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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186 vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
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189 jseq.setStart(jal.getSequenceAt(i).getStart());
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190 jseq.setEnd(jal.getSequenceAt(i).getEnd());
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192 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
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196 if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
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198 Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements();
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199 while(en.hasMoreElements())
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201 Features features = new Features();
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202 jalview.datamodel.SequenceFeature sf
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203 = (jalview.datamodel.SequenceFeature)en.nextElement();
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205 features.setBegin(sf.getBegin());
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206 features.setEnd(sf.getEnd());
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207 features.setDescription(sf.getDescription());
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208 features.setStatus(sf.getStatus());
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209 features.setType(sf.getType());
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210 features.setFeatureGroup(sf.getFeatureGroup());
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211 jseq.addFeatures(features);
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215 if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
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217 Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
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218 while(en.hasMoreElements())
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220 Pdbids pdb = new Pdbids();
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221 jalview.datamodel.PDBEntry entry
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222 = (jalview.datamodel.PDBEntry)en.nextElement();
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224 pdb.setId(entry.getId());
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225 pdb.setType(entry.getType());
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227 if(entry.getProperty()!=null)
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229 PdbentryItem item = new PdbentryItem();
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230 Hashtable properties = entry.getProperty();
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231 Enumeration en2 = properties.keys();
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232 while(en2.hasMoreElements())
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234 Property prop = new Property();
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235 String key = en2.nextElement().toString();
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237 prop.setValue( properties.get(key).toString() );
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238 item.addProperty(prop);
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240 pdb.addPdbentryItem(item);
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243 jseq.addPdbids(pdb);
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248 vamsasSet.addSequence(vamsasSeq);
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253 ///////////////////////////////////
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254 if (af.viewport.currentTree != null)
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256 // FIND ANY ASSOCIATED TREES
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257 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
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258 if (Desktop.desktop != null)
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260 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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262 for (int t = 0; t < frames.length; t++)
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264 if (frames[t] instanceof TreePanel)
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266 TreePanel tp = (TreePanel) frames[t];
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268 if (tp.treeCanvas.av.alignment == jal)
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270 Tree tree = new Tree();
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271 tree.setTitle(tp.getTitle());
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272 tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
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273 tree.setNewick(tp.getTree().toString());
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274 tree.setThreshold(tp.treeCanvas.threshold);
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276 tree.setFitToWindow(tp.fitToWindow.getState());
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277 tree.setFontName(tp.getTreeFont().getName());
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278 tree.setFontSize(tp.getTreeFont().getSize());
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279 tree.setFontStyle(tp.getTreeFont().getStyle());
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280 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
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282 tree.setShowBootstrap(tp.bootstrapMenu.getState());
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283 tree.setShowDistances(tp.distanceMenu.getState());
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285 tree.setHeight(tp.getHeight());
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286 tree.setWidth(tp.getWidth());
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287 tree.setXpos(tp.getX());
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288 tree.setYpos(tp.getY());
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298 if (jal.getAlignmentAnnotation() != null)
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300 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
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302 for (int i = 0; i < aa.length; i++)
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304 if (aa[i].label.equals("Quality") ||
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305 aa[i].label.equals("Conservation") ||
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306 aa[i].label.equals("Consensus"))
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311 Annotation an = new Annotation();
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312 an.setDescription(aa[i].description);
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316 an.setGraphType(aa[i].graph);
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318 an.setLabel(aa[i].label);
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320 AnnotationElement ae;
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322 for (int a = 0; a < aa[i].annotations.length; a++)
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324 if ((aa[i] == null) || (aa[i].annotations[a] == null))
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329 ae = new AnnotationElement();
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330 ae.setDescription(aa[i].annotations[a].description);
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331 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
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332 ae.setValue(aa[i].annotations[a].value);
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334 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
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336 an.addAnnotationElement(ae);
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339 vamsasSet.addAnnotation(an);
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344 if (jal.getGroups() != null)
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346 JGroup[] groups = new JGroup[jal.getGroups().size()];
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348 for (int i = 0; i < groups.length; i++)
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350 groups[i] = new JGroup();
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352 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
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354 groups[i].setStart(sg.getStartRes());
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355 groups[i].setEnd(sg.getEndRes());
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356 groups[i].setName(sg.getName());
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359 if (sg.cs.conservationApplied())
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361 groups[i].setConsThreshold(sg.cs.getConservationInc());
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363 if (sg.cs instanceof jalview.schemes.UserColourScheme)
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365 groups[i].setColour(SetUserColourScheme(sg.cs,
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371 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
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375 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
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377 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
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382 groups[i].setColour(ColourSchemeProperty.getColourName(
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386 groups[i].setPidThreshold(sg.cs.getThreshold());
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389 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
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390 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
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391 groups[i].setDisplayText(sg.getDisplayText());
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392 groups[i].setColourText(sg.getColourText());
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394 for (int s = 0; s < sg.getSize(); s++)
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396 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
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397 int index = seqids.indexOf(seq);
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398 groups[i].addSeq(index);
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402 jms.setJGroup(groups);
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406 ///////////SAVE VIEWPORT
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407 Viewport view = new Viewport();
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408 view.setTitle(af.getTitle());
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409 view.setXpos(af.getX());
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410 view.setYpos(af.getY());
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411 view.setWidth(af.getWidth());
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412 view.setHeight(af.getHeight());
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413 view.setStartRes(av.startRes);
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414 view.setStartSeq(av.startSeq);
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416 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
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418 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
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419 userColours, jms));
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423 view.setBgColour(ColourSchemeProperty.getColourName(
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424 av.getGlobalColourScheme()));
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427 ColourSchemeI cs = av.getGlobalColourScheme();
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431 if (cs.conservationApplied())
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433 view.setConsThreshold(cs.getConservationInc());
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434 if (cs instanceof jalview.schemes.UserColourScheme)
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435 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
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438 if (cs instanceof ResidueColourScheme)
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440 view.setPidThreshold(cs.getThreshold());
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444 view.setConservationSelected(av.getConservationSelected());
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445 view.setPidSelected(av.getAbovePIDThreshold());
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446 view.setFontName(av.font.getName());
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447 view.setFontSize(av.font.getSize());
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448 view.setFontStyle(av.font.getStyle());
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449 view.setRenderGaps(av.renderGaps);
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450 view.setShowAnnotation(av.getShowAnnotation());
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451 view.setShowBoxes(av.getShowBoxes());
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452 view.setShowColourText(av.getColourText());
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453 view.setShowConservation(av.showConservation);
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454 view.setShowFullId(av.getShowJVSuffix());
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455 view.setShowIdentity(av.showIdentity);
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456 view.setShowQuality(av.showQuality);
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457 view.setShowSequenceFeatures(av.showSequenceFeatures);
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458 view.setShowText(av.getShowText());
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459 view.setWrapAlignment(av.getWrapAlignment());
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461 if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
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463 jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
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465 Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
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466 while (e.hasMoreElements())
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468 String type = e.nextElement().toString();
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469 Setting setting = new Setting();
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470 setting.setType(type);
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472 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()
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474 setting.setDisplay(
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475 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type)
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478 fs.addSetting(setting);
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481 jms.setFeatureSettings(fs);
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485 jms.addViewport(view);
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488 object.setJalviewModelSequence(jms);
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489 object.getVamsasModel().addSequenceSet(vamsasSet);
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493 if (!fileName.endsWith(".xml"))
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495 fileName = fileName + ".xml";
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498 JarEntry entry = new JarEntry(fileName);
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499 jout.putNextEntry(entry);
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501 object.marshal(out);
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503 catch (Exception ex)
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505 ex.printStackTrace();
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509 static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
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510 Vector userColours, JalviewModelSequence jms)
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513 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
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515 if (!userColours.contains(ucs))
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517 userColours.add(ucs);
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519 java.awt.Color[] colours = ucs.getColours();
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520 jalview.binding.UserColours uc = new jalview.binding.UserColours();
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521 jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
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523 for (int i = 0; i < colours.length; i++)
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525 jalview.binding.Colour col = new jalview.binding.Colour();
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526 col.setRGB(jalview.util.Format.getHexString(colours[i]));
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527 jbucs.addColour(col);
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530 id = "ucs" + userColours.indexOf(ucs);
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532 uc.setUserColourScheme(jbucs);
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533 jms.addUserColours(uc);
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539 static jalview.schemes.UserColourScheme GetUserColourScheme(
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540 JalviewModelSequence jms, String id)
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542 UserColours[] uc = jms.getUserColours();
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543 UserColours colours = null;
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545 for (int i = 0; i < uc.length; i++)
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547 if (uc[i].getId().equals(id))
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555 int csize = colours.getUserColourScheme().getColourCount();
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556 java.awt.Color[] newColours = new java.awt.Color[csize];
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558 for (int i = 0; i < csize; i++)
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560 newColours[i] = new java.awt.Color(Integer.parseInt(
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561 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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564 return new jalview.schemes.UserColourScheme(newColours);
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570 * @param file DOCUMENT ME!
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572 public static AlignFrame LoadJalviewAlign(String file)
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574 JalviewModel object = new JalviewModel();
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575 jalview.gui.AlignFrame af = null;
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579 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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582 if (file.startsWith("http://"))
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584 url = new URL(file);
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587 JarInputStream jin = null;
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588 JarEntry jarentry = null;
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589 int entryCount = 1;
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595 jin = new JarInputStream(url.openStream());
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599 jin = new JarInputStream(new FileInputStream(file));
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602 for (int i = 0; i < entryCount; i++)
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604 jarentry = jin.getNextJarEntry();
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607 if (jarentry != null)
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609 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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610 object = (JalviewModel) object.unmarshal(in);
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611 af = LoadFromObject(object);
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615 while (jarentry != null);
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617 catch(java.net.UnknownHostException ex)
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619 ex.printStackTrace();
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620 System.err.println("Couldn't locate Jalview XML file : " +
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622 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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623 "Couldn't locate " + file,
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625 JOptionPane.WARNING_MESSAGE);
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628 catch (Exception ex)
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630 ex.printStackTrace();
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631 System.err.println("Exception whilst loading jalview XML file : " +
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633 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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634 "Error loading " + file,
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635 "Error loading Jalview file",
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636 JOptionPane.WARNING_MESSAGE);
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643 static AlignFrame LoadFromObject(JalviewModel object)
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645 Vector seqids = new Vector();
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646 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
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647 Sequence[] vamsasSeq = vamsasSet.getSequence();
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649 JalviewModelSequence jms = object.getJalviewModelSequence();
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651 //////////////////////////////////
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653 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
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654 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
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655 for (int i = 0; i < vamsasSeq.length; i++)
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657 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
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658 vamsasSeq[i].getSequence());
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659 jseqs[i].setDescription( vamsasSeq[i].getDescription() );
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661 jseqs[i].setStart(JSEQ[i].getStart());
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662 jseqs[i].setEnd(JSEQ[i].getEnd());
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663 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
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664 seqids.add(jseqs[i]);
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667 ///SequenceFeatures are added to the DatasetSequence,
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668 // so we must create the dataset before loading features
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669 /////////////////////////////////
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670 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
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671 al.setDataset(null);
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672 /////////////////////////////////
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674 for (int i = 0; i < vamsasSeq.length; i++)
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676 if (JSEQ[i].getFeaturesCount() > 0)
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678 Features[] features = JSEQ[i].getFeatures();
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679 for (int f = 0; f < features.length; f++)
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681 //features[f].getBegin()
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682 jalview.datamodel.SequenceFeature sf
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683 = new jalview.datamodel.SequenceFeature(features[f].getType(),
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684 features[f].getDescription(), features[f].getStatus(),
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685 features[f].getBegin(), features[f].getEnd());
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686 sf.setFeatureGroup(features[f].getFeatureGroup());
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687 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
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690 if (JSEQ[i].getPdbidsCount() > 0)
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692 Pdbids[] ids = JSEQ[i].getPdbids();
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693 for (int p = 0; p < ids.length; p++)
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695 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
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696 entry.setId(ids[p].getId());
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697 entry.setType(ids[p].getType());
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698 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
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703 /////////////////////////////////
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704 //////////////////////////////////
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706 if (vamsasSet.getAnnotation() != null)
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708 Annotation[] an = vamsasSet.getAnnotation();
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710 for (int i = 0; i < an.length; i++)
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712 AnnotationElement[] ae = an[i].getAnnotationElement();
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713 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
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715 for (int aa = 0; aa < ae.length; aa++)
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717 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
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718 ae[aa].getDescription(),
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719 ae[aa].getSecondaryStructure().charAt(0),
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720 ae[aa].getValue());
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723 jalview.datamodel.AlignmentAnnotation jaa = null;
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725 if (an[i].getGraph())
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727 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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728 an[i].getDescription(), anot, 0, 0,
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729 an[i].getGraphType());
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733 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
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734 an[i].getDescription(), anot);
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737 al.addAnnotation(jaa);
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741 /////////////////////////////////
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743 Viewport[] views = jms.getViewport();
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744 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
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746 AlignFrame af = new AlignFrame(al);
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749 // af.changeColour() );
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750 /////////////////////////
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752 if (jms.getJGroupCount() > 0)
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754 JGroup[] groups = jms.getJGroup();
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756 for (int i = 0; i < groups.length; i++)
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758 ColourSchemeI cs = null;
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760 if (groups[i].getColour() != null)
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762 if (groups[i].getColour().startsWith("ucs"))
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764 cs = GetUserColourScheme(jms, groups[i].getColour());
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768 cs = ColourSchemeProperty.getColour(al,
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769 groups[i].getColour());
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772 cs.setThreshold(groups[i].getPidThreshold(), true);
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775 Vector seqs = new Vector();
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776 int[] ids = groups[i].getSeq();
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778 for (int s = 0; s < ids.length; s++)
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780 seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
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784 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
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785 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
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786 groups[i].getDisplayText(), groups[i].getColourText(),
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787 groups[i].getStart(), groups[i].getEnd());
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789 sg.setOutlineColour(new java.awt.Color(
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790 groups[i].getOutlineColour()));
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792 if (groups[i].getConsThreshold() != 0)
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794 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
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795 ResidueProperties.propHash, 3, sg.sequences, 0,
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796 sg.getWidth() - 1);
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798 c.verdict(false, 25);
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799 sg.cs.setConservation(c);
\r
807 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
\r
809 af.viewport.setStartRes(view.getStartRes());
\r
810 af.viewport.setStartSeq(view.getStartSeq());
\r
811 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
812 af.viewport.showConservation = view.getShowConservation();
\r
813 af.viewport.showQuality = view.getShowQuality();
\r
814 af.viewport.showIdentity = view.getShowIdentity();
\r
815 af.viewport.setAbovePIDThreshold(view.getPidSelected());
\r
816 af.abovePIDThreshold.setSelected(view.getPidSelected());
\r
817 af.viewport.setColourText(view.getShowColourText());
\r
818 af.colourTextMenuItem.setSelected(view.getShowColourText());
\r
819 af.viewport.setConservationSelected(view.getConservationSelected());
\r
820 af.conservationMenuItem.setSelected(view.getConservationSelected());
\r
822 af.viewport.setShowJVSuffix(view.getShowFullId());
\r
823 af.seqLimits.setSelected(view.getShowFullId());
\r
825 af.viewport.setFont(new java.awt.Font(view.getFontName(),
\r
826 view.getFontStyle(), view.getFontSize()));
\r
827 af.alignPanel.fontChanged();
\r
829 af.viewport.setRenderGaps(view.getRenderGaps());
\r
830 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
\r
832 af.viewport.setWrapAlignment(view.getWrapAlignment());
\r
833 af.wrapMenuItem.setSelected(view.getWrapAlignment());
\r
835 if (view.getWrapAlignment())
\r
837 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
\r
841 af.annotationPanelMenuItem.setState(view.getShowAnnotation());
\r
842 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
843 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
\r
846 af.viewport.setShowBoxes(view.getShowBoxes());
\r
847 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
\r
848 af.viewport.setShowText(view.getShowText());
\r
849 af.viewTextMenuItem.setSelected(view.getShowText());
\r
851 ColourSchemeI cs = null;
\r
853 if (view.getBgColour() != null)
\r
855 if (view.getBgColour().startsWith("ucs"))
\r
857 cs = GetUserColourScheme(jms, view.getBgColour());
\r
861 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
\r
866 cs.setThreshold(view.getPidThreshold(), true);
\r
867 cs.setConsensus(af.viewport.vconsensus);
\r
871 af.setColourSelected(view.getBgColour());
\r
872 af.viewport.setGlobalColourScheme(cs);
\r
873 af.viewport.setColourAppliesToAllGroups(false);
\r
874 af.changeColour(cs);
\r
875 if (view.getConservationSelected() && cs!=null)
\r
877 cs.setConservationInc(view.getConsThreshold());
\r
880 af.viewport.setColourAppliesToAllGroups(true);
\r
882 if (view.getShowSequenceFeatures())
\r
884 af.viewport.showSequenceFeatures = true;
\r
885 af.showSeqFeatures.setSelected(true);
\r
888 if(jms.getFeatureSettings()!=null)
\r
890 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector();
\r
891 // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)
\r
892 // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
\r
893 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
\r
895 Setting setting = jms.getFeatureSettings().getSetting(fs);
\r
897 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
\r
898 new java.awt.Color(setting.getColour()));
\r
899 if(setting.getDisplay())
\r
900 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.addElement(setting.getType());
\r
904 Desktop.addInternalFrame(af, view.getTitle(),
\r
905 view.getWidth(), view.getHeight());
\r
908 ///////////////////////////////////////
\r
909 if (jms.getTreeCount() > 0)
\r
913 for (int t = 0; t < jms.getTreeCount(); t++)
\r
916 Tree tree = jms.getTree(t);
\r
918 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
\r
919 tree.getNewick()), tree.getTitle(),
\r
920 tree.getWidth(), tree.getHeight(),
\r
921 tree.getXpos(), tree.getYpos());
\r
923 tp.fitToWindow.setState(tree.getFitToWindow());
\r
924 tp.fitToWindow_actionPerformed(null);
\r
926 if(tree.getFontName()!=null)
\r
927 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
\r
928 tree.getFontStyle(),
\r
929 tree.getFontSize()));
\r
931 tp.setTreeFont(new java.awt.Font(view.getFontName(),
\r
932 view.getFontStyle(),
\r
933 tree.getFontSize()));
\r
935 tp.showPlaceholders(tree.getMarkUnlinked());
\r
936 tp.showBootstrap(tree.getShowBootstrap());
\r
937 tp.showDistances(tree.getShowDistances());
\r
939 tp.treeCanvas.threshold = tree.getThreshold();
\r
941 if (tree.getCurrentTree())
\r
942 af.viewport.setCurrentTree(tp.getTree());
\r
946 catch (Exception ex)
\r
948 ex.printStackTrace();
\r