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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30 import java.util.jar.*;
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32 import javax.swing.*;
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34 import jalview.binding.*;
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41 * @version $Revision$
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43 public class Jalview2XML
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45 // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
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46 public static void SaveState(File statefile)
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48 long creation = System.currentTimeMillis();
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49 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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58 FileOutputStream fos = new FileOutputStream(statefile);
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59 JarOutputStream jout = new JarOutputStream(fos);
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61 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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62 ////////////////////////////////////////////////////
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63 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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66 Vector shortNames = new Vector();
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69 for (int i = frames.length - 1; i > -1; i--)
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71 if (frames[i] instanceof AlignFrame)
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73 AlignFrame af = (AlignFrame) frames[i];
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75 String shortName = af.getTitle();
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77 if (shortName.indexOf(File.separatorChar) > -1)
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79 shortName = shortName.substring(shortName.lastIndexOf(
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80 File.separatorChar) + 1);
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85 while (shortNames.contains(shortName))
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87 if (shortName.endsWith("_" + (count - 1)))
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89 shortName = shortName.substring(0,
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90 shortName.lastIndexOf("_"));
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93 shortName = shortName.concat("_" + count);
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97 shortNames.addElement(shortName);
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99 if (!shortName.endsWith(".xml"))
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101 shortName = shortName + ".xml";
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104 SaveState(af, creation, shortName, jout, out);
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111 catch (Exception ex)
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113 ex.printStackTrace();
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117 // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
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118 public static void SaveAlignment(AlignFrame af, String jarFile,
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123 FileOutputStream fos = new FileOutputStream(jarFile);
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124 JarOutputStream jout = new JarOutputStream(fos);
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126 //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
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127 ////////////////////////////////////////////////////
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128 PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
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131 SaveState(af, System.currentTimeMillis(), fileName, jout, out);
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135 catch (Exception ex)
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137 ex.printStackTrace();
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144 * @param af DOCUMENT ME!
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145 * @param timeStamp DOCUMENT ME!
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146 * @param fileName DOCUMENT ME!
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147 * @param jout DOCUMENT ME!
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148 * @param out DOCUMENT ME!
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150 public static void SaveState(AlignFrame af, long timeStamp,
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151 String fileName, JarOutputStream jout, PrintWriter out)
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153 Vector seqids = new Vector();
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154 Vector userColours = new Vector();
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156 AlignViewport av = af.viewport;
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158 JalviewModel object = new JalviewModel();
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159 object.setVamsasModel(new VamsasModel());
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161 object.setCreationDate(new java.util.Date(timeStamp));
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162 object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
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164 jalview.datamodel.AlignmentI jal = af.viewport.alignment;
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166 SequenceSet vamsasSet = new SequenceSet();
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167 Sequence vamsasSeq;
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168 JalviewModelSequence jms = new JalviewModelSequence();
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170 vamsasSet.setGapChar(jal.getGapCharacter() + "");
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177 for (int i = 0; i < jal.getHeight(); i++)
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179 seqids.add(jal.getSequenceAt(i));
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181 vamsasSeq = new Sequence();
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182 vamsasSeq.setId(id + "");
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183 vamsasSeq.setName(jal.getSequenceAt(i).getName());
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184 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
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187 jseq.setStart(jal.getSequenceAt(i).getStart());
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188 jseq.setEnd(jal.getSequenceAt(i).getEnd());
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190 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
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195 vamsasSet.addSequence(vamsasSeq);
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200 ///////////////////////////////////
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201 if (af.viewport.currentTree != null)
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203 // FIND ANY ASSOCIATED TREES
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204 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
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205 if (Desktop.desktop != null)
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207 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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209 for (int t = 0; t < frames.length; t++)
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211 if (frames[t] instanceof TreePanel)
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213 TreePanel tp = (TreePanel) frames[t];
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215 if (tp.treeCanvas.av.alignment == jal)
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217 Tree tree = new Tree();
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218 tree.setTitle(tp.getTitle());
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219 tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
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220 tree.setNewick(tp.getTree().toString());
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221 tree.setThreshold(tp.treeCanvas.threshold);
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223 tree.setFitToWindow(tp.fitToWindow.getState());
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224 tree.setFontSize(tp.treeCanvas.fontSize);
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225 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
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226 tree.setShowBootstrap(tp.bootstrapMenu.getState());
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227 tree.setShowDistances(tp.distanceMenu.getState());
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229 tree.setHeight(tp.getHeight());
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230 tree.setWidth(tp.getWidth());
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231 tree.setXpos(tp.getX());
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232 tree.setYpos(tp.getY());
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242 if (jal.getAlignmentAnnotation() != null)
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244 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
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246 for (int i = 0; i < aa.length; i++)
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248 if (aa[i].label.equals("Quality") ||
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249 aa[i].label.equals("Conservation") ||
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250 aa[i].label.equals("Consensus"))
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255 Annotation an = new Annotation();
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256 an.setDescription(aa[i].description);
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257 an.setGraph(aa[i].isGraph);
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258 an.setLabel(aa[i].label);
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260 AnnotationElement ae;
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262 for (int a = 0; a < aa[i].annotations.length; a++)
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264 if ((aa[i] == null) || (aa[i].annotations[a] == null))
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269 ae = new AnnotationElement();
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270 ae.setDescription(aa[i].annotations[a].description);
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271 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
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272 ae.setValue(aa[i].annotations[a].value);
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274 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
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276 an.addAnnotationElement(ae);
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279 vamsasSet.addAnnotation(an);
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284 if (jal.getGroups() != null)
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286 JGroup[] groups = new JGroup[jal.getGroups().size()];
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288 for (int i = 0; i < groups.length; i++)
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290 groups[i] = new JGroup();
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292 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
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294 groups[i].setStart(sg.getStartRes());
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295 groups[i].setEnd(sg.getEndRes());
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296 groups[i].setName(sg.getName());
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299 if (sg.cs.conservationApplied())
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301 groups[i].setConsThreshold(sg.cs.getConservationInc());
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303 if (sg.cs instanceof jalview.schemes.UserColourScheme)
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305 groups[i].setColour(SetUserColourScheme(sg.cs,
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311 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
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315 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
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317 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
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322 groups[i].setColour(ColourSchemeProperty.getColourName(
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326 groups[i].setPidThreshold(sg.cs.getThreshold());
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329 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
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330 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
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331 groups[i].setDisplayText(sg.getDisplayText());
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332 groups[i].setColourText(sg.getColourText());
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334 for (int s = 0; s < sg.getSize(); s++)
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336 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
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337 int index = seqids.indexOf(seq);
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338 groups[i].addSeq(index);
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342 jms.setJGroup(groups);
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345 ///////////SAVE VIEWPORT
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346 Viewport view = new Viewport();
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347 view.setTitle(af.getTitle());
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348 view.setXpos(af.getX());
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349 view.setYpos(af.getY());
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350 view.setWidth(af.getWidth());
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351 view.setHeight(af.getHeight());
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352 view.setStartRes(av.startRes);
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353 view.setStartSeq(av.startSeq);
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355 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
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357 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
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358 userColours, jms));
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362 view.setBgColour(ColourSchemeProperty.getColourName(
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363 av.getGlobalColourScheme()));
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366 ColourSchemeI cs = av.getGlobalColourScheme();
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370 if (cs.conservationApplied())
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372 view.setConsThreshold(cs.getConservationInc());
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373 if (cs instanceof jalview.schemes.UserColourScheme)
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374 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
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377 if (cs instanceof ResidueColourScheme)
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379 view.setPidThreshold(cs.getThreshold());
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383 view.setConservationSelected(av.getConservationSelected());
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384 view.setPidSelected(av.getAbovePIDThreshold());
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385 view.setFontName(av.font.getName());
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386 view.setFontSize(av.font.getSize());
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387 view.setFontStyle(av.font.getStyle());
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388 view.setRenderGaps(av.renderGaps);
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389 view.setShowAnnotation(av.getShowAnnotation());
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390 view.setShowBoxes(av.getShowBoxes());
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391 view.setShowColourText(av.getColourText());
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392 view.setShowConservation(av.showConservation);
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393 view.setShowFullId(av.getShowFullId());
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394 view.setShowIdentity(av.showIdentity);
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395 view.setShowQuality(av.showQuality);
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396 view.setShowSequenceFeatures(av.showSequenceFeatures);
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397 view.setShowText(av.getShowText());
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398 view.setWrapAlignment(av.getWrapAlignment());
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400 jms.addViewport(view);
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402 object.setJalviewModelSequence(jms);
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403 object.getVamsasModel().addSequenceSet(vamsasSet);
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407 if (!fileName.endsWith(".xml"))
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409 fileName = fileName + ".xml";
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412 JarEntry entry = new JarEntry(fileName);
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413 jout.putNextEntry(entry);
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415 object.marshal(out);
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417 catch (Exception ex)
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419 ex.printStackTrace();
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423 static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
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424 Vector userColours, JalviewModelSequence jms)
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427 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
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429 if (!userColours.contains(ucs))
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431 userColours.add(ucs);
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433 java.awt.Color[] colours = ucs.getColours();
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434 jalview.binding.UserColours uc = new jalview.binding.UserColours();
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435 jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
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437 for (int i = 0; i < colours.length; i++)
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439 jalview.binding.Colour col = new jalview.binding.Colour();
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440 col.setRGB(jalview.util.Format.getHexString(colours[i]));
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441 jbucs.addColour(col);
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444 id = "ucs" + userColours.indexOf(ucs);
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446 uc.setUserColourScheme(jbucs);
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447 jms.addUserColours(uc);
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453 static jalview.schemes.UserColourScheme GetUserColourScheme(
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454 JalviewModelSequence jms, String id)
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456 UserColours[] uc = jms.getUserColours();
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457 UserColours colours = null;
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459 for (int i = 0; i < uc.length; i++)
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461 if (uc[i].getId().equals(id))
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469 int csize = colours.getUserColourScheme().getColourCount();
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470 java.awt.Color[] newColours = new java.awt.Color[csize];
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472 for (int i = 0; i < csize; i++)
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474 newColours[i] = new java.awt.Color(Integer.parseInt(
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475 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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478 return new jalview.schemes.UserColourScheme(newColours);
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484 * @param file DOCUMENT ME!
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486 public static AlignFrame LoadJalviewAlign(String file)
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488 JalviewModel object = new JalviewModel();
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489 jalview.gui.AlignFrame af = null;
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493 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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496 if (file.startsWith("http://"))
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498 url = new URL(file);
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501 JarInputStream jin = null;
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502 JarEntry jarentry = null;
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503 int entryCount = 1;
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509 jin = new JarInputStream(url.openStream());
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513 jin = new JarInputStream(new FileInputStream(file));
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516 for (int i = 0; i < entryCount; i++)
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518 jarentry = jin.getNextJarEntry();
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521 if (jarentry != null)
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523 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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524 object = (JalviewModel) object.unmarshal(in);
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525 af = LoadFromObject(object);
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529 while (jarentry != null);
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531 catch (Exception ex)
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533 ex.printStackTrace();
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534 System.err.println("Exception whilst loading jalview XML file : " +
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536 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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537 "Couldn't locate " + file,
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539 JOptionPane.WARNING_MESSAGE);
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546 static AlignFrame LoadFromObject(JalviewModel object)
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548 Vector seqids = new Vector();
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549 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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550 Sequence[] vamsasSeq = vamsasSet.getSequence();
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552 JalviewModelSequence jms = object.getJalviewModelSequence();
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554 //////////////////////////////////
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556 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
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557 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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559 for (int i = 0; i < vamsasSeq.length; i++)
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561 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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562 vamsasSeq[i].getSequence());
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564 jseqs[i].setStart(JSEQ[i].getStart());
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565 jseqs[i].setEnd(JSEQ[i].getEnd());
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566 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
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567 seqids.add(jseqs[i]);
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570 /////////////////////////////////
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571 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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573 /////////////////////////////////
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574 //////////////////////////////////
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576 if (vamsasSet.getAnnotation() != null)
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578 Annotation[] an = vamsasSet.getAnnotation();
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580 for (int i = 0; i < an.length; i++)
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582 AnnotationElement[] ae = an[i].getAnnotationElement();
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583 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
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585 for (int aa = 0; aa < ae.length; aa++)
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587 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
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588 ae[aa].getDescription(),
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589 ae[aa].getSecondaryStructure().charAt(0),
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590 ae[aa].getValue());
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593 jalview.datamodel.AlignmentAnnotation jaa = null;
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595 if (an[i].getGraph())
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597 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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598 an[i].getDescription(), anot, 0, 0, 1);
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602 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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603 an[i].getDescription(), anot);
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606 al.addAnnotation(jaa);
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610 /////////////////////////////////
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612 Viewport[] views = jms.getViewport();
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613 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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615 AlignFrame af = new AlignFrame(al);
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617 // af.changeColour() );
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618 /////////////////////////
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620 if (jms.getJGroupCount() > 0)
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622 JGroup[] groups = jms.getJGroup();
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624 for (int i = 0; i < groups.length; i++)
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626 ColourSchemeI cs = null;
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628 if (groups[i].getColour() != null)
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630 if (groups[i].getColour().startsWith("ucs"))
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632 cs = GetUserColourScheme(jms, groups[i].getColour());
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636 cs = ColourSchemeProperty.getColour(al,
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637 groups[i].getColour());
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640 cs.setThreshold(groups[i].getPidThreshold(), true);
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643 Vector seqs = new Vector();
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644 int[] ids = groups[i].getSeq();
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646 for (int s = 0; s < ids.length; s++)
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648 seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
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652 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
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653 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
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654 groups[i].getDisplayText(), groups[i].getColourText(),
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655 groups[i].getStart(), groups[i].getEnd());
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657 sg.setOutlineColour(new java.awt.Color(
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658 groups[i].getOutlineColour()));
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660 if (groups[i].getConsThreshold() != 0)
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662 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
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663 ResidueProperties.propHash, 3, sg.sequences, 0,
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664 sg.getWidth() - 1);
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666 c.verdict(false, 25);
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667 sg.cs.setConservation(c);
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675 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
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677 af.viewport.setStartRes(view.getStartRes());
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678 af.viewport.setStartSeq(view.getStartSeq());
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679 af.viewport.showConservation = view.getShowConservation();
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680 af.viewport.showQuality = view.getShowQuality();
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681 af.viewport.showIdentity = view.getShowIdentity();
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682 af.viewport.setAbovePIDThreshold(view.getPidSelected());
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683 af.abovePIDThreshold.setSelected(view.getPidSelected());
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684 af.viewport.setColourText(view.getShowColourText());
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685 af.colourTextMenuItem.setSelected(view.getShowColourText());
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686 af.viewport.setConservationSelected(view.getConservationSelected());
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687 af.conservationMenuItem.setSelected(view.getConservationSelected());
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689 af.viewport.setShowFullId(view.getShowFullId());
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690 af.fullSeqId.setSelected(view.getShowFullId());
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692 af.viewport.setFont(new java.awt.Font(view.getFontName(),
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693 view.getFontStyle(), view.getFontSize()));
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694 af.alignPanel.fontChanged();
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696 af.viewport.setRenderGaps(view.getRenderGaps());
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697 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
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699 af.viewport.setWrapAlignment(view.getWrapAlignment());
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700 af.wrapMenuItem.setSelected(view.getWrapAlignment());
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702 if (view.getWrapAlignment())
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704 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
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708 af.annotationPanelMenuItem.setState(view.getShowAnnotation());
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709 af.viewport.setShowAnnotation(view.getShowAnnotation());
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710 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
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713 af.viewport.setShowBoxes(view.getShowBoxes());
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714 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
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715 af.viewport.setShowText(view.getShowText());
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716 af.viewTextMenuItem.setSelected(view.getShowText());
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718 ColourSchemeI cs = null;
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720 if (view.getBgColour() != null)
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722 if (view.getBgColour().startsWith("ucs"))
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724 cs = GetUserColourScheme(jms, view.getBgColour());
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728 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
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733 cs.setThreshold(view.getPidThreshold(), true);
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734 cs.setConsensus(af.viewport.vconsensus);
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738 af.setColourSelected(view.getBgColour());
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739 af.viewport.setGlobalColourScheme(cs);
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740 af.viewport.setColourAppliesToAllGroups(false);
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741 af.changeColour(cs);
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742 if (view.getConservationSelected() && cs!=null)
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744 cs.setConservationInc(view.getConsThreshold());
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747 af.viewport.setColourAppliesToAllGroups(true);
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749 if (view.getShowSequenceFeatures())
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751 af.viewport.showSequenceFeatures = true;
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752 af.sequenceFeatures.setSelected(true);
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753 new SequenceFeatureFetcher(al, af.alignPanel);
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754 al.featuresAdded = true;
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757 Desktop.addInternalFrame(af, view.getTitle(),
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758 view.getWidth(), view.getHeight());
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761 ///////////////////////////////////////
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762 if (jms.getTreeCount() > 0)
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766 for (int t = 0; t < jms.getTreeCount(); t++)
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769 Tree tree = jms.getTree(t);
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771 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
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772 tree.getNewick()), tree.getTitle(),
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773 tree.getWidth(), tree.getHeight(),
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774 tree.getXpos(), tree.getYpos());
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776 tp.fitToWindow.setState(tree.getFitToWindow());
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777 tp.fitToWindow_actionPerformed(null);
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778 tp.treeCanvas.fontSize = tree.getFontSize();
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779 tp.fontSize.setText("Font Size - " + tree.getFontSize());
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780 tp.placeholdersMenu.setState(tree.getMarkUnlinked());
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781 tp.placeholdersMenu_actionPerformed(null);
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782 tp.bootstrapMenu.setState(tree.getShowBootstrap());
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783 tp.bootstrapMenu_actionPerformed(null);
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784 tp.distanceMenu.setState(tree.getShowDistances());
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785 tp.distanceMenu_actionPerformed(null);
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786 tp.treeCanvas.threshold = tree.getThreshold();
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788 if (tree.getCurrentTree())
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789 af.viewport.setCurrentTree(tp.getTree());
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793 catch (Exception ex)
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795 ex.printStackTrace();
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