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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22 import jalview.schemes.*;
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24 import jalview.gui.*;
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32 import java.util.jar.*;
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34 import javax.swing.*;
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36 import org.exolab.castor.xml.*;
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38 import jalview.schemabinding.version2.*;
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47 * @version $Revision$
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49 public class Jalview2XML
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51 // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
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52 public void SaveState(File statefile)
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54 long creation = System.currentTimeMillis();
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55 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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64 FileOutputStream fos = new FileOutputStream(statefile);
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65 JarOutputStream jout = new JarOutputStream(fos);
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67 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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68 ////////////////////////////////////////////////////
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69 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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72 Vector shortNames = new Vector();
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75 for (int i = frames.length - 1; i > -1; i--)
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77 if (frames[i] instanceof AlignFrame)
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79 AlignFrame af = (AlignFrame) frames[i];
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81 String shortName = af.getTitle();
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83 if (shortName.indexOf(File.separatorChar) > -1)
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85 shortName = shortName.substring(shortName.lastIndexOf(
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86 File.separatorChar) + 1);
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91 while (shortNames.contains(shortName))
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93 if (shortName.endsWith("_" + (count - 1)))
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95 shortName = shortName.substring(0,
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96 shortName.lastIndexOf("_"));
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99 shortName = shortName.concat("_" + count);
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103 shortNames.addElement(shortName);
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105 if (!shortName.endsWith(".xml"))
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107 shortName = shortName + ".xml";
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110 SaveState(af, creation, shortName, jout, out);
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117 catch (Exception ex)
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119 ex.printStackTrace();
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123 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
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124 public void SaveAlignment(AlignFrame af, String jarFile,
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129 FileOutputStream fos = new FileOutputStream(jarFile);
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130 JarOutputStream jout = new JarOutputStream(fos);
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132 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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133 ////////////////////////////////////////////////////
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134 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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137 SaveState(af, System.currentTimeMillis(), fileName, jout, out);
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141 catch (Exception ex)
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143 ex.printStackTrace();
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150 * @param af DOCUMENT ME!
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151 * @param timeStamp DOCUMENT ME!
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152 * @param fileName DOCUMENT ME!
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153 * @param jout DOCUMENT ME!
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154 * @param out DOCUMENT ME!
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156 public void SaveState(AlignFrame af, long timeStamp,
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157 String fileName, JarOutputStream jout, PrintWriter out)
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159 Vector seqids = new Vector();
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160 Vector userColours = new Vector();
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162 AlignViewport av = af.viewport;
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164 JalviewModel object = new JalviewModel();
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165 object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
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167 object.setCreationDate(new java.util.Date(timeStamp));
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168 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
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170 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
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172 SequenceSet vamsasSet = new SequenceSet();
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173 Sequence vamsasSeq;
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174 JalviewModelSequence jms = new JalviewModelSequence();
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176 vamsasSet.setGapChar(jal.getGapCharacter() + "");
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183 for (int i = 0; i < jal.getHeight(); i++)
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185 seqids.add(jal.getSequenceAt(i));
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187 vamsasSeq = new Sequence();
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188 vamsasSeq.setId(id + "");
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189 vamsasSeq.setName(jal.getSequenceAt(i).getName());
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190 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
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191 vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
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194 jseq.setStart(jal.getSequenceAt(i).getStart());
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195 jseq.setEnd(jal.getSequenceAt(i).getEnd());
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197 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
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201 if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
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203 jalview.datamodel.SequenceFeature[] sf
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204 = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
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206 while(index < sf.length)
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208 Features features = new Features();
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210 features.setBegin(sf[index].getBegin());
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211 features.setEnd(sf[index].getEnd());
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212 features.setDescription(sf[index].getDescription());
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213 features.setType(sf[index].getType());
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214 features.setFeatureGroup(sf[index].getFeatureGroup());
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215 jseq.addFeatures(features);
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220 if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
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222 Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
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223 while(en.hasMoreElements())
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225 Pdbids pdb = new Pdbids();
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226 jalview.datamodel.PDBEntry entry
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227 = (jalview.datamodel.PDBEntry)en.nextElement();
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229 pdb.setId(entry.getId());
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230 pdb.setType(entry.getType());
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232 if(entry.getProperty()!=null)
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234 PdbentryItem item = new PdbentryItem();
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235 Hashtable properties = entry.getProperty();
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236 Enumeration en2 = properties.keys();
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237 while(en2.hasMoreElements())
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239 Property prop = new Property();
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240 String key = en2.nextElement().toString();
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242 prop.setValue( properties.get(key).toString() );
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243 item.addProperty(prop);
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245 pdb.addPdbentryItem(item);
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248 jseq.addPdbids(pdb);
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253 vamsasSet.addSequence(vamsasSeq);
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258 ///////////////////////////////////
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259 if (af.viewport.currentTree != null)
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261 // FIND ANY ASSOCIATED TREES
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262 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
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263 if (Desktop.desktop != null)
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265 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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267 for (int t = 0; t < frames.length; t++)
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269 if (frames[t] instanceof TreePanel)
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271 TreePanel tp = (TreePanel) frames[t];
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273 if (tp.treeCanvas.av.alignment == jal)
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275 Tree tree = new Tree();
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276 tree.setTitle(tp.getTitle());
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277 tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
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278 tree.setNewick(tp.getTree().toString());
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279 tree.setThreshold(tp.treeCanvas.threshold);
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281 tree.setFitToWindow(tp.fitToWindow.getState());
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282 tree.setFontName(tp.getTreeFont().getName());
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283 tree.setFontSize(tp.getTreeFont().getSize());
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284 tree.setFontStyle(tp.getTreeFont().getStyle());
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285 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
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287 tree.setShowBootstrap(tp.bootstrapMenu.getState());
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288 tree.setShowDistances(tp.distanceMenu.getState());
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290 tree.setHeight(tp.getHeight());
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291 tree.setWidth(tp.getWidth());
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292 tree.setXpos(tp.getX());
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293 tree.setYpos(tp.getY());
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303 if (jal.getAlignmentAnnotation() != null)
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305 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
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307 for (int i = 0; i < aa.length; i++)
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309 Annotation an = new Annotation();
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311 if (aa[i].label.equals("Quality") ||
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312 aa[i].label.equals("Conservation") ||
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313 aa[i].label.equals("Consensus"))
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315 an.setLabel(aa[i].label);
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317 vamsasSet.addAnnotation(an);
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322 an.setDescription(aa[i].description);
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324 if(aa[i].sequenceRef!=null)
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326 an.setSequenceRef(aa[i].sequenceRef.getName());
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332 an.setGraphType(aa[i].graph);
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333 an.setGraphGroup(aa[i].graphGroup);
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334 if(aa[i].getThreshold()!=null)
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336 ThresholdLine line = new ThresholdLine();
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337 line.setLabel(aa[i].getThreshold().label);
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338 line.setValue(aa[i].getThreshold().value);
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339 line.setColour(aa[i].getThreshold().colour.getRGB());
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340 an.setThresholdLine(line);
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344 an.setGraph(false);
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346 an.setLabel(aa[i].label);
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348 AnnotationElement ae;
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350 for (int a = 0; a < aa[i].annotations.length; a++)
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352 if ((aa[i] == null) || (aa[i].annotations[a] == null))
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357 ae = new AnnotationElement();
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358 ae.setDescription(aa[i].annotations[a].description);
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359 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
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360 ae.setValue(aa[i].annotations[a].value);
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362 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
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365 if(aa[i].annotations[a].colour!=java.awt.Color.black)
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366 ae.setColour(aa[i].annotations[a].colour.getRGB());
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368 an.addAnnotationElement(ae);
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371 vamsasSet.addAnnotation(an);
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376 if (jal.getGroups() != null)
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378 JGroup[] groups = new JGroup[jal.getGroups().size()];
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380 for (int i = 0; i < groups.length; i++)
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382 groups[i] = new JGroup();
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384 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
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386 groups[i].setStart(sg.getStartRes());
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387 groups[i].setEnd(sg.getEndRes());
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388 groups[i].setName(sg.getName());
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391 if (sg.cs.conservationApplied())
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393 groups[i].setConsThreshold(sg.cs.getConservationInc());
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395 if (sg.cs instanceof jalview.schemes.UserColourScheme)
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397 groups[i].setColour(SetUserColourScheme(sg.cs,
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403 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
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407 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
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409 groups[i].setColour(
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410 ColourSchemeProperty.getColourName(
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411 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
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413 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
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415 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
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420 groups[i].setColour(ColourSchemeProperty.getColourName(
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424 groups[i].setPidThreshold(sg.cs.getThreshold());
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427 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
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428 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
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429 groups[i].setDisplayText(sg.getDisplayText());
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430 groups[i].setColourText(sg.getColourText());
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432 for (int s = 0; s < sg.getSize(false); s++)
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434 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
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435 int index = seqids.indexOf(seq);
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436 groups[i].addSeq(index);
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440 jms.setJGroup(groups);
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444 ///////////SAVE VIEWPORT
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445 Viewport view = new Viewport();
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446 view.setTitle(af.getTitle());
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447 view.setXpos(af.getX());
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448 view.setYpos(af.getY());
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449 view.setWidth(af.getWidth());
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450 view.setHeight(af.getHeight());
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451 view.setStartRes(av.startRes);
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452 view.setStartSeq(av.startSeq);
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454 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
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456 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
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457 userColours, jms));
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459 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
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461 jalview.schemes.AnnotationColourGradient acg
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462 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
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464 AnnotationColours ac = new AnnotationColours();
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465 ac.setAboveThreshold(acg.getAboveThreshold());
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466 ac.setThreshold(acg.getAnnotationThreshold());
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467 ac.setAnnotation(acg.getAnnotation());
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468 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
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469 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
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470 userColours, jms));
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472 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
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474 ac.setMaxColour(acg.getMaxColour().getRGB());
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475 ac.setMinColour(acg.getMinColour().getRGB());
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476 view.setAnnotationColours(ac);
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477 view.setBgColour("AnnotationColourGradient");
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481 view.setBgColour(ColourSchemeProperty.getColourName(
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482 av.getGlobalColourScheme()));
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485 ColourSchemeI cs = av.getGlobalColourScheme();
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489 if (cs.conservationApplied())
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491 view.setConsThreshold(cs.getConservationInc());
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492 if (cs instanceof jalview.schemes.UserColourScheme)
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493 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
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496 if (cs instanceof ResidueColourScheme)
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498 view.setPidThreshold(cs.getThreshold());
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502 view.setConservationSelected(av.getConservationSelected());
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503 view.setPidSelected(av.getAbovePIDThreshold());
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504 view.setFontName(av.font.getName());
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505 view.setFontSize(av.font.getSize());
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506 view.setFontStyle(av.font.getStyle());
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507 view.setRenderGaps(av.renderGaps);
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508 view.setShowAnnotation(av.getShowAnnotation());
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509 view.setShowBoxes(av.getShowBoxes());
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510 view.setShowColourText(av.getColourText());
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511 view.setShowConservation(av.showConservation);
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512 view.setShowFullId(av.getShowJVSuffix());
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513 view.setShowIdentity(av.showIdentity);
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514 view.setShowQuality(av.showQuality);
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515 view.setShowSequenceFeatures(av.showSequenceFeatures);
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516 view.setShowText(av.getShowText());
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517 view.setWrapAlignment(av.getWrapAlignment());
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519 if(av.featuresDisplayed!=null)
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521 jalview.schemabinding.version2.FeatureSettings fs
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522 = new jalview.schemabinding.version2.FeatureSettings();
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524 String [] renderOrder =
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525 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
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526 for(int ro=0; ro<renderOrder.length; ro++)
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528 Setting setting = new Setting();
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529 setting.setType(renderOrder[ro]);
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531 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
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534 setting.setDisplay(
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535 av.featuresDisplayed.containsKey(renderOrder[ro])
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538 fs.addSetting(setting);
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541 jms.setFeatureSettings(fs);
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545 jms.addViewport(view);
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548 object.setJalviewModelSequence(jms);
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549 object.getVamsasModel().addSequenceSet(vamsasSet);
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553 if (!fileName.endsWith(".xml"))
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555 fileName = fileName + ".xml";
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558 JarEntry entry = new JarEntry(fileName);
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559 jout.putNextEntry(entry);
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561 object.marshal(out);
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563 catch (Exception ex)
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565 ex.printStackTrace();
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569 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
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570 Vector userColours, JalviewModelSequence jms)
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573 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
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575 if (!userColours.contains(ucs))
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577 userColours.add(ucs);
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579 java.awt.Color[] colours = ucs.getColours();
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580 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
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581 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
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583 for (int i = 0; i < colours.length; i++)
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585 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
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586 col.setRGB(jalview.util.Format.getHexString(colours[i]));
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587 jbucs.addColour(col);
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590 id = "ucs" + userColours.indexOf(ucs);
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592 uc.setUserColourScheme(jbucs);
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593 jms.addUserColours(uc);
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599 jalview.schemes.UserColourScheme GetUserColourScheme(
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600 JalviewModelSequence jms, String id)
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602 UserColours[] uc = jms.getUserColours();
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603 UserColours colours = null;
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605 for (int i = 0; i < uc.length; i++)
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607 if (uc[i].getId().equals(id))
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615 int csize = colours.getUserColourScheme().getColourCount();
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616 java.awt.Color[] newColours = new java.awt.Color[csize];
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618 for (int i = 0; i < csize; i++)
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620 newColours[i] = new java.awt.Color(Integer.parseInt(
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621 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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624 return new jalview.schemes.UserColourScheme(newColours);
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630 * @param file DOCUMENT ME!
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632 public AlignFrame LoadJalviewAlign(String file)
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635 jalview.gui.AlignFrame af = null;
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639 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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642 if (file.startsWith("http://"))
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644 url = new URL(file);
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647 JarInputStream jin = null;
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648 JarEntry jarentry = null;
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649 int entryCount = 1;
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655 jin = new JarInputStream(url.openStream());
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659 jin = new JarInputStream(new FileInputStream(file));
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662 for (int i = 0; i < entryCount; i++)
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664 jarentry = jin.getNextJarEntry();
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669 class NoDescIDResolver implements IDResolver
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671 public Object resolve(String idref)
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673 System.out.println(idref+" used");
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679 if (jarentry != null)
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681 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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682 JalviewModel object = new JalviewModel();
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684 Unmarshaller unmar = new Unmarshaller(object);
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685 unmar.setValidation(false);
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686 object = (JalviewModel) unmar.unmarshal( in );
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688 af = LoadFromObject(object);
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692 while (jarentry != null);
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694 catch(java.net.UnknownHostException ex)
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696 ex.printStackTrace();
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697 System.err.println("Couldn't locate Jalview XML file : " +
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699 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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700 "Couldn't locate " + file,
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702 JOptionPane.WARNING_MESSAGE);
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705 catch (Exception ex)
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707 //Is Version 1 Jar file?
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708 af = new Jalview2XML_V1().LoadJalviewAlign(file);
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712 System.out.println("Successfully loaded archive file");
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715 ex.printStackTrace();
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716 System.err.println("Exception whilst loading jalview XML file : " +
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718 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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719 "Error loading " + file,
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720 "Error loading Jalview file",
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721 JOptionPane.WARNING_MESSAGE);
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728 AlignFrame LoadFromObject(JalviewModel object)
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730 Vector seqids = new Vector();
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731 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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732 Sequence[] vamsasSeq = vamsasSet.getSequence();
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734 JalviewModelSequence jms = object.getJalviewModelSequence();
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736 //////////////////////////////////
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738 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
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739 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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740 for (int i = 0; i < vamsasSeq.length; i++)
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742 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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743 vamsasSeq[i].getSequence());
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744 jseqs[i].setDescription( vamsasSeq[i].getDescription() );
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746 jseqs[i].setStart(JSEQ[i].getStart());
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747 jseqs[i].setEnd(JSEQ[i].getEnd());
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748 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
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749 seqids.add(jseqs[i]);
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752 ///SequenceFeatures are added to the DatasetSequence,
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753 // so we must create the dataset before loading features
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754 /////////////////////////////////
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755 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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756 al.setDataset(null);
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757 /////////////////////////////////
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759 for (int i = 0; i < vamsasSeq.length; i++)
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761 if (JSEQ[i].getFeaturesCount() > 0)
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763 Features[] features = JSEQ[i].getFeatures();
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764 for (int f = 0; f < features.length; f++)
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766 jalview.datamodel.SequenceFeature sf
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767 = new jalview.datamodel.SequenceFeature(features[f].getType(),
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768 features[f].getDescription(), features[f].getStatus(),
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769 features[f].getBegin(), features[f].getEnd(),
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770 features[f].getFeatureGroup());
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772 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
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775 if (JSEQ[i].getPdbidsCount() > 0)
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777 Pdbids[] ids = JSEQ[i].getPdbids();
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778 for (int p = 0; p < ids.length; p++)
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780 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
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781 entry.setId(ids[p].getId());
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782 entry.setType(ids[p].getType());
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783 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
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790 /////////////////////////////////
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791 //////////////////////////////////
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793 boolean hideQuality = true,
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794 hideConservation = true,
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795 hideConsensus = true;
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797 if (vamsasSet.getAnnotation() != null)
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799 Annotation[] an = vamsasSet.getAnnotation();
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801 for (int i = 0; i < an.length; i++)
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803 if (an[i].getLabel().equals("Quality"))
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805 hideQuality = false;
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808 else if(an[i].getLabel().equals("Conservation"))
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810 hideConservation = false;
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813 else if(an[i].getLabel().equals("Consensus"))
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815 hideConsensus = false;
\r
819 AnnotationElement[] ae = an[i].getAnnotationElement();
\r
820 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
\r
822 for (int aa = 0; aa < ae.length; aa++)
\r
824 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
\r
825 ae[aa].getDescription(),
\r
826 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
\r
827 ae[aa].getValue());
\r
828 anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
\r
831 jalview.datamodel.AlignmentAnnotation jaa = null;
\r
833 if (an[i].getGraph())
\r
835 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
\r
836 an[i].getDescription(), anot, 0, 0,
\r
837 an[i].getGraphType());
\r
839 jaa.graphGroup = an[i].getGraphGroup();
\r
841 if (an[i].getThresholdLine() != null)
\r
843 jaa.setThreshold(new jalview.datamodel.GraphLine(
\r
844 an[i].getThresholdLine().getValue(),
\r
845 an[i].getThresholdLine().getLabel(),
\r
846 new java.awt.Color(an[i].getThresholdLine().getColour()))
\r
854 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
\r
855 an[i].getDescription(), anot);
\r
858 if(an[i].getSequenceRef()!=null)
\r
860 jaa.createSequenceMapping(
\r
861 al.findName(an[i].getSequenceRef()), 1
\r
863 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
\r
866 al.addAnnotation(jaa);
\r
871 // af.changeColour() );
\r
872 /////////////////////////
\r
874 if (jms.getJGroupCount() > 0)
\r
876 JGroup[] groups = jms.getJGroup();
\r
878 for (int i = 0; i < groups.length; i++)
\r
880 ColourSchemeI cs = null;
\r
882 if (groups[i].getColour() != null)
\r
884 if (groups[i].getColour().startsWith("ucs"))
\r
886 cs = GetUserColourScheme(jms, groups[i].getColour());
\r
890 cs = ColourSchemeProperty.getColour(al,
\r
891 groups[i].getColour());
\r
895 cs.setThreshold(groups[i].getPidThreshold(), true);
\r
898 Vector seqs = new Vector();
\r
899 int[] ids = groups[i].getSeq();
\r
901 for (int s = 0; s < ids.length; s++)
\r
903 seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
\r
907 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
\r
908 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
\r
909 groups[i].getDisplayText(), groups[i].getColourText(),
\r
910 groups[i].getStart(), groups[i].getEnd());
\r
912 sg.setOutlineColour(new java.awt.Color(
\r
913 groups[i].getOutlineColour()));
\r
915 if (groups[i].getConsThreshold() != 0)
\r
917 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
\r
918 ResidueProperties.propHash, 3, sg.getSequences(false), 0,
\r
919 sg.getWidth() - 1);
\r
921 c.verdict(false, 25);
\r
922 sg.cs.setConservation(c);
\r
930 /////////////////////////////////
\r
932 Viewport[] views = jms.getViewport();
\r
933 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
\r
935 AlignFrame af = new AlignFrame(al);
\r
936 if(hideConsensus || hideQuality || hideConservation)
\r
938 int hSize = al.getAlignmentAnnotation().length;
\r
939 for (int h = 0; h < hSize; h++)
\r
943 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
\r
946 al.getAlignmentAnnotation()[h].label.equals("Quality"))
\r
948 (hideConservation &&
\r
949 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
\r
951 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
\r
956 af.alignPanel.adjustAnnotationHeight();
\r
959 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
\r
961 af.viewport.setStartRes(view.getStartRes());
\r
962 af.viewport.setStartSeq(view.getStartSeq());
\r
963 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
964 af.viewport.showConservation = view.getShowConservation();
\r
965 af.viewport.showQuality = view.getShowQuality();
\r
966 af.viewport.showIdentity = view.getShowIdentity();
\r
967 af.viewport.setAbovePIDThreshold(view.getPidSelected());
\r
968 af.abovePIDThreshold.setSelected(view.getPidSelected());
\r
969 af.viewport.setColourText(view.getShowColourText());
\r
970 af.colourTextMenuItem.setSelected(view.getShowColourText());
\r
971 af.viewport.setConservationSelected(view.getConservationSelected());
\r
972 af.conservationMenuItem.setSelected(view.getConservationSelected());
\r
974 af.viewport.setShowJVSuffix(view.getShowFullId());
\r
975 af.seqLimits.setSelected(view.getShowFullId());
\r
977 af.viewport.setFont(new java.awt.Font(view.getFontName(),
\r
978 view.getFontStyle(), view.getFontSize()));
\r
979 af.alignPanel.fontChanged();
\r
981 af.viewport.setRenderGaps(view.getRenderGaps());
\r
982 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
\r
984 af.viewport.setWrapAlignment(view.getWrapAlignment());
\r
985 af.wrapMenuItem.setSelected(view.getWrapAlignment());
\r
987 if (view.getWrapAlignment())
\r
989 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
\r
993 af.annotationPanelMenuItem.setState(view.getShowAnnotation());
\r
994 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
995 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
\r
998 af.viewport.setShowBoxes(view.getShowBoxes());
\r
999 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
\r
1000 af.viewport.setShowText(view.getShowText());
\r
1001 af.viewTextMenuItem.setSelected(view.getShowText());
\r
1003 ColourSchemeI cs = null;
\r
1005 if (view.getBgColour() != null)
\r
1007 if (view.getBgColour().startsWith("ucs"))
\r
1009 cs = GetUserColourScheme(jms, view.getBgColour());
\r
1011 else if(view.getBgColour().startsWith("Annotation"))
\r
1013 //int find annotation
\r
1014 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
\r
1016 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
\r
1017 equals(view.getAnnotationColours().getAnnotation()))
\r
1019 if (af.viewport.alignment.getAlignmentAnnotation()[i].
\r
1020 getThreshold() == null)
\r
1022 af.viewport.alignment.getAlignmentAnnotation()[i].
\r
1024 new jalview.datamodel.GraphLine(
\r
1025 view.getAnnotationColours().getThreshold(),
\r
1026 "Threshold", java.awt.Color.black)
\r
1032 if (view.getAnnotationColours().getColourScheme().equals(
\r
1035 cs = new AnnotationColourGradient(
\r
1036 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1037 new java.awt.Color(view.getAnnotationColours().
\r
1039 new java.awt.Color(view.getAnnotationColours().
\r
1041 view.getAnnotationColours().getAboveThreshold());
\r
1043 else if (view.getAnnotationColours().getColourScheme().
\r
1044 startsWith("ucs"))
\r
1046 cs = new AnnotationColourGradient(
\r
1047 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1048 GetUserColourScheme(jms, view.getAnnotationColours().
\r
1049 getColourScheme()),
\r
1050 view.getAnnotationColours().getAboveThreshold()
\r
1055 cs = new AnnotationColourGradient(
\r
1056 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1057 ColourSchemeProperty.getColour(al,
\r
1058 view.getAnnotationColours().getColourScheme()),
\r
1059 view.getAnnotationColours().getAboveThreshold()
\r
1063 // Also use these settings for all the groups
\r
1064 if (al.getGroups() != null)
\r
1065 for (int g = 0; g < al.getGroups().size(); g++)
\r
1067 jalview.datamodel.SequenceGroup sg
\r
1068 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
\r
1074 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
\r
1076 sg.cs = new AnnotationColourGradient(
\r
1077 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1078 new java.awt.Color(view.getAnnotationColours().
\r
1080 new java.awt.Color(view.getAnnotationColours().
\r
1082 view.getAnnotationColours().getAboveThreshold());
\r
1086 sg.cs = new AnnotationColourGradient(
\r
1087 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1089 view.getAnnotationColours().getAboveThreshold()
\r
1103 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
\r
1108 cs.setThreshold(view.getPidThreshold(), true);
\r
1109 cs.setConsensus(af.viewport.vconsensus);
\r
1113 af.setColourSelected(view.getBgColour());
\r
1114 af.viewport.setGlobalColourScheme(cs);
\r
1115 af.viewport.setColourAppliesToAllGroups(false);
\r
1116 af.changeColour(cs);
\r
1117 if (view.getConservationSelected() && cs!=null)
\r
1119 cs.setConservationInc(view.getConsThreshold());
\r
1122 af.viewport.setColourAppliesToAllGroups(true);
\r
1124 if (view.getShowSequenceFeatures())
\r
1126 af.viewport.showSequenceFeatures = true;
\r
1127 af.showSeqFeatures.setSelected(true);
\r
1130 if(jms.getFeatureSettings()!=null)
\r
1132 af.viewport.featuresDisplayed = new Hashtable();
\r
1133 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
\r
1134 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
\r
1136 Setting setting = jms.getFeatureSettings().getSetting(fs);
\r
1138 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
\r
1139 new java.awt.Color(setting.getColour()));
\r
1141 renderOrder[fs] = setting.getType();
\r
1143 if(setting.getDisplay())
\r
1144 af.viewport.featuresDisplayed.put(
\r
1145 setting.getType(), new Integer(setting.getColour()));
\r
1147 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
\r
1151 Desktop.addInternalFrame(af, view.getTitle(),
\r
1152 view.getWidth(), view.getHeight());
\r
1155 ///////////////////////////////////////
\r
1156 if (jms.getTreeCount() > 0)
\r
1160 for (int t = 0; t < jms.getTreeCount(); t++)
\r
1163 Tree tree = jms.getTree(t);
\r
1165 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
\r
1166 tree.getNewick()), tree.getTitle(),
\r
1167 tree.getWidth(), tree.getHeight(),
\r
1168 tree.getXpos(), tree.getYpos());
\r
1170 tp.fitToWindow.setState(tree.getFitToWindow());
\r
1171 tp.fitToWindow_actionPerformed(null);
\r
1173 if(tree.getFontName()!=null)
\r
1174 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
\r
1175 tree.getFontStyle(),
\r
1176 tree.getFontSize()));
\r
1178 tp.setTreeFont(new java.awt.Font(view.getFontName(),
\r
1179 view.getFontStyle(),
\r
1180 tree.getFontSize()));
\r
1182 tp.showPlaceholders(tree.getMarkUnlinked());
\r
1183 tp.showBootstrap(tree.getShowBootstrap());
\r
1184 tp.showDistances(tree.getShowDistances());
\r
1186 tp.treeCanvas.threshold = tree.getThreshold();
\r
1188 if (tree.getCurrentTree())
\r
1189 af.viewport.setCurrentTree(tp.getTree());
\r
1193 catch (Exception ex)
\r
1195 ex.printStackTrace();
\r