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.
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;
29 import java.awt.BasicStroke;
30 import java.awt.BorderLayout;
31 import java.awt.Color;
32 import java.awt.FontMetrics;
33 import java.awt.Graphics;
34 import java.awt.Graphics2D;
35 import java.awt.RenderingHints;
36 import java.awt.Shape;
37 import java.awt.image.BufferedImage;
38 import java.util.List;
40 import javax.swing.JComponent;
48 public class SeqCanvas extends JComponent
50 final FeatureRenderer fr;
52 final SequenceRenderer sr;
64 SearchResults searchResults = null;
66 boolean fastPaint = false;
77 * Creates a new SeqCanvas object.
82 public SeqCanvas(AlignmentPanel ap)
86 fr = new FeatureRenderer(ap);
87 sr = new SequenceRenderer(av);
88 setLayout(new BorderLayout());
89 PaintRefresher.Register(this, av.getSequenceSetId());
90 setBackground(Color.white);
93 public SequenceRenderer getSequenceRenderer()
98 public FeatureRenderer getFeatureRenderer()
103 int charHeight = 0, charWidth = 0;
105 private void updateViewport()
107 charHeight = av.getCharHeight();
108 charWidth = av.getCharWidth();
122 private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
125 int scalestartx = startx - (startx % 10) + 10;
127 g.setColor(Color.black);
129 for (int i = scalestartx; i < endx; i += 10)
132 if (av.hasHiddenColumns())
134 value = av.getColumnSelection().adjustForHiddenColumns(value);
137 g.drawString(String.valueOf(value), (i - startx - 1) * charWidth,
138 ypos - (charHeight / 2));
140 g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
141 (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
159 void drawWestScale(Graphics g, int startx, int endx, int ypos)
161 FontMetrics fm = getFontMetrics(av.getFont());
164 if (av.hasHiddenColumns())
166 startx = av.getColumnSelection().adjustForHiddenColumns(startx);
167 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
170 int maxwidth = av.getAlignment().getWidth();
171 if (av.hasHiddenColumns())
173 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
177 for (int i = 0; i < av.getAlignment().getHeight(); i++)
179 SequenceI seq = av.getAlignment().getSequenceAt(i);
185 if (Comparison.isGap(seq.getCharAt(index)))
192 value = av.getAlignment().getSequenceAt(i).findPosition(index);
199 int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
201 g.drawString(value + "", x, (ypos + (i * charHeight))
219 void drawEastScale(Graphics g, int startx, int endx, int ypos)
223 if (av.hasHiddenColumns())
225 endx = av.getColumnSelection().adjustForHiddenColumns(endx);
230 for (int i = 0; i < av.getAlignment().getHeight(); i++)
232 seq = av.getAlignment().getSequenceAt(i);
236 while (index > startx)
238 if (Comparison.isGap(seq.getCharAt(index)))
245 value = seq.findPosition(index);
252 g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
258 boolean fastpainting = false;
261 * need to make this thread safe move alignment rendering in response to
267 * shift up or down in repaint
269 public void fastPaint(int horizontal, int vertical)
271 if (fastpainting || gg == null)
278 gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
279 imgHeight, -horizontal * charWidth, -vertical * charHeight);
281 int sr = av.startRes;
283 int ss = av.startSeq;
288 if (horizontal > 0) // scrollbar pulled right, image to the left
291 transX = (er - sr - horizontal) * charWidth;
292 sr = er - horizontal;
294 else if (horizontal < 0)
296 er = sr - horizontal - 1;
298 else if (vertical > 0) // scroll down
302 if (ss < av.startSeq)
303 { // ie scrolling too fast, more than a page at a time
308 transY = imgHeight - (vertical * charHeight);
311 else if (vertical < 0)
321 gg.translate(transX, transY);
322 drawPanel(gg, sr, er, ss, es, 0);
323 gg.translate(-transX, -transY);
326 fastpainting = false;
330 * Definitions of startx and endx (hopefully): SMJS This is what I'm working
331 * towards! startx is the first residue (starting at 0) to display. endx is
332 * the last residue to display (starting at 0). starty is the first sequence
333 * to display (starting at 0). endy is the last sequence to display (starting
334 * at 0). NOTE 1: The av limits are set in setFont in this class and in the
335 * adjustment listener in SeqPanel when the scrollbars move.
338 // Set this to false to force a full panel paint
339 public void paintComponent(Graphics g)
342 BufferedImage lcimg = img; // take reference since other threads may null
343 // img and call later.
344 super.paintComponent(g);
348 || (getVisibleRect().width != g.getClipBounds().width) || (getVisibleRect().height != g
349 .getClipBounds().height)))
351 g.drawImage(lcimg, 0, 0, this);
356 // this draws the whole of the alignment
357 imgWidth = getWidth();
358 imgHeight = getHeight();
360 imgWidth -= (imgWidth % charWidth);
361 imgHeight -= (imgHeight % charHeight);
363 if ((imgWidth < 1) || (imgHeight < 1))
368 if (lcimg == null || imgWidth != lcimg.getWidth()
369 || imgHeight != lcimg.getHeight())
373 lcimg = img = new BufferedImage(imgWidth, imgHeight,
374 BufferedImage.TYPE_INT_RGB);
375 gg = (Graphics2D) img.getGraphics();
376 gg.setFont(av.getFont());
377 } catch (OutOfMemoryError er)
380 System.err.println("SeqCanvas OutOfMemory Redraw Error.\n" + er);
381 new OOMWarning("Creating alignment image for display", er);
389 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
390 RenderingHints.VALUE_ANTIALIAS_ON);
393 gg.setColor(Color.white);
394 gg.fillRect(0, 0, imgWidth, imgHeight);
396 if (av.getWrapAlignment())
398 drawWrappedPanel(gg, getWidth(), getHeight(), av.startRes);
402 drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
405 g.drawImage(lcimg, 0, 0, this);
415 * @return DOCUMENT ME!
417 public int getWrappedCanvasWidth(int cwidth)
419 FontMetrics fm = getFontMetrics(av.getFont());
424 if (av.getScaleRightWrapped())
426 LABEL_EAST = fm.stringWidth(getMask());
429 if (av.getScaleLeftWrapped())
431 LABEL_WEST = fm.stringWidth(getMask());
434 return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
438 * Generates a string of zeroes.
447 for (int i = 0; i < av.getAlignment().getHeight(); i++)
449 tmp = av.getAlignment().getSequenceAt(i).getEnd();
456 for (int i = maxWidth; i > 0; i /= 10)
470 * @param canvasHeight
475 public void drawWrappedPanel(Graphics g, int canvasWidth,
476 int canvasHeight, int startRes)
479 AlignmentI al = av.getAlignment();
481 FontMetrics fm = getFontMetrics(av.getFont());
483 if (av.getScaleRightWrapped())
485 LABEL_EAST = fm.stringWidth(getMask());
488 if (av.getScaleLeftWrapped())
490 LABEL_WEST = fm.stringWidth(getMask());
493 int hgap = charHeight;
494 if (av.getScaleAboveWrapped())
499 int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
500 int cHeight = av.getAlignment().getHeight() * charHeight;
502 av.setWrappedWidth(cWidth);
504 av.endRes = av.startRes + cWidth;
508 int maxwidth = av.getAlignment().getWidth() - 1;
510 if (av.hasHiddenColumns())
512 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
515 while ((ypos <= canvasHeight) && (startRes < maxwidth))
517 endx = startRes + cWidth - 1;
524 g.setFont(av.getFont());
525 g.setColor(Color.black);
527 if (av.getScaleLeftWrapped())
529 drawWestScale(g, startRes, endx, ypos);
532 if (av.getScaleRightWrapped())
534 g.translate(canvasWidth - LABEL_EAST, 0);
535 drawEastScale(g, startRes, endx, ypos);
536 g.translate(-(canvasWidth - LABEL_EAST), 0);
539 g.translate(LABEL_WEST, 0);
541 if (av.getScaleAboveWrapped())
543 drawNorthScale(g, startRes, endx, ypos);
546 if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
548 g.setColor(Color.blue);
550 for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
553 res = av.getColumnSelection().findHiddenRegionPosition(i)
556 if (res < 0 || res > endx - startRes)
561 gg.fillPolygon(new int[]
562 { res * charWidth - charHeight / 4,
563 res * charWidth + charHeight / 4, res * charWidth },
565 { ypos - (charHeight / 2), ypos - (charHeight / 2),
566 ypos - (charHeight / 2) + 8 }, 3);
571 // When printing we have an extra clipped region,
572 // the Printable page which we need to account for here
573 Shape clip = g.getClip();
577 g.setClip(0, 0, cWidth * charWidth, canvasHeight);
581 g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
582 (int) clip.getBounds().getHeight());
585 drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
587 if (av.isShowAnnotation())
589 g.translate(0, cHeight + ypos + 3);
590 if (annotations == null)
592 annotations = new AnnotationPanel(av);
595 annotations.renderer.drawComponent(annotations, av, g,
596 -1, startRes, endx + 1);
597 g.translate(0, -cHeight - ypos - 3);
600 g.translate(-LABEL_WEST, 0);
602 ypos += cHeight + getAnnotationHeight() + hgap;
608 AnnotationPanel annotations;
610 int getAnnotationHeight()
612 if (!av.isShowAnnotation())
617 if (annotations == null)
619 annotations = new AnnotationPanel(av);
622 return annotations.adjustPanelHeight();
641 public void drawPanel(Graphics g1, int startRes, int endRes,
643 int endSeq, int offset)
646 if (!av.hasHiddenColumns())
648 draw(g1, startRes, endRes, startSeq, endSeq, offset);
652 List<int[]> regions = av.getColumnSelection().getHiddenColumns();
655 int blockStart = startRes;
656 int blockEnd = endRes;
658 for (int[] region : regions)
660 int hideStart = region[0];
661 int hideEnd = region[1];
663 if (hideStart <= blockStart)
665 blockStart += (hideEnd - hideStart) + 1;
669 blockEnd = hideStart - 1;
671 g1.translate(screenY * charWidth, 0);
673 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
675 if (av.getShowHiddenMarkers())
677 g1.setColor(Color.blue);
679 g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
680 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
681 (endSeq - startSeq) * charHeight + offset);
684 g1.translate(-screenY * charWidth, 0);
685 screenY += blockEnd - blockStart + 1;
686 blockStart = hideEnd + 1;
689 if (screenY <= (endRes - startRes))
691 blockEnd = blockStart + (endRes - startRes) - screenY;
692 g1.translate(screenY * charWidth, 0);
693 draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
695 g1.translate(-screenY * charWidth, 0);
701 // int startRes, int endRes, int startSeq, int endSeq, int x, int y,
702 // int x1, int x2, int y1, int y2, int startx, int starty,
703 private void draw(Graphics g, int startRes, int endRes, int startSeq,
707 g.setFont(av.getFont());
708 sr.prepare(g, av.isRenderGaps());
712 // / First draw the sequences
713 // ///////////////////////////
714 for (int i = startSeq; i < endSeq; i++)
716 nextSeq = av.getAlignment().getSequenceAt(i);
719 // occasionally, a race condition occurs such that the alignment row is
723 sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
724 startRes, endRes, offset + ((i - startSeq) * charHeight));
726 if (av.isShowSequenceFeatures())
728 fr.drawSequence(g, nextSeq, startRes, endRes, offset
729 + ((i - startSeq) * charHeight));
732 // / Highlight search Results once all sequences have been drawn
733 // ////////////////////////////////////////////////////////
734 if (searchResults != null)
736 int[] visibleResults = searchResults.getResults(nextSeq, startRes,
738 if (visibleResults != null)
740 for (int r = 0; r < visibleResults.length; r += 2)
742 sr.drawHighlightedText(nextSeq, visibleResults[r],
743 visibleResults[r + 1], (visibleResults[r] - startRes)
745 + ((i - startSeq) * charHeight));
750 if (av.cursorMode && cursorY == i && cursorX >= startRes
751 && cursorX <= endRes)
753 sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
754 offset + ((i - startSeq) * charHeight));
758 if (av.getSelectionGroup() != null
759 || av.getAlignment().getGroups().size() > 0)
761 drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
766 void drawGroupsBoundaries(Graphics g1, int startRes, int endRes,
767 int startSeq, int endSeq, int offset)
769 Graphics2D g = (Graphics2D) g1;
771 // ///////////////////////////////////
772 // Now outline any areas if necessary
773 // ///////////////////////////////////
774 SequenceGroup group = av.getSelectionGroup();
780 int visWidth = (endRes - startRes + 1) * charWidth;
782 if ((group == null) && (av.getAlignment().getGroups().size() > 0))
784 group = av.getAlignment().getGroups().get(0);
794 boolean inGroup = false;
798 for (i = startSeq; i < endSeq; i++)
800 sx = (group.getStartRes() - startRes) * charWidth;
801 sy = offset + ((i - startSeq) * charHeight);
802 ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
804 if (sx + ex < 0 || sx > visWidth)
809 if ((sx <= (endRes - startRes) * charWidth)
810 && group.getSequences(null).contains(
811 av.getAlignment().getSequenceAt(i)))
814 && !group.getSequences(null).contains(
815 av.getAlignment().getSequenceAt(i + 1)))
817 bottom = sy + charHeight;
822 if (((top == -1) && (i == 0))
823 || !group.getSequences(null).contains(
824 av.getAlignment().getSequenceAt(i - 1)))
832 if (group == av.getSelectionGroup())
834 g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
835 BasicStroke.JOIN_ROUND, 3f, new float[]
837 g.setColor(Color.RED);
841 g.setStroke(new BasicStroke());
842 g.setColor(group.getOutlineColour());
850 if (sx >= 0 && sx < visWidth)
852 g.drawLine(sx, oldY, sx, sy);
855 if (sx + ex < visWidth)
857 g.drawLine(sx + ex, oldY, sx + ex, sy);
866 if (sx + ex > visWidth)
871 else if (sx + ex >= (endRes - startRes + 1) * charWidth)
873 ex = (endRes - startRes + 1) * charWidth;
878 g.drawLine(sx, top, sx + ex, top);
884 g.drawLine(sx, bottom, sx + ex, bottom);
895 sy = offset + ((i - startSeq) * charHeight);
896 if (sx >= 0 && sx < visWidth)
898 g.drawLine(sx, oldY, sx, sy);
901 if (sx + ex < visWidth)
903 g.drawLine(sx + ex, oldY, sx + ex, sy);
912 if (sx + ex > visWidth)
916 else if (sx + ex >= (endRes - startRes + 1) * charWidth)
918 ex = (endRes - startRes + 1) * charWidth;
923 g.drawLine(sx, top, sx + ex, top);
929 g.drawLine(sx, bottom - 1, sx + ex, bottom - 1);
938 g.setStroke(new BasicStroke());
940 if (groupIndex >= av.getAlignment().getGroups().size())
945 group = av.getAlignment().getGroups()
948 } while (groupIndex < av.getAlignment().getGroups().size());
960 public void highlightSearchResults(SearchResults results)
964 searchResults = results;