2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 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
21 import jalview.datamodel.*;
23 import jalview.schemes.*;
33 public class SequenceRenderer
37 boolean renderGaps = true;
38 SequenceGroup currentSequenceGroup = null;
39 SequenceGroup[] allGroups = null;
42 boolean monospacedFont;
43 boolean forOverview = false;
46 * Creates a new SequenceRenderer object.
48 * @param av DOCUMENT ME!
50 public SequenceRenderer(AlignViewport av)
58 * @param b DOCUMENT ME!
60 public void prepare(Graphics g, boolean renderGaps)
63 fm = g.getFontMetrics();
65 // If EPS graphics, stringWidth will be a double, not an int
66 double dwidth = fm.getStringBounds("M", g).getWidth();
69 (dwidth == fm.getStringBounds("|",g).getWidth()
70 && (float)av.charWidth == dwidth);
72 this.renderGaps = renderGaps;
76 public Color getResidueBoxColour(SequenceI seq, int i)
78 allGroups = av.alignment.findAllGroups(seq);
80 if (inCurrentSequenceGroup(i))
82 if (currentSequenceGroup.getDisplayBoxes())
84 getBoxColour(currentSequenceGroup.cs, seq, i);
87 else if (av.getShowBoxes())
89 getBoxColour(av.globalColourScheme, seq, i);
99 * @param cs DOCUMENT ME!
100 * @param seq DOCUMENT ME!
101 * @param i DOCUMENT ME!
103 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
107 resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
109 else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
111 resBoxColour = Color.lightGray;
115 resBoxColour = Color.white;
122 * @param g DOCUMENT ME!
123 * @param seq DOCUMENT ME!
124 * @param sg DOCUMENT ME!
125 * @param start DOCUMENT ME!
126 * @param end DOCUMENT ME!
127 * @param x1 DOCUMENT ME!
128 * @param y1 DOCUMENT ME!
129 * @param width DOCUMENT ME!
130 * @param height DOCUMENT ME!
132 public void drawSequence(SequenceI seq, SequenceGroup[] sg,
133 int start, int end, int y1)
137 drawBoxes(seq, start, end, y1);
139 if (av.validCharWidth)
140 drawText(seq, start, end, y1);
146 * @param seq DOCUMENT ME!
147 * @param start DOCUMENT ME!
148 * @param end DOCUMENT ME!
149 * @param x1 DOCUMENT ME!
150 * @param y1 DOCUMENT ME!
151 * @param width DOCUMENT ME!
152 * @param height DOCUMENT ME!
154 public synchronized void drawBoxes(SequenceI seq, int start, int end, int y1)
157 int length = seq.getLength();
160 int curWidth = av.charWidth;
162 Color tempColour = null;
166 resBoxColour = Color.white;
170 if (inCurrentSequenceGroup(i))
172 if (currentSequenceGroup.getDisplayBoxes())
174 getBoxColour(currentSequenceGroup.cs, seq, i);
177 else if (av.getShowBoxes())
179 getBoxColour(av.globalColourScheme, seq, i);
184 if (resBoxColour != tempColour)
186 if (tempColour != null)
188 graphics.fillRect( av.charWidth * (curStart - start), y1,
189 curWidth, av.charHeight);
192 graphics.setColor(resBoxColour);
195 curWidth = av.charWidth;
196 tempColour = resBoxColour;
200 curWidth += av.charWidth;
206 graphics.fillRect( av.charWidth * (curStart - start), y1, curWidth,
214 * @param seq DOCUMENT ME!
215 * @param start DOCUMENT ME!
216 * @param end DOCUMENT ME!
217 * @param x1 DOCUMENT ME!
218 * @param y1 DOCUMENT ME!
219 * @param width DOCUMENT ME!
220 * @param height DOCUMENT ME!
222 public void drawText(SequenceI seq, int start, int end, int y1)
224 y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
228 if(end+1>=seq.getLength())
229 end = seq.getLength()-1;
230 graphics.setColor(Color.black);
233 if(monospacedFont && av.showText && allGroups.length==0 && !av.getColourText())
236 graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
239 char gap = av.getGapCharacter();
240 graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);
245 for (int i = start; i <= end; i++)
247 graphics.setColor(Color.black);
248 s = seq.getCharAt(i);
249 if (!renderGaps && jalview.util.Comparison.isGap(s))
254 if (inCurrentSequenceGroup(i))
256 if (!currentSequenceGroup.getDisplayText())
261 if (currentSequenceGroup.getColourText())
263 getBoxColour(currentSequenceGroup.cs, seq, i);
264 graphics.setColor(resBoxColour.darker());
269 if (!av.getShowText())
274 if (av.getColourText())
276 getBoxColour(av.globalColourScheme, seq, i);
278 if (av.getShowBoxes())
280 graphics.setColor(resBoxColour.darker());
284 graphics.setColor(resBoxColour);
289 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
291 // System.out.print(s);
292 graphics.drawString(String.valueOf(s),
293 charOffset + av.charWidth * (i - start),
297 // System.out.println("\n");
304 * @param res DOCUMENT ME!
306 * @return DOCUMENT ME!
308 boolean inCurrentSequenceGroup(int res)
310 if (allGroups == null)
315 for (int i = 0; i < allGroups.length; i++)
317 if ((allGroups[i].getStartRes() <= res) &&
318 (allGroups[i].getEndRes() >= res))
320 currentSequenceGroup = allGroups[i];
332 * @param seq DOCUMENT ME!
333 * @param start DOCUMENT ME!
334 * @param end DOCUMENT ME!
335 * @param x1 DOCUMENT ME!
336 * @param y1 DOCUMENT ME!
337 * @param width DOCUMENT ME!
338 * @param height DOCUMENT ME!
340 public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
342 int pady = av.charHeight / 5;
344 graphics.setColor(Color.BLACK);
345 graphics.fillRect(x1, y1, av.charWidth * (end - start + 1), av.charHeight);
346 graphics.setColor(Color.white);
350 // Need to find the sequence position here.
351 if(av.validCharWidth)
353 for (int i = start; i <= end; i++)
355 if (i < seq.getLength())
357 s = seq.getSequence().charAt(i);
360 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
361 graphics.drawString(String.valueOf(s),
362 charOffset + x1 + (av.charWidth * (i - start)),
363 (y1 + av.charHeight) - pady);
368 public void drawCursor(SequenceI seq, int res, int x1, int y1)
370 int pady = av.charHeight / 5;
372 graphics.setColor(Color.black);
373 graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
375 if(av.validCharWidth)
377 graphics.setColor(Color.white);
379 char s = seq.getCharAt(res);
381 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
382 graphics.drawString(String.valueOf(s),
384 (y1 + av.charHeight) - pady);