2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
22 import jalview.datamodel.*;
23 import jalview.schemes.*;
31 public class SequenceRenderer implements jalview.api.SequenceRenderer
37 boolean renderGaps = true;
39 SequenceGroup currentSequenceGroup = null;
41 SequenceGroup[] allGroups = null;
47 boolean monospacedFont;
49 boolean forOverview = false;
52 * Creates a new SequenceRenderer object.
57 public SequenceRenderer(AlignViewport av)
68 public void prepare(Graphics g, boolean renderGaps)
71 fm = g.getFontMetrics();
73 // If EPS graphics, stringWidth will be a double, not an int
74 double dwidth = fm.getStringBounds("M", g).getWidth();
76 monospacedFont = (dwidth == fm.getStringBounds("|", g).getWidth() && (float) av.charWidth == dwidth);
78 this.renderGaps = renderGaps;
81 public Color getResidueBoxColour(SequenceI seq, int i)
83 allGroups = av.alignment.findAllGroups(seq);
85 if (inCurrentSequenceGroup(i))
87 if (currentSequenceGroup.getDisplayBoxes())
89 getBoxColour(currentSequenceGroup.cs, seq, i);
92 else if (av.getShowBoxes())
94 getBoxColour(av.globalColourScheme, seq, i);
110 void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
114 resBoxColour = cs.findColour(seq.getCharAt(i), i);
117 && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
119 resBoxColour = Color.lightGray;
123 resBoxColour = Color.white;
149 public void drawSequence(SequenceI seq, SequenceGroup[] sg, int start,
154 drawBoxes(seq, start, end, y1);
156 if (av.validCharWidth)
158 drawText(seq, start, end, y1);
180 public synchronized void drawBoxes(SequenceI seq, int start, int end,
184 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.getShowNonconserved()) // 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
387 private char getDisplayChar(AlignmentAnnotation consensus, int position,
390 char conschar = consensus.annotations[position].displayCharacter
392 if (conschar != '-' && s == conschar)
405 * @return DOCUMENT ME!
407 boolean inCurrentSequenceGroup(int res)
409 if (allGroups == null)
414 for (int i = 0; i < allGroups.length; i++)
416 if ((allGroups[i].getStartRes() <= res)
417 && (allGroups[i].getEndRes() >= res))
419 currentSequenceGroup = allGroups[i];
446 public void drawHighlightedText(SequenceI seq, int start, int end,
449 int pady = av.charHeight / 5;
451 graphics.setColor(Color.BLACK);
452 graphics.fillRect(x1, y1, av.charWidth * (end - start + 1),
454 graphics.setColor(Color.white);
458 // Need to find the sequence position here.
459 if (av.validCharWidth)
461 for (int i = start; i <= end; i++)
463 if (i < seq.getLength())
465 s = seq.getCharAt(i);
468 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
469 graphics.drawString(String.valueOf(s), charOffset + x1
470 + (av.charWidth * (i - start)), (y1 + av.charHeight) - pady);
475 public void drawCursor(SequenceI seq, int res, int x1, int y1)
477 int pady = av.charHeight / 5;
479 graphics.setColor(Color.black);
480 graphics.fillRect(x1, y1, av.charWidth, av.charHeight);
482 if (av.validCharWidth)
484 graphics.setColor(Color.white);
486 char s = seq.getCharAt(res);
488 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
489 graphics.drawString(String.valueOf(s), charOffset + x1,
490 (y1 + av.charHeight) - pady);