2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 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
36 boolean renderGaps = true;
37 SequenceGroup currentSequenceGroup = null;
38 SequenceGroup[] allGroups = null;
41 boolean monospacedFont;
42 boolean forOverview = false;
45 * Creates a new SequenceRenderer object.
47 * @param av DOCUMENT ME!
49 public SequenceRenderer(AlignViewport av)
57 * @param b DOCUMENT ME!
59 public void prepare(Graphics g, boolean renderGaps)
62 fm = g.getFontMetrics();
64 // If EPS graphics, stringWidth will be a double, not an int
65 double dwidth = fm.getStringBounds("M", g).getWidth();
68 (dwidth == fm.getStringBounds("|", g).getWidth()
69 && (float) av.charWidth == dwidth);
71 this.renderGaps = renderGaps;
74 public Color getResidueBoxColour(SequenceI seq, int i)
76 allGroups = av.alignment.findAllGroups(seq);
78 if (inCurrentSequenceGroup(i))
80 if (currentSequenceGroup.getDisplayBoxes())
82 getBoxColour(currentSequenceGroup.cs, seq, i);
85 else if (av.getShowBoxes())
87 getBoxColour(av.globalColourScheme, seq, i);
96 * @param cs DOCUMENT ME!
97 * @param seq DOCUMENT ME!
98 * @param i DOCUMENT ME!
100 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
104 resBoxColour = cs.findColour(seq.getCharAt(i), i);
106 else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
108 resBoxColour = Color.lightGray;
112 resBoxColour = Color.white;
119 * @param g DOCUMENT ME!
120 * @param seq DOCUMENT ME!
121 * @param sg DOCUMENT ME!
122 * @param start DOCUMENT ME!
123 * @param end DOCUMENT ME!
124 * @param x1 DOCUMENT ME!
125 * @param y1 DOCUMENT ME!
126 * @param width DOCUMENT ME!
127 * @param height DOCUMENT ME!
129 public void drawSequence(SequenceI seq, SequenceGroup[] sg,
130 int start, int end, int y1)
134 drawBoxes(seq, start, end, y1);
136 if (av.validCharWidth)
138 drawText(seq, start, end, y1);
145 * @param seq DOCUMENT ME!
146 * @param start DOCUMENT ME!
147 * @param end DOCUMENT ME!
148 * @param x1 DOCUMENT ME!
149 * @param y1 DOCUMENT ME!
150 * @param width DOCUMENT ME!
151 * @param height DOCUMENT ME!
153 public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
156 int length = seq.getLength();
159 int curWidth = av.charWidth;
161 Color tempColour = null;
165 resBoxColour = Color.white;
169 if (inCurrentSequenceGroup(i))
171 if (currentSequenceGroup.getDisplayBoxes())
173 getBoxColour(currentSequenceGroup.cs, seq, i);
176 else if (av.getShowBoxes())
178 getBoxColour(av.globalColourScheme, seq, i);
183 if (resBoxColour != tempColour)
185 if (tempColour != null)
187 graphics.fillRect(av.charWidth * (curStart - start), y1,
188 curWidth, av.charHeight);
191 graphics.setColor(resBoxColour);
194 curWidth = av.charWidth;
195 tempColour = resBoxColour;
199 curWidth += av.charWidth;
205 graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
213 * @param seq DOCUMENT ME!
214 * @param start DOCUMENT ME!
215 * @param end DOCUMENT ME!
216 * @param x1 DOCUMENT ME!
217 * @param y1 DOCUMENT ME!
218 * @param width DOCUMENT ME!
219 * @param height DOCUMENT ME!
221 public void drawText(SequenceI seq, int start, int end, int y1)
223 y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
227 if (end + 1 >= seq.getLength())
229 end = seq.getLength() - 1;
231 graphics.setColor(av.textColour);
235 && allGroups.length == 0
236 && !av.getColourText()
237 && av.thresholdTextColour == 0)
241 graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
245 char gap = av.getGapCharacter();
246 graphics.drawString(seq.getSequenceAsString(start, end + 1).replace(gap,
252 boolean getboxColour = false;
253 for (int i = start; i <= end; i++)
255 graphics.setColor(av.textColour);
256 getboxColour = false;
257 s = seq.getCharAt(i);
258 if (!renderGaps && jalview.util.Comparison.isGap(s))
263 if (inCurrentSequenceGroup(i))
265 if (!currentSequenceGroup.getDisplayText())
270 if (currentSequenceGroup.thresholdTextColour > 0
271 || currentSequenceGroup.getColourText())
274 getBoxColour(currentSequenceGroup.cs, seq, i);
276 if (currentSequenceGroup.getColourText())
278 graphics.setColor(resBoxColour.darker());
281 if (currentSequenceGroup.thresholdTextColour > 0)
283 if (resBoxColour.getRed() +
284 resBoxColour.getBlue() +
285 resBoxColour.getGreen() <
286 currentSequenceGroup.thresholdTextColour)
288 graphics.setColor(currentSequenceGroup.textColour2);
294 graphics.setColor(currentSequenceGroup.textColour);
300 if (!av.getShowText())
305 if (av.getColourText())
308 getBoxColour(av.globalColourScheme, seq, i);
310 if (av.getShowBoxes())
312 graphics.setColor(resBoxColour.darker());
316 graphics.setColor(resBoxColour);
320 if (av.thresholdTextColour > 0)
324 getBoxColour(av.globalColourScheme, seq, i);
327 if (resBoxColour.getRed() +
328 resBoxColour.getBlue() +
329 resBoxColour.getGreen() < av.thresholdTextColour)
331 graphics.setColor(av.textColour2);
337 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
338 graphics.drawString(String.valueOf(s),
339 charOffset + av.charWidth * (i - start),
349 * @param res DOCUMENT ME!
351 * @return DOCUMENT ME!
353 boolean inCurrentSequenceGroup(int res)
355 if (allGroups == null)
360 for (int i = 0; i < allGroups.length; i++)
362 if ( (allGroups[i].getStartRes() <= res) &&
363 (allGroups[i].getEndRes() >= res))
365 currentSequenceGroup = allGroups[i];
377 * @param seq DOCUMENT ME!
378 * @param start DOCUMENT ME!
379 * @param end DOCUMENT ME!
380 * @param x1 DOCUMENT ME!
381 * @param y1 DOCUMENT ME!
382 * @param width DOCUMENT ME!
383 * @param height DOCUMENT ME!
385 public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
388 int pady = av.charHeight / 5;
390 graphics.setColor(Color.BLACK);
391 graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
392 graphics.setColor(Color.white);
396 // Need to find the sequence position here.
397 if (av.validCharWidth)
399 for (int i = start; i <= end; i++)
401 if (i < seq.getLength())
403 s = seq.getCharAt(i);
406 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
407 graphics.drawString(String.valueOf(s),
408 charOffset + x1 + (av.charWidth * (i - start)),
409 (y1 + av.charHeight) - pady);
414 public void drawCursor(SequenceI seq, int res, int x1, int y1)
416 int pady = av.charHeight / 5;
418 graphics.setColor(Color.black);
419 graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
421 if (av.validCharWidth)
423 graphics.setColor(Color.white);
425 char s = seq.getCharAt(res);
427 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
428 graphics.drawString(String.valueOf(s),
430 (y1 + av.charHeight) - pady);