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;
64 List<SequenceI> searchResults;
68 AnnotationLabels labels = null;
75 * Creates a new IdCanvas object.
80 public IdCanvas(AlignViewport av)
82 setLayout(new BorderLayout());
84 PaintRefresher.Register(this, av.getSequenceSetId());
85 av.getRanges().addPropertyChangeListener(this);
94 * true - check and display hidden row marker if need be
104 public void drawIdString(Graphics2D gg, boolean hiddenRows, SequenceI s,
105 int i, int starty, int ypos)
108 int panelWidth = getWidth();
109 int charHeight = av.getCharHeight();
111 if ((searchResults != null) && searchResults.contains(s))
113 gg.setColor(Color.black);
114 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
116 gg.setColor(Color.white);
118 else if ((av.getSelectionGroup() != null)
119 && av.getSelectionGroup().getSequences(null).contains(s))
121 gg.setColor(Color.lightGray);
122 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
124 gg.setColor(Color.white);
128 gg.setColor(av.getSequenceColour(s));
129 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(),
131 gg.setColor(Color.black);
134 if (av.isRightAlignIds())
137 - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4;
140 gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos,
141 (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));
145 drawMarker(i, starty, ypos);
156 public void fastPaint(int vertical)
159 * for now, not attempting fast paint of wrapped ids...
161 if (gg == null || av.getWrapAlignment())
168 ViewportRanges ranges = av.getRanges();
170 gg.copyArea(0, 0, getWidth(), imgHeight, 0,
171 -vertical * av.getCharHeight());
173 int ss = ranges.getStartSeq();
174 int es = ranges.getEndSeq();
177 if (vertical > 0) // scroll down
181 if (ss < ranges.getStartSeq())
182 { // ie scrolling too fast, more than a page at a time
183 ss = ranges.getStartSeq();
187 transY = imgHeight - ((vertical + 1) * av.getCharHeight());
190 else if (vertical < 0) // scroll up
194 if (es > ranges.getEndSeq())
196 es = ranges.getEndSeq();
200 gg.translate(0, transY);
204 gg.translate(0, -transY);
217 public void paintComponent(Graphics g)
219 g.setColor(Color.white);
220 g.fillRect(0, 0, getWidth(), getHeight());
225 g.drawImage(image, 0, 0, this);
230 int oldHeight = imgHeight;
232 imgHeight = getHeight();
233 imgHeight -= (imgHeight % av.getCharHeight());
240 if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
242 image = new BufferedImage(getWidth(), imgHeight,
243 BufferedImage.TYPE_INT_RGB);
246 gg = (Graphics2D) image.getGraphics();
248 // Fill in the background
249 gg.setColor(Color.white);
250 gg.fillRect(0, 0, getWidth(), imgHeight);
252 drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
254 g.drawImage(image, 0, 0, this);
265 void drawIds(int starty, int endy)
267 if (av.isSeqNameItalics())
269 setIdfont(new Font(av.getFont().getName(), Font.ITALIC,
270 av.getFont().getSize()));
274 setIdfont(av.getFont());
277 gg.setFont(getIdfont());
278 fm = gg.getFontMetrics();
282 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
283 RenderingHints.VALUE_ANTIALIAS_ON);
286 Color currentColor = Color.white;
287 Color currentTextColor = Color.black;
289 boolean hasHiddenRows = av.hasHiddenRows();
291 if (av.getWrapAlignment())
293 drawIdsWrapped(starty, hasHiddenRows);
297 // No need to hang on to labels if we're not wrapped
300 // Now draw the id strings
301 int panelWidth = getWidth();
305 // Now draw the id strings
306 for (int i = starty; i <= endy; i++)
308 sequence = av.getAlignment().getSequenceAt(i);
310 if (sequence == null)
315 if (hasHiddenRows || av.isDisplayReferenceSeq())
317 setHiddenFont(sequence);
320 // Selected sequence colours
321 if ((searchResults != null) && searchResults.contains(sequence))
323 currentColor = Color.black;
324 currentTextColor = Color.white;
326 else if ((av.getSelectionGroup() != null) && av.getSelectionGroup()
327 .getSequences(null).contains(sequence))
329 currentColor = Color.lightGray;
330 currentTextColor = Color.black;
334 currentColor = av.getSequenceColour(sequence);
335 currentTextColor = Color.black;
338 gg.setColor(currentColor);
340 gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
343 gg.setColor(currentTextColor);
345 String string = sequence.getDisplayId(av.getShowJVSuffix());
347 if (av.isRightAlignIds())
349 xPos = panelWidth - fm.stringWidth(string) - 4;
352 gg.drawString(string, xPos,
353 (((i - starty) * av.getCharHeight()) + av.getCharHeight())
354 - (av.getCharHeight() / 5));
358 drawMarker(i, starty, 0);
364 * Draws sequence ids in wrapped mode
367 * @param hasHiddenRows
369 protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
371 int maxwidth = av.getAlignment().getWidth();
372 int alheight = av.getAlignment().getHeight();
374 if (av.hasHiddenColumns())
376 maxwidth = av.getAlignment().getHiddenColumns()
377 .findColumnPosition(maxwidth) - 1;
380 int annotationHeight = 0;
382 if (av.isShowAnnotation())
386 ap = new AnnotationPanel(av);
389 annotationHeight = ap.adjustPanelHeight();
392 labels = new AnnotationLabels(av);
396 int hgap = av.getCharHeight();
397 if (av.getScaleAboveWrapped())
399 hgap += av.getCharHeight();
402 int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
404 ViewportRanges ranges = av.getRanges();
406 int rowSize = ranges.getViewportWidth();
409 * draw repeating sequence ids until out of sequence data or
410 * out of visible space, whichever comes first
413 int row = ranges.getStartRes();
414 while ((ypos <= getHeight()) && (row < maxwidth))
416 for (int i = starty; i < alheight; i++)
418 SequenceI s = av.getAlignment().getSequenceAt(i);
419 if (hasHiddenRows || av.isDisplayReferenceSeq())
425 gg.setFont(getIdfont());
428 drawIdString(gg, hasHiddenRows, s, i, 0, ypos);
431 if (labels != null && av.isShowAnnotation())
433 gg.translate(0, ypos + (alheight * av.getCharHeight()));
434 labels.drawComponent(gg, getWidth());
435 gg.translate(0, -ypos - (alheight * av.getCharHeight()));
443 void drawMarker(int i, int starty, int yoffset)
446 SequenceI[] hseqs = av.getAlignment()
447 .getHiddenSequences().hiddenSequences;
448 // Use this method here instead of calling hiddenSeq adjust
450 int hSize = hseqs.length;
453 int lastIndex = i - 1;
454 int nextIndex = i + 1;
456 for (int j = 0; j < hSize; j++)
458 if (hseqs[j] != null)
460 if (j - 1 < hiddenIndex)
464 if (j - 1 < lastIndex)
468 if (j - 1 < nextIndex)
475 boolean below = (hiddenIndex > lastIndex + 1);
476 boolean above = (nextIndex > hiddenIndex + 1);
478 gg.setColor(Color.blue);
483 { getWidth() - av.getCharHeight(),
484 getWidth() - av.getCharHeight(), getWidth() },
486 { (i - starty) * av.getCharHeight() + yoffset,
487 (i - starty) * av.getCharHeight() + yoffset
488 + av.getCharHeight() / 4,
489 (i - starty) * av.getCharHeight() + yoffset },
496 { getWidth() - av.getCharHeight(),
497 getWidth() - av.getCharHeight(), getWidth() },
499 { (i - starty + 1) * av.getCharHeight() + yoffset,
500 (i - starty + 1) * av.getCharHeight() + yoffset
501 - av.getCharHeight() / 4,
502 (i - starty + 1) * av.getCharHeight() + yoffset },
508 void setHiddenFont(SequenceI seq)
510 Font bold = new Font(av.getFont().getName(), Font.BOLD,
511 av.getFont().getSize());
513 if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
519 gg.setFont(getIdfont());
529 public void setHighlighted(List<SequenceI> list)
531 searchResults = list;
535 public Font getIdfont()
540 public void setIdfont(Font idfont)
542 this.idfont = idfont;
546 * Respond to viewport range changes (e.g. alignment panel was scrolled). Both
547 * scrolling and resizing change viewport ranges. Scrolling changes both start
548 * and end points, but resize only changes end values. Here we only want to
549 * fastpaint on a scroll, with resize using a normal paint, so scroll events
550 * are identified as changes to the horizontal or vertical start value.
552 * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
553 * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
554 * provided, but it generates a change of "startres" which does require an
558 public void propertyChange(PropertyChangeEvent evt)
560 String propertyName = evt.getPropertyName();
561 if (propertyName.equals(ViewportRanges.STARTSEQ)
562 || (av.getWrapAlignment()
563 && propertyName.equals(ViewportRanges.STARTRES)))
565 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());