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);
208 av.getAlignPanel().alignFrame.repaint();
218 public void paintComponent(Graphics g)
220 super.paintComponent(g);
222 g.setColor(Color.white);
223 g.fillRect(0, 0, getWidth(), getHeight());
228 g.drawImage(image, 0, 0, this);
233 int oldHeight = imgHeight;
235 imgHeight = getHeight();
236 imgHeight -= (imgHeight % av.getCharHeight());
243 if (oldHeight != imgHeight || image.getWidth(this) != getWidth())
245 image = new BufferedImage(getWidth(), imgHeight,
246 BufferedImage.TYPE_INT_RGB);
249 gg = (Graphics2D) image.getGraphics();
251 // Fill in the background
252 gg.setColor(Color.white);
253 gg.fillRect(0, 0, getWidth(), imgHeight);
255 drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
257 g.drawImage(image, 0, 0, this);
268 void drawIds(int starty, int endy)
270 if (av.isSeqNameItalics())
272 setIdfont(new Font(av.getFont().getName(), Font.ITALIC,
273 av.getFont().getSize()));
277 setIdfont(av.getFont());
280 gg.setFont(getIdfont());
281 fm = gg.getFontMetrics();
285 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
286 RenderingHints.VALUE_ANTIALIAS_ON);
289 Color currentColor = Color.white;
290 Color currentTextColor = Color.black;
292 boolean hasHiddenRows = av.hasHiddenRows();
294 if (av.getWrapAlignment())
296 drawIdsWrapped(starty, hasHiddenRows);
300 // No need to hang on to labels if we're not wrapped
303 // Now draw the id strings
304 int panelWidth = getWidth();
308 // Now draw the id strings
309 for (int i = starty; i <= endy; i++)
311 sequence = av.getAlignment().getSequenceAt(i);
313 if (sequence == null)
318 if (hasHiddenRows || av.isDisplayReferenceSeq())
320 setHiddenFont(sequence);
323 // Selected sequence colours
324 if ((searchResults != null) && searchResults.contains(sequence))
326 currentColor = Color.black;
327 currentTextColor = Color.white;
329 else if ((av.getSelectionGroup() != null) && av.getSelectionGroup()
330 .getSequences(null).contains(sequence))
332 currentColor = Color.lightGray;
333 currentTextColor = Color.black;
337 currentColor = av.getSequenceColour(sequence);
338 currentTextColor = Color.black;
341 gg.setColor(currentColor);
343 gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
346 gg.setColor(currentTextColor);
348 String string = sequence.getDisplayId(av.getShowJVSuffix());
350 if (av.isRightAlignIds())
352 xPos = panelWidth - fm.stringWidth(string) - 4;
355 gg.drawString(string, xPos,
356 (((i - starty) * av.getCharHeight()) + av.getCharHeight())
357 - (av.getCharHeight() / 5));
361 drawMarker(i, starty, 0);
367 * Draws sequence ids in wrapped mode
370 * @param hasHiddenRows
372 protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
374 int maxwidth = av.getAlignment().getWidth();
375 int alheight = av.getAlignment().getHeight();
377 if (av.hasHiddenColumns())
379 maxwidth = av.getAlignment().getHiddenColumns()
380 .findColumnPosition(maxwidth) - 1;
383 int annotationHeight = 0;
385 if (av.isShowAnnotation())
389 ap = new AnnotationPanel(av);
392 annotationHeight = ap.adjustPanelHeight();
395 labels = new AnnotationLabels(av);
399 int hgap = av.getCharHeight();
400 if (av.getScaleAboveWrapped())
402 hgap += av.getCharHeight();
405 int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
407 ViewportRanges ranges = av.getRanges();
409 int rowSize = ranges.getViewportWidth();
412 * draw repeating sequence ids until out of sequence data or
413 * out of visible space, whichever comes first
416 int row = ranges.getStartRes();
417 while ((ypos <= getHeight()) && (row < maxwidth))
419 for (int i = starty; i < alheight; i++)
421 SequenceI s = av.getAlignment().getSequenceAt(i);
422 if (hasHiddenRows || av.isDisplayReferenceSeq())
428 gg.setFont(getIdfont());
431 drawIdString(gg, hasHiddenRows, s, i, 0, ypos);
434 if (labels != null && av.isShowAnnotation())
436 gg.translate(0, ypos + (alheight * av.getCharHeight()));
437 labels.drawComponent(gg, getWidth());
438 gg.translate(0, -ypos - (alheight * av.getCharHeight()));
446 void drawMarker(int i, int starty, int yoffset)
449 SequenceI[] hseqs = av.getAlignment()
450 .getHiddenSequences().hiddenSequences;
451 // Use this method here instead of calling hiddenSeq adjust
453 int hSize = hseqs.length;
456 int lastIndex = i - 1;
457 int nextIndex = i + 1;
459 for (int j = 0; j < hSize; j++)
461 if (hseqs[j] != null)
463 if (j - 1 < hiddenIndex)
467 if (j - 1 < lastIndex)
471 if (j - 1 < nextIndex)
478 boolean below = (hiddenIndex > lastIndex + 1);
479 boolean above = (nextIndex > hiddenIndex + 1);
481 gg.setColor(Color.blue);
486 { getWidth() - av.getCharHeight(),
487 getWidth() - av.getCharHeight(), getWidth() },
489 { (i - starty) * av.getCharHeight() + yoffset,
490 (i - starty) * av.getCharHeight() + yoffset
491 + av.getCharHeight() / 4,
492 (i - starty) * av.getCharHeight() + yoffset },
499 { getWidth() - av.getCharHeight(),
500 getWidth() - av.getCharHeight(), getWidth() },
502 { (i - starty + 1) * av.getCharHeight() + yoffset,
503 (i - starty + 1) * av.getCharHeight() + yoffset
504 - av.getCharHeight() / 4,
505 (i - starty + 1) * av.getCharHeight() + yoffset },
511 void setHiddenFont(SequenceI seq)
513 Font bold = new Font(av.getFont().getName(), Font.BOLD,
514 av.getFont().getSize());
516 if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
522 gg.setFont(getIdfont());
532 public void setHighlighted(List<SequenceI> list)
534 searchResults = list;
538 public Font getIdfont()
543 public void setIdfont(Font idfont)
545 this.idfont = idfont;
549 * Respond to viewport range changes (e.g. alignment panel was scrolled). Both
550 * scrolling and resizing change viewport ranges. Scrolling changes both start
551 * and end points, but resize only changes end values. Here we only want to
552 * fastpaint on a scroll, with resize using a normal paint, so scroll events
553 * are identified as changes to the horizontal or vertical start value.
555 * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
556 * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
557 * provided, but it generates a change of "startres" which does require an
561 public void propertyChange(PropertyChangeEvent evt)
563 String propertyName = evt.getPropertyName();
564 if (propertyName.equals(ViewportRanges.STARTSEQ)
565 || (av.getWrapAlignment()
566 && propertyName.equals(ViewportRanges.STARTRES)))
568 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
570 else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ))
572 fastPaint(((int[]) evt.getNewValue())[1]
573 - ((int[]) evt.getOldValue())[1]);