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 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(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
256 g.drawImage(image, 0, 0, this);
267 void drawIds(int starty, int endy)
269 if (av.isSeqNameItalics())
271 setIdfont(new Font(av.getFont().getName(), Font.ITALIC,
272 av.getFont().getSize()));
276 setIdfont(av.getFont());
279 gg.setFont(getIdfont());
280 fm = gg.getFontMetrics();
284 gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
285 RenderingHints.VALUE_ANTIALIAS_ON);
288 Color currentColor = Color.white;
289 Color currentTextColor = Color.black;
291 boolean hasHiddenRows = av.hasHiddenRows();
293 if (av.getWrapAlignment())
295 drawIdsWrapped(starty, hasHiddenRows);
299 // No need to hang on to labels if we're not wrapped
302 // Now draw the id strings
303 int panelWidth = getWidth();
307 // Now draw the id strings
308 for (int i = starty; i <= endy; i++)
310 sequence = av.getAlignment().getSequenceAt(i);
312 if (sequence == null)
317 if (hasHiddenRows || av.isDisplayReferenceSeq())
319 setHiddenFont(sequence);
322 // Selected sequence colours
323 if ((searchResults != null) && searchResults.contains(sequence))
325 currentColor = Color.black;
326 currentTextColor = Color.white;
328 else if ((av.getSelectionGroup() != null) && av.getSelectionGroup()
329 .getSequences(null).contains(sequence))
331 currentColor = Color.lightGray;
332 currentTextColor = Color.black;
336 currentColor = av.getSequenceColour(sequence);
337 currentTextColor = Color.black;
340 gg.setColor(currentColor);
342 gg.fillRect(0, (i - starty) * av.getCharHeight(), getWidth(),
345 gg.setColor(currentTextColor);
347 String string = sequence.getDisplayId(av.getShowJVSuffix());
349 if (av.isRightAlignIds())
351 xPos = panelWidth - fm.stringWidth(string) - 4;
354 gg.drawString(string, xPos,
355 (((i - starty) * av.getCharHeight()) + av.getCharHeight())
356 - (av.getCharHeight() / 5));
360 drawMarker(i, starty, 0);
366 * Draws sequence ids in wrapped mode
369 * @param hasHiddenRows
371 protected void drawIdsWrapped(int starty, boolean hasHiddenRows)
373 int maxwidth = av.getAlignment().getWidth();
374 int alheight = av.getAlignment().getHeight();
376 if (av.hasHiddenColumns())
378 maxwidth = av.getAlignment().getHiddenColumns()
379 .findColumnPosition(maxwidth) - 1;
382 int annotationHeight = 0;
384 if (av.isShowAnnotation())
388 ap = new AnnotationPanel(av);
391 annotationHeight = ap.adjustPanelHeight();
394 labels = new AnnotationLabels(av);
398 int hgap = av.getCharHeight();
399 if (av.getScaleAboveWrapped())
401 hgap += av.getCharHeight();
404 int cHeight = alheight * av.getCharHeight() + hgap + annotationHeight;
406 ViewportRanges ranges = av.getRanges();
408 int rowSize = ranges.getViewportWidth();
411 * draw repeating sequence ids until out of sequence data or
412 * out of visible space, whichever comes first
415 int row = ranges.getStartRes();
416 while ((ypos <= getHeight()) && (row < maxwidth))
418 for (int i = starty; i < alheight; i++)
420 SequenceI s = av.getAlignment().getSequenceAt(i);
421 if (hasHiddenRows || av.isDisplayReferenceSeq())
427 gg.setFont(getIdfont());
430 drawIdString(gg, hasHiddenRows, s, i, 0, ypos);
433 if (labels != null && av.isShowAnnotation())
435 gg.translate(0, ypos + (alheight * av.getCharHeight()));
436 labels.drawComponent(gg, getWidth());
437 gg.translate(0, -ypos - (alheight * av.getCharHeight()));
445 void drawMarker(int i, int starty, int yoffset)
448 SequenceI[] hseqs = av.getAlignment()
449 .getHiddenSequences().hiddenSequences;
450 // Use this method here instead of calling hiddenSeq adjust
452 int hSize = hseqs.length;
455 int lastIndex = i - 1;
456 int nextIndex = i + 1;
458 for (int j = 0; j < hSize; j++)
460 if (hseqs[j] != null)
462 if (j - 1 < hiddenIndex)
466 if (j - 1 < lastIndex)
470 if (j - 1 < nextIndex)
477 boolean below = (hiddenIndex > lastIndex + 1);
478 boolean above = (nextIndex > hiddenIndex + 1);
480 gg.setColor(Color.blue);
485 { getWidth() - av.getCharHeight(),
486 getWidth() - av.getCharHeight(), getWidth() },
488 { (i - starty) * av.getCharHeight() + yoffset,
489 (i - starty) * av.getCharHeight() + yoffset
490 + av.getCharHeight() / 4,
491 (i - starty) * av.getCharHeight() + yoffset },
498 { getWidth() - av.getCharHeight(),
499 getWidth() - av.getCharHeight(), getWidth() },
501 { (i - starty + 1) * av.getCharHeight() + yoffset,
502 (i - starty + 1) * av.getCharHeight() + yoffset
503 - av.getCharHeight() / 4,
504 (i - starty + 1) * av.getCharHeight() + yoffset },
510 void setHiddenFont(SequenceI seq)
512 Font bold = new Font(av.getFont().getName(), Font.BOLD,
513 av.getFont().getSize());
515 if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
521 gg.setFont(getIdfont());
531 public void setHighlighted(List<SequenceI> list)
533 searchResults = list;
537 public Font getIdfont()
542 public void setIdfont(Font idfont)
544 this.idfont = idfont;
548 * Respond to viewport range changes (e.g. alignment panel was scrolled). Both
549 * scrolling and resizing change viewport ranges. Scrolling changes both start
550 * and end points, but resize only changes end values. Here we only want to
551 * fastpaint on a scroll, with resize using a normal paint, so scroll events
552 * are identified as changes to the horizontal or vertical start value.
554 * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
555 * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
556 * provided, but it generates a change of "startres" which does require an
560 public void propertyChange(PropertyChangeEvent evt)
562 String propertyName = evt.getPropertyName();
563 if (propertyName.equals(ViewportRanges.STARTSEQ)
564 || (av.getWrapAlignment()
565 && propertyName.equals(ViewportRanges.STARTRES)))
567 fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
569 else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ))
571 fastPaint(((int[]) evt.getNewValue())[1]
572 - ((int[]) evt.getOldValue())[1]);