2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2007 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.appletgui;
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25 import jalview.datamodel.*;
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31 * @version $Revision$
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33 public class FeatureRenderer
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37 Hashtable featureColours = new Hashtable();
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39 // A higher level for grouping features of a
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41 Hashtable featureGroups = null;
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43 // Holds web links for feature groups and feature types
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44 // in the form label|link
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45 Hashtable featureLinks = null;
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47 // This is actually an Integer held in the hashtable,
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48 // Retrieved using the key feature type
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49 Object currentColour;
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51 String[] renderOrder;
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56 float transparency = 1f;
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58 TransparencySetter transparencySetter = null;
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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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69 if (!System.getProperty("java.version").startsWith("1.1"))
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71 transparencySetter = new TransparencySetter();
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75 public void transferSettings(FeatureRenderer fr)
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77 renderOrder = fr.renderOrder;
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78 featureGroups = fr.featureGroups;
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79 featureColours = fr.featureColours;
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80 transparency = fr.transparency;
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83 public Color findFeatureColour(Color initialCol, SequenceI seq, int i)
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86 if (!av.showSequenceFeatures)
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92 sequenceFeatures = lastSequence.getSequenceFeatures();
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93 if (sequenceFeatures == null)
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98 sfSize = sequenceFeatures.length;
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100 if (jalview.util.Comparison.isGap(lastSequence.getCharAt(i)))
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102 return Color.white;
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105 currentColour = null;
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107 drawSequence(null, lastSequence, lastSequence.findPosition(i), -1, -1);
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109 if (currentColour == null)
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114 return new Color( ( (Integer) currentColour).intValue());
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118 * This is used by the Molecule Viewer to get the accurate colour
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119 * of the rendered sequence
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121 boolean overview = false;
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123 int white = Color.white.getRGB();
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124 public int findFeatureColour(int initialCol, int seqIndex, int column)
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126 if (!av.showSequenceFeatures)
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131 if (seqIndex != lastSequenceIndex)
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133 lastSequence = av.alignment.getSequenceAt(seqIndex);
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134 lastSequenceIndex = seqIndex;
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135 sequenceFeatures = lastSequence.getSequenceFeatures();
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136 if (sequenceFeatures == null)
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141 sfSize = sequenceFeatures.length;
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144 if (jalview.util.Comparison.isGap(lastSequence.getCharAt(column)))
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146 return Color.white.getRGB();
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149 currentColour = null;
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151 drawSequence(null, lastSequence, lastSequence.findPosition(column), -1, -1);
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153 if (currentColour == null)
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158 return ( (Integer) currentColour).intValue();
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164 * @param g DOCUMENT ME!
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165 * @param seq DOCUMENT ME!
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166 * @param sg DOCUMENT ME!
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167 * @param start DOCUMENT ME!
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168 * @param end DOCUMENT ME!
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169 * @param x1 DOCUMENT ME!
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170 * @param y1 DOCUMENT ME!
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171 * @param width DOCUMENT ME!
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172 * @param height DOCUMENT ME!
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175 // SequenceFeature sf;
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176 int lastSequenceIndex = -1;
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177 SequenceI lastSequence;
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178 SequenceFeature[] sequenceFeatures;
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179 int sfSize, sfindex, spos, epos;
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181 public void drawSequence(Graphics g, SequenceI seq,
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182 int start, int end, int y1)
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184 if (seq.getSequenceFeatures() == null
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185 || seq.getSequenceFeatures().length == 0)
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190 if (transparencySetter != null && g != null)
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192 transparencySetter.setTransparency(g, transparency);
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195 if (av.featuresDisplayed == null || renderOrder == null)
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198 if (av.featuresDisplayed.size() < 1)
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203 sequenceFeatures = seq.getSequenceFeatures();
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204 sfSize = sequenceFeatures.length;
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206 if (lastSequence == null || seq != lastSequence)
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208 lastSequence = seq;
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209 sequenceFeatures = seq.getSequenceFeatures();
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210 sfSize = sequenceFeatures.length;
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214 spos = lastSequence.findPosition(start);
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215 epos = lastSequence.findPosition(end);
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218 fm = g.getFontMetrics();
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222 for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)
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224 type = renderOrder[renderIndex];
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225 if (!av.featuresDisplayed.containsKey(type))
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230 // loop through all features in sequence to find
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231 // current feature to render
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232 for (sfindex = 0; sfindex < sfSize; sfindex++)
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234 if (!sequenceFeatures[sfindex].type.equals(type))
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239 if (featureGroups != null
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240 && sequenceFeatures[sfindex].featureGroup != null
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242 featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
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244 ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].
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251 if (!overview && (sequenceFeatures[sfindex].getBegin() > epos
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252 || sequenceFeatures[sfindex].getEnd() < spos))
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259 if (sequenceFeatures[sfindex].begin <= start &&
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260 sequenceFeatures[sfindex].end >= start)
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262 currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
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267 else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
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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].begin) - 1,
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273 new Color( ( (Integer) av.featuresDisplayed.get(
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274 sequenceFeatures[sfindex].type)).intValue()),
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276 renderFeature(g, seq,
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277 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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278 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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279 new Color( ( (Integer) av.featuresDisplayed.get(
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280 sequenceFeatures[sfindex].type)).intValue()),
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286 renderFeature(g, seq,
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287 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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288 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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289 getColour(sequenceFeatures[sfindex].type),
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296 if (transparencySetter != null && g != null)
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298 transparencySetter.setTransparency(g, 1.0f);
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304 void renderFeature(Graphics g, SequenceI seq,
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305 int fstart, int fend, Color featureColour, int start,
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309 if ( ( (fstart <= end) && (fend >= start)))
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311 if (fstart < start)
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312 { // fix for if the feature we have starts before the sequence start,
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313 fstart = start; // but the feature end is still valid!!
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321 for (i = fstart; i <= fend; i++)
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323 s = seq.getCharAt(i);
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325 if (jalview.util.Comparison.isGap(s))
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330 g.setColor(featureColour);
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332 g.fillRect( (i - start) * av.charWidth, y1, av.charWidth, av.charHeight);
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334 if (!av.validCharWidth)
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339 g.setColor(Color.white);
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340 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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341 g.drawString(String.valueOf(s),
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342 charOffset + (av.charWidth * (i - start)),
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343 (y1 + av.charHeight) - av.charHeight / 5); //pady = height / 5;
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349 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 av.featuresDisplayed = new Hashtable();
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355 Vector allfeatures = new Vector();
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356 for (int i = 0; i < av.alignment.getHeight(); i++)
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358 SequenceFeature[] features = av.alignment.getSequenceAt(i).
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359 getSequenceFeatures();
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361 if (features == null)
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367 while (index < features.length)
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369 if (!av.featuresDisplayed.containsKey(features[index].getType()))
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371 if (getColour(features[index].getType()) == null)
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373 featureColours.put(features[index].getType(),
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374 ucs.createColourFromName(features[index].
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378 av.featuresDisplayed.put(features[index].getType(),
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379 new Integer(getColour(features[index].
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380 getType()).getRGB()));
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381 allfeatures.addElement(features[index].getType());
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387 renderOrder = new String[allfeatures.size()];
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388 Enumeration en = allfeatures.elements();
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389 int i = allfeatures.size() - 1;
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390 while (en.hasMoreElements())
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392 renderOrder[i] = en.nextElement().toString();
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397 public Color getColour(String featureType)
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399 return (Color) featureColours.get(featureType);
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402 public void addNewFeature(String name, Color col)
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405 setColour(name, col);
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406 if (av.featuresDisplayed == null)
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408 av.featuresDisplayed = new Hashtable();
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411 av.featuresDisplayed.put(name, "NOGROUP");
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414 public void setColour(String featureType, Color col)
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416 featureColours.put(featureType, col);
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419 public void setFeaturePriority(Object[][] data)
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421 // The feature table will display high priority
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422 // features at the top, but theses are the ones
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423 // we need to render last, so invert the data
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424 if (av.featuresDisplayed != null)
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426 av.featuresDisplayed.clear();
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429 renderOrder = new String[data.length];
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431 if (data.length > 0)
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433 for (int i = 0; i < data.length; i++)
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435 String type = data[i][0].toString();
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436 setColour(type, (Color) data[i][1]);
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437 if ( ( (Boolean) data[i][2]).booleanValue())
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439 av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
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442 renderOrder[data.length - i - 1] = type;
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448 class TransparencySetter
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450 void setTransparency(Graphics g, float value)
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452 Graphics2D g2 = (Graphics2D) g;
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454 AlphaComposite.getInstance(
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455 AlphaComposite.SRC_OVER, value));
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