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.SequenceI;
24 import jalview.viewmodel.ViewportListenerI;
25 import jalview.viewmodel.ViewportRanges;
27 import java.awt.BorderLayout;
28 import java.awt.Color;
30 import java.awt.FontMetrics;
31 import java.awt.Graphics;
32 import java.awt.Graphics2D;
33 import java.awt.RenderingHints;
34 import java.awt.image.BufferedImage;
35 import java.beans.PropertyChangeEvent;
36 import java.util.List;
38 import javax.swing.JPanel;
46 public class IdCanvas extends JPanel implements ViewportListenerI
48 protected AlignViewport av;
50 protected boolean showScores = true;
52 protected int maxIdLength = -1;
54 protected String maxIdStr = null;
62 boolean fastPaint = false;
69 * Creates a new IdCanvas object.
74 public IdCanvas(AlignViewport av)
76 setLayout(new BorderLayout());
78 PaintRefresher.Register(this, av.getSequenceSetId());
79 av.getRanges().addPropertyChangeListener(this);
88 * true - check and display hidden row marker if need be
98 public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s,
99 int i, int starty, int ypos)
102 int panelWidth = getWidth();
103 int charHeight = av.getCharHeight();
104 List<SequenceI> searchResults = av.getHighlightedSeqs();
105 if ((searchResults != null) && searchResults.contains(s))
107 g.setColor(Color.black);
108 g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
110 g.setColor(Color.white);
112 else if ((av.getSelectionGroup() != null)
113 && av.getSelectionGroup().getSequences(null).contains(s))
115 g.setColor(Color.lightGray);
116 g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
118 g.setColor(Color.white);
122 g.setColor(av.getSequenceColour(s));
123 g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
125 g.setColor(Color.black);
128 if (av.isRightAlignIds())
130 FontMetrics fm = g.getFontMetrics();
132 - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
135 g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
136 (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
140 drawMarker(g, av, i, starty, ypos);
151 public void fastPaint(int vertical)
154 * for now, not attempting fast paint of wrapped ids...
156 if (gg == null || av.getWrapAlignment())
163 ViewportRanges ranges = av.getRanges();
164 List<SequenceI> searchResults = av.getHighlightedSeqs();
166 gg.copyArea(0, 0, getWidth(), imgHeight, 0,
167 -vertical * av.getCharHeight());
169 int ss = ranges.getStartSeq();
170 int es = ranges.getEndSeq();
173 if (vertical > 0) // scroll down
177 if (ss < ranges.getStartSeq())
178 { // ie scrolling too fast, more than a page at a time
179 ss = ranges.getStartSeq();
183 transY = imgHeight - ((vertical + 1) * av.getCharHeight());
186 else if (vertical < 0) // scroll up
190 if (es > ranges.getEndSeq())
192 es = ranges.getEndSeq();
196 gg.translate(0, transY);
198 drawIds(gg, av, ss, es, searchResults);
200 gg.translate(0, -transY);
204 // Call repaint on alignment panel so that repaints from other alignment
205 // panel components can be aggregated. Otherwise performance of the overview
206 // window and others may be adversely affected.
207 av.getAlignPanel().repaint();
217 public void paintComponent(Graphics g)
219 super.paintComponent(g);
221 g.setColor(Color.white);
222 g.fillRect(0, 0, getWidth(), getHeight());
227 g.drawImage(image, 0, 0, this);
232 int oldHeight = imgHeight;
234 imgHeight = getHeight();
235 imgHeight -= (imgHeight % av.getCharHeight());
242 if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
244 image = new BufferedImage(getWidth(), imgHeight,
245 BufferedImage.TYPE_INT_RGB);
248 gg = (Graphics2D) image.getGraphics();
250 // Fill in the background
251 gg.setColor(Color.white);
252 gg.fillRect(0, 0, getWidth(), imgHeight);
254 drawIds(gg, av, av.getRanges().getStartSeq(),
255 av.getRanges().getEndSeq(), av.getHighlightedSeqs());
257 g.drawImage(image, 0, 0, this);
261 * Draws sequence ids from sequence index startSeq to endSeq (inclusive), with
262 * the font and other display settings configured on the viewport. Ids of
263 * sequences included in the selection are coloured grey, otherwise the
264 * current id colour for the sequence id is used.
267 * @param alignViewport
272 void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq,
273 final int endSeq, List<SequenceI> selection)
275 Font font = alignViewport.getFont();
276 if (alignViewport.isSeqNameItalics())
278 setIdfont(new Font(font.getName(), Font.ITALIC,
286 g.setFont(getIdfont());
287 FontMetrics fm = g.getFontMetrics();
289 if (alignViewport.antiAlias)
291 g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
292 RenderingHints.VALUE_ANTIALIAS_ON);
295 Color currentColor = Color.white;
296 Color currentTextColor = Color.black;
298 boolean hasHiddenRows = alignViewport.hasHiddenRows();
300 if (alignViewport.getWrapAlignment())
302 drawIdsWrapped(g, alignViewport, startSeq, getHeight());
306 // Now draw the id strings
307 int panelWidth = getWidth();
310 // Now draw the id strings
311 for (int i = startSeq; i <= endSeq; i++)
313 SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i);
315 if (sequence == null)
320 if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
322 g.setFont(getHiddenFont(sequence, alignViewport));
325 // Selected sequence colours
326 if (selection != null && selection.contains(sequence))
328 currentColor = Color.black;
329 currentTextColor = Color.white;
331 else if ((alignViewport.getSelectionGroup() != null) && alignViewport
332 .getSelectionGroup().getSequences(null).contains(sequence))
334 currentColor = Color.lightGray;
335 currentTextColor = Color.black;
339 currentColor = alignViewport.getSequenceColour(sequence);
340 currentTextColor = Color.black;
343 g.setColor(currentColor);
345 int charHeight = alignViewport.getCharHeight();
346 g.fillRect(0, (i - startSeq) * charHeight,
347 getWidth(), charHeight);
349 g.setColor(currentTextColor);
351 String string = sequence
352 .getDisplayId(alignViewport.getShowJVSuffix());
354 if (alignViewport.isRightAlignIds())
356 xPos = panelWidth - fm.stringWidth(string) - 4;
359 g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight)
364 drawMarker(g, alignViewport, i, startSeq, 0);
370 * Draws sequence ids, and annotation labels if annotations are shown, in
374 * @param alignViewport
377 void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport,
378 int startSeq, int pageHeight)
380 int alignmentWidth = alignViewport.getAlignment().getWidth();
381 final int alheight = alignViewport.getAlignment().getHeight();
383 if (alignViewport.hasHiddenColumns())
385 alignmentWidth = alignViewport.getAlignment().getHiddenColumns()
386 .absoluteToVisibleColumn(alignmentWidth) - 1;
389 int annotationHeight = 0;
391 AnnotationLabels labels = null;
392 if (alignViewport.isShowAnnotation())
396 ap = new AnnotationPanel(alignViewport);
398 annotationHeight = ap.adjustPanelHeight();
399 labels = new AnnotationLabels(alignViewport);
402 final int charHeight = alignViewport.getCharHeight();
403 int hgap = charHeight;
404 if (alignViewport.getScaleAboveWrapped())
410 * height of alignment + gap + annotations (if shown)
412 int cHeight = alheight * charHeight + hgap
415 ViewportRanges ranges = alignViewport.getRanges();
417 int rowSize = ranges.getViewportWidth();
420 * draw repeating sequence ids until out of sequence data or
421 * out of visible space, whichever comes first
423 boolean hasHiddenRows = alignViewport.hasHiddenRows();
425 int rowStartRes = ranges.getStartRes();
426 while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth))
428 for (int i = startSeq; i < alheight; i++)
430 SequenceI s = alignViewport.getAlignment().getSequenceAt(i);
431 if (hasHiddenRows || alignViewport.isDisplayReferenceSeq())
433 g.setFont(getHiddenFont(s, alignViewport));
437 g.setFont(getIdfont());
439 drawIdString(g, hasHiddenRows, s, i, 0, ypos);
442 if (labels != null && alignViewport.isShowAnnotation())
444 g.translate(0, ypos + (alheight * charHeight));
445 labels.drawComponent(g, getWidth());
446 g.translate(0, -ypos - (alheight * charHeight));
450 rowStartRes += rowSize;
455 * Draws a marker (a blue right-pointing triangle) between sequences to
456 * indicate hidden sequences.
459 * @param alignViewport
464 void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset)
466 SequenceI[] hseqs = alignViewport.getAlignment()
467 .getHiddenSequences().hiddenSequences;
468 // Use this method here instead of calling hiddenSeq adjust
470 int hSize = hseqs.length;
472 int hiddenIndex = seqIndex;
473 int lastIndex = seqIndex - 1;
474 int nextIndex = seqIndex + 1;
476 for (int j = 0; j < hSize; j++)
478 if (hseqs[j] != null)
480 if (j - 1 < hiddenIndex)
484 if (j - 1 < lastIndex)
488 if (j - 1 < nextIndex)
496 * are we below or above the hidden sequences?
498 boolean below = (hiddenIndex > lastIndex + 1);
499 boolean above = (nextIndex > hiddenIndex + 1);
501 g.setColor(Color.blue);
502 int charHeight = av.getCharHeight();
505 * vertices of the triangle, below or above hidden seqs
507 int[] xPoints = new int[]
508 { getWidth() - charHeight,
509 getWidth() - charHeight, getWidth() };
510 int yShift = seqIndex - starty;
514 int[] yPoints = new int[] { yShift * charHeight + yoffset,
515 yShift * charHeight + yoffset + charHeight / 4,
516 yShift * charHeight + yoffset };
517 g.fillPolygon(xPoints, yPoints, 3);
522 int[] yPoints = new int[] { yShift * charHeight + yoffset,
523 yShift * charHeight + yoffset - charHeight / 4,
524 yShift * charHeight + yoffset };
525 g.fillPolygon(xPoints, yPoints, 3);
530 * Answers the standard sequence id font, or a bold font if the sequence is
531 * set as reference or a hidden group representative
534 * @param alignViewport
537 private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport)
539 if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
541 return new Font(av.getFont().getName(), Font.BOLD,
542 av.getFont().getSize());
547 public Font getIdfont()
552 public void setIdfont(Font idfont)
554 this.idfont = idfont;
558 * Respond to viewport range changes (e.g. alignment panel was scrolled). Both
559 * scrolling and resizing change viewport ranges. Scrolling changes both start
560 * and end points, but resize only changes end values. Here we only want to
561 * fastpaint on a scroll, with resize using a normal paint, so scroll events
562 * are identified as changes to the horizontal or vertical start value.
564 * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
565 * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
566 * provided, but it generates a change of "startres" which does require an
570 public void propertyChange(PropertyChangeEvent evt)
572 String propertyName = evt.getPropertyName();
573 if (propertyName.equals(ViewportRanges.STARTSEQ)
574 || (av.getWrapAlignment()
575 && propertyName.equals(ViewportRanges.STARTRES)))
577 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
579 else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ))
581 fastPaint(((int[]) evt.getNewValue())[1]
582 - ((int[]) evt.getOldValue())[1]);
584 else if (propertyName.equals(ViewportRanges.MOVE_VIEWPORT))