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.viewmodel.AlignmentViewport;
29 import java.awt.Color;
30 import java.awt.FontMetrics;
31 import java.awt.Graphics;
32 import java.awt.Image;
33 import java.awt.Panel;
35 public class SeqCanvas extends Panel
51 SearchResults searchResults = null;
53 boolean fastPaint = false;
59 public SeqCanvas(AlignViewport av)
62 fr = new FeatureRenderer(av);
63 sr = new SequenceRenderer(av);
64 PaintRefresher.Register(this, av.getSequenceSetId());
68 int avcharHeight = 0, avcharWidth = 0;
70 private void updateViewport()
72 avcharHeight = av.getCharHeight();
73 avcharWidth = av.getCharWidth();
76 public AlignmentViewport getViewport()
81 public FeatureRenderer getFeatureRenderer()
86 public SequenceRenderer getSequenceRenderer()
91 private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
93 int scalestartx = startx - startx % 10 + 10;
95 g.setColor(Color.black);
98 for (int i = scalestartx; i < endx; i += 10)
101 if (av.hasHiddenColumns())
103 value = av.getColumnSelection().adjustForHiddenColumns(value);
106 g.drawString(String.valueOf(value), (i - startx - 1) * avcharWidth,
107 ypos - (avcharHeight / 2));
109 g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
110 (ypos + 2) - (avcharHeight / 2),
111 ((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
116 private void drawWestScale(Graphics g, int startx, int endx, int ypos)
118 FontMetrics fm = getFontMetrics(av.getFont());
119 ypos += avcharHeight;
120 if (av.hasHiddenColumns())
122 startx = av.getColumnSelection().adjustForHiddenColumns(startx);
123 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
126 int maxwidth = av.getAlignment().getWidth();
127 if (av.hasHiddenColumns())
129 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
133 for (int i = 0; i < av.getAlignment().getHeight(); i++)
135 SequenceI seq = av.getAlignment().getSequenceAt(i);
141 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
148 value = av.getAlignment().getSequenceAt(i).findPosition(index);
155 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
157 g.drawString(value + "", x, (ypos + (i * avcharHeight))
158 - (avcharHeight / 5));
163 private void drawEastScale(Graphics g, int startx, int endx, int ypos)
165 ypos += avcharHeight;
167 if (av.hasHiddenColumns())
169 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
174 for (int i = 0; i < av.getAlignment().getHeight(); i++)
176 seq = av.getAlignment().getSequenceAt(i);
180 while (index > startx)
182 if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
189 value = seq.findPosition(index);
196 g.drawString(String.valueOf(value), 0, (ypos + (i * avcharHeight))
197 - (avcharHeight / 5));
204 void fastPaint(int horizontal, int vertical)
206 if (fastPaint || gg == null)
213 // Its possible on certain browsers that the call to fastpaint
214 // is faster than it can paint, so this check here catches
216 if (lastsr + horizontal != av.startRes)
218 horizontal = av.startRes - lastsr;
221 lastsr = av.startRes;
224 gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight, imgWidth
225 - horizontal * avcharWidth,
226 imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
227 -vertical * avcharHeight);
229 int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
231 if (horizontal > 0) // scrollbar pulled right, image to the left
233 transX = (er - sr - horizontal) * avcharWidth;
234 sr = er - horizontal;
236 else if (horizontal < 0)
238 er = sr - horizontal;
241 else if (vertical > 0) // scroll down
244 if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
250 transY = imgHeight - vertical * avcharHeight;
253 else if (vertical < 0)
262 gg.translate(transX, transY);
264 drawPanel(gg, sr, er, ss, es, 0);
265 gg.translate(-transX, -transY);
272 * Definitions of startx and endx (hopefully): SMJS This is what I'm working
273 * towards! startx is the first residue (starting at 0) to display. endx is
274 * the last residue to display (starting at 0). starty is the first sequence
275 * to display (starting at 0). endy is the last sequence to display (starting
276 * at 0). NOTE 1: The av limits are set in setFont in this class and in the
277 * adjustment listener in SeqPanel when the scrollbars move.
280 public void update(Graphics g)
286 public void paint(Graphics g)
290 && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
291 .getClipBounds().height)))
293 g.drawImage(img, 0, 0, this);
300 g.drawImage(img, 0, 0, this);
306 // this draws the whole of the alignment
307 imgWidth = this.getSize().width;
308 imgHeight = this.getSize().height;
310 imgWidth -= imgWidth % avcharWidth;
311 imgHeight -= imgHeight % avcharHeight;
313 if (imgWidth < 1 || imgHeight < 1)
318 if (img == null || imgWidth != img.getWidth(this)
319 || imgHeight != img.getHeight(this))
321 img = createImage(imgWidth, imgHeight);
322 gg = img.getGraphics();
323 gg.setFont(av.getFont());
326 gg.setColor(Color.white);
327 gg.fillRect(0, 0, imgWidth, imgHeight);
329 if (av.getWrapAlignment())
331 drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
335 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
338 g.drawImage(img, 0, 0, this);
342 int LABEL_WEST, LABEL_EAST;
344 public int getWrappedCanvasWidth(int cwidth)
346 cwidth -= cwidth % av.getCharWidth();
348 FontMetrics fm = getFontMetrics(av.getFont());
353 if (av.getScaleRightWrapped())
355 LABEL_EAST = fm.stringWidth(getMask());
358 if (av.getScaleLeftWrapped())
360 LABEL_WEST = fm.stringWidth(getMask());
363 return (cwidth - LABEL_EAST - LABEL_WEST) / av.getCharWidth();
367 * Generates a string of zeroes.
376 AlignmentI alignment = av.getAlignment();
377 for (int i = 0; i < alignment.getHeight(); i++)
379 tmp = alignment.getSequenceAt(i).getEnd();
386 for (int i = maxWidth; i > 0; i /= 10)
393 private void drawWrappedPanel(Graphics g, int canvasWidth,
394 int canvasHeight, int startRes)
396 AlignmentI al = av.getAlignment();
398 FontMetrics fm = getFontMetrics(av.getFont());
400 if (av.getScaleRightWrapped())
402 LABEL_EAST = fm.stringWidth(getMask());
405 if (av.getScaleLeftWrapped())
407 LABEL_WEST = fm.stringWidth(getMask());
410 int hgap = avcharHeight;
411 if (av.getScaleAboveWrapped())
413 hgap += avcharHeight;
416 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
417 int cHeight = av.getAlignment().getHeight() * avcharHeight;
419 av.setWrappedWidth(cWidth);
421 av.endRes = av.startRes + cWidth;
426 int maxwidth = av.getAlignment().getWidth() - 1;
428 if (av.hasHiddenColumns())
430 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
433 while ((ypos <= canvasHeight) && (startRes < maxwidth))
435 endx = startRes + cWidth - 1;
442 g.setColor(Color.black);
444 if (av.getScaleLeftWrapped())
446 drawWestScale(g, startRes, endx, ypos);
449 if (av.getScaleRightWrapped())
451 g.translate(canvasWidth - LABEL_EAST, 0);
452 drawEastScale(g, startRes, endx, ypos);
453 g.translate(-(canvasWidth - LABEL_EAST), 0);
456 g.translate(LABEL_WEST, 0);
458 if (av.getScaleAboveWrapped())
460 drawNorthScale(g, startRes, endx, ypos);
462 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
464 g.setColor(Color.blue);
466 for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
469 res = av.getColumnSelection().findHiddenRegionPosition(i)
472 if (res < 0 || res > endx - startRes)
477 gg.fillPolygon(new int[] { res * avcharWidth - avcharHeight / 4,
478 res * avcharWidth + avcharHeight / 4, res * avcharWidth },
479 new int[] { ypos - (avcharHeight / 2),
480 ypos - (avcharHeight / 2),
481 ypos - (avcharHeight / 2) + 8 }, 3);
486 if (g.getClip() == null)
488 g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
491 drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
494 if (av.isShowAnnotation())
496 g.translate(0, cHeight + ypos + 4);
497 if (annotations == null)
499 annotations = new AnnotationPanel(av);
502 annotations.drawComponent(g, startRes, endx + 1);
503 g.translate(0, -cHeight - ypos - 4);
505 g.translate(-LABEL_WEST, 0);
507 ypos += cHeight + getAnnotationHeight() + hgap;
514 AnnotationPanel annotations;
516 int getAnnotationHeight()
518 if (!av.isShowAnnotation())
523 if (annotations == null)
525 annotations = new AnnotationPanel(av);
528 return annotations.adjustPanelHeight();
531 private void drawPanel(Graphics g1, int startRes, int endRes,
532 int startSeq, int endSeq, int offset)
535 if (!av.hasHiddenColumns())
537 draw(g1, startRes, endRes, startSeq, endSeq, offset);
543 int blockStart = startRes;
544 int blockEnd = endRes;
546 if (av.hasHiddenColumns())
548 for (int[] region : av.getColumnSelection().getHiddenColumns())
550 int hideStart = region[0];
551 int hideEnd = region[1];
553 if (hideStart <= blockStart)
555 blockStart += (hideEnd - hideStart) + 1;
559 blockEnd = hideStart - 1;
561 g1.translate(screenY * avcharWidth, 0);
563 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
565 if (av.getShowHiddenMarkers())
567 g1.setColor(Color.blue);
568 g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
569 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
570 - 1, (endSeq - startSeq) * avcharHeight
574 g1.translate(-screenY * avcharWidth, 0);
575 screenY += blockEnd - blockStart + 1;
576 blockStart = hideEnd + 1;
578 if (screenY > (endRes - startRes))
580 // already rendered last block
585 if (screenY <= (endRes - startRes))
587 // remaining visible region to render
588 blockEnd = blockStart + (endRes - startRes) - screenY;
589 g1.translate(screenY * avcharWidth, 0);
590 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
592 g1.translate(-screenY * avcharWidth, 0);
598 // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
599 // int x1, int x2, int y1, int y2, int startx, int starty,
600 void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
603 g.setFont(av.getFont());
604 sr.prepare(g, av.isRenderGaps());
608 // / First draw the sequences
609 // ///////////////////////////
610 for (int i = startSeq; i < endSeq; i++)
612 nextSeq = av.getAlignment().getSequenceAt(i);
619 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
620 startRes, endRes, offset + ((i - startSeq) * avcharHeight));
622 if (av.isShowSequenceFeatures())
624 fr.drawSequence(g, nextSeq, startRes, endRes, offset
625 + ((i - startSeq) * avcharHeight));
628 // / Highlight search Results once all sequences have been drawn
629 // ////////////////////////////////////////////////////////
630 if (searchResults != null)
632 int[] visibleResults = searchResults.getResults(nextSeq, startRes,
634 if (visibleResults != null)
636 for (int r = 0; r < visibleResults.length; r += 2)
638 sr.drawHighlightedText(nextSeq, visibleResults[r],
639 visibleResults[r + 1], (visibleResults[r] - startRes)
640 * avcharWidth, offset
641 + ((i - startSeq) * avcharHeight));
646 if (av.cursorMode && cursorY == i && cursorX >= startRes
647 && cursorX <= endRes)
649 sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
650 offset + ((i - startSeq) * avcharHeight));
654 if (av.getSelectionGroup() != null
655 || av.getAlignment().getGroups().size() > 0)
657 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
662 private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
663 int startSeq, int endSeq, int offset)
666 // ///////////////////////////////////
667 // Now outline any areas if necessary
668 // ///////////////////////////////////
669 SequenceGroup group = av.getSelectionGroup();
676 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
678 group = av.getAlignment().getGroups().get(0);
688 boolean inGroup = false;
691 int alHeight = av.getAlignment().getHeight() - 1;
693 for (i = startSeq; i < endSeq; i++)
695 sx = (group.getStartRes() - startRes) * avcharWidth;
696 sy = offset + ((i - startSeq) * avcharHeight);
697 ex = (((group.getEndRes() + 1) - group.getStartRes()) * avcharWidth) - 1;
699 if (sx + ex < 0 || sx > imgWidth)
704 if ((sx <= (endRes - startRes) * avcharWidth)
705 && group.getSequences(null).contains(
706 av.getAlignment().getSequenceAt(i)))
709 && (i >= alHeight || !group.getSequences(null)
711 av.getAlignment().getSequenceAt(i + 1))))
713 bottom = sy + avcharHeight;
718 if (((top == -1) && (i == 0))
719 || !group.getSequences(null).contains(
720 av.getAlignment().getSequenceAt(i - 1)))
728 if (group == av.getSelectionGroup())
730 g.setColor(Color.red);
734 g.setColor(group.getOutlineColour());
742 if (sx >= 0 && sx < imgWidth)
744 g.drawLine(sx, oldY, sx, sy);
747 if (sx + ex < imgWidth)
749 g.drawLine(sx + ex, oldY, sx + ex, sy);
758 if (sx + ex > imgWidth)
763 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
765 ex = (endRes - startRes + 1) * avcharWidth;
770 g.drawLine(sx, top, sx + ex, top);
776 g.drawLine(sx, bottom, sx + ex, bottom);
787 sy = offset + ((i - startSeq) * avcharHeight);
788 if (sx >= 0 && sx < imgWidth)
790 g.drawLine(sx, oldY, sx, sy);
793 if (sx + ex < imgWidth)
795 g.drawLine(sx + ex, oldY, sx + ex, sy);
804 if (sx + ex > imgWidth)
808 else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
810 ex = (endRes - startRes + 1) * avcharWidth;
815 g.drawLine(sx, top, sx + ex, top);
821 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
830 if (groupIndex >= av.getAlignment().getGroups().size())
835 group = av.getAlignment().getGroups().get(groupIndex);
836 } while (groupIndex < av.getAlignment().getGroups().size());
841 public void highlightSearchResults(SearchResults results)
843 searchResults = results;