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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21 import jalview.io.*;
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23 import jalview.schemes.*;
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31 import java.util.jar.*;
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33 import javax.swing.*;
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35 import jalview.binding.*;
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42 * @version $Revision$
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44 public class Jalview2XML
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46 // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
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47 public static void SaveState(File statefile)
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49 long creation = System.currentTimeMillis();
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50 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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59 FileOutputStream fos = new FileOutputStream(statefile);
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60 JarOutputStream jout = new JarOutputStream(fos);
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62 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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63 ////////////////////////////////////////////////////
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64 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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67 Vector shortNames = new Vector();
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70 for (int i = frames.length - 1; i > -1; i--)
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72 if (frames[i] instanceof AlignFrame)
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74 AlignFrame af = (AlignFrame) frames[i];
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76 String shortName = af.getTitle();
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78 if (shortName.indexOf(File.separatorChar) > -1)
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80 shortName = shortName.substring(shortName.lastIndexOf(
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81 File.separatorChar) + 1);
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86 while (shortNames.contains(shortName))
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88 if (shortName.endsWith("_" + (count - 1)))
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90 shortName = shortName.substring(0,
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91 shortName.lastIndexOf("_"));
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94 shortName = shortName.concat("_" + count);
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98 shortNames.addElement(shortName);
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100 if (!shortName.endsWith(".xml"))
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102 shortName = shortName + ".xml";
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105 SaveState(af, creation, shortName, jout, out);
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112 catch (Exception ex)
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114 ex.printStackTrace();
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118 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
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119 public static void SaveAlignment(AlignFrame af, String jarFile,
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124 FileOutputStream fos = new FileOutputStream(jarFile);
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125 JarOutputStream jout = new JarOutputStream(fos);
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127 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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128 ////////////////////////////////////////////////////
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129 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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132 SaveState(af, System.currentTimeMillis(), fileName, jout, out);
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136 catch (Exception ex)
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138 ex.printStackTrace();
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145 * @param af DOCUMENT ME!
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146 * @param timeStamp DOCUMENT ME!
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147 * @param fileName DOCUMENT ME!
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148 * @param jout DOCUMENT ME!
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149 * @param out DOCUMENT ME!
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151 public static void SaveState(AlignFrame af, long timeStamp,
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152 String fileName, JarOutputStream jout, PrintWriter out)
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154 Vector seqids = new Vector();
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155 Vector userColours = new Vector();
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157 AlignViewport av = af.viewport;
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159 JalviewModel object = new JalviewModel();
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160 object.setVamsasModel(new jalview.binding.VamsasModel());
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162 object.setCreationDate(new java.util.Date(timeStamp));
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163 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
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165 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
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167 SequenceSet vamsasSet = new SequenceSet();
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168 Sequence vamsasSeq;
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169 JalviewModelSequence jms = new JalviewModelSequence();
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171 vamsasSet.setGapChar(jal.getGapCharacter() + "");
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178 for (int i = 0; i < jal.getHeight(); i++)
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180 seqids.add(jal.getSequenceAt(i));
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182 vamsasSeq = new Sequence();
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183 vamsasSeq.setId(id + "");
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184 vamsasSeq.setName(jal.getSequenceAt(i).getName());
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185 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
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188 jseq.setStart(jal.getSequenceAt(i).getStart());
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189 jseq.setEnd(jal.getSequenceAt(i).getEnd());
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191 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
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196 vamsasSet.addSequence(vamsasSeq);
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201 ///////////////////////////////////
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202 if (af.viewport.currentTree != null)
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204 // FIND ANY ASSOCIATED TREES
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205 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
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206 if (Desktop.desktop != null)
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208 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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210 for (int t = 0; t < frames.length; t++)
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212 if (frames[t] instanceof TreePanel)
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214 TreePanel tp = (TreePanel) frames[t];
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216 if (tp.treeCanvas.av.alignment == jal)
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218 Tree tree = new Tree();
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219 tree.setTitle(tp.getTitle());
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220 tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
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221 tree.setNewick(tp.getTree().toString());
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222 tree.setThreshold(tp.treeCanvas.threshold);
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224 tree.setFitToWindow(tp.fitToWindow.getState());
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225 tree.setFontName(tp.getTreeFont().getName());
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226 tree.setFontSize(tp.getTreeFont().getSize());
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227 tree.setFontStyle(tp.getTreeFont().getStyle());
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228 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
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230 tree.setShowBootstrap(tp.bootstrapMenu.getState());
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231 tree.setShowDistances(tp.distanceMenu.getState());
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233 tree.setHeight(tp.getHeight());
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234 tree.setWidth(tp.getWidth());
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235 tree.setXpos(tp.getX());
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236 tree.setYpos(tp.getY());
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246 if (jal.getAlignmentAnnotation() != null)
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248 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
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250 for (int i = 0; i < aa.length; i++)
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252 if (aa[i].label.equals("Quality") ||
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253 aa[i].label.equals("Conservation") ||
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254 aa[i].label.equals("Consensus"))
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259 Annotation an = new Annotation();
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260 an.setDescription(aa[i].description);
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261 an.setGraph(aa[i].isGraph);
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262 an.setLabel(aa[i].label);
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264 AnnotationElement ae;
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266 for (int a = 0; a < aa[i].annotations.length; a++)
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268 if ((aa[i] == null) || (aa[i].annotations[a] == null))
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273 ae = new AnnotationElement();
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274 ae.setDescription(aa[i].annotations[a].description);
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275 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
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276 ae.setValue(aa[i].annotations[a].value);
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278 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
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280 an.addAnnotationElement(ae);
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283 vamsasSet.addAnnotation(an);
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288 if (jal.getGroups() != null)
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290 JGroup[] groups = new JGroup[jal.getGroups().size()];
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292 for (int i = 0; i < groups.length; i++)
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294 groups[i] = new JGroup();
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296 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
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298 groups[i].setStart(sg.getStartRes());
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299 groups[i].setEnd(sg.getEndRes());
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300 groups[i].setName(sg.getName());
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303 if (sg.cs.conservationApplied())
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305 groups[i].setConsThreshold(sg.cs.getConservationInc());
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307 if (sg.cs instanceof jalview.schemes.UserColourScheme)
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309 groups[i].setColour(SetUserColourScheme(sg.cs,
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315 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
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319 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
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321 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
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326 groups[i].setColour(ColourSchemeProperty.getColourName(
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330 groups[i].setPidThreshold(sg.cs.getThreshold());
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333 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
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334 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
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335 groups[i].setDisplayText(sg.getDisplayText());
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336 groups[i].setColourText(sg.getColourText());
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338 for (int s = 0; s < sg.getSize(); s++)
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340 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
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341 int index = seqids.indexOf(seq);
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342 groups[i].addSeq(index);
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346 jms.setJGroup(groups);
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349 ///////////SAVE VIEWPORT
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350 Viewport view = new Viewport();
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351 view.setTitle(af.getTitle());
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352 view.setXpos(af.getX());
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353 view.setYpos(af.getY());
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354 view.setWidth(af.getWidth());
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355 view.setHeight(af.getHeight());
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356 view.setStartRes(av.startRes);
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357 view.setStartSeq(av.startSeq);
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359 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
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361 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
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362 userColours, jms));
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366 view.setBgColour(ColourSchemeProperty.getColourName(
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367 av.getGlobalColourScheme()));
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370 ColourSchemeI cs = av.getGlobalColourScheme();
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374 if (cs.conservationApplied())
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376 view.setConsThreshold(cs.getConservationInc());
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377 if (cs instanceof jalview.schemes.UserColourScheme)
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378 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
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381 if (cs instanceof ResidueColourScheme)
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383 view.setPidThreshold(cs.getThreshold());
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387 view.setConservationSelected(av.getConservationSelected());
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388 view.setPidSelected(av.getAbovePIDThreshold());
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389 view.setFontName(av.font.getName());
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390 view.setFontSize(av.font.getSize());
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391 view.setFontStyle(av.font.getStyle());
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392 view.setRenderGaps(av.renderGaps);
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393 view.setShowAnnotation(av.getShowAnnotation());
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394 view.setShowBoxes(av.getShowBoxes());
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395 view.setShowColourText(av.getColourText());
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396 view.setShowConservation(av.showConservation);
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397 view.setShowFullId(av.getShowJVSuffix());
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398 view.setShowIdentity(av.showIdentity);
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399 view.setShowQuality(av.showQuality);
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400 view.setShowSequenceFeatures(av.showSequenceFeatures);
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401 view.setShowText(av.getShowText());
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402 view.setWrapAlignment(av.getWrapAlignment());
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404 jms.addViewport(view);
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406 object.setJalviewModelSequence(jms);
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407 object.getVamsasModel().addSequenceSet(vamsasSet);
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411 if (!fileName.endsWith(".xml"))
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413 fileName = fileName + ".xml";
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416 JarEntry entry = new JarEntry(fileName);
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417 jout.putNextEntry(entry);
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419 object.marshal(out);
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421 catch (Exception ex)
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423 ex.printStackTrace();
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427 static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
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428 Vector userColours, JalviewModelSequence jms)
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431 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
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433 if (!userColours.contains(ucs))
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435 userColours.add(ucs);
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437 java.awt.Color[] colours = ucs.getColours();
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438 jalview.binding.UserColours uc = new jalview.binding.UserColours();
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439 jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
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441 for (int i = 0; i < colours.length; i++)
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443 jalview.binding.Colour col = new jalview.binding.Colour();
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444 col.setRGB(jalview.util.Format.getHexString(colours[i]));
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445 jbucs.addColour(col);
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448 id = "ucs" + userColours.indexOf(ucs);
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450 uc.setUserColourScheme(jbucs);
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451 jms.addUserColours(uc);
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457 static jalview.schemes.UserColourScheme GetUserColourScheme(
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458 JalviewModelSequence jms, String id)
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460 UserColours[] uc = jms.getUserColours();
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461 UserColours colours = null;
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463 for (int i = 0; i < uc.length; i++)
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465 if (uc[i].getId().equals(id))
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473 int csize = colours.getUserColourScheme().getColourCount();
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474 java.awt.Color[] newColours = new java.awt.Color[csize];
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476 for (int i = 0; i < csize; i++)
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478 newColours[i] = new java.awt.Color(Integer.parseInt(
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479 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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482 return new jalview.schemes.UserColourScheme(newColours);
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488 * @param file DOCUMENT ME!
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490 public static AlignFrame LoadJalviewAlign(String file)
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492 JalviewModel object = new JalviewModel();
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493 jalview.gui.AlignFrame af = null;
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497 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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500 if (file.startsWith("http://"))
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502 url = new URL(file);
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505 JarInputStream jin = null;
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506 JarEntry jarentry = null;
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507 int entryCount = 1;
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513 jin = new JarInputStream(url.openStream());
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517 jin = new JarInputStream(new FileInputStream(file));
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520 for (int i = 0; i < entryCount; i++)
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522 jarentry = jin.getNextJarEntry();
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525 if (jarentry != null)
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527 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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528 object = (JalviewModel) object.unmarshal(in);
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529 af = LoadFromObject(object);
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533 while (jarentry != null);
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535 catch(java.net.UnknownHostException ex)
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537 ex.printStackTrace();
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538 System.err.println("Couldn't locate Jalview XML file : " +
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540 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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541 "Couldn't locate " + file,
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543 JOptionPane.WARNING_MESSAGE);
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546 catch (Exception ex)
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548 ex.printStackTrace();
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549 System.err.println("Exception whilst loading jalview XML file : " +
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551 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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552 "Error loading " + file,
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553 "Error loading Jalview file",
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554 JOptionPane.WARNING_MESSAGE);
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561 static AlignFrame LoadFromObject(JalviewModel object)
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563 Vector seqids = new Vector();
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564 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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565 Sequence[] vamsasSeq = vamsasSet.getSequence();
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567 JalviewModelSequence jms = object.getJalviewModelSequence();
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569 //////////////////////////////////
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571 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
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572 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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574 for (int i = 0; i < vamsasSeq.length; i++)
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576 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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577 vamsasSeq[i].getSequence());
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579 jseqs[i].setStart(JSEQ[i].getStart());
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580 jseqs[i].setEnd(JSEQ[i].getEnd());
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581 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
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582 seqids.add(jseqs[i]);
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585 /////////////////////////////////
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586 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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588 /////////////////////////////////
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589 //////////////////////////////////
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591 if (vamsasSet.getAnnotation() != null)
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593 Annotation[] an = vamsasSet.getAnnotation();
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595 for (int i = 0; i < an.length; i++)
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597 AnnotationElement[] ae = an[i].getAnnotationElement();
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598 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
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600 for (int aa = 0; aa < ae.length; aa++)
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602 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
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603 ae[aa].getDescription(),
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604 ae[aa].getSecondaryStructure().charAt(0),
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605 ae[aa].getValue());
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608 jalview.datamodel.AlignmentAnnotation jaa = null;
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610 if (an[i].getGraph())
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612 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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613 an[i].getDescription(), anot, 0, 0, 1);
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617 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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618 an[i].getDescription(), anot);
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621 al.addAnnotation(jaa);
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625 /////////////////////////////////
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627 Viewport[] views = jms.getViewport();
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628 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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630 AlignFrame af = new AlignFrame(al);
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632 // af.changeColour() );
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633 /////////////////////////
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635 if (jms.getJGroupCount() > 0)
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637 JGroup[] groups = jms.getJGroup();
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639 for (int i = 0; i < groups.length; i++)
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641 ColourSchemeI cs = null;
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643 if (groups[i].getColour() != null)
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645 if (groups[i].getColour().startsWith("ucs"))
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647 cs = GetUserColourScheme(jms, groups[i].getColour());
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651 cs = ColourSchemeProperty.getColour(al,
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652 groups[i].getColour());
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655 cs.setThreshold(groups[i].getPidThreshold(), true);
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658 Vector seqs = new Vector();
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659 int[] ids = groups[i].getSeq();
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661 for (int s = 0; s < ids.length; s++)
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663 seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
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667 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
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668 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
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669 groups[i].getDisplayText(), groups[i].getColourText(),
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670 groups[i].getStart(), groups[i].getEnd());
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672 sg.setOutlineColour(new java.awt.Color(
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673 groups[i].getOutlineColour()));
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675 if (groups[i].getConsThreshold() != 0)
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677 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
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678 ResidueProperties.propHash, 3, sg.sequences, 0,
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679 sg.getWidth() - 1);
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681 c.verdict(false, 25);
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682 sg.cs.setConservation(c);
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690 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
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692 af.viewport.setStartRes(view.getStartRes());
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693 af.viewport.setStartSeq(view.getStartSeq());
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694 af.viewport.showConservation = view.getShowConservation();
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695 af.viewport.showQuality = view.getShowQuality();
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696 af.viewport.showIdentity = view.getShowIdentity();
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697 af.viewport.setAbovePIDThreshold(view.getPidSelected());
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698 af.abovePIDThreshold.setSelected(view.getPidSelected());
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699 af.viewport.setColourText(view.getShowColourText());
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700 af.colourTextMenuItem.setSelected(view.getShowColourText());
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701 af.viewport.setConservationSelected(view.getConservationSelected());
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702 af.conservationMenuItem.setSelected(view.getConservationSelected());
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704 af.viewport.setShowJVSuffix(view.getShowFullId());
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705 af.seqLimits.setSelected(view.getShowFullId());
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707 af.viewport.setFont(new java.awt.Font(view.getFontName(),
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708 view.getFontStyle(), view.getFontSize()));
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709 af.alignPanel.fontChanged();
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711 af.viewport.setRenderGaps(view.getRenderGaps());
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712 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
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714 af.viewport.setWrapAlignment(view.getWrapAlignment());
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715 af.wrapMenuItem.setSelected(view.getWrapAlignment());
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717 if (view.getWrapAlignment())
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719 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
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723 af.annotationPanelMenuItem.setState(view.getShowAnnotation());
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724 af.viewport.setShowAnnotation(view.getShowAnnotation());
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725 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
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728 af.viewport.setShowBoxes(view.getShowBoxes());
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729 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
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730 af.viewport.setShowText(view.getShowText());
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731 af.viewTextMenuItem.setSelected(view.getShowText());
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733 ColourSchemeI cs = null;
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735 if (view.getBgColour() != null)
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737 if (view.getBgColour().startsWith("ucs"))
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739 cs = GetUserColourScheme(jms, view.getBgColour());
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743 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
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748 cs.setThreshold(view.getPidThreshold(), true);
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749 cs.setConsensus(af.viewport.vconsensus);
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753 af.setColourSelected(view.getBgColour());
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754 af.viewport.setGlobalColourScheme(cs);
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755 af.viewport.setColourAppliesToAllGroups(false);
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756 af.changeColour(cs);
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757 if (view.getConservationSelected() && cs!=null)
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759 cs.setConservationInc(view.getConsThreshold());
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762 af.viewport.setColourAppliesToAllGroups(true);
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764 if (view.getShowSequenceFeatures())
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766 af.viewport.showSequenceFeatures = true;
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767 af.sequenceFeatures.setSelected(true);
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768 new SequenceFeatureFetcher(al, af.alignPanel);
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769 al.featuresAdded = true;
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772 Desktop.addInternalFrame(af, view.getTitle(),
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773 view.getWidth(), view.getHeight());
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776 ///////////////////////////////////////
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777 if (jms.getTreeCount() > 0)
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781 for (int t = 0; t < jms.getTreeCount(); t++)
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784 Tree tree = jms.getTree(t);
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786 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
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787 tree.getNewick()), tree.getTitle(),
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788 tree.getWidth(), tree.getHeight(),
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789 tree.getXpos(), tree.getYpos());
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791 tp.fitToWindow.setState(tree.getFitToWindow());
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792 tp.fitToWindow_actionPerformed(null);
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794 if(tree.getFontName()!=null)
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795 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
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796 tree.getFontStyle(),
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797 tree.getFontSize()));
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799 tp.setTreeFont(new java.awt.Font(view.getFontName(),
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800 view.getFontStyle(),
\r
801 tree.getFontSize()));
\r
803 tp.showPlaceholders(tree.getMarkUnlinked());
\r
804 tp.showBootstrap(tree.getShowBootstrap());
\r
805 tp.showDistances(tree.getShowDistances());
\r
807 tp.treeCanvas.threshold = tree.getThreshold();
\r
809 if (tree.getCurrentTree())
\r
810 af.viewport.setCurrentTree(tp.getTree());
\r
814 catch (Exception ex)
\r
816 ex.printStackTrace();
\r