2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.gui;
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24 import java.util.jar.*;
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26 import javax.swing.*;
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28 import jalview.binding.*;
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29 import jalview.io.*;
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30 import jalview.schemes.*;
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32 public class Jalview2XML
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34 // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
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35 public static void SaveState(File statefile)
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37 long creation = System.currentTimeMillis();
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38 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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47 FileOutputStream fos = new FileOutputStream(statefile);
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48 JarOutputStream jout = new JarOutputStream(fos);
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50 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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51 ////////////////////////////////////////////////////
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52 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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55 Vector shortNames = new Vector();
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58 for (int i = frames.length - 1; i > -1; i--)
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60 if (frames[i] instanceof AlignFrame)
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62 AlignFrame af = (AlignFrame) frames[i];
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64 String shortName = af.getTitle();
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66 if (shortName.indexOf(File.separatorChar) > -1)
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68 shortName = shortName.substring(shortName.lastIndexOf(
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69 File.separatorChar) + 1);
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74 while (shortNames.contains(shortName))
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76 if (shortName.endsWith("_" + (count - 1)))
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78 shortName = shortName.substring(0,
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79 shortName.lastIndexOf("_"));
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82 shortName = shortName.concat("_" + count);
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86 shortNames.addElement(shortName);
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88 if (!shortName.endsWith(".xml"))
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90 shortName = shortName + ".xml";
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93 SaveState(af, creation, shortName, jout, out);
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100 catch (Exception ex)
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102 ex.printStackTrace();
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106 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
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107 public static void SaveState(AlignFrame af, String jarFile, String fileName)
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111 FileOutputStream fos = new FileOutputStream(jarFile);
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112 JarOutputStream jout = new JarOutputStream(fos);
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114 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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115 ////////////////////////////////////////////////////
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116 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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119 SaveState(af, System.currentTimeMillis(), fileName, jout, out);
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123 catch (Exception ex)
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128 public static void SaveState(AlignFrame af, long timeStamp,
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129 String fileName, JarOutputStream jout,
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132 Vector seqids = new Vector();
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133 Vector userColours = new Vector();
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135 AlignViewport av = af.viewport;
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137 JalviewModel object = new JalviewModel();
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138 object.setVamsasModel(new VamsasModel());
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140 object.setCreationDate(new java.util.Date(timeStamp));
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142 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
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144 SequenceSet vamsasSet = new SequenceSet();
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145 Sequence vamsasSeq;
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146 JalviewModelSequence jms = new JalviewModelSequence();
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148 vamsasSet.setGapChar(jal.getGapCharacter() + "");
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155 for (int i = 0; i < jal.getHeight(); i++)
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157 seqids.add(jal.getSequenceAt(i));
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159 vamsasSeq = new Sequence();
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160 vamsasSeq.setId(id + "");
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161 vamsasSeq.setName(jal.getSequenceAt(i).getName());
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162 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
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165 jseq.setStart(jal.getSequenceAt(i).getStart());
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166 jseq.setEnd(jal.getSequenceAt(i).getEnd());
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168 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
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173 vamsasSet.addSequence(vamsasSeq);
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178 if (af.viewport.currentTree != null)
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180 object.getVamsasModel().addTree(af.viewport.currentTree.toString());
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184 if (jal.getAlignmentAnnotation() != null)
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186 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
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188 for (int i = 0; i < aa.length; i++)
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190 if (aa[i].label.equals("Quality") ||
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191 aa[i].label.equals("Conservation") ||
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192 aa[i].label.equals("Consensus"))
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197 Annotation an = new Annotation();
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198 an.setDescription(aa[i].description);
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199 an.setGraph(aa[i].isGraph);
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200 an.setLabel(aa[i].label);
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202 AnnotationElement ae;
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204 for (int a = 0; a < aa[i].annotations.length; a++)
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206 if ( (aa[i] == null) || (aa[i].annotations[a] == null))
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211 ae = new AnnotationElement();
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212 ae.setDescription(aa[i].annotations[a].description);
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213 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
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214 ae.setValue(aa[i].annotations[a].value);
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216 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
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218 an.addAnnotationElement(ae);
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221 vamsasSet.addAnnotation(an);
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226 if (jal.getGroups() != null)
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228 JGroup[] groups = new JGroup[jal.getGroups().size()];
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230 for (int i = 0; i < groups.length; i++)
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232 groups[i] = new JGroup();
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234 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
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237 groups[i].setStart(sg.getStartRes());
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238 groups[i].setEnd(sg.getEndRes());
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239 groups[i].setName(sg.getName());
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241 if (sg.cs instanceof ConservationColourScheme)
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243 groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);
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246 if (sg.cs instanceof ResidueColourScheme)
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248 groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).
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251 else if (sg.cs instanceof ScoreColourScheme)
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253 groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
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256 if (sg.cs instanceof jalview.schemes.UserColourScheme)
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258 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
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263 groups[i].setColour(ColourSchemeProperty.getColourName(
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267 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
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268 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
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269 groups[i].setDisplayText(sg.getDisplayText());
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270 groups[i].setColourText(sg.getColourText());
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272 for (int s = 0; s < sg.getSize(); s++)
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274 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.
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276 int index = seqids.indexOf(seq);
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277 groups[i].addSeq(index);
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281 jms.setJGroup(groups);
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284 ///////////SAVE VIEWPORT
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285 Viewport view = new Viewport();
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286 view.setTitle(af.getTitle());
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287 view.setXpos(af.getX());
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288 view.setYpos(af.getY());
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289 view.setWidth(af.getWidth());
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290 view.setHeight(af.getHeight());
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291 view.setStartRes(av.startRes);
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292 view.setStartSeq(av.startSeq);
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294 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
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296 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
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297 userColours, jms));
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301 view.setBgColour(ColourSchemeProperty.getColourName(
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302 av.getGlobalColourScheme()));
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305 ColourSchemeI cs = av.getGlobalColourScheme();
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307 if (cs instanceof ConservationColourScheme)
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309 view.setConsThreshold( ( (ConservationColourScheme) cs).inc);
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312 if (cs instanceof ResidueColourScheme)
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314 view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
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316 else if (cs instanceof ScoreColourScheme)
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318 view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
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321 view.setConservationSelected(av.getConservationSelected());
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322 view.setPidSelected(av.getAbovePIDThreshold());
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323 view.setFontName(av.font.getFontName());
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324 view.setFontSize(av.font.getSize());
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325 view.setFontStyle(av.font.getStyle());
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326 view.setRenderGaps(av.renderGaps);
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327 view.setShowAnnotation(av.getShowAnnotation());
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328 view.setShowBoxes(av.getShowBoxes());
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329 view.setShowColourText(av.getColourText());
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330 view.setShowConservation(av.showConservation);
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331 view.setShowFullId(av.getShowFullId());
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332 view.setShowIdentity(av.showIdentity);
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333 view.setShowQuality(av.showQuality);
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334 view.setShowSequenceFeatures(av.showSequenceFeatures);
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335 view.setShowText(av.getShowText());
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336 view.setWrapAlignment(av.getWrapAlignment());
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338 jms.addViewport(view);
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340 object.setJalviewModelSequence(jms);
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341 object.getVamsasModel().addSequenceSet(vamsasSet);
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345 if (!fileName.endsWith(".xml"))
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347 fileName = fileName + ".xml";
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350 JarEntry entry = new JarEntry(fileName);
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351 jout.putNextEntry(entry);
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353 object.marshal(out);
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355 catch (Exception ex)
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357 ex.printStackTrace();
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361 static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
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362 Vector userColours,
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363 JalviewModelSequence jms)
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366 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
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369 if (!userColours.contains(ucs))
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371 userColours.add(ucs);
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373 java.awt.Color[] colours = ucs.getColours();
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374 jalview.binding.UserColours uc = new jalview.binding.UserColours();
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375 jalview.binding.UserColourScheme jbucs = new jalview.binding.
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376 UserColourScheme();
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378 for (int i = 0; i < colours.length; i++)
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380 jalview.binding.Colour col = new jalview.binding.Colour();
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381 col.setRGB(jalview.util.Format.getHexString(colours[i]));
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382 jbucs.addColour(col);
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385 id = "ucs" + userColours.indexOf(ucs);
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387 uc.setUserColourScheme(jbucs);
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388 jms.addUserColours(uc);
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394 static jalview.schemes.UserColourScheme GetUserColourScheme(
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395 JalviewModelSequence jms, String id)
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397 UserColours[] uc = jms.getUserColours();
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398 UserColours colours = null;
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400 for (int i = 0; i < uc.length; i++)
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402 if (uc[i].getId().equals(id))
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410 int csize = colours.getUserColourScheme().getColourCount();
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411 java.awt.Color[] newColours = new java.awt.Color[csize];
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413 for (int i = 0; i < csize; i++)
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415 newColours[i] = new java.awt.Color(Integer.parseInt(
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416 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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419 return new jalview.schemes.UserColourScheme(newColours);
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422 public static void LoadJalviewAlign(String file)
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424 JalviewModel object = new JalviewModel();
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428 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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431 if (file.startsWith("http://"))
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433 url = new URL(file);
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436 JarInputStream jin = null;
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437 JarEntry jarentry = null;
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438 int entryCount = 1;
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444 jin = new JarInputStream(url.openStream());
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448 jin = new JarInputStream(new FileInputStream(file));
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451 for (int i = 0; i < entryCount; i++)
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453 jarentry = jin.getNextJarEntry();
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456 if (jarentry != null)
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458 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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459 object = (JalviewModel) object.unmarshal(in);
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460 LoadFromObject(object);
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464 while (jarentry != null);
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466 catch (Exception ex)
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468 System.err.println("Exception whilst loading jalview XML file : " +
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470 ex.printStackTrace();
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476 static void LoadFromObject(JalviewModel object)
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478 Vector seqids = new Vector();
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479 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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480 Sequence[] vamsasSeq = vamsasSet.getSequence();
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482 JalviewModelSequence jms = object.getJalviewModelSequence();
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484 //////////////////////////////////
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486 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[
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488 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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490 for (int i = 0; i < vamsasSeq.length; i++)
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492 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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493 vamsasSeq[i].getSequence());
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495 jseqs[i].setStart(JSEQ[i].getStart());
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496 jseqs[i].setEnd(JSEQ[i].getEnd());
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497 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
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498 seqids.add(jseqs[i]);
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501 /////////////////////////////////
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502 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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504 /////////////////////////////////
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505 //////////////////////////////////
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507 if (vamsasSet.getAnnotation() != null)
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509 Annotation[] an = vamsasSet.getAnnotation();
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511 for (int i = 0; i < an.length; i++)
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513 AnnotationElement[] ae = an[i].getAnnotationElement();
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514 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
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517 for (int aa = 0; aa < ae.length; aa++)
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519 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
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520 getDisplayCharacter(),
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521 ae[aa].getDescription(),
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522 ae[aa].getSecondaryStructure().charAt(0),
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523 ae[aa].getValue());
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526 jalview.datamodel.AlignmentAnnotation jaa = null;
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528 if (an[i].getGraph())
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530 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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531 an[i].getDescription(), anot, 0, 0, 1);
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535 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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536 an[i].getDescription(), anot);
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539 al.addAnnotation(jaa);
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543 /////////////////////////////////
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545 Viewport[] views = jms.getViewport();
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546 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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548 AlignFrame af = new AlignFrame(al);
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550 // af.changeColour() );
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551 /////////////////////////
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553 if (jms.getJGroupCount() > 0)
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555 JGroup[] groups = jms.getJGroup();
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557 for (int i = 0; i < groups.length; i++)
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559 ColourSchemeI cs = null;
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561 if (groups[i].getColour() != null)
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563 if (groups[i].getColour().startsWith("ucs"))
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565 cs = GetUserColourScheme(jms, groups[i].getColour());
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569 cs = ColourSchemeProperty.getColour(al,
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570 groups[i].getColour());
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573 if (cs instanceof ResidueColourScheme)
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575 ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
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577 else if (cs instanceof ScoreColourScheme)
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579 ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
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583 Vector seqs = new Vector();
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584 int[] ids = groups[i].getSeq();
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586 for (int s = 0; s < ids.length; s++)
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588 seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(
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592 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
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593 SequenceGroup(seqs, groups[i].getName(),
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594 cs, groups[i].getDisplayBoxes(),
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595 groups[i].getDisplayText(), groups[i].getColourText(),
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596 groups[i].getStart(), groups[i].getEnd());
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598 sg.setOutlineColour(new java.awt.Color(
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599 groups[i].getOutlineColour()));
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602 if (groups[i].getConsThreshold() != 0)
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604 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
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606 ResidueProperties.propHash, 3, sg.sequences, 0,
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607 sg.getWidth() - 1);
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609 c.verdict(false, 25);
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610 cs = new ConservationColourScheme(c, cs);
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618 Desktop.addInternalFrame(af, view.getTitle(),
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619 AlignFrame.NEW_WINDOW_WIDTH,
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620 AlignFrame.NEW_WINDOW_HEIGHT);
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621 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
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623 af.viewport.setStartRes(view.getStartRes());
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624 af.viewport.setStartSeq(view.getStartSeq());
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625 af.viewport.showConservation = view.getShowConservation();
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626 af.viewport.showQuality = view.getShowQuality();
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627 af.viewport.showIdentity = view.getShowIdentity();
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628 af.viewport.setAbovePIDThreshold(view.getPidSelected());
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629 af.viewport.setColourText(view.getShowColourText());
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630 af.viewport.setConservationSelected(view.getConservationSelected());
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631 af.viewport.setShowFullId(view.getShowFullId());
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632 af.viewport.setFont(new java.awt.Font(view.getFontName(),
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633 view.getFontStyle(), view.getFontSize()));
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634 af.alignPanel.fontChanged();
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636 af.viewport.setRenderGaps(view.getRenderGaps());
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638 af.viewport.setWrapAlignment(view.getWrapAlignment());
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640 if (view.getWrapAlignment())
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642 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
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646 af.viewport.setShowAnnotation(view.getShowAnnotation());
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647 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
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650 af.viewport.setShowBoxes(view.getShowBoxes());
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651 af.viewport.setShowText(view.getShowText());
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653 ColourSchemeI cs = null;
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655 if (view.getBgColour() != null)
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657 if (view.getBgColour().startsWith("ucs"))
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659 cs = GetUserColourScheme(jms, view.getBgColour());
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663 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
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666 if (cs instanceof ConservationColourScheme)
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668 ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
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671 if (cs instanceof ResidueColourScheme)
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673 ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
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675 else if (cs instanceof ScoreColourScheme)
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677 ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
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681 af.viewport.setGlobalColourScheme(cs);
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683 af.viewport.setColourAppliesToAllGroups(false);
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684 af.changeColour(af.viewport.getGlobalColourScheme());
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685 af.viewport.setColourAppliesToAllGroups(true);
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687 if (view.getShowSequenceFeatures())
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689 af.viewport.showSequenceFeatures = true;
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690 SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al,
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692 al.featuresAdded = true;
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695 //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE
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696 if (object.getVamsasModel().getTreeCount() > 0)
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700 af.ShowNewickTree(new jalview.io.NewickFile(
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701 (String) object.getVamsasModel().getTree(0)), "Tree");
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703 catch (Exception ex)
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705 ex.printStackTrace();
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