm.stringWidth(getMask());
405 int hgap = avcharHeight;
406 if (av.getScaleAboveWrapped())
408 hgap += avcharHeight;
411 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
412 int cHeight = av.getAlignment().getHeight() * avcharHeight;
414 av.setWrappedWidth(cWidth);
416 av.endRes = av.startRes + cWidth;
421 int maxwidth = av.getAlignment().getWidth() - 1;
423 if (av.hasHiddenColumns())
425 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
428 while ((ypos <= canvasHeight) && (startRes < maxwidth))
430 endx = startRes + cWidth - 1;
437 g.setColor(Color.black);
439 if (av.getScaleLeftWrapped())
441 drawWestScale(g, startRes, endx, ypos);
444 if (av.getScaleRightWrapped())
446 g.translate(canvasWidth - LABEL_EAST, 0);
447 drawEastScale(g, startRes, endx, ypos);
448 g.translate(-(canvasWidth - LABEL_EAST), 0);
451 g.translate(LABEL_WEST, 0);
453 if (av.getScaleAboveWrapped())
455 drawNorthScale(g, startRes, endx, ypos);
457 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
459 g.setColor(Color.blue);
461 for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
464 res = av.getColumnSelection().findHiddenRegionPosition(i)
467 if (res < 0 || res > endx - startRes)
472 gg.fillPolygon(new int[]
473 { res * avcharWidth - avcharHeight / 4,
474 res * avcharWidth + avcharHeight / 4, res * avcharWidth },
476 { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
477 ypos - (avcharHeight / 2) + 8 }, 3);
482 if (g.getClip() == null)
484 g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
487 drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
490 if (av.isShowAnnotation())
492 g.translate(0, cHeight + ypos + 4);
493 if (annotations == null)
495 annotations = new AnnotationPanel(av);
498 annotations.drawComponent(g, startRes, endx + 1);
499 g.translate(0, -cHeight - ypos - 4);
501 g.translate(-LABEL_WEST, 0);
503 ypos += cHeight + getAnnotationHeight() + hgap;
510 AnnotationPanel annotations;
512 int getAnnotationHeight()
514 if (!av.isShowAnnotation())
519 if (annotations == null)
521 annotations = new AnnotationPanel(av);
524 return annotations.adjustPanelHeight();
527 private void drawPanel(Graphics g1, int startRes, int endRes,
529 int endSeq, int offset)
533 if (!av.hasHiddenColumns())
535 draw(g1, startRes, endRes, startSeq, endSeq, offset);
541 int blockStart = startRes;
542 int blockEnd = endRes;
544 if (av.hasHiddenColumns())
546 for (int[] region : av.getColumnSelection().getHiddenColumns())
548 int hideStart = region[0];
549 int hideEnd = region[1];
551 if (hideStart <= blockStart)
553 blockStart += (hideEnd - hideStart) + 1;
557 blockEnd = hideStart - 1;
559 g1.translate(screenY * avcharWidth, 0);
561 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
563 if (av.getShowHiddenMarkers())
565 g1.setColor(Color.blue);
566 g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
567 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
568 - 1, (endSeq - startSeq) * avcharHeight
572 g1.translate(-screenY * avcharWidth, 0);
573 screenY += blockEnd - blockStart + 1;
574 blockStart = hideEnd + 1;
577 if (screenY <= (endRes - startRes))
579 blockEnd = blockStart + (endRes - startRes) - screenY;
580 g1.translate(screenY * avcharWidth, 0);
581 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
583 g1.translate(-screenY * avcharWidth, 0);
589 // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
590 // int x1, int x2, int y1, int y2, int startx, int starty,
591 void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
594 g.setFont(av.getFont());
595 sr.prepare(g, av.isRenderGaps());
599 // / First draw the sequences
600 // ///////////////////////////
601 for (int i = startSeq; i < endSeq; i++)
603 nextSeq = av.getAlignment().getSequenceAt(i);
610 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
611 startRes, endRes, offset + ((i - startSeq) * avcharHeight));
613 if (av.isShowSequenceFeatures())
615 fr.drawSequence(g, nextSeq, startRes, endRes, offset
616 + ((i - startSeq) * avcharHeight));
619 // / Highlight search Results once all sequences have been drawn
620 // ////////////////////////////////////////////////////////
621 if (searchResults != null)
623 int[] visibleResults = searchResults.getResults(nextSeq, startRes,
625 if (visibleResults != null)
627 for (int r = 0; r < visibleResults.length; r += 2)
629 sr.drawHighlightedText(nextSeq, visibleResults[r],
630 visibleResults[r + 1], (visibleResults[r] - startRes)
631 * avcharWidth, offset
632 + ((i - startSeq) * avcharHeight));
637 if (av.cursorMode && cursorY == i && cursorX >= startRes
638 && cursorX <= endRes)
640 sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
641 offset + ((i - startSeq) * avcharHeight));
645 if (av.getSelectionGroup() != null
646 || av.getAlignment().getGroups().size() > 0)
648 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
653 private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
654 int startSeq, int endSeq, int offset)
657 // ///////////////////////////////////
658 // Now outline any areas if necessary
659 // ///////////////////////////////////
660 SequenceGroup group = av.getSelectionGroup();
667 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
669 group = av.getAlignment().getGroups().get(0);
679 boolean inGroup = false;
682 int alHeight = av.getAlignment().getHeight() - 1;
684 for (i = startSeq; i < endSeq; i++)
686 sx = (group.getStartRes() - startRes) * avcharWidth;
687 sy = offset + ((i - startSeq) * avcharHeight);
688 ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;
690 if (sx + ex < 0 || sx > imgWidth)
695 if ((sx <= (endRes - startRes) * avcharWidth)
696 && group.getSequences(null).contains(
697 av.getAlignment().getSequenceAt(i)))
700 && (i >= alHeight || !group.getSequences(null)
702 av.getAlignment().getSequenceAt(i + 1))))
704 bottom = sy + avcharHeight;
709 if (((top == -1) && (i == 0))
710 || !group.getSequences(null).contains(
711 av.getAlignment().getSequenceAt(i - 1)))
719 if (group == av.getSelectionGroup())
721 g.setColor(Color.red);
725 g.setColor(group.getOutlineColour());
733 if (sx >= 0 && sx < imgWidth)
735 g.drawLine(sx, oldY, sx, sy);
738 if (sx + ex < imgWidth)
740 g.drawLine(sx + ex, oldY, sx + ex, sy);
749 if (sx + ex > imgWidth)
754 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
756 ex = (endRes - startRes + 1) * avcharWidth;
761 g.drawLine(sx, top, sx + ex, top);
767 g.drawLine(sx, bottom, sx + ex, bottom);
778 sy = offset + ((i - startSeq) * avcharHeight);
779 if (sx >= 0 && sx < imgWidth)
781 g.drawLine(sx, oldY, sx, sy);
784 if (sx + ex < imgWidth)
786 g.drawLine(sx + ex, oldY, sx + ex, sy);
795 if (sx + ex > imgWidth)
799 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
801 ex = (endRes - startRes + 1) * avcharWidth;
806 g.drawLine(sx, top, sx + ex, top);
812 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
821 if (groupIndex >= av.getAlignment().getGroups().size())
826 group = av.getAlignment().getGroups()
828 } while (groupIndex < av.getAlignment().getGroups().size());
833 public void highlightSearchResults(SearchResults results)
835 searchResults = results;