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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28 import javax.swing.*;
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29 import javax.swing.JOptionPane;
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30 import java.awt.event.*;
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37 * @version $Revision$
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39 public class FeatureRenderer
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43 float transparency = 1.0f;
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47 Hashtable featureColours = new Hashtable();
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50 // A higher level for grouping features of a
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52 Hashtable featureGroups = null;
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54 // This is actually an Integer held in the hashtable,
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55 // Retrieved using the key feature type
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56 Object currentColour;
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58 String [] renderOrder;
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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 return new Color( findFeatureColour (initialCol.getRGB(),
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87 * This is used by the Molecule Viewer and Overview to
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88 * get the accurate colourof the rendered sequence
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90 public int findFeatureColour(int initialCol, SequenceI seq, int column)
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92 if(!av.showSequenceFeatures)
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98 sequenceFeatures = lastSeq.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(lastSeq.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 lastSeq.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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161 SequenceFeature [] sequenceFeatures;
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162 int sfSize, sfindex, spos, epos;
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164 public void drawSequence(Graphics g, SequenceI seq,
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165 int start, int end, int y1)
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167 if ( seq.getDatasetSequence().getSequenceFeatures() == null
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168 || seq.getDatasetSequence().getSequenceFeatures().length==0)
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172 fm = g.getFontMetrics();
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175 if (av.featuresDisplayed == null
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176 || renderOrder==null
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177 || newFeatureAdded)
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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(lastSeq==null || seq!=lastSeq)
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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 = lastSeq.findPosition(start);
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206 epos = lastSeq.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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215 if(type==null || !av.featuresDisplayed.containsKey(type))
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218 // loop through all features in sequence to find
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219 // current feature to render
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220 for (sfindex = 0; sfindex < sfSize; sfindex++)
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222 if(sequenceFeatures.length<=sfindex)
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226 if (!sequenceFeatures[sfindex].type.equals(type))
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229 if (featureGroups != null
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230 && sequenceFeatures[sfindex].featureGroup != null
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232 featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
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234 ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
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240 if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
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241 || sequenceFeatures[sfindex].getEnd() < spos))
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244 if (offscreenRender && offscreenImage==null)
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246 if (sequenceFeatures[sfindex].begin <= start &&
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247 sequenceFeatures[sfindex].end >= start)
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249 currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
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253 else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
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256 renderFeature(g, seq,
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257 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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258 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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259 new Color( ( (Integer) av.featuresDisplayed.get(
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260 sequenceFeatures[sfindex].type)).intValue()),
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262 renderFeature(g, seq,
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263 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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264 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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265 new Color( ( (Integer) av.featuresDisplayed.get(
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266 sequenceFeatures[sfindex].type)).intValue()),
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271 renderFeature(g, seq,
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272 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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273 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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274 getColour(sequenceFeatures[sfindex].type),
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282 if(transparency!=1.0f && g!=null)
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284 Graphics2D g2 = (Graphics2D) g;
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286 AlphaComposite.getInstance(
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287 AlphaComposite.SRC_OVER, 1.0f));
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294 void renderFeature(Graphics g, SequenceI seq,
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295 int fstart, int fend, Color featureColour, int start, int end, int y1)
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298 if (((fstart <= end) && (fend >= start)))
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300 if (fstart < start)
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301 { // fix for if the feature we have starts before the sequence start,
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302 fstart = start; // but the feature end is still valid!!
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309 int pady = (y1 + av.charHeight) - av.charHeight / 5;
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310 for (i = fstart; i <= fend; i++)
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312 s = seq.getCharAt(i);
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314 if (jalview.util.Comparison.isGap(s))
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319 g.setColor(featureColour);
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321 g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
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323 if(offscreenRender || !av.validCharWidth)
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326 g.setColor(Color.white);
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327 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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328 g.drawString(String.valueOf(s),
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329 charOffset + (av.charWidth * (i - start)),
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337 boolean newFeatureAdded = false;
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339 public void featuresAdded()
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344 boolean findingFeatures = false;
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345 synchronized void findAllFeatures()
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347 newFeatureAdded = false;
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349 if(findingFeatures)
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351 newFeatureAdded = true;
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355 findingFeatures = true;
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356 jalview.schemes.UserColourScheme ucs = new
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357 jalview.schemes.UserColourScheme();
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359 if(av.featuresDisplayed==null)
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360 av.featuresDisplayed = new Hashtable();
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362 av.featuresDisplayed.clear();
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364 Vector allfeatures = new Vector();
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365 for (int i = 0; i < av.alignment.getHeight(); i++)
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367 SequenceFeature [] features
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368 = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
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370 if (features == null)
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374 while (index < features.length)
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376 if (!av.featuresDisplayed.containsKey(features[index].getType()))
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378 if(!(features[index].begin == 0 && features[index].end ==0))
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380 // If beginning and end are 0, the feature is for the whole sequence
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381 // and we don't want to render the feature in the normal way
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383 if (getColour(features[index].getType()) == null)
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385 featureColours.put(features[index].getType(),
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386 ucs.createColourFromName(features[index].
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390 av.featuresDisplayed.put(features[index].getType(),
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391 new Integer(getColour(features[index].
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392 getType()).getRGB()));
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393 allfeatures.addElement(features[index].getType());
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400 renderOrder = new String[allfeatures.size()];
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401 Enumeration en = allfeatures.elements();
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402 int i = allfeatures.size()-1;
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403 while(en.hasMoreElements())
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405 renderOrder[i] = en.nextElement().toString();
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409 findingFeatures = false;
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412 public Color getColour(String featureType)
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414 Color colour = (Color)featureColours.get(featureType);
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419 static String lastFeatureAdded;
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420 static String lastFeatureGroupAdded;
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421 static String lastDescriptionAdded;
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423 public boolean createNewFeatures(SequenceI[] sequences,
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424 SequenceFeature [] features)
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426 return amendFeatures(sequences, features, true, null);
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429 int featureIndex = 0;
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430 boolean amendFeatures(final SequenceI[] sequences,
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431 final SequenceFeature[] features,
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432 boolean newFeatures,
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433 final AlignmentPanel ap)
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435 JPanel bigPanel = new JPanel(new BorderLayout());
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436 final JComboBox name = new JComboBox();
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437 final JComboBox source = new JComboBox();
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438 final JTextArea description = new JTextArea(3,25);
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439 final JSpinner start = new JSpinner();
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440 final JSpinner end = new JSpinner();
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441 start.setPreferredSize(new Dimension(80,20));
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442 end.setPreferredSize(new Dimension(80,20));
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443 final JPanel colour = new JPanel();
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444 colour.setBorder(BorderFactory.createEtchedBorder());
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445 colour.setMaximumSize(new Dimension(40,10));
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446 colour.addMouseListener(new MouseAdapter()
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448 public void mousePressed(MouseEvent evt)
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450 colour.setBackground(
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451 JColorChooser.showDialog(Desktop.desktop,
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452 "Select Feature Colour",
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453 colour.getBackground()));
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457 JPanel panel = new JPanel(new GridLayout(3, 2));
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458 panel.add(new JLabel("Sequence Feature Name: ",JLabel.RIGHT));
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460 panel.add(new JLabel("Feature Group: ", JLabel.RIGHT));
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462 panel.add(new JLabel("Feature Colour: ", JLabel.RIGHT));
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463 JPanel tmp = new JPanel();
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465 colour.setPreferredSize(new Dimension(150,15));
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467 name.setEditable(true);
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468 source.setEditable(true);
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470 bigPanel.add(panel, BorderLayout.NORTH);
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471 panel = new JPanel();
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472 panel.add(new JLabel("Description: ", JLabel.RIGHT));
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473 description.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
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474 description.setLineWrap(true);
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475 panel.add(new JScrollPane(description));
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479 bigPanel.add(panel, BorderLayout.SOUTH);
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481 panel = new JPanel();
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482 panel.add(new JLabel(" Start:", JLabel.RIGHT));
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484 panel.add(new JLabel(" End:", JLabel.RIGHT));
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486 bigPanel.add(panel, BorderLayout.CENTER);
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489 bigPanel.add(panel, BorderLayout.CENTER);
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491 if (lastFeatureAdded == null)
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492 if (features[0].type != null)
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493 lastFeatureAdded = features[0].type;
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495 lastFeatureAdded = "feature_1";
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497 if (lastFeatureGroupAdded == null)
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498 if (features[0].featureGroup != null)
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499 lastFeatureGroupAdded = features[0].featureGroup;
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501 lastFeatureAdded = "Jalview";
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505 if (featureGroups != null)
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507 en = featureGroups.keys();
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508 while (en.hasMoreElements())
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510 source.addItem(en.nextElement().toString());
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516 if(av.featuresDisplayed != null)
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518 en = av.featuresDisplayed.keys();
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519 while (en.hasMoreElements())
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521 name.addItem(en.nextElement().toString());
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525 name.setSelectedItem(lastFeatureAdded);
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526 source.setSelectedItem(lastFeatureGroupAdded);
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527 description.setText(
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528 lastDescriptionAdded == null ?
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529 features[0].description : lastDescriptionAdded);
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531 if (getColour(lastFeatureAdded) != null)
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533 colour.setBackground(getColour(lastFeatureAdded));
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537 colour.setBackground(new Color(60, 160, 115));
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541 else if (!newFeatures)
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544 for(int f=0; f<features.length; f++)
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546 name.addItem(features[f].getType().toString());
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549 description.setText(features[0].getDescription());
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550 source.setSelectedItem(features[0].getFeatureGroup());
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551 start.setValue(new Integer(features[0].getBegin()));
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552 end.setValue(new Integer(features[0].getEnd()));
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553 colour.setBackground(
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554 getColour(name.getSelectedItem().toString()));
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555 name.addItemListener(new ItemListener()
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557 public void itemStateChanged(ItemEvent e)
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559 int index = name.getSelectedIndex();
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562 featureIndex = index;
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563 description.setText(features[index].getDescription());
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564 source.setSelectedItem(features[index].getFeatureGroup());
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565 start.setValue(new Integer(features[index].getBegin()));
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566 end.setValue(new Integer(features[index].getEnd()));
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567 colour.setBackground(
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568 getColour(name.getSelectedItem().toString()));
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570 SearchResults highlight = new SearchResults();
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571 highlight.addResult(sequences[0],
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572 features[index].getBegin(),
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573 features[index].getEnd());
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575 ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
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578 Color col = getColour(name.getSelectedItem().toString());
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581 jalview.schemes.UserColourScheme()
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582 .createColourFromName(name.getSelectedItem().toString());
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584 colour.setBackground(col);
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593 options = new Object[]{"Amend", "Delete", "Cancel"};
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595 options = new Object[]{"OK", "Cancel"};
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597 String title = newFeatures ? "Create New Sequence Feature(s)" :
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598 "Amend/Delete Features for "
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599 +sequences[0].getName();
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601 int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
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604 JOptionPane.YES_NO_CANCEL_OPTION,
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605 JOptionPane.QUESTION_MESSAGE,
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609 jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
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611 if (reply == JOptionPane.OK_OPTION
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612 && name.getSelectedItem() != null
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613 && source.getSelectedItem() != null)
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615 //This ensures that the last sequence
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616 //is refreshed and new features are rendered
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618 lastFeatureAdded = name.getSelectedItem().toString();
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619 lastFeatureGroupAdded = source.getSelectedItem().toString();
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620 lastDescriptionAdded = description.getText().replaceAll("\n", " ");
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625 SequenceFeature sf = features[featureIndex];
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627 if(reply==JOptionPane.NO_OPTION)
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628 sequences[0].getDatasetSequence().deleteFeature(sf);
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629 else if(reply==JOptionPane.YES_OPTION)
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631 sf.type = lastFeatureAdded;
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632 sf.featureGroup = lastFeatureGroupAdded;
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633 sf.description = lastDescriptionAdded;
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634 setColour(sf.type, colour.getBackground());
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636 sf.begin = ((Integer)start.getValue()).intValue();
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637 sf.end = ((Integer)end.getValue()).intValue();
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638 }catch(NumberFormatException ex)
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641 ffile.parseDescriptionHTML(sf, false);
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646 if (reply == JOptionPane.OK_OPTION
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647 && name.getSelectedItem() != null
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648 && source.getSelectedItem() != null)
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650 for (int i = 0; i < sequences.length; i++)
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652 features[i].type = lastFeatureAdded;
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653 features[i].featureGroup = lastFeatureGroupAdded;
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654 features[i].description = lastDescriptionAdded;
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655 sequences[i].addSequenceFeature(features[i]);
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656 ffile.parseDescriptionHTML(features[i], false);
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659 if (av.featuresDisplayed == null)
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660 av.featuresDisplayed = new Hashtable();
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662 if (featureGroups == null)
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663 featureGroups = new Hashtable();
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665 featureGroups.put(lastFeatureGroupAdded, new Boolean(true));
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667 Color col = colour.getBackground();
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668 setColour(lastFeatureAdded, colour.getBackground());
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670 av.featuresDisplayed.put(lastFeatureGroupAdded,
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671 new Integer(col.getRGB()));
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681 if(name.getSelectedIndex()==-1)
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688 public void setColour(String featureType, Color col)
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690 featureColours.put(featureType, col);
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693 public void setTransparency(float value)
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695 transparency = value;
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698 public float getTransparency()
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700 return transparency;
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703 public void setFeaturePriority(Object [][] data)
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705 // The feature table will display high priority
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706 // features at the top, but theses are the ones
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707 // we need to render last, so invert the data
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708 if(av.featuresDisplayed!=null)
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709 av.featuresDisplayed.clear();
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711 av.featuresDisplayed = new Hashtable();
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713 renderOrder = new String[data.length];
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715 if (data.length > 0)
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716 for (int i = 0; i < data.length; i++)
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718 String type = data[i][0].toString();
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719 setColour(type, (Color) data[i][1]);
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720 if ( ( (Boolean) data[i][2]).booleanValue())
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722 av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
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725 renderOrder[data.length - i - 1] = type;
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