2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
23 import jalview.datamodel.*;
24 import jalview.schemes.*;
32 public class SequenceRenderer
38 boolean renderGaps = true;
40 SequenceGroup currentSequenceGroup = null;
42 SequenceGroup[] allGroups = null;
48 boolean monospacedFont;
50 boolean forOverview = false;
53 * Creates a new SequenceRenderer object.
58 public SequenceRenderer(AlignViewport av)
69 public void prepare(Graphics g, boolean renderGaps)
72 fm = g.getFontMetrics();
74 // If EPS graphics, stringWidth will be a double, not an int
75 double dwidth = fm.getStringBounds("M", g).getWidth();
77 monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth);
79 this.renderGaps = renderGaps;
82 public Color getResidueBoxColour(SequenceI seq, int i)
84 allGroups = av.alignment.findAllGroups(seq);
86 if (inCurrentSequenceGroup(i))
88 if (currentSequenceGroup.getDisplayBoxes())
90 getBoxColour(currentSequenceGroup.cs, seq, i);
93 else if (av.getShowBoxes())
95 getBoxColour(av.globalColourScheme, seq, i);
111 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
115 resBoxColour = cs.findColour(seq.getCharAt(i), i);
118 && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
120 resBoxColour = Color.lightGray;
124 resBoxColour = Color.white;
150 public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
155 drawBoxes(seq, start, end, y1);
157 if (av.validCharWidth)
159 drawText(seq, start, end, y1);
181 public synchronized void drawBoxes(SequenceI seq, int start, int end,
184 if (seq==null) return; // fix for racecondition
186 int length = seq.getLength();
189 int curWidth = av.charWidth;
191 Color tempColour = null;
195 resBoxColour = Color.white;
199 if (inCurrentSequenceGroup(i))
201 if (currentSequenceGroup.getDisplayBoxes())
203 getBoxColour(currentSequenceGroup.cs, seq, i);
206 else if (av.getShowBoxes())
208 getBoxColour(av.globalColourScheme, seq, i);
213 if (resBoxColour != tempColour)
215 if (tempColour != null)
217 graphics.fillRect(av.charWidth * (curStart - start), y1,
218 curWidth, av.charHeight);
221 graphics.setColor(resBoxColour);
224 curWidth = av.charWidth;
225 tempColour = resBoxColour;
229 curWidth += av.charWidth;
235 graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
258 public void drawText(SequenceI seq, int start, int end, int y1)
260 y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
264 if (end + 1 >= seq.getLength())
266 end = seq.getLength() - 1;
268 graphics.setColor(av.textColour);
270 if (monospacedFont && av.showText && allGroups.length == 0
271 && !av.getColourText() && av.thresholdTextColour == 0)
275 graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
279 char gap = av.getGapCharacter();
280 graphics.drawString(seq.getSequenceAsString(start, end + 1)
281 .replace(gap, ' '), 0, y1);
286 boolean getboxColour = false;
287 for (int i = start; i <= end; i++)
289 graphics.setColor(av.textColour);
290 getboxColour = false;
291 s = seq.getCharAt(i);
292 if (!renderGaps && jalview.util.Comparison.isGap(s))
297 if (inCurrentSequenceGroup(i))
299 if (!currentSequenceGroup.getDisplayText())
304 if (currentSequenceGroup.thresholdTextColour > 0
305 || currentSequenceGroup.getColourText())
308 getBoxColour(currentSequenceGroup.cs, seq, i);
310 if (currentSequenceGroup.getColourText())
312 graphics.setColor(resBoxColour.darker());
315 if (currentSequenceGroup.thresholdTextColour > 0)
317 if (resBoxColour.getRed() + resBoxColour.getBlue()
318 + resBoxColour.getGreen() < currentSequenceGroup.thresholdTextColour)
320 graphics.setColor(currentSequenceGroup.textColour2);
326 graphics.setColor(currentSequenceGroup.textColour);
328 if (currentSequenceGroup.getShowunconserved()) // todo optimize
330 // todo - use sequence group consensus
331 s = getDisplayChar(av.consensus, i, s, '.');
338 if (!av.getShowText())
343 if (av.getColourText())
346 getBoxColour(av.globalColourScheme, seq, i);
348 if (av.getShowBoxes())
350 graphics.setColor(resBoxColour.darker());
354 graphics.setColor(resBoxColour);
358 if (av.thresholdTextColour > 0)
362 getBoxColour(av.globalColourScheme, seq, i);
365 if (resBoxColour.getRed() + resBoxColour.getBlue()
366 + resBoxColour.getGreen() < av.thresholdTextColour)
368 graphics.setColor(av.textColour2);
371 if (av.showUnconserved)
373 s = getDisplayChar(av.consensus, i, s, '.');
379 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
380 graphics.drawString(String.valueOf(s), charOffset + av.charWidth
386 private char getDisplayChar(AlignmentAnnotation consensus, int position, char s, char c)
388 char conschar = consensus.annotations[position].displayCharacter.charAt(0);
389 if (conschar!='-' && s==conschar)
402 * @return DOCUMENT ME!
404 boolean inCurrentSequenceGroup(int res)
406 if (allGroups == null)
411 for (int i = 0; i < allGroups.length; i++)
413 if ((allGroups[i].getStartRes() <= res)
414 && (allGroups[i].getEndRes() >= res))
416 currentSequenceGroup = allGroups[i];
443 public void drawHighlightedText(SequenceI seq, int start, int end,
446 int pady = av.charHeight / 5;
448 graphics.setColor(Color.BLACK);
449 graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
451 graphics.setColor(Color.white);
455 // Need to find the sequence position here.
456 if (av.validCharWidth)
458 for (int i = start; i <= end; i++)
460 if (i < seq.getLength())
462 s = seq.getCharAt(i);
465 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
467 .drawString(String.valueOf(s), charOffset + x1
468 + (av.charWidth * (i - start)),
469 (y1 + av.charHeight) - pady);
474 public void drawCursor(SequenceI seq, int res, int x1, int y1)
476 int pady = av.charHeight / 5;
478 graphics.setColor(Color.black);
479 graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
481 if (av.validCharWidth)
483 graphics.setColor(Color.white);
485 char s = seq.getCharAt(res);
487 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
488 graphics.drawString(String.valueOf(s), charOffset + x1,
489 (y1 + av.charHeight) - pady);