2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 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 Hashtable featureColours = new Hashtable();
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47 // A higher level for grouping features of a
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49 Hashtable featureGroups = null;
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51 // This is actually an Integer held in the hashtable,
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52 // Retrieved using the key feature type
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53 Object currentColour;
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55 String [] renderOrder;
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58 * Creates a new FeatureRenderer object.
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60 * @param av DOCUMENT ME!
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62 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 return new Color( findFeatureColour (initialCol.getRGB(),
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84 * This is used by the Molecule Viewer and Overview to
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85 * get the accurate colourof the rendered sequence
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87 public int findFeatureColour(int initialCol, SequenceI seq, int column)
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89 if(!av.showSequenceFeatures)
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95 sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
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96 if(sequenceFeatures==null)
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99 sfSize = sequenceFeatures.length;
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102 if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
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103 return Color.white.getRGB();
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106 //Only bother making an offscreen image if transparency is applied
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107 if(transparency!=1.0f && offscreenImage==null)
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109 offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
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112 currentColour = null;
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114 offscreenRender = true;
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116 if(offscreenImage!=null)
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118 offscreenImage.setRGB(0,0,initialCol);
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119 drawSequence(offscreenImage.getGraphics(),
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123 return offscreenImage.getRGB(0,0);
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129 lastSeq.findPosition(column),
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132 if (currentColour == null)
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135 return ((Integer)currentColour).intValue();
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145 * @param g DOCUMENT ME!
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146 * @param seq DOCUMENT ME!
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147 * @param sg DOCUMENT ME!
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148 * @param start DOCUMENT ME!
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149 * @param end DOCUMENT ME!
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150 * @param x1 DOCUMENT ME!
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151 * @param y1 DOCUMENT ME!
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152 * @param width DOCUMENT ME!
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153 * @param height DOCUMENT ME!
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156 // SequenceFeature sf;
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158 SequenceFeature [] sequenceFeatures;
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159 int sfSize, sfindex, spos, epos;
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161 public void drawSequence(Graphics g, SequenceI seq,
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162 int start, int end, int y1)
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164 if ( seq.getDatasetSequence().getSequenceFeatures() == null
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165 || seq.getDatasetSequence().getSequenceFeatures().length==0)
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169 fm = g.getFontMetrics();
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172 if (av.featuresDisplayed == null
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173 || renderOrder==null
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174 || newFeatureAdded)
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177 if(av.featuresDisplayed.size()<1)
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180 sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
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181 sfSize = sequenceFeatures.length;
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184 if(lastSeq==null || seq!=lastSeq)
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187 sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
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188 sfSize = sequenceFeatures.length;
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192 if (transparency != 1 && g!=null)
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194 Graphics2D g2 = (Graphics2D) g;
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196 AlphaComposite.getInstance(
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197 AlphaComposite.SRC_OVER, transparency));
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200 if(!offscreenRender)
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202 spos = lastSeq.findPosition(start);
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203 epos = lastSeq.findPosition(end);
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208 for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
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210 type = renderOrder[renderIndex];
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212 if(!av.featuresDisplayed.containsKey(type))
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215 // loop through all features in sequence to find
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216 // current feature to render
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217 for (sfindex = 0; sfindex < sfSize; sfindex++)
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219 if(sequenceFeatures.length<=sfindex)
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223 if (!sequenceFeatures[sfindex].type.equals(type))
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226 if (featureGroups != null
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227 && sequenceFeatures[sfindex].featureGroup != null
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229 featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
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231 ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
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237 if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
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238 || sequenceFeatures[sfindex].getEnd() < spos))
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241 if (offscreenRender && offscreenImage==null)
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243 if (sequenceFeatures[sfindex].begin <= start &&
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244 sequenceFeatures[sfindex].end >= start)
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246 currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
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250 else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
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253 renderFeature(g, seq,
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254 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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255 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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256 new Color( ( (Integer) av.featuresDisplayed.get(
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257 sequenceFeatures[sfindex].type)).intValue()),
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259 renderFeature(g, seq,
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260 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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261 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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262 new Color( ( (Integer) av.featuresDisplayed.get(
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263 sequenceFeatures[sfindex].type)).intValue()),
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268 renderFeature(g, seq,
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269 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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270 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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271 getColour(sequenceFeatures[sfindex].type),
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279 if(transparency!=1.0f && g!=null)
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281 Graphics2D g2 = (Graphics2D) g;
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283 AlphaComposite.getInstance(
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284 AlphaComposite.SRC_OVER, 1.0f));
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291 void renderFeature(Graphics g, SequenceI seq,
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292 int fstart, int fend, Color featureColour, int start, int end, int y1)
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295 if (((fstart <= end) && (fend >= start)))
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297 if (fstart < start)
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298 { // fix for if the feature we have starts before the sequence start,
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299 fstart = start; // but the feature end is still valid!!
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306 int pady = (y1 + av.charHeight) - av.charHeight / 5;
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307 for (i = fstart; i <= fend; i++)
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309 s = seq.getSequence().charAt(i);
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311 if (jalview.util.Comparison.isGap(s))
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316 g.setColor(featureColour);
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318 g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
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320 if(offscreenRender || !av.validCharWidth)
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323 g.setColor(Color.white);
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324 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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325 g.drawString(String.valueOf(s),
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326 charOffset + (av.charWidth * (i - start)),
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334 boolean newFeatureAdded = false;
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336 public void featuresAdded()
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341 boolean findingFeatures = false;
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342 synchronized void findAllFeatures()
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344 newFeatureAdded = false;
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346 if(findingFeatures)
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348 newFeatureAdded = true;
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352 findingFeatures = true;
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353 jalview.schemes.UserColourScheme ucs = new
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354 jalview.schemes.UserColourScheme();
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356 if(av.featuresDisplayed==null)
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357 av.featuresDisplayed = new Hashtable();
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359 av.featuresDisplayed.clear();
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361 Vector allfeatures = new Vector();
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362 for (int i = 0; i < av.alignment.getHeight(); i++)
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364 SequenceFeature [] features
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365 = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
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367 if (features == null)
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371 while (index < features.length)
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373 if (!av.featuresDisplayed.containsKey(features[index].getType()))
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375 if(!(features[index].begin == 0 && features[index].end ==0))
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377 // If beginning and end are 0, the feature is for the whole sequence
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378 // and we don't want to render the feature in the normal way
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380 if (getColour(features[index].getType()) == null)
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382 featureColours.put(features[index].getType(),
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383 ucs.createColourFromName(features[index].
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387 av.featuresDisplayed.put(features[index].getType(),
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388 new Integer(getColour(features[index].
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389 getType()).getRGB()));
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390 allfeatures.addElement(features[index].getType());
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397 renderOrder = new String[allfeatures.size()];
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398 Enumeration en = allfeatures.elements();
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399 int i = allfeatures.size()-1;
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400 while(en.hasMoreElements())
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402 renderOrder[i] = en.nextElement().toString();
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406 findingFeatures = false;
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409 public Color getColour(String featureType)
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411 Color colour = (Color)featureColours.get(featureType);
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416 public void addNewFeature(String name, Color col, String group)
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419 setColour(name, col);
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420 if(av.featuresDisplayed==null)
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421 av.featuresDisplayed = new Hashtable();
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426 av.featuresDisplayed.put(name, new Integer(col.getRGB()));
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429 public void setColour(String featureType, Color col)
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431 featureColours.put(featureType, col);
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434 public void setTransparency(float value)
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436 transparency = value;
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439 public float getTransparency()
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441 return transparency;
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444 public void setFeaturePriority(Object [][] data)
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446 // The feature table will display high priority
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447 // features at the top, but theses are the ones
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448 // we need to render last, so invert the data
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449 if(av.featuresDisplayed!=null)
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450 av.featuresDisplayed.clear();
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452 av.featuresDisplayed = new Hashtable();
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454 renderOrder = new String[data.length];
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456 if (data.length > 0)
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457 for (int i = 0; i < data.length; i++)
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459 String type = data[i][0].toString();
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460 setColour(type, (Color) data[i][1]);
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461 if ( ( (Boolean) data[i][2]).booleanValue())
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463 av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
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466 renderOrder[data.length - i - 1] = type;
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