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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44 // A higher level for grouping features of a
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46 Hashtable featureGroups = null;
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49 // This is actually an Integer held in the hashtable,
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50 // Retrieved using the key feature type
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51 Object currentColour;
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53 String [] renderOrder;
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57 * Creates a new FeatureRenderer object.
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59 * @param av DOCUMENT ME!
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61 public FeatureRenderer(AlignViewport av)
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67 public void transferSettings(FeatureRenderer fr)
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69 renderOrder = fr.renderOrder;
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70 featureGroups = fr.featureGroups;
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71 featureColours = fr.featureColours;
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72 transparency = fr.transparency;
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75 BufferedImage offscreenImage;
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76 boolean offscreenRender = false;
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77 public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
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79 int seqindex = av.alignment.findIndex(seq);
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81 return new Color( findFeatureColour (initialCol.getRGB(),
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86 * This is used by the Molecule Viewer to get the accurate colour
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87 * of the rendered sequence
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89 public int findFeatureColour(int initialCol, int seqIndex, int column)
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91 if(!av.showSequenceFeatures)
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94 if(seqIndex!=lastSequenceIndex)
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96 lastSequence = av.alignment.getSequenceAt(seqIndex);
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97 lastSequenceIndex = seqIndex;
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98 sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
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99 if(sequenceFeatures==null)
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102 sfSize = sequenceFeatures.length;
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105 if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
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106 return Color.white.getRGB();
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109 //Only bother making an offscreen image if transparency is applied
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110 if(transparency!=1.0f && offscreenImage==null)
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112 offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
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115 currentColour = null;
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117 offscreenRender = true;
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119 if(offscreenImage!=null)
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121 offscreenImage.setRGB(0,0,initialCol);
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122 drawSequence(offscreenImage.getGraphics(),
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126 return offscreenImage.getRGB(0,0);
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132 lastSequence.findPosition(column),
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135 if (currentColour == null)
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138 return ((Integer)currentColour).intValue();
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148 * @param g DOCUMENT ME!
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149 * @param seq DOCUMENT ME!
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150 * @param sg DOCUMENT ME!
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151 * @param start DOCUMENT ME!
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152 * @param end DOCUMENT ME!
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153 * @param x1 DOCUMENT ME!
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154 * @param y1 DOCUMENT ME!
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155 * @param width DOCUMENT ME!
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156 * @param height DOCUMENT ME!
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159 // SequenceFeature sf;
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160 int lastSequenceIndex=-1;
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161 SequenceI lastSequence;
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162 SequenceFeature [] sequenceFeatures;
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163 int sfSize, sfindex, spos, epos;
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165 public void drawSequence(Graphics g, SequenceI seq,
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166 int start, int end, int y1)
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168 if ( seq.getDatasetSequence().getSequenceFeatures() == null
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169 || seq.getDatasetSequence().getSequenceFeatures().length==0)
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174 fm = g.getFontMetrics();
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177 if (av.featuresDisplayed == null || renderOrder==null)
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180 if(av.featuresDisplayed.size()<1)
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183 sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
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184 sfSize = sequenceFeatures.length;
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187 if(lastSequence==null || seq!=lastSequence)
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189 lastSequence = seq;
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190 sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
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191 sfSize = sequenceFeatures.length;
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195 if (transparency != 1 && g!=null)
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197 Graphics2D g2 = (Graphics2D) g;
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199 AlphaComposite.getInstance(
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200 AlphaComposite.SRC_OVER, transparency));
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203 if(!offscreenRender)
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205 spos = lastSequence.findPosition(start);
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206 epos = lastSequence.findPosition(end);
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211 for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
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213 type = renderOrder[renderIndex];
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214 if(!av.featuresDisplayed.containsKey(type))
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217 // loop through all features in sequence to find
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218 // current feature to render
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219 for (sfindex = 0; sfindex < sfSize; sfindex++)
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221 if(sequenceFeatures.length<=sfindex)
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225 if (!sequenceFeatures[sfindex].type.equals(type))
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228 if (featureGroups != null
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229 && sequenceFeatures[sfindex].featureGroup != null
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231 featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
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233 ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
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239 if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
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240 || sequenceFeatures[sfindex].getEnd() < spos))
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243 if (offscreenRender && offscreenImage==null)
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245 if (sequenceFeatures[sfindex].begin <= start &&
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246 sequenceFeatures[sfindex].end >= start)
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248 currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
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252 else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
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255 renderFeature(g, seq,
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256 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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257 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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258 new Color( ( (Integer) av.featuresDisplayed.get(
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259 sequenceFeatures[sfindex].type)).intValue()),
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261 renderFeature(g, seq,
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262 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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263 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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264 new Color( ( (Integer) av.featuresDisplayed.get(
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265 sequenceFeatures[sfindex].type)).intValue()),
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270 renderFeature(g, seq,
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271 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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272 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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273 getColour(sequenceFeatures[sfindex].type),
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281 if(transparency!=1.0f && g!=null)
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283 Graphics2D g2 = (Graphics2D) g;
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285 AlphaComposite.getInstance(
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286 AlphaComposite.SRC_OVER, 1.0f));
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293 void renderFeature(Graphics g, SequenceI seq,
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294 int fstart, int fend, Color featureColour, int start, int end, int y1)
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297 if (((fstart <= end) && (fend >= start)))
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299 if (fstart < start)
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300 { // fix for if the feature we have starts before the sequence start,
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301 fstart = start; // but the feature end is still valid!!
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308 int pady = (y1 + av.charHeight) - av.charHeight / 5;
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309 for (i = fstart; i <= fend; i++)
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311 s = seq.getSequence().charAt(i);
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313 if (jalview.util.Comparison.isGap(s))
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318 g.setColor(featureColour);
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320 g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
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322 if(offscreenRender || !av.validCharWidth)
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325 g.setColor(Color.white);
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326 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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327 g.drawString(String.valueOf(s),
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328 charOffset + (av.charWidth * (i - start)),
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335 void findAllFeatures()
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337 av.featuresDisplayed = new Hashtable();
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338 Vector allfeatures = new Vector();
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339 for (int i = 0; i < av.alignment.getHeight(); i++)
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341 SequenceFeature [] features
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342 = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
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344 if (features == null)
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348 while (index < features.length)
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350 if (!av.featuresDisplayed.containsKey(features[index].getType()))
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352 av.featuresDisplayed.put(features[index].getType(),
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353 new Integer( getColour(features[index].getType()).getRGB()) );
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354 allfeatures.addElement(features[index].getType());
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360 renderOrder = new String[allfeatures.size()];
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361 Enumeration en = allfeatures.elements();
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362 int i = allfeatures.size()-1;
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363 while(en.hasMoreElements())
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365 renderOrder[i] = en.nextElement().toString();
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370 public Color getColour(String featureType)
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372 return (Color)featureColours.get(featureType);
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375 public void addNewFeature(String name, Color col, String group)
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378 setColour(name, col);
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379 if(av.featuresDisplayed==null)
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380 av.featuresDisplayed = new Hashtable();
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385 av.featuresDisplayed.put(name, new Integer(col.getRGB()));
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388 public void setColour(String featureType, Color col)
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390 featureColours.put(featureType, col);
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393 public void setTransparency(float value)
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395 transparency = value;
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398 public float getTransparency()
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400 return transparency;
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403 public void setFeaturePriority(Object [][] data)
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405 // The feature table will display high priority
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406 // features at the top, but theses are the ones
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407 // we need to render last, so invert the data
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408 if(av.featuresDisplayed!=null)
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409 av.featuresDisplayed.clear();
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411 av.featuresDisplayed = new Hashtable();
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413 renderOrder = new String[data.length];
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415 if (data.length > 0)
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416 for (int i = 0; i < data.length; i++)
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418 String type = data[i][0].toString();
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419 setColour(type, (Color) data[i][1]);
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420 if ( ( (Boolean) data[i][2]).booleanValue())
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422 av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
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425 renderOrder[data.length - i - 1] = type;
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430 Hashtable featureColours = new Hashtable();
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433 featureColours.put("active site", new Color(255, 75, 0));
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434 featureColours.put("binding site", new Color(245, 85, 0));
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435 featureColours.put("calcium-binding region", new Color(235, 95, 0));
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436 featureColours.put("chain", new Color(225, 105, 0));
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437 featureColours.put("coiled-coil region", new Color(215, 115, 0));
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438 featureColours.put("compositionally biased region", new Color(205, 125, 0));
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439 featureColours.put("cross-link", new Color(195, 135, 0));
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440 featureColours.put("disulfide bond", new Color(230,230,0));
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441 featureColours.put("DNA-binding region", new Color(175, 155, 0));
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442 featureColours.put("domain", new Color(165, 165, 0));
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443 featureColours.put("glycosylation site", new Color(155, 175, 0));
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444 featureColours.put("helix", new Color(145, 185, 0));
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445 featureColours.put("initiator methionine", new Color(135, 195, 5));
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446 featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));
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447 featureColours.put("metal ion-binding site", new Color(115, 215, 25));
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448 featureColours.put("modified residue", new Color(105, 225, 35));
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449 featureColours.put("mutagenesis site", new Color(95, 235, 45));
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450 featureColours.put("non-consecutive residues", new Color(85, 245, 55));
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451 featureColours.put("non-terminal residue", new Color(75, 255, 65));
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452 featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));
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453 featureColours.put("peptide", new Color(55, 235, 85));
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454 featureColours.put("propeptide", new Color(45, 225, 95));
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455 featureColours.put("region of interest", new Color(35, 215, 105));
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456 featureColours.put("repeat", new Color(25, 205, 115));
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457 featureColours.put("selenocysteine", new Color(15, 195, 125));
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458 featureColours.put("sequence conflict", new Color(5, 185, 135));
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459 featureColours.put("sequence variant", new Color(0, 175, 145));
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460 featureColours.put("short sequence motif", new Color(0, 165, 155));
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461 featureColours.put("signal peptide", new Color(0, 155, 165));
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462 featureColours.put("site", new Color(0, 145, 175));
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463 featureColours.put("splice variant", new Color(0, 135, 185));
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464 featureColours.put("strand", new Color(0, 125, 195));
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465 featureColours.put("topological domain", new Color(0, 115, 205));
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466 featureColours.put("transit peptide", new Color(0, 105, 215));
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467 featureColours.put("transmembrane region", new Color(0, 95, 225));
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468 featureColours.put("turn", new Color(0, 85, 235));
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469 featureColours.put("unsure residue", new Color(0, 75, 245));
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470 featureColours.put("zinc finger region", new Color(0, 65, 255));
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