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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59 for (int i = frames.length - 1; i > -1; i--)
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61 if (frames[i] instanceof AlignFrame)
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63 AlignFrame af = (AlignFrame) frames[i];
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65 String shortName = af.getTitle();
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67 if (shortName.indexOf(File.separatorChar) > -1)
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69 shortName = shortName.substring(shortName.lastIndexOf(
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70 File.separatorChar) + 1);
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75 while (shortNames.contains(shortName))
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77 if (shortName.endsWith("_" + (count - 1)))
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79 shortName = shortName.substring(0,
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80 shortName.lastIndexOf("_"));
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83 shortName = shortName.concat("_" + count);
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87 shortNames.addElement(shortName);
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89 if (!shortName.endsWith(".xml"))
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91 shortName = shortName + ".xml";
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94 SaveState(af, creation, shortName, jout, out);
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101 catch (Exception ex)
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103 ex.printStackTrace();
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108 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
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109 public static void SaveAlignment(AlignFrame af, String jarFile, String fileName)
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113 FileOutputStream fos = new FileOutputStream(jarFile);
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114 JarOutputStream jout = new JarOutputStream(fos);
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116 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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117 ////////////////////////////////////////////////////
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118 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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121 SaveState(af, System.currentTimeMillis(), fileName, jout, out);
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125 catch (Exception ex)
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130 public static void SaveState(AlignFrame af, long timeStamp,
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131 String fileName, JarOutputStream jout,
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134 Vector seqids = new Vector();
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135 Vector userColours = new Vector();
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137 AlignViewport av = af.viewport;
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139 JalviewModel object = new JalviewModel();
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140 object.setVamsasModel(new VamsasModel());
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142 object.setCreationDate(new java.util.Date(timeStamp));
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143 object.setVersion(jalview.bin.Cache.VERSION);
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145 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
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147 SequenceSet vamsasSet = new SequenceSet();
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148 Sequence vamsasSeq;
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149 JalviewModelSequence jms = new JalviewModelSequence();
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151 vamsasSet.setGapChar(jal.getGapCharacter() + "");
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158 for (int i = 0; i < jal.getHeight(); i++)
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160 seqids.add(jal.getSequenceAt(i));
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162 vamsasSeq = new Sequence();
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163 vamsasSeq.setId(id + "");
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164 vamsasSeq.setName(jal.getSequenceAt(i).getName());
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165 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
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168 jseq.setStart(jal.getSequenceAt(i).getStart());
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169 jseq.setEnd(jal.getSequenceAt(i).getEnd());
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171 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
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176 vamsasSet.addSequence(vamsasSeq);
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181 ///////////////////////////////////
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182 if (af.viewport.currentTree != null)
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184 // FIND ANY ASSOCIATED TREES
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185 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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186 for(int t=0; t<frames.length; t++)
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188 if (frames[t] instanceof TreePanel)
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190 TreePanel tp = (TreePanel) frames[t];
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191 if(tp.treeCanvas.av.alignment==jal)
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193 Tree tree = new Tree();
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194 tree.setTitle(tp.getTitle());
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195 tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
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196 tree.setNewick(tp.getTree().toString());
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197 tree.setThreshold(tp.treeCanvas.threshold);
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199 tree.setFitToWindow(tp.fitToWindow.getState());
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200 tree.setFontSize(tp.treeCanvas.fontSize);
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201 tree.setMarkUnlinked( tp.placeholdersMenu.getState() );
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202 tree.setShowBootstrap( tp.bootstrapMenu.getState() );
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203 tree.setShowDistances( tp.distanceMenu.getState() );
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205 tree.setHeight(tp.getHeight());
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206 tree.setWidth(tp.getWidth());
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207 tree.setXpos(tp.getX());
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208 tree.setYpos(tp.getY());
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217 if (jal.getAlignmentAnnotation() != null)
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219 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
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221 for (int i = 0; i < aa.length; i++)
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223 if (aa[i].label.equals("Quality") ||
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224 aa[i].label.equals("Conservation") ||
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225 aa[i].label.equals("Consensus"))
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230 Annotation an = new Annotation();
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231 an.setDescription(aa[i].description);
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232 an.setGraph(aa[i].isGraph);
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233 an.setLabel(aa[i].label);
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235 AnnotationElement ae;
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237 for (int a = 0; a < aa[i].annotations.length; a++)
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239 if ( (aa[i] == null) || (aa[i].annotations[a] == null))
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244 ae = new AnnotationElement();
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245 ae.setDescription(aa[i].annotations[a].description);
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246 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
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247 ae.setValue(aa[i].annotations[a].value);
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249 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
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251 an.addAnnotationElement(ae);
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254 vamsasSet.addAnnotation(an);
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259 if (jal.getGroups() != null)
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261 JGroup[] groups = new JGroup[jal.getGroups().size()];
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263 for (int i = 0; i < groups.length; i++)
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265 groups[i] = new JGroup();
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267 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
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270 groups[i].setStart(sg.getStartRes());
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271 groups[i].setEnd(sg.getEndRes());
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272 groups[i].setName(sg.getName());
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274 if (sg.cs instanceof ConservationColourScheme)
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276 groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);
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279 if (sg.cs instanceof ResidueColourScheme)
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281 groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).
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284 else if (sg.cs instanceof ScoreColourScheme)
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286 groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
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289 if (sg.cs instanceof jalview.schemes.UserColourScheme)
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291 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
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296 groups[i].setColour(ColourSchemeProperty.getColourName(
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300 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
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301 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
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302 groups[i].setDisplayText(sg.getDisplayText());
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303 groups[i].setColourText(sg.getColourText());
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305 for (int s = 0; s < sg.getSize(); s++)
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307 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.
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309 int index = seqids.indexOf(seq);
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310 groups[i].addSeq(index);
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314 jms.setJGroup(groups);
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317 ///////////SAVE VIEWPORT
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318 Viewport view = new Viewport();
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319 view.setTitle(af.getTitle());
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320 view.setXpos(af.getX());
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321 view.setYpos(af.getY());
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322 view.setWidth(af.getWidth());
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323 view.setHeight(af.getHeight());
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324 view.setStartRes(av.startRes);
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325 view.setStartSeq(av.startSeq);
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327 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
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329 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
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330 userColours, jms));
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334 view.setBgColour(ColourSchemeProperty.getColourName(
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335 av.getGlobalColourScheme()));
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338 ColourSchemeI cs = av.getGlobalColourScheme();
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340 if (cs instanceof ConservationColourScheme)
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342 view.setConsThreshold( ( (ConservationColourScheme) cs).inc);
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345 if (cs instanceof ResidueColourScheme)
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347 view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
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349 else if (cs instanceof ScoreColourScheme)
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351 view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
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354 view.setConservationSelected(av.getConservationSelected());
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355 view.setPidSelected(av.getAbovePIDThreshold());
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356 view.setFontName(av.font.getFontName());
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357 view.setFontSize(av.font.getSize());
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358 view.setFontStyle(av.font.getStyle());
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359 view.setRenderGaps(av.renderGaps);
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360 view.setShowAnnotation(av.getShowAnnotation());
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361 view.setShowBoxes(av.getShowBoxes());
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362 view.setShowColourText(av.getColourText());
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363 view.setShowConservation(av.showConservation);
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364 view.setShowFullId(av.getShowFullId());
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365 view.setShowIdentity(av.showIdentity);
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366 view.setShowQuality(av.showQuality);
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367 view.setShowSequenceFeatures(av.showSequenceFeatures);
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368 view.setShowText(av.getShowText());
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369 view.setWrapAlignment(av.getWrapAlignment());
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371 jms.addViewport(view);
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373 object.setJalviewModelSequence(jms);
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374 object.getVamsasModel().addSequenceSet(vamsasSet);
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378 if (!fileName.endsWith(".xml"))
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380 fileName = fileName + ".xml";
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383 JarEntry entry = new JarEntry(fileName);
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384 jout.putNextEntry(entry);
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386 object.marshal(out);
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388 catch (Exception ex)
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390 ex.printStackTrace();
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394 static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
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395 Vector userColours,
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396 JalviewModelSequence jms)
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399 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
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402 if (!userColours.contains(ucs))
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404 userColours.add(ucs);
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406 java.awt.Color[] colours = ucs.getColours();
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407 jalview.binding.UserColours uc = new jalview.binding.UserColours();
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408 jalview.binding.UserColourScheme jbucs = new jalview.binding.
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409 UserColourScheme();
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411 for (int i = 0; i < colours.length; i++)
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413 jalview.binding.Colour col = new jalview.binding.Colour();
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414 col.setRGB(jalview.util.Format.getHexString(colours[i]));
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415 jbucs.addColour(col);
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418 id = "ucs" + userColours.indexOf(ucs);
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420 uc.setUserColourScheme(jbucs);
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421 jms.addUserColours(uc);
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427 static jalview.schemes.UserColourScheme GetUserColourScheme(
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428 JalviewModelSequence jms, String id)
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430 UserColours[] uc = jms.getUserColours();
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431 UserColours colours = null;
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433 for (int i = 0; i < uc.length; i++)
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435 if (uc[i].getId().equals(id))
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443 int csize = colours.getUserColourScheme().getColourCount();
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444 java.awt.Color[] newColours = new java.awt.Color[csize];
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446 for (int i = 0; i < csize; i++)
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448 newColours[i] = new java.awt.Color(Integer.parseInt(
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449 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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452 return new jalview.schemes.UserColourScheme(newColours);
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455 public static void LoadJalviewAlign(String file)
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457 JalviewModel object = new JalviewModel();
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461 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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464 if (file.startsWith("http://"))
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466 url = new URL(file);
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469 JarInputStream jin = null;
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470 JarEntry jarentry = null;
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471 int entryCount = 1;
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477 jin = new JarInputStream(url.openStream());
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481 jin = new JarInputStream(new FileInputStream(file));
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484 for (int i = 0; i < entryCount; i++)
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486 jarentry = jin.getNextJarEntry();
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489 if (jarentry != null)
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491 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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492 object = (JalviewModel) object.unmarshal(in);
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493 LoadFromObject(object);
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497 while (jarentry != null);
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499 catch (Exception ex)
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501 System.err.println("Exception whilst loading jalview XML file : " +
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503 ex.printStackTrace();
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509 static void LoadFromObject(JalviewModel object)
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511 Vector seqids = new Vector();
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512 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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513 Sequence[] vamsasSeq = vamsasSet.getSequence();
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515 JalviewModelSequence jms = object.getJalviewModelSequence();
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517 //////////////////////////////////
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519 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[
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521 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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523 for (int i = 0; i < vamsasSeq.length; i++)
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525 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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526 vamsasSeq[i].getSequence());
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528 jseqs[i].setStart(JSEQ[i].getStart());
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529 jseqs[i].setEnd(JSEQ[i].getEnd());
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530 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
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531 seqids.add(jseqs[i]);
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534 /////////////////////////////////
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535 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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537 /////////////////////////////////
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538 //////////////////////////////////
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540 if (vamsasSet.getAnnotation() != null)
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542 Annotation[] an = vamsasSet.getAnnotation();
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544 for (int i = 0; i < an.length; i++)
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546 AnnotationElement[] ae = an[i].getAnnotationElement();
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547 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
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550 for (int aa = 0; aa < ae.length; aa++)
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552 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
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553 getDisplayCharacter(),
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554 ae[aa].getDescription(),
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555 ae[aa].getSecondaryStructure().charAt(0),
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556 ae[aa].getValue());
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559 jalview.datamodel.AlignmentAnnotation jaa = null;
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561 if (an[i].getGraph())
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563 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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564 an[i].getDescription(), anot, 0, 0, 1);
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568 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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569 an[i].getDescription(), anot);
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572 al.addAnnotation(jaa);
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576 /////////////////////////////////
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578 Viewport[] views = jms.getViewport();
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579 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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581 AlignFrame af = new AlignFrame(al);
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583 // af.changeColour() );
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584 /////////////////////////
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586 if (jms.getJGroupCount() > 0)
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588 JGroup[] groups = jms.getJGroup();
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590 for (int i = 0; i < groups.length; i++)
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592 ColourSchemeI cs = null;
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594 if (groups[i].getColour() != null)
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596 if (groups[i].getColour().startsWith("ucs"))
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598 cs = GetUserColourScheme(jms, groups[i].getColour());
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602 cs = ColourSchemeProperty.getColour(al,
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603 groups[i].getColour());
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606 if (cs instanceof ResidueColourScheme)
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608 ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
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610 else if (cs instanceof ScoreColourScheme)
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612 ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
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616 Vector seqs = new Vector();
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617 int[] ids = groups[i].getSeq();
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619 for (int s = 0; s < ids.length; s++)
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621 seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(
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625 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
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626 SequenceGroup(seqs, groups[i].getName(),
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627 cs, groups[i].getDisplayBoxes(),
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628 groups[i].getDisplayText(), groups[i].getColourText(),
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629 groups[i].getStart(), groups[i].getEnd());
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631 sg.setOutlineColour(new java.awt.Color(
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632 groups[i].getOutlineColour()));
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635 if (groups[i].getConsThreshold() != 0)
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637 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
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639 ResidueProperties.propHash, 3, sg.sequences, 0,
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640 sg.getWidth() - 1);
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642 c.verdict(false, 25);
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643 cs = new ConservationColourScheme(c, cs);
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651 Desktop.addInternalFrame(af, view.getTitle(),
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652 AlignFrame.NEW_WINDOW_WIDTH,
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653 AlignFrame.NEW_WINDOW_HEIGHT);
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654 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
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656 af.viewport.setStartRes(view.getStartRes());
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657 af.viewport.setStartSeq(view.getStartSeq());
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658 af.viewport.showConservation = view.getShowConservation();
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659 af.viewport.showQuality = view.getShowQuality();
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660 af.viewport.showIdentity = view.getShowIdentity();
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661 af.viewport.setAbovePIDThreshold(view.getPidSelected());
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662 af.abovePIDThreshold.setSelected(view.getPidSelected());
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663 af.viewport.setColourText(view.getShowColourText());
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664 af.colourTextMenuItem.setSelected(view.getShowColourText());
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665 af.viewport.setConservationSelected(view.getConservationSelected());
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666 af.conservationMenuItem.setSelected(view.getConservationSelected());
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668 af.viewport.setShowFullId(view.getShowFullId());
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669 af.fullSeqId.setSelected(view.getShowFullId());
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671 af.viewport.setFont(new java.awt.Font(view.getFontName(),
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672 view.getFontStyle(), view.getFontSize()));
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673 af.alignPanel.fontChanged();
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675 af.viewport.setRenderGaps(view.getRenderGaps());
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676 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
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678 af.viewport.setWrapAlignment(view.getWrapAlignment());
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679 af.wrapMenuItem.setSelected(view.getWrapAlignment());
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681 if (view.getWrapAlignment())
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683 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
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687 af.viewport.setShowAnnotation(view.getShowAnnotation());
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688 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
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691 af.viewport.setShowBoxes(view.getShowBoxes());
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692 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
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693 af.viewport.setShowText(view.getShowText());
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694 af.viewTextMenuItem.setSelected(view.getShowText());
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696 ColourSchemeI cs = null;
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698 if (view.getBgColour() != null)
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700 if (view.getBgColour().startsWith("ucs"))
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702 cs = GetUserColourScheme(jms, view.getBgColour());
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706 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
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709 if (cs instanceof ConservationColourScheme)
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711 ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
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714 if (cs instanceof ResidueColourScheme)
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716 ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
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718 else if (cs instanceof ScoreColourScheme)
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720 ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
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724 af.viewport.setGlobalColourScheme(cs);
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726 af.viewport.setColourAppliesToAllGroups(false);
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727 af.changeColour(af.viewport.getGlobalColourScheme());
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728 af.viewport.setColourAppliesToAllGroups(true);
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730 if (view.getShowSequenceFeatures())
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732 af.viewport.showSequenceFeatures = true;
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733 af.sequenceFeatures.setSelected(true);
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734 new SequenceFeatureFetcher(al, af.alignPanel);
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735 al.featuresAdded = true;
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739 ///////////////////////////////////////
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740 /* JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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741 for(int t=0; t<frames.length; t++)
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743 if (frames[t] instanceof TreePanel)
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745 TreePanel tp = (TreePanel) frames[t];
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746 if(tp.treeCanvas.av.alignment==jal)
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748 Tree tree = new Tree();
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749 tree.setTitle(tp.getTitle());
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750 tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
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751 tree.setNewick(tp.getTree().toString());
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752 tree.setThreshold(tp.treeCanvas.threshold);
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754 tree.setHeight(tp.getHeight());
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755 tree.setWidth(tp.getWidth());
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756 tree.setXpos(tp.getX());
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757 tree.setYpos(tp.getY());
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762 if (jms.getTreeCount() > 0)
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766 for(int t = 0; t<jms.getTreeCount(); t++)
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768 Tree tree = jms.getTree(t);
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770 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
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771 tree.getNewick()), tree.getTitle());
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773 tp.setBounds( tree.getXpos(),
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778 tp.fitToWindow.setState(tree.getFitToWindow());
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779 tp.fitToWindow_actionPerformed(null);
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780 tp.treeCanvas.fontSize = tree.getFontSize();
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781 tp.fontSize.setText("Font Size - "+tree.getFontSize());
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782 tp.placeholdersMenu.setState(tree.getMarkUnlinked());
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783 tp.placeholdersMenu_actionPerformed(null);
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784 tp.bootstrapMenu.setState(tree.getShowBootstrap());
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785 tp.bootstrapMenu_actionPerformed(null);
\r
786 tp.distanceMenu.setState(tree.getShowDistances());
\r
787 tp.distanceMenu_actionPerformed(null);
\r
788 tp.treeCanvas.threshold = tree.getThreshold();
\r
789 if(tree.getCurrentTree());
\r
790 af.viewport.setCurrentTree(tp.getTree());
\r
793 catch (Exception ex)
\r
795 ex.printStackTrace();
\r