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.
21 package jalview.appletgui;
23 import jalview.datamodel.SequenceI;
25 import java.awt.Color;
27 import java.awt.Graphics;
28 import java.awt.Image;
29 import java.awt.Panel;
30 import java.util.List;
32 public class IdCanvas extends Panel
34 protected AlignViewport av;
36 protected boolean showScores = true;
38 protected int maxIdLength = -1;
40 protected String maxIdStr = null;
48 boolean fastPaint = false;
50 List<SequenceI> searchResults;
52 public IdCanvas(AlignViewport av)
56 PaintRefresher.Register(this, av.getSequenceSetId());
59 public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
62 int charHeight = av.getCharHeight();
64 if (searchResults != null && searchResults.contains(s))
66 gg.setColor(Color.black);
67 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
69 gg.setColor(Color.white);
71 else if (av.getSelectionGroup() != null
72 && av.getSelectionGroup().getSequences(null).contains(s))
74 gg.setColor(Color.lightGray);
75 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
77 gg.setColor(Color.white);
81 gg.setColor(av.getSequenceColour(s));
82 gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
84 gg.setColor(Color.black);
87 gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
88 ((i - starty) * charHeight) + ypos + charHeight
91 if (av.hasHiddenRows() && av.getShowHiddenMarkers())
93 drawMarker(i, starty, ypos);
98 public void fastPaint(int vertical)
106 gg.copyArea(0, 0, getSize().width, imgHeight, 0,
107 -vertical * av.getCharHeight());
109 int ss = av.startSeq, es = av.endSeq, transY = 0;
110 if (vertical > 0) // scroll down
113 if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
119 transY = imgHeight - vertical * av.getCharHeight();
122 else if (vertical < 0)
131 gg.translate(0, transY);
135 gg.translate(0, -transY);
141 public void update(Graphics g)
146 public void paint(Graphics g)
148 if (getSize().height < 0 || getSize().width < 0)
155 g.drawImage(image, 0, 0, this);
159 imgHeight = getSize().height;
160 imgHeight -= imgHeight % av.getCharHeight();
167 if (image == null || imgHeight != image.getHeight(this))
169 image = createImage(getSize().width, imgHeight);
170 gg = image.getGraphics();
171 gg.setFont(av.getFont());
174 // Fill in the background
175 gg.setColor(Color.white);
176 Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
177 .getFont().getSize());
180 gg.fillRect(0, 0, getSize().width, getSize().height);
181 drawIds(av.startSeq, av.endSeq);
182 g.drawImage(image, 0, 0, this);
186 * local copy of av.getCharHeight set at top of drawIds
188 private int avcharHeight;
189 void drawIds(int starty, int endy)
191 // hardwired italic IDs in applet currently
192 Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
193 .getFont().getSize());
194 // temp variable for speed
195 avcharHeight = av.getCharHeight();
199 Color currentColor = Color.white;
200 Color currentTextColor = Color.black;
202 if (av.getWrapAlignment())
204 int maxwidth = av.getAlignment().getWidth();
205 int alheight = av.getAlignment().getHeight();
207 if (av.hasHiddenColumns())
209 maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
212 int annotationHeight = 0;
213 AnnotationLabels labels = null;
215 if (av.isShowAnnotation())
217 AnnotationPanel ap = new AnnotationPanel(av);
218 annotationHeight = ap.adjustPanelHeight();
219 labels = new AnnotationLabels(av);
221 int hgap = avcharHeight;
222 if (av.getScaleAboveWrapped())
224 hgap += avcharHeight;
227 int cHeight = alheight * avcharHeight + hgap + annotationHeight;
229 int rowSize = av.getEndRes() - av.getStartRes();
231 // Draw the rest of the panels
232 for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
233 && (row < maxwidth); ypos += cHeight, row += rowSize)
235 for (int i = starty; i < alheight; i++)
238 SequenceI s = av.getAlignment().getSequenceAt(i);
240 if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
244 drawIdString(gg, s, i, 0, ypos);
249 gg.translate(0, ypos + (alheight * avcharHeight));
250 labels.drawComponent(gg, getSize().width);
251 gg.translate(0, -ypos - (alheight * avcharHeight));
258 // Now draw the id strings
260 for (int i = starty; i < endy; i++)
263 seq = av.getAlignment().getSequenceAt(i);
269 // boolean isrep=false;
270 if (av.isDisplayReferenceSeq() || av.hasHiddenRows())
276 // Selected sequence colours
277 if ((searchResults != null) && searchResults.contains(seq))
279 currentColor = Color.black;
280 currentTextColor = Color.white;
282 else if ((av.getSelectionGroup() != null)
283 && av.getSelectionGroup().getSequences(null).contains(seq))
285 currentColor = Color.lightGray;
286 currentTextColor = Color.black;
290 currentColor = av.getSequenceColour(seq);
291 currentTextColor = Color.black;
294 gg.setColor(currentColor);
295 // TODO: isrep could be used to highlight the representative in a
297 gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
299 gg.setColor(currentTextColor);
301 gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
302 (((i - starty) * avcharHeight) + avcharHeight)
303 - (avcharHeight / 5));
305 if (av.hasHiddenRows() && av.getShowHiddenMarkers())
307 drawMarker(i, starty, 0);
313 public void setHighlighted(List<SequenceI> list)
315 searchResults = list;
319 void drawMarker(int i, int starty, int yoffset)
321 SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
322 // Use this method here instead of calling hiddenSeq adjust
324 int hSize = hseqs.length;
327 int lastIndex = i - 1;
328 int nextIndex = i + 1;
330 for (int j = 0; j < hSize; j++)
332 if (hseqs[j] != null)
334 if (j - 1 < hiddenIndex)
338 if (j - 1 < lastIndex)
342 if (j - 1 < nextIndex)
349 boolean below = (hiddenIndex > lastIndex + 1);
350 boolean above = (nextIndex > hiddenIndex + 1);
352 gg.setColor(Color.blue);
355 gg.fillPolygon(new int[]
356 { getSize().width - avcharHeight, getSize().width - avcharHeight,
357 getSize().width }, new int[]
358 { (i - starty) * avcharHeight + yoffset,
359 (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
360 (i - starty) * avcharHeight + yoffset }, 3);
364 gg.fillPolygon(new int[]
365 { getSize().width - avcharHeight, getSize().width - avcharHeight,
366 getSize().width }, new int[]
367 { (i - starty + 1) * avcharHeight + yoffset,
368 (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
369 (i - starty + 1) * avcharHeight + yoffset }, 3);
374 boolean setHiddenFont(SequenceI seq)
376 Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
379 if (av.isHiddenRepSequence(seq))