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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21 import jalview.datamodel.*;
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27 import java.awt.image.*;
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34 * @version $Revision$
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36 public class FeatureRenderer
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40 float transparency = 1.0f;
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43 boolean drawText = true;
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45 // The following vector holds the features which are
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46 // to be added, in the correct order or rendering
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47 Vector featuresDisplayed = null;
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49 // A higher level for grouping features of a
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51 Hashtable featureGroups = null;
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55 * Creates a new FeatureRenderer object.
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57 * @param av DOCUMENT ME!
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59 public FeatureRenderer(AlignViewport av)
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66 * This is used by the Molecule Viewer to get the accurate colour
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67 * of the rendered sequence
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70 public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
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72 if(!av.showSequenceFeatures)
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76 bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);
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78 bi.setRGB(0,0, initialCol.getRGB());
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82 drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);
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85 return new Color(bi.getRGB(0, 0));
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92 * @param g DOCUMENT ME!
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93 * @param seq DOCUMENT ME!
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94 * @param sg DOCUMENT ME!
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95 * @param start DOCUMENT ME!
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96 * @param end DOCUMENT ME!
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97 * @param x1 DOCUMENT ME!
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98 * @param y1 DOCUMENT ME!
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99 * @param width DOCUMENT ME!
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100 * @param height DOCUMENT ME!
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102 public void drawSequence(Graphics g, SequenceI seq,
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103 int start, int end, int x1, int y1, int width, int height)
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106 //System.out.println(start+" "+end+" "+x1+" "+y1);
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107 if (seq.getDatasetSequence().getSequenceFeatures() == null
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108 || seq.getDatasetSequence().getSequenceFeatures().size()==0)
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111 fm = g.getFontMetrics();
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113 if (transparency != 1)
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115 Graphics2D g2 = (Graphics2D) g;
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117 AlphaComposite.getInstance(
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118 AlphaComposite.SRC_OVER, transparency));
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122 SequenceFeature sf;
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123 if (featuresDisplayed == null)
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126 Enumeration e = featuresDisplayed.elements(), e2;
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128 // Loop through each visible feature
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129 while (e.hasMoreElements())
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132 type = e.nextElement().toString();
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133 e2 = seq.getDatasetSequence().getSequenceFeatures().elements();
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134 // loop through all features in sequence to find
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135 // current feature to render
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136 while (e2.hasMoreElements())
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139 sf = (SequenceFeature) e2.nextElement();
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140 if (!type.equals(sf.getType()))
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143 if(featureGroups!=null
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144 && sf.getFeatureGroup()!=null
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145 && featureGroups.containsKey(sf.getFeatureGroup())
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146 && !((Boolean)featureGroups.get(sf.getFeatureGroup())).booleanValue())
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151 if (sf.getBegin() > seq.getEnd())
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154 if (type.equals("disulfide bond"))
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157 renderFeature(g, seq,
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158 seq.findIndex(sf.getBegin()) - 1,
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159 seq.findIndex(sf.getBegin()) - 1,
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160 type, start, end, x1, y1, width, height);
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161 renderFeature(g, seq,
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162 seq.findIndex(sf.getEnd()) - 1,
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163 seq.findIndex(sf.getEnd()) - 1,
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164 type, start, end, x1, y1, width, height);
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168 renderFeature(g, seq,
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169 seq.findIndex(sf.getBegin()) - 1,
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170 seq.findIndex(sf.getEnd()) - 1,
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171 type, start, end, x1, y1, width, height);
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175 if(transparency!=1.0f)
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177 Graphics2D g2 = (Graphics2D) g;
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179 AlphaComposite.getInstance(
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180 AlphaComposite.SRC_OVER, 1.0f));
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185 void renderFeature(Graphics g, SequenceI seq,
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186 int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)
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189 if (((fstart <= end) && (fend >= start)))
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191 if (fstart < start)
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192 { // fix for if the feature we have starts before the sequence start,
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193 fstart = start; // but the feature end is still valid!!
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200 for (int i = fstart; i <= fend; i++)
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202 char s = seq.getSequence().charAt(i);
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204 if (jalview.util.Comparison.isGap(s))
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209 g.setColor(getColour(type));
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211 g.fillRect( (i - start) * width, y1, width, height);
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215 g.setColor(Color.white);
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216 charOffset = (width - fm.charWidth(s)) / 2;
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217 g.drawString(String.valueOf(s),
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218 charOffset + x1 + (width * (i - start)),
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219 (y1 + height) - height / 5); //pady = height / 5;
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225 void findAllFeatures()
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227 Vector features = new Vector();
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228 SequenceFeature sf;
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229 featuresDisplayed = new Vector();
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231 for (int i = 0; i < av.alignment.getHeight(); i++)
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233 features = av.alignment.getSequenceAt(i).getDatasetSequence().
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234 getSequenceFeatures();
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235 if (features == null)
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238 e = features.elements();
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239 while (e.hasMoreElements())
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241 sf = (SequenceFeature) e.nextElement();
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242 if (!featuresDisplayed.contains(sf.getType()))
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244 featuresDisplayed.addElement(sf.getType());
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250 public Color getColour(String featureType)
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252 return (Color)featureColours.get(featureType);
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255 public void addNewFeature(String name, Color col)
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257 setColour(name, col);
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258 if(featuresDisplayed==null)
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259 featuresDisplayed = new Vector();
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260 featuresDisplayed.insertElementAt(name, 0);
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263 public void setColour(String featureType, Color col)
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265 featureColours.put(featureType, col);
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268 public void setTransparency(float value)
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270 transparency = value;
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273 public float getTransparency()
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275 return transparency;
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278 public void setFeaturePriority(Object [][] data)
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280 // The feature table will display high priority
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281 // features at the top, but theses are the ones
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282 // we need to render last, so invert the data
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283 featuresDisplayed.clear();
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284 for(int i=data.length-1; i>-1; i--)
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286 String type = data[i][0].toString();
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287 setColour(type, (Color)data[i][1]);
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288 if( ((Boolean)data[i][2]).booleanValue() )
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289 featuresDisplayed.addElement(type);
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293 Hashtable featureColours = new Hashtable();
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296 featureColours.put("active site", new Color(255, 75, 0));
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297 featureColours.put("binding site", new Color(245, 85, 0));
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298 featureColours.put("calcium-binding region", new Color(235, 95, 0));
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299 featureColours.put("chain", new Color(225, 105, 0));
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300 featureColours.put("coiled-coil region", new Color(215, 115, 0));
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301 featureColours.put("compositionally biased region", new Color(205, 125, 0));
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302 featureColours.put("cross-link", new Color(195, 135, 0));
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303 featureColours.put("disulfide bond", new Color(230,230,0));
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304 featureColours.put("DNA-binding region", new Color(175, 155, 0));
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305 featureColours.put("domain", new Color(165, 165, 0));
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306 featureColours.put("glycosylation site", new Color(155, 175, 0));
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307 featureColours.put("helix", new Color(145, 185, 0));
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308 featureColours.put("initiator methionine", new Color(135, 195, 5));
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309 featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));
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310 featureColours.put("metal ion-binding site", new Color(115, 215, 25));
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311 featureColours.put("modified residue", new Color(105, 225, 35));
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312 featureColours.put("mutagenesis site", new Color(95, 235, 45));
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313 featureColours.put("non-consecutive residues", new Color(85, 245, 55));
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314 featureColours.put("non-terminal residue", new Color(75, 255, 65));
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315 featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));
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316 featureColours.put("peptide", new Color(55, 235, 85));
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317 featureColours.put("propeptide", new Color(45, 225, 95));
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318 featureColours.put("region of interest", new Color(35, 215, 105));
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319 featureColours.put("repeat", new Color(25, 205, 115));
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320 featureColours.put("selenocysteine", new Color(15, 195, 125));
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321 featureColours.put("sequence conflict", new Color(5, 185, 135));
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322 featureColours.put("sequence variant", new Color(0, 175, 145));
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323 featureColours.put("short sequence motif", new Color(0, 165, 155));
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324 featureColours.put("signal peptide", new Color(0, 155, 165));
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325 featureColours.put("site", new Color(0, 145, 175));
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326 featureColours.put("splice variant", new Color(0, 135, 185));
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327 featureColours.put("strand", new Color(0, 125, 195));
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328 featureColours.put("topological domain", new Color(0, 115, 205));
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329 featureColours.put("transit peptide", new Color(0, 105, 215));
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330 featureColours.put("transmembrane region", new Color(0, 95, 225));
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331 featureColours.put("turn", new Color(0, 85, 235));
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332 featureColours.put("unsure residue", new Color(0, 75, 245));
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333 featureColours.put("zinc finger region", new Color(0, 65, 255));
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