2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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25 import jalview.datamodel.*;
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27 public class FeatureRenderer
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30 SequenceGroup currentSequenceGroup = null;
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31 SequenceGroup[] allGroups = null;
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35 public FeatureRenderer(AlignViewport av)
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40 public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
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41 int start, int end, int x1, int y1, int width,
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44 Vector features = seq.getSequenceFeatures();
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45 Enumeration e = features.elements();
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47 while (e.hasMoreElements())
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49 SequenceFeature sf = (SequenceFeature) e.nextElement();
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51 if (sf.getStart() > seq.getEnd())
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56 int fstart = seq.findIndex(sf.getStart()) - 1;
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57 int fend = seq.findIndex(sf.getEnd()) - 1;
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59 if ( ( (fstart <= end) && (fend >= start)))
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62 { // fix for if the feature we have starts before the sequence start,
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63 fstart = 0; // but the feature end is still valid!!
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68 g.setColor(Color.red);
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69 g.fillRoundRect( (fstart - start) * width, y1, width,
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71 g.setColor(Color.white);
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73 char s = seq.getSequence().charAt(fstart);
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74 FontMetrics fm = g.getFontMetrics();
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75 int charOffset = (width - fm.charWidth(s)) / 2;
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76 int pady = height / 5;
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77 g.drawString(String.valueOf(s),
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78 charOffset + x1 + (width * (fstart - start)),
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79 (y1 + height) - pady);
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83 for (int i = fstart; i <= fend; i++)
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85 char s = seq.getSequence().charAt(i);
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87 if (jalview.util.Comparison.isGap(s))
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92 g.setColor(Color.blue);
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93 g.fillRect( (i - start) * width, y1, width, height);
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95 g.setColor(Color.white);
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97 FontMetrics fm = g.getFontMetrics();
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98 int charOffset = (width - fm.charWidth(s)) / 2;
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99 int pady = height / 5;
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100 g.drawString(String.valueOf(s),
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101 charOffset + x1 + (width * (i - start)),
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102 (y1 + height) - pady);
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