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.gui;
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24 import java.util.jar.*;
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26 import javax.swing.*;
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28 import org.exolab.castor.xml.*;
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29 import jalview.binding.*;
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30 import jalview.schemes.*;
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36 * @version $Revision$
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38 public class Jalview2XML_V1
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40 jalview.schemes.UserColourScheme GetUserColourScheme(
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41 JalviewModelSequence jms, String id)
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43 UserColours[] uc = jms.getUserColours();
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44 UserColours colours = null;
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46 for (int i = 0; i < uc.length; i++)
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48 if (uc[i].getId().equals(id))
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56 int csize = colours.getUserColourScheme().getColourCount();
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57 java.awt.Color[] newColours = new java.awt.Color[csize];
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59 for (int i = 0; i < csize; i++)
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61 newColours[i] = new java.awt.Color(Integer.parseInt(
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62 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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65 return new jalview.schemes.UserColourScheme(newColours);
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71 * @param file DOCUMENT ME!
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73 public AlignFrame LoadJalviewAlign(final String file)
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76 jalview.gui.AlignFrame af = null;
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80 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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83 if (file.startsWith("http://"))
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85 url = new URL(file);
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88 JarInputStream jin = null;
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89 JarEntry jarentry = null;
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96 jin = new JarInputStream(url.openStream());
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100 jin = new JarInputStream(new FileInputStream(file));
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103 for (int i = 0; i < entryCount; i++)
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105 jarentry = jin.getNextJarEntry();
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108 class NoDescIDResolver
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109 implements IDResolver
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111 public Object resolve(String idref)
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113 System.out.println(idref + " used");
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118 if (jarentry != null)
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120 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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121 JalviewModel object = new JalviewModel();
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123 object = (JalviewModel) object.unmarshal(in);
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125 af = LoadFromObject(object, file);
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129 while (jarentry != null);
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131 catch (final java.net.UnknownHostException ex)
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133 ex.printStackTrace();
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134 javax.swing.SwingUtilities.invokeLater(new Runnable()
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139 System.err.println("Couldn't locate Jalview XML file : " +
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141 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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142 "Couldn't locate " + file,
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144 JOptionPane.WARNING_MESSAGE);
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148 catch (Exception ex)
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150 ex.printStackTrace();
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151 System.err.println("Exception whilst loading jalview XML file : " +
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153 javax.swing.SwingUtilities.invokeLater(new Runnable()
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158 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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159 "Error loading " + file,
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160 "Error loading Jalview file",
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161 JOptionPane.WARNING_MESSAGE);
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169 AlignFrame LoadFromObject(JalviewModel object, String file)
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171 Vector seqids = new Vector();
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172 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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173 Sequence[] vamsasSeq = vamsasSet.getSequence();
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175 JalviewModelSequence jms = object.getJalviewModelSequence();
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177 //////////////////////////////////
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179 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[
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181 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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182 for (int i = 0; i < vamsasSeq.length; i++)
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184 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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185 vamsasSeq[i].getSequence());
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186 jseqs[i].setStart(JSEQ[i].getStart());
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187 jseqs[i].setEnd(JSEQ[i].getEnd());
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188 seqids.add(jseqs[i]);
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191 ///SequenceFeatures are added to the DatasetSequence,
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192 // so we must create the dataset before loading features
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193 /////////////////////////////////
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194 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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195 al.setDataset(null);
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196 /////////////////////////////////
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198 for (int i = 0; i < vamsasSeq.length; i++)
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200 if (JSEQ[i].getFeaturesCount() > 0)
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202 Features[] features = JSEQ[i].getFeatures();
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203 for (int f = 0; f < features.length; f++)
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205 jalview.datamodel.SequenceFeature sf
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206 = new jalview.datamodel.SequenceFeature(features[f].getType(),
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207 features[f].getDescription(), features[f].getStatus(),
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208 features[f].getBegin(), features[f].getEnd(),
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211 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
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214 if (JSEQ[i].getPdbidsCount() > 0)
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216 Pdbids[] ids = JSEQ[i].getPdbids();
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217 for (int p = 0; p < ids.length; p++)
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219 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
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220 entry.setId(ids[p].getId());
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221 entry.setType(ids[p].getType());
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222 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
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228 /////////////////////////////////
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229 //////////////////////////////////
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231 if (vamsasSet.getAnnotation() != null)
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233 Annotation[] an = vamsasSet.getAnnotation();
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235 for (int i = 0; i < an.length; i++)
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237 AnnotationElement[] ae = an[i].getAnnotationElement();
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238 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
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241 for (int aa = 0; aa < ae.length; aa++)
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243 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
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244 getDisplayCharacter(),
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245 ae[aa].getDescription(),
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246 ae[aa].getSecondaryStructure().charAt(0),
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247 ae[aa].getValue());
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250 jalview.datamodel.AlignmentAnnotation jaa = null;
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252 if (an[i].getGraph())
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254 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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255 an[i].getDescription(), anot, 0, 0,
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256 jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
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260 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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261 an[i].getDescription(), anot);
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264 al.addAnnotation(jaa);
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268 /////////////////////////////////
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270 Viewport[] views = jms.getViewport();
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271 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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273 AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
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275 af.setFileName(file, "Jalview");
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277 for (int i = 0; i < JSEQ.length; i++)
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279 af.viewport.setSequenceColour(
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280 af.viewport.alignment.getSequenceAt(i),
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281 new java.awt.Color(
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282 JSEQ[i].getColour()));
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285 // af.changeColour() );
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286 /////////////////////////
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288 if (jms.getJGroupCount() > 0)
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290 JGroup[] groups = jms.getJGroup();
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292 for (int i = 0; i < groups.length; i++)
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294 ColourSchemeI cs = null;
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296 if (groups[i].getColour() != null)
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298 if (groups[i].getColour().startsWith("ucs"))
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300 cs = GetUserColourScheme(jms, groups[i].getColour());
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304 cs = ColourSchemeProperty.getColour(al,
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305 groups[i].getColour());
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310 cs.setThreshold(groups[i].getPidThreshold(), true);
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315 Vector seqs = new Vector();
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316 int[] ids = groups[i].getSeq();
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318 for (int s = 0; s < ids.length; s++)
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320 seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(
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324 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
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325 SequenceGroup(seqs,
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326 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
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327 groups[i].getDisplayText(), groups[i].getColourText(),
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328 groups[i].getStart(), groups[i].getEnd());
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330 sg.setOutlineColour(new java.awt.Color(
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331 groups[i].getOutlineColour()));
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333 if (groups[i].getConsThreshold() != 0)
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335 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
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337 ResidueProperties.propHash, 3, sg.getSequences(null), 0,
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338 sg.getWidth() - 1);
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340 c.verdict(false, 25);
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341 sg.cs.setConservation(c);
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348 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
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350 af.viewport.setStartRes(view.getStartRes());
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351 af.viewport.setStartSeq(view.getStartSeq());
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352 af.viewport.setShowAnnotation(view.getShowAnnotation());
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353 af.viewport.setAbovePIDThreshold(view.getPidSelected());
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354 af.viewport.setColourText(view.getShowColourText());
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355 af.viewport.setConservationSelected(view.getConservationSelected());
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356 af.viewport.setShowJVSuffix(view.getShowFullId());
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357 af.viewport.setFont(new java.awt.Font(view.getFontName(),
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358 view.getFontStyle(), view.getFontSize()));
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359 af.alignPanel.fontChanged();
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361 af.viewport.setRenderGaps(view.getRenderGaps());
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362 af.viewport.setWrapAlignment(view.getWrapAlignment());
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363 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
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364 af.viewport.setShowAnnotation(view.getShowAnnotation());
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365 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
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366 af.viewport.setShowBoxes(view.getShowBoxes());
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367 af.viewport.setShowText(view.getShowText());
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369 ColourSchemeI cs = null;
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371 if (view.getBgColour() != null)
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373 if (view.getBgColour().startsWith("ucs"))
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375 cs = GetUserColourScheme(jms, view.getBgColour());
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379 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
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384 cs.setThreshold(view.getPidThreshold(), true);
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385 cs.setConsensus(af.viewport.hconsensus);
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389 af.viewport.setGlobalColourScheme(cs);
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390 af.viewport.setColourAppliesToAllGroups(false);
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391 af.changeColour(cs);
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392 if (view.getConservationSelected() && cs != null)
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394 cs.setConservationInc(view.getConsThreshold());
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397 af.viewport.setColourAppliesToAllGroups(true);
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398 af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
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400 if (jms.getFeatureSettings() != null)
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402 af.viewport.featuresDisplayed = new Hashtable();
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403 String[] renderOrder = new String[jms.getFeatureSettings().
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404 getSettingCount()];
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405 for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
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407 Setting setting = jms.getFeatureSettings().getSetting(fs);
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409 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
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411 new java.awt.Color(setting.getColour()));
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413 renderOrder[fs] = setting.getType();
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415 if (setting.getDisplay())
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417 af.viewport.featuresDisplayed.put(
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418 setting.getType(), new Integer(setting.getColour()));
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421 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
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425 af.setMenusFromViewport(af.viewport);
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427 Desktop.addInternalFrame(af, view.getTitle(),
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428 view.getWidth(), view.getHeight());
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431 ///////////////////////////////////////
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432 if (jms.getTreeCount() > 0)
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436 for (int t = 0; t < jms.getTreeCount(); t++)
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439 Tree tree = jms.getTree(t);
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441 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
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442 tree.getNewick()), tree.getTitle(),
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443 tree.getWidth(), tree.getHeight(),
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444 tree.getXpos(), tree.getYpos());
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446 tp.fitToWindow.setState(tree.getFitToWindow());
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447 tp.fitToWindow_actionPerformed(null);
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449 if (tree.getFontName() != null)
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451 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
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452 tree.getFontStyle(),
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453 tree.getFontSize()));
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457 tp.setTreeFont(new java.awt.Font(view.getFontName(),
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458 view.getFontStyle(),
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459 tree.getFontSize()));
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462 tp.showPlaceholders(tree.getMarkUnlinked());
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463 tp.showBootstrap(tree.getShowBootstrap());
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464 tp.showDistances(tree.getShowDistances());
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466 tp.treeCanvas.threshold = tree.getThreshold();
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468 if (tree.getCurrentTree())
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470 af.viewport.setCurrentTree(tp.getTree());
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475 catch (Exception ex)
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477 ex.printStackTrace();
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