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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144 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
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146 SequenceSet vamsasSet = new SequenceSet();
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147 Sequence vamsasSeq;
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148 JalviewModelSequence jms = new JalviewModelSequence();
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150 vamsasSet.setGapChar(jal.getGapCharacter() + "");
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157 for (int i = 0; i < jal.getHeight(); i++)
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159 seqids.add(jal.getSequenceAt(i));
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161 vamsasSeq = new Sequence();
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162 vamsasSeq.setId(id + "");
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163 vamsasSeq.setName(jal.getSequenceAt(i).getName());
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164 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
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167 jseq.setStart(jal.getSequenceAt(i).getStart());
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168 jseq.setEnd(jal.getSequenceAt(i).getEnd());
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170 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
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175 vamsasSet.addSequence(vamsasSeq);
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180 ///////////////////////////////////
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181 if (af.viewport.currentTree != null)
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183 // FIND ANY ASSOCIATED TREES
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184 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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185 for(int t=0; t<frames.length; t++)
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187 if (frames[t] instanceof TreePanel)
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189 TreePanel tp = (TreePanel) frames[t];
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190 if(tp.treeCanvas.av.alignment==jal)
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192 Tree tree = new Tree();
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193 tree.setTitle(tp.getTitle());
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194 tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
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195 tree.setNewick(tp.getTree().toString());
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196 tree.setThreshold(tp.treeCanvas.threshold);
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198 tree.setFitToWindow(tp.fitToWindow.getState());
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199 tree.setFontSize(tp.treeCanvas.fontSize);
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200 tree.setMarkUnlinked( tp.placeholdersMenu.getState() );
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201 tree.setShowBootstrap( tp.bootstrapMenu.getState() );
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202 tree.setShowDistances( tp.distanceMenu.getState() );
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204 tree.setHeight(tp.getHeight());
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205 tree.setWidth(tp.getWidth());
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206 tree.setXpos(tp.getX());
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207 tree.setYpos(tp.getY());
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216 if (jal.getAlignmentAnnotation() != null)
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218 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
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220 for (int i = 0; i < aa.length; i++)
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222 if (aa[i].label.equals("Quality") ||
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223 aa[i].label.equals("Conservation") ||
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224 aa[i].label.equals("Consensus"))
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229 Annotation an = new Annotation();
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230 an.setDescription(aa[i].description);
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231 an.setGraph(aa[i].isGraph);
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232 an.setLabel(aa[i].label);
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234 AnnotationElement ae;
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236 for (int a = 0; a < aa[i].annotations.length; a++)
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238 if ( (aa[i] == null) || (aa[i].annotations[a] == null))
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243 ae = new AnnotationElement();
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244 ae.setDescription(aa[i].annotations[a].description);
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245 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
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246 ae.setValue(aa[i].annotations[a].value);
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248 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
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250 an.addAnnotationElement(ae);
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253 vamsasSet.addAnnotation(an);
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258 if (jal.getGroups() != null)
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260 JGroup[] groups = new JGroup[jal.getGroups().size()];
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262 for (int i = 0; i < groups.length; i++)
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264 groups[i] = new JGroup();
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266 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
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269 groups[i].setStart(sg.getStartRes());
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270 groups[i].setEnd(sg.getEndRes());
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271 groups[i].setName(sg.getName());
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273 if (sg.cs instanceof ConservationColourScheme)
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275 groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);
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278 if (sg.cs instanceof ResidueColourScheme)
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280 groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).
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283 else if (sg.cs instanceof ScoreColourScheme)
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285 groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());
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288 if (sg.cs instanceof jalview.schemes.UserColourScheme)
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290 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
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295 groups[i].setColour(ColourSchemeProperty.getColourName(
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299 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
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300 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
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301 groups[i].setDisplayText(sg.getDisplayText());
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302 groups[i].setColourText(sg.getColourText());
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304 for (int s = 0; s < sg.getSize(); s++)
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306 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.
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308 int index = seqids.indexOf(seq);
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309 groups[i].addSeq(index);
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313 jms.setJGroup(groups);
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316 ///////////SAVE VIEWPORT
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317 Viewport view = new Viewport();
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318 view.setTitle(af.getTitle());
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319 view.setXpos(af.getX());
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320 view.setYpos(af.getY());
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321 view.setWidth(af.getWidth());
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322 view.setHeight(af.getHeight());
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323 view.setStartRes(av.startRes);
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324 view.setStartSeq(av.startSeq);
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326 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
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328 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
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329 userColours, jms));
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333 view.setBgColour(ColourSchemeProperty.getColourName(
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334 av.getGlobalColourScheme()));
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337 ColourSchemeI cs = av.getGlobalColourScheme();
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339 if (cs instanceof ConservationColourScheme)
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341 view.setConsThreshold( ( (ConservationColourScheme) cs).inc);
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344 if (cs instanceof ResidueColourScheme)
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346 view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());
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348 else if (cs instanceof ScoreColourScheme)
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350 view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());
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353 view.setConservationSelected(av.getConservationSelected());
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354 view.setPidSelected(av.getAbovePIDThreshold());
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355 view.setFontName(av.font.getFontName());
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356 view.setFontSize(av.font.getSize());
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357 view.setFontStyle(av.font.getStyle());
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358 view.setRenderGaps(av.renderGaps);
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359 view.setShowAnnotation(av.getShowAnnotation());
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360 view.setShowBoxes(av.getShowBoxes());
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361 view.setShowColourText(av.getColourText());
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362 view.setShowConservation(av.showConservation);
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363 view.setShowFullId(av.getShowFullId());
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364 view.setShowIdentity(av.showIdentity);
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365 view.setShowQuality(av.showQuality);
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366 view.setShowSequenceFeatures(av.showSequenceFeatures);
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367 view.setShowText(av.getShowText());
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368 view.setWrapAlignment(av.getWrapAlignment());
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370 jms.addViewport(view);
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372 object.setJalviewModelSequence(jms);
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373 object.getVamsasModel().addSequenceSet(vamsasSet);
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377 if (!fileName.endsWith(".xml"))
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379 fileName = fileName + ".xml";
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382 JarEntry entry = new JarEntry(fileName);
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383 jout.putNextEntry(entry);
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385 object.marshal(out);
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387 catch (Exception ex)
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389 ex.printStackTrace();
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393 static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
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394 Vector userColours,
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395 JalviewModelSequence jms)
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398 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
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401 if (!userColours.contains(ucs))
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403 userColours.add(ucs);
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405 java.awt.Color[] colours = ucs.getColours();
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406 jalview.binding.UserColours uc = new jalview.binding.UserColours();
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407 jalview.binding.UserColourScheme jbucs = new jalview.binding.
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408 UserColourScheme();
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410 for (int i = 0; i < colours.length; i++)
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412 jalview.binding.Colour col = new jalview.binding.Colour();
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413 col.setRGB(jalview.util.Format.getHexString(colours[i]));
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414 jbucs.addColour(col);
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417 id = "ucs" + userColours.indexOf(ucs);
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419 uc.setUserColourScheme(jbucs);
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420 jms.addUserColours(uc);
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426 static jalview.schemes.UserColourScheme GetUserColourScheme(
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427 JalviewModelSequence jms, String id)
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429 UserColours[] uc = jms.getUserColours();
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430 UserColours colours = null;
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432 for (int i = 0; i < uc.length; i++)
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434 if (uc[i].getId().equals(id))
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442 int csize = colours.getUserColourScheme().getColourCount();
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443 java.awt.Color[] newColours = new java.awt.Color[csize];
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445 for (int i = 0; i < csize; i++)
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447 newColours[i] = new java.awt.Color(Integer.parseInt(
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448 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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451 return new jalview.schemes.UserColourScheme(newColours);
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454 public static void LoadJalviewAlign(String file)
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456 JalviewModel object = new JalviewModel();
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460 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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463 if (file.startsWith("http://"))
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465 url = new URL(file);
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468 JarInputStream jin = null;
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469 JarEntry jarentry = null;
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470 int entryCount = 1;
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476 jin = new JarInputStream(url.openStream());
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480 jin = new JarInputStream(new FileInputStream(file));
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483 for (int i = 0; i < entryCount; i++)
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485 jarentry = jin.getNextJarEntry();
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488 if (jarentry != null)
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490 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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491 object = (JalviewModel) object.unmarshal(in);
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492 LoadFromObject(object);
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496 while (jarentry != null);
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498 catch (Exception ex)
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500 System.err.println("Exception whilst loading jalview XML file : " +
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502 ex.printStackTrace();
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508 static void LoadFromObject(JalviewModel object)
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510 Vector seqids = new Vector();
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511 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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512 Sequence[] vamsasSeq = vamsasSet.getSequence();
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514 JalviewModelSequence jms = object.getJalviewModelSequence();
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516 //////////////////////////////////
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518 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[
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520 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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522 for (int i = 0; i < vamsasSeq.length; i++)
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524 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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525 vamsasSeq[i].getSequence());
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527 jseqs[i].setStart(JSEQ[i].getStart());
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528 jseqs[i].setEnd(JSEQ[i].getEnd());
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529 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
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530 seqids.add(jseqs[i]);
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533 /////////////////////////////////
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534 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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536 /////////////////////////////////
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537 //////////////////////////////////
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539 if (vamsasSet.getAnnotation() != null)
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541 Annotation[] an = vamsasSet.getAnnotation();
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543 for (int i = 0; i < an.length; i++)
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545 AnnotationElement[] ae = an[i].getAnnotationElement();
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546 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
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549 for (int aa = 0; aa < ae.length; aa++)
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551 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
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552 getDisplayCharacter(),
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553 ae[aa].getDescription(),
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554 ae[aa].getSecondaryStructure().charAt(0),
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555 ae[aa].getValue());
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558 jalview.datamodel.AlignmentAnnotation jaa = null;
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560 if (an[i].getGraph())
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562 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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563 an[i].getDescription(), anot, 0, 0, 1);
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567 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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568 an[i].getDescription(), anot);
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571 al.addAnnotation(jaa);
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575 /////////////////////////////////
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577 Viewport[] views = jms.getViewport();
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578 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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580 AlignFrame af = new AlignFrame(al);
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582 // af.changeColour() );
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583 /////////////////////////
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585 if (jms.getJGroupCount() > 0)
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587 JGroup[] groups = jms.getJGroup();
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589 for (int i = 0; i < groups.length; i++)
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591 ColourSchemeI cs = null;
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593 if (groups[i].getColour() != null)
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595 if (groups[i].getColour().startsWith("ucs"))
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597 cs = GetUserColourScheme(jms, groups[i].getColour());
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601 cs = ColourSchemeProperty.getColour(al,
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602 groups[i].getColour());
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605 if (cs instanceof ResidueColourScheme)
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607 ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());
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609 else if (cs instanceof ScoreColourScheme)
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611 ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());
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615 Vector seqs = new Vector();
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616 int[] ids = groups[i].getSeq();
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618 for (int s = 0; s < ids.length; s++)
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620 seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(
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624 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
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625 SequenceGroup(seqs, groups[i].getName(),
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626 cs, groups[i].getDisplayBoxes(),
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627 groups[i].getDisplayText(), groups[i].getColourText(),
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628 groups[i].getStart(), groups[i].getEnd());
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630 sg.setOutlineColour(new java.awt.Color(
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631 groups[i].getOutlineColour()));
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634 if (groups[i].getConsThreshold() != 0)
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636 jalview.analysis.Conservation c = new jalview.analysis.Conservation(
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638 ResidueProperties.propHash, 3, sg.sequences, 0,
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639 sg.getWidth() - 1);
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641 c.verdict(false, 25);
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642 cs = new ConservationColourScheme(c, cs);
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650 Desktop.addInternalFrame(af, view.getTitle(),
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651 AlignFrame.NEW_WINDOW_WIDTH,
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652 AlignFrame.NEW_WINDOW_HEIGHT);
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653 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
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655 af.viewport.setStartRes(view.getStartRes());
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656 af.viewport.setStartSeq(view.getStartSeq());
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657 af.viewport.showConservation = view.getShowConservation();
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658 af.viewport.showQuality = view.getShowQuality();
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659 af.viewport.showIdentity = view.getShowIdentity();
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660 af.viewport.setAbovePIDThreshold(view.getPidSelected());
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661 af.abovePIDThreshold.setSelected(view.getPidSelected());
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662 af.viewport.setColourText(view.getShowColourText());
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663 af.colourTextMenuItem.setSelected(view.getShowColourText());
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664 af.viewport.setConservationSelected(view.getConservationSelected());
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665 af.conservationMenuItem.setSelected(view.getConservationSelected());
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667 af.viewport.setShowFullId(view.getShowFullId());
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668 af.fullSeqId.setSelected(view.getShowFullId());
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670 af.viewport.setFont(new java.awt.Font(view.getFontName(),
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671 view.getFontStyle(), view.getFontSize()));
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672 af.alignPanel.fontChanged();
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674 af.viewport.setRenderGaps(view.getRenderGaps());
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675 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
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677 af.viewport.setWrapAlignment(view.getWrapAlignment());
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678 af.wrapMenuItem.setSelected(view.getWrapAlignment());
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680 if (view.getWrapAlignment())
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682 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
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686 af.viewport.setShowAnnotation(view.getShowAnnotation());
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687 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
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690 af.viewport.setShowBoxes(view.getShowBoxes());
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691 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
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692 af.viewport.setShowText(view.getShowText());
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693 af.viewTextMenuItem.setSelected(view.getShowText());
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695 ColourSchemeI cs = null;
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697 if (view.getBgColour() != null)
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699 if (view.getBgColour().startsWith("ucs"))
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701 cs = GetUserColourScheme(jms, view.getBgColour());
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705 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
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708 if (cs instanceof ConservationColourScheme)
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710 ( (ConservationColourScheme) cs).inc = view.getConsThreshold();
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713 if (cs instanceof ResidueColourScheme)
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715 ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());
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717 else if (cs instanceof ScoreColourScheme)
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719 ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());
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723 af.viewport.setGlobalColourScheme(cs);
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725 af.viewport.setColourAppliesToAllGroups(false);
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726 af.changeColour(af.viewport.getGlobalColourScheme());
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727 af.viewport.setColourAppliesToAllGroups(true);
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729 if (view.getShowSequenceFeatures())
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731 af.viewport.showSequenceFeatures = true;
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732 af.sequenceFeatures.setSelected(true);
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733 new SequenceFeatureFetcher(al, af.alignPanel);
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734 al.featuresAdded = true;
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738 ///////////////////////////////////////
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739 /* JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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740 for(int t=0; t<frames.length; t++)
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742 if (frames[t] instanceof TreePanel)
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744 TreePanel tp = (TreePanel) frames[t];
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745 if(tp.treeCanvas.av.alignment==jal)
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747 Tree tree = new Tree();
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748 tree.setTitle(tp.getTitle());
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749 tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));
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750 tree.setNewick(tp.getTree().toString());
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751 tree.setThreshold(tp.treeCanvas.threshold);
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753 tree.setHeight(tp.getHeight());
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754 tree.setWidth(tp.getWidth());
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755 tree.setXpos(tp.getX());
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756 tree.setYpos(tp.getY());
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761 if (jms.getTreeCount() > 0)
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765 for(int t = 0; t<jms.getTreeCount(); t++)
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767 Tree tree = jms.getTree(t);
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769 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
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770 tree.getNewick()), tree.getTitle());
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772 tp.setBounds( tree.getXpos(),
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777 tp.fitToWindow.setState(tree.getFitToWindow());
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778 tp.fitToWindow_actionPerformed(null);
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779 tp.treeCanvas.fontSize = tree.getFontSize();
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780 tp.fontSize.setText("Font Size - "+tree.getFontSize());
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781 tp.placeholdersMenu.setState(tree.getMarkUnlinked());
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782 tp.placeholdersMenu_actionPerformed(null);
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783 tp.bootstrapMenu.setState(tree.getShowBootstrap());
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784 tp.bootstrapMenu_actionPerformed(null);
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785 tp.distanceMenu.setState(tree.getShowDistances());
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786 tp.distanceMenu_actionPerformed(null);
\r
787 tp.treeCanvas.threshold = tree.getThreshold();
\r
788 if(tree.getCurrentTree());
\r
789 af.viewport.setCurrentTree(tp.getTree());
\r
792 catch (Exception ex)
\r
794 ex.printStackTrace();
\r