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 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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57 boolean newFeatureAdded = false;
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61 * Creates a new FeatureRenderer object.
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63 * @param av DOCUMENT ME!
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65 public FeatureRenderer(AlignViewport av)
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70 public void transferSettings(FeatureRenderer fr)
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72 renderOrder = fr.renderOrder;
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73 featureGroups = fr.featureGroups;
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74 featureColours = fr.featureColours;
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75 transparency = fr.transparency;
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78 BufferedImage offscreenImage;
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79 boolean offscreenRender = false;
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80 public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
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82 int seqindex = av.alignment.findIndex(seq);
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84 return new Color( findFeatureColour (initialCol.getRGB(),
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89 * This is used by the Molecule Viewer to get the accurate colour
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90 * of the rendered sequence
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92 public int findFeatureColour(int initialCol, int seqIndex, int column)
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94 if(!av.showSequenceFeatures)
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97 if(seqIndex!=lastSequenceIndex)
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99 lastSequence = av.alignment.getSequenceAt(seqIndex);
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100 lastSequenceIndex = seqIndex;
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101 sequenceFeatures = lastSequence.getDatasetSequence().getSequenceFeatures();
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102 if(sequenceFeatures==null)
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105 sfSize = sequenceFeatures.length;
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108 if(jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
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109 return Color.white.getRGB();
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112 //Only bother making an offscreen image if transparency is applied
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113 if(transparency!=1.0f && offscreenImage==null)
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115 offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
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118 currentColour = null;
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120 offscreenRender = true;
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122 if(offscreenImage!=null)
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124 offscreenImage.setRGB(0,0,initialCol);
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125 drawSequence(offscreenImage.getGraphics(),
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129 return offscreenImage.getRGB(0,0);
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135 lastSequence.findPosition(column),
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138 if (currentColour == null)
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141 return ((Integer)currentColour).intValue();
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151 * @param g DOCUMENT ME!
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152 * @param seq DOCUMENT ME!
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153 * @param sg DOCUMENT ME!
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154 * @param start DOCUMENT ME!
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155 * @param end DOCUMENT ME!
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156 * @param x1 DOCUMENT ME!
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157 * @param y1 DOCUMENT ME!
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158 * @param width DOCUMENT ME!
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159 * @param height DOCUMENT ME!
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162 // SequenceFeature sf;
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163 int lastSequenceIndex=-1;
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164 SequenceI lastSequence;
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165 SequenceFeature [] sequenceFeatures;
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166 int sfSize, sfindex, spos, epos;
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168 public void drawSequence(Graphics g, SequenceI seq,
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169 int start, int end, int y1)
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171 if ( seq.getDatasetSequence().getSequenceFeatures() == null
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172 || seq.getDatasetSequence().getSequenceFeatures().length==0)
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177 fm = g.getFontMetrics();
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180 if (av.featuresDisplayed == null
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181 || renderOrder==null
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182 || newFeatureAdded)
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185 if(av.featuresDisplayed.size()<1)
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188 sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
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189 sfSize = sequenceFeatures.length;
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192 if(lastSequence==null || seq!=lastSequence)
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194 lastSequence = seq;
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195 sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
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196 sfSize = sequenceFeatures.length;
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200 if (transparency != 1 && g!=null)
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202 Graphics2D g2 = (Graphics2D) g;
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204 AlphaComposite.getInstance(
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205 AlphaComposite.SRC_OVER, transparency));
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208 if(!offscreenRender)
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210 spos = lastSequence.findPosition(start);
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211 epos = lastSequence.findPosition(end);
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216 for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
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218 type = renderOrder[renderIndex];
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220 if(!av.featuresDisplayed.containsKey(type))
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223 // loop through all features in sequence to find
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224 // current feature to render
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225 for (sfindex = 0; sfindex < sfSize; sfindex++)
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227 if(sequenceFeatures.length<=sfindex)
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231 if (!sequenceFeatures[sfindex].type.equals(type))
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234 if (featureGroups != null
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235 && sequenceFeatures[sfindex].featureGroup != null
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237 featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
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239 ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
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245 if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
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246 || sequenceFeatures[sfindex].getEnd() < spos))
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249 if (offscreenRender && offscreenImage==null)
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251 if (sequenceFeatures[sfindex].begin <= start &&
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252 sequenceFeatures[sfindex].end >= start)
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254 currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
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258 else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
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261 renderFeature(g, seq,
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262 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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263 seq.findIndex(sequenceFeatures[sfindex].begin) - 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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267 renderFeature(g, seq,
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268 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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269 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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270 new Color( ( (Integer) av.featuresDisplayed.get(
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271 sequenceFeatures[sfindex].type)).intValue()),
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276 renderFeature(g, seq,
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277 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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278 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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279 getColour(sequenceFeatures[sfindex].type),
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287 if(transparency!=1.0f && g!=null)
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289 Graphics2D g2 = (Graphics2D) g;
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291 AlphaComposite.getInstance(
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292 AlphaComposite.SRC_OVER, 1.0f));
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299 void renderFeature(Graphics g, SequenceI seq,
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300 int fstart, int fend, Color featureColour, int start, int end, int y1)
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303 if (((fstart <= end) && (fend >= start)))
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305 if (fstart < start)
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306 { // fix for if the feature we have starts before the sequence start,
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307 fstart = start; // but the feature end is still valid!!
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314 int pady = (y1 + av.charHeight) - av.charHeight / 5;
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315 for (i = fstart; i <= fend; i++)
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317 s = seq.getSequence().charAt(i);
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319 if (jalview.util.Comparison.isGap(s))
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324 g.setColor(featureColour);
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326 g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
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328 if(offscreenRender || !av.validCharWidth)
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331 g.setColor(Color.white);
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332 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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333 g.drawString(String.valueOf(s),
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334 charOffset + (av.charWidth * (i - start)),
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342 synchronized public void featuresAdded()
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344 newFeatureAdded = true;
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346 newFeatureAdded = false;
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349 synchronized void findAllFeatures()
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351 jalview.schemes.UserColourScheme ucs = new
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352 jalview.schemes.UserColourScheme();
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354 if(av.featuresDisplayed==null)
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355 av.featuresDisplayed = new Hashtable();
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357 av.featuresDisplayed.clear();
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359 Vector allfeatures = new Vector();
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360 for (int i = 0; i < av.alignment.getHeight(); i++)
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362 SequenceFeature [] features
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363 = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
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365 if (features == null)
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369 while (index < features.length)
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371 if (!av.featuresDisplayed.containsKey(features[index].getType()))
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373 if(!(features[index].begin == 0 && features[index].end ==0))
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375 // If beginning and end are 0, the feature is for the whole sequence
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376 // and we don't want to render the feature in the normal way
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378 if (getColour(features[index].getType()) == null)
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380 featureColours.put(features[index].getType(),
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381 ucs.createColourFromName(features[index].
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385 av.featuresDisplayed.put(features[index].getType(),
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386 new Integer(getColour(features[index].
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387 getType()).getRGB()));
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388 allfeatures.addElement(features[index].getType());
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395 renderOrder = new String[allfeatures.size()];
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396 Enumeration en = allfeatures.elements();
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397 int i = allfeatures.size()-1;
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398 while(en.hasMoreElements())
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400 renderOrder[i] = en.nextElement().toString();
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405 public Color getColour(String featureType)
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407 Color colour = (Color)featureColours.get(featureType);
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412 public void addNewFeature(String name, Color col, String group)
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415 setColour(name, col);
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416 if(av.featuresDisplayed==null)
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417 av.featuresDisplayed = new Hashtable();
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422 av.featuresDisplayed.put(name, new Integer(col.getRGB()));
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425 public void setColour(String featureType, Color col)
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427 featureColours.put(featureType, col);
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430 public void setTransparency(float value)
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432 transparency = value;
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435 public float getTransparency()
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437 return transparency;
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440 public void setFeaturePriority(Object [][] data)
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442 // The feature table will display high priority
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443 // features at the top, but theses are the ones
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444 // we need to render last, so invert the data
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445 if(av.featuresDisplayed!=null)
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446 av.featuresDisplayed.clear();
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448 av.featuresDisplayed = new Hashtable();
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450 renderOrder = new String[data.length];
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452 if (data.length > 0)
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453 for (int i = 0; i < data.length; i++)
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455 String type = data[i][0].toString();
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456 setColour(type, (Color) data[i][1]);
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457 if ( ( (Boolean) data[i][2]).booleanValue())
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459 av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
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462 renderOrder[data.length - i - 1] = type;
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