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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20 package jalview.appletgui;
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22 import jalview.datamodel.*;
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26 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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41 public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height)
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43 Vector features = seq.getSequenceFeatures();
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44 Enumeration e = features.elements();
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45 while( e.hasMoreElements() )
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47 SequenceFeature sf = (SequenceFeature)e.nextElement();
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48 if(sf.getStart()>seq.getEnd())
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51 int fstart = seq.findIndex(sf.getStart())-1;
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52 int fend = seq.findIndex(sf.getEnd())-1;
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54 if( (fstart<=end && fend>=start) )
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56 if(fstart<0) // fix for if the feature we have starts before the sequence start,
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57 fstart = 0;// but the feature end is still valid!!
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61 g.setColor(Color.red);
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62 g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
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63 g.setColor(Color.white);
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65 char s = seq.getSequence().charAt(fstart);
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66 FontMetrics fm = g.getFontMetrics();
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67 int charOffset = (width - fm.charWidth(s))/2;
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68 int pady = height/5;
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69 g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);
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74 for (int i = fstart; i <= fend; i++)
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76 char s = seq.getSequence().charAt(i);
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77 if( jalview.util.Comparison.isGap(s) )
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80 g.setColor(Color.blue);
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81 g.fillRect( (i-start) * width, y1, width, height);
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83 g.setColor(Color.white);
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85 FontMetrics fm = g.getFontMetrics();
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86 int charOffset = (width - fm.charWidth(s)) / 2;
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87 int pady = height / 5;
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88 g.drawString(String.valueOf(s),
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89 charOffset + x1 + width * (i-start),
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90 y1 + height - pady);
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