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.JComboBox;
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29 import javax.swing.JPanel;
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30 import javax.swing.JLabel;
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31 import javax.swing.JOptionPane;
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38 * @version $Revision$
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40 public class FeatureRenderer
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44 float transparency = 1.0f;
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48 Hashtable featureColours = new Hashtable();
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51 // A higher level for grouping features of a
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53 Hashtable featureGroups = null;
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55 // This is actually an Integer held in the hashtable,
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56 // Retrieved using the key feature type
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57 Object currentColour;
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59 String [] renderOrder;
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62 * Creates a new FeatureRenderer object.
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64 * @param av DOCUMENT ME!
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66 public FeatureRenderer(AlignViewport av)
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71 public void transferSettings(FeatureRenderer fr)
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73 renderOrder = fr.renderOrder;
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74 featureGroups = fr.featureGroups;
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75 featureColours = fr.featureColours;
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76 transparency = fr.transparency;
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79 BufferedImage offscreenImage;
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80 boolean offscreenRender = false;
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81 public Color findFeatureColour(Color initialCol, SequenceI seq, int res)
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83 return new Color( findFeatureColour (initialCol.getRGB(),
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88 * This is used by the Molecule Viewer and Overview to
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89 * get the accurate colourof the rendered sequence
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91 public int findFeatureColour(int initialCol, SequenceI seq, int column)
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93 if(!av.showSequenceFeatures)
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99 sequenceFeatures = lastSeq.getDatasetSequence().getSequenceFeatures();
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100 if(sequenceFeatures==null)
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103 sfSize = sequenceFeatures.length;
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106 if(jalview.util.Comparison.isGap(lastSeq.getCharAt(column)))
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107 return Color.white.getRGB();
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110 //Only bother making an offscreen image if transparency is applied
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111 if(transparency!=1.0f && offscreenImage==null)
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113 offscreenImage = new BufferedImage(1,1,BufferedImage.TYPE_INT_ARGB);
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116 currentColour = null;
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118 offscreenRender = true;
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120 if(offscreenImage!=null)
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122 offscreenImage.setRGB(0,0,initialCol);
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123 drawSequence(offscreenImage.getGraphics(),
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127 return offscreenImage.getRGB(0,0);
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133 lastSeq.findPosition(column),
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136 if (currentColour == null)
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139 return ((Integer)currentColour).intValue();
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149 * @param g DOCUMENT ME!
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150 * @param seq DOCUMENT ME!
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151 * @param sg DOCUMENT ME!
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152 * @param start DOCUMENT ME!
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153 * @param end DOCUMENT ME!
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154 * @param x1 DOCUMENT ME!
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155 * @param y1 DOCUMENT ME!
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156 * @param width DOCUMENT ME!
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157 * @param height DOCUMENT ME!
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160 // SequenceFeature sf;
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162 SequenceFeature [] sequenceFeatures;
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163 int sfSize, sfindex, spos, epos;
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165 public void drawSequence(Graphics g, SequenceI seq,
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166 int start, int end, int y1)
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168 if ( seq.getDatasetSequence().getSequenceFeatures() == null
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169 || seq.getDatasetSequence().getSequenceFeatures().length==0)
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173 fm = g.getFontMetrics();
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176 if (av.featuresDisplayed == null
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177 || renderOrder==null
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178 || newFeatureAdded)
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181 if(av.featuresDisplayed.size()<1)
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184 sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
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185 sfSize = sequenceFeatures.length;
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188 if(lastSeq==null || seq!=lastSeq)
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191 sequenceFeatures = seq.getDatasetSequence().getSequenceFeatures();
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192 sfSize = sequenceFeatures.length;
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196 if (transparency != 1 && g!=null)
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198 Graphics2D g2 = (Graphics2D) g;
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200 AlphaComposite.getInstance(
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201 AlphaComposite.SRC_OVER, transparency));
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204 if(!offscreenRender)
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206 spos = lastSeq.findPosition(start);
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207 epos = lastSeq.findPosition(end);
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212 for(int renderIndex=0; renderIndex<renderOrder.length; renderIndex++)
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214 type = renderOrder[renderIndex];
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216 if(!av.featuresDisplayed.containsKey(type))
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219 // loop through all features in sequence to find
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220 // current feature to render
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221 for (sfindex = 0; sfindex < sfSize; sfindex++)
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223 if(sequenceFeatures.length<=sfindex)
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227 if (!sequenceFeatures[sfindex].type.equals(type))
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230 if (featureGroups != null
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231 && sequenceFeatures[sfindex].featureGroup != null
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233 featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)
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235 ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].featureGroup)).
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241 if (!offscreenRender && (sequenceFeatures[sfindex].getBegin() > epos
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242 || sequenceFeatures[sfindex].getEnd() < spos))
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245 if (offscreenRender && offscreenImage==null)
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247 if (sequenceFeatures[sfindex].begin <= start &&
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248 sequenceFeatures[sfindex].end >= start)
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250 currentColour = av.featuresDisplayed.get(sequenceFeatures[sfindex].
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254 else if (sequenceFeatures[sfindex].type.equals("disulfide bond"))
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257 renderFeature(g, seq,
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258 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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259 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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260 new Color( ( (Integer) av.featuresDisplayed.get(
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261 sequenceFeatures[sfindex].type)).intValue()),
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263 renderFeature(g, seq,
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264 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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265 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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266 new Color( ( (Integer) av.featuresDisplayed.get(
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267 sequenceFeatures[sfindex].type)).intValue()),
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272 renderFeature(g, seq,
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273 seq.findIndex(sequenceFeatures[sfindex].begin) - 1,
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274 seq.findIndex(sequenceFeatures[sfindex].end) - 1,
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275 getColour(sequenceFeatures[sfindex].type),
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283 if(transparency!=1.0f && g!=null)
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285 Graphics2D g2 = (Graphics2D) g;
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287 AlphaComposite.getInstance(
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288 AlphaComposite.SRC_OVER, 1.0f));
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295 void renderFeature(Graphics g, SequenceI seq,
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296 int fstart, int fend, Color featureColour, int start, int end, int y1)
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299 if (((fstart <= end) && (fend >= start)))
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301 if (fstart < start)
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302 { // fix for if the feature we have starts before the sequence start,
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303 fstart = start; // but the feature end is still valid!!
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310 int pady = (y1 + av.charHeight) - av.charHeight / 5;
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311 for (i = fstart; i <= fend; i++)
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313 s = seq.getSequence().charAt(i);
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315 if (jalview.util.Comparison.isGap(s))
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320 g.setColor(featureColour);
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322 g.fillRect( (i - start) * av.charWidth, y1, av.charWidth,av.charHeight);
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324 if(offscreenRender || !av.validCharWidth)
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327 g.setColor(Color.white);
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328 charOffset = (av.charWidth - fm.charWidth(s)) / 2;
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329 g.drawString(String.valueOf(s),
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330 charOffset + (av.charWidth * (i - start)),
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338 boolean newFeatureAdded = false;
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340 public void featuresAdded()
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345 boolean findingFeatures = false;
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346 synchronized void findAllFeatures()
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348 newFeatureAdded = false;
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350 if(findingFeatures)
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352 newFeatureAdded = true;
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356 findingFeatures = true;
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357 jalview.schemes.UserColourScheme ucs = new
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358 jalview.schemes.UserColourScheme();
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360 if(av.featuresDisplayed==null)
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361 av.featuresDisplayed = new Hashtable();
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363 av.featuresDisplayed.clear();
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365 Vector allfeatures = new Vector();
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366 for (int i = 0; i < av.alignment.getHeight(); i++)
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368 SequenceFeature [] features
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369 = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
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371 if (features == null)
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375 while (index < features.length)
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377 if (!av.featuresDisplayed.containsKey(features[index].getType()))
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379 if(!(features[index].begin == 0 && features[index].end ==0))
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381 // If beginning and end are 0, the feature is for the whole sequence
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382 // and we don't want to render the feature in the normal way
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384 if (getColour(features[index].getType()) == null)
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386 featureColours.put(features[index].getType(),
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387 ucs.createColourFromName(features[index].
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391 av.featuresDisplayed.put(features[index].getType(),
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392 new Integer(getColour(features[index].
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393 getType()).getRGB()));
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394 allfeatures.addElement(features[index].getType());
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401 renderOrder = new String[allfeatures.size()];
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402 Enumeration en = allfeatures.elements();
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403 int i = allfeatures.size()-1;
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404 while(en.hasMoreElements())
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406 renderOrder[i] = en.nextElement().toString();
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410 findingFeatures = false;
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413 public Color getColour(String featureType)
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415 Color colour = (Color)featureColours.get(featureType);
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420 static String lastFeatureAdded = "feature_1";
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421 static String lastSourceAdded = "Jalview";
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423 public boolean createNewFeatures(SequenceI[] sequences,
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424 SequenceFeature [] features)
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427 JComboBox name = new JComboBox();
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428 JComboBox source = new JComboBox();
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430 JPanel panel = new JPanel(new GridLayout(2, 2));
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431 panel.add(new JLabel("New Sequence Feature Name"));
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433 panel.add(new JLabel("Source:"));
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435 // name.setPreferredSize(new Dimension(300, 20));
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436 name.setEditable(true);
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437 source.setEditable(true);
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440 if (av.featuresDisplayed != null)
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442 en = av.featuresDisplayed.keys();
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443 while (en.hasMoreElements())
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445 name.addItem(en.nextElement().toString());
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449 if (featureGroups != null)
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451 en = featureGroups.keys();
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452 while (en.hasMoreElements())
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454 source.addItem(en.nextElement().toString());
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458 name.setSelectedItem(lastFeatureAdded);
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459 source.setSelectedItem(lastSourceAdded);
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461 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
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462 panel, "Create New Sequence Feature(s)",
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463 JOptionPane.OK_CANCEL_OPTION);
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466 if(reply==JOptionPane.OK_OPTION
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467 && name.getSelectedItem()!=null
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468 && source.getSelectedItem()!=null)
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470 lastFeatureAdded = name.getSelectedItem().toString();
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471 lastSourceAdded = source.getSelectedItem().toString();
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472 for(int i=0; i<sequences.length; i++)
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474 features[i].type = lastFeatureAdded;
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475 features[i].featureGroup = lastSourceAdded;
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476 sequences[i].addSequenceFeature(features[i]);
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479 if (av.featuresDisplayed == null)
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480 av.featuresDisplayed = new Hashtable();
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482 if(featureGroups==null)
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483 featureGroups = new Hashtable();
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485 featureGroups.put(lastSourceAdded, new Boolean(true));
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487 Color col = getColour(lastFeatureAdded);
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490 col = new Color(60, 160, 115);
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491 setColour(lastFeatureAdded, col);
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494 av.featuresDisplayed.put(lastSourceAdded, new Integer(col.getRGB()));
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503 public void setColour(String featureType, Color col)
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505 featureColours.put(featureType, col);
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508 public void setTransparency(float value)
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510 transparency = value;
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513 public float getTransparency()
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515 return transparency;
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518 public void setFeaturePriority(Object [][] data)
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520 // The feature table will display high priority
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521 // features at the top, but theses are the ones
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522 // we need to render last, so invert the data
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523 if(av.featuresDisplayed!=null)
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524 av.featuresDisplayed.clear();
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526 av.featuresDisplayed = new Hashtable();
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528 renderOrder = new String[data.length];
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530 if (data.length > 0)
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531 for (int i = 0; i < data.length; i++)
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533 String type = data[i][0].toString();
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534 setColour(type, (Color) data[i][1]);
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535 if ( ( (Boolean) data[i][2]).booleanValue())
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537 av.featuresDisplayed.put(type, new Integer(getColour(type).getRGB()));
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540 renderOrder[data.length - i - 1] = type;
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