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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171 jalview.datamodel.AlignmentI jalhidden = null;
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173 if(av.hasHiddenRows)
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176 jal = jal.getHiddenSequences().getFullAlignment();
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180 SequenceSet vamsasSet = new SequenceSet();
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181 Sequence vamsasSeq;
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182 JalviewModelSequence jms = new JalviewModelSequence();
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184 vamsasSet.setGapChar(jal.getGapCharacter() + "");
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187 Vector pdbfiles = null;
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191 for (int i = 0; i < jal.getHeight(); i++)
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193 seqids.add(jal.getSequenceAt(i));
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194 vamsasSeq = new Sequence();
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195 vamsasSeq.setId(id + "");
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196 vamsasSeq.setName(jal.getSequenceAt(i).getName());
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197 vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());
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198 vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());
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200 if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)
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202 jalview.datamodel.DBRefEntry [] dbrefs =
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203 jal.getSequenceAt(i).getDatasetSequence().getDBRef();
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205 for(int d=0; d<dbrefs.length; d++)
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207 DBRef dbref = new DBRef();
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208 dbref.setSource( dbrefs[d].getSource() );
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209 dbref.setVersion( dbrefs[d].getVersion());
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210 dbref.setAccessionId(dbrefs[d].getAccessionId());
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211 vamsasSeq.addDBRef(dbref);
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216 jseq.setStart(jal.getSequenceAt(i).getStart());
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217 jseq.setEnd(jal.getSequenceAt(i).getEnd());
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218 jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());
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222 if (av.hasHiddenRows)
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224 jseq.setHidden(jalhidden.getHiddenSequences().isHidden(
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225 jal.getSequenceAt(i)));
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227 if(jal.getSequenceAt(i).getHiddenSequences()!=null)
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229 jalview.datamodel.SequenceI [] reps =
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230 jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
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232 for(int h=0; h<reps.length; h++)
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234 jseq.addHiddenSequences(
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235 jal.findIndex(reps[h])
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242 if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)
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244 jalview.datamodel.SequenceFeature[] sf
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245 = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();
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247 while(index < sf.length)
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249 Features features = new Features();
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251 features.setBegin(sf[index].getBegin());
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252 features.setEnd(sf[index].getEnd());
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253 features.setDescription(sf[index].getDescription());
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254 features.setType(sf[index].getType());
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255 features.setFeatureGroup(sf[index].getFeatureGroup());
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256 features.setScore(sf[index].getScore());
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257 if(sf[index].links!=null)
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259 for(int l=0; l<sf[index].links.size(); l++)
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261 OtherData keyValue = new OtherData();
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262 keyValue.setKey("LINK_"+l);
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263 keyValue.setValue(sf[index].links.elementAt(l).toString());
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264 features.addOtherData(keyValue);
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267 if(sf[index].otherDetails!=null)
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270 Enumeration keys = sf[index].otherDetails.keys();
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271 while(keys.hasMoreElements())
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273 key = keys.nextElement().toString();
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274 OtherData keyValue = new OtherData();
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275 keyValue.setKey( key );
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277 sf[index].otherDetails.get(key).toString());
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278 features.addOtherData(keyValue);
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282 jseq.addFeatures(features);
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287 if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)
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289 Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();
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290 while(en.hasMoreElements())
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292 Pdbids pdb = new Pdbids();
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293 jalview.datamodel.PDBEntry entry
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294 = (jalview.datamodel.PDBEntry)en.nextElement();
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296 pdb.setId(entry.getId());
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297 pdb.setType(entry.getType());
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299 if(entry.getFile()!=null)
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302 pdbfiles = new Vector();
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305 if(!pdbfiles.contains(entry.getId()))
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307 pdbfiles.addElement(entry.getId());
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310 File file = new File(entry.getFile());
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313 byte[] data = new byte[ (int) file.length()];
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314 jout.putNextEntry(new JarEntry(entry.getId()));
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315 DataInputStream dis = new DataInputStream(new
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316 FileInputStream(file));
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317 dis.readFully(data);
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319 DataOutputStream dout = new DataOutputStream(jout);
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320 dout.write(data, 0, data.length);
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324 catch (Exception ex)
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326 ex.printStackTrace();
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332 if(entry.getProperty()!=null)
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334 PdbentryItem item = new PdbentryItem();
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335 Hashtable properties = entry.getProperty();
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336 Enumeration en2 = properties.keys();
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337 while(en2.hasMoreElements())
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339 Property prop = new Property();
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340 String key = en2.nextElement().toString();
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342 prop.setValue( properties.get(key).toString() );
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343 item.addProperty(prop);
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345 pdb.addPdbentryItem(item);
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348 jseq.addPdbids(pdb);
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353 vamsasSet.addSequence(vamsasSeq);
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358 ///////////////////////////////////
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359 if (af.viewport.currentTree != null)
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361 // FIND ANY ASSOCIATED TREES
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362 // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
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363 if (Desktop.desktop != null)
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365 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
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367 for (int t = 0; t < frames.length; t++)
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369 if (frames[t] instanceof TreePanel)
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371 TreePanel tp = (TreePanel) frames[t];
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373 if (tp.treeCanvas.av.alignment == jal)
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375 Tree tree = new Tree();
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376 tree.setTitle(tp.getTitle());
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377 tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));
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378 tree.setNewick(tp.getTree().toString());
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379 tree.setThreshold(tp.treeCanvas.threshold);
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381 tree.setFitToWindow(tp.fitToWindow.getState());
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382 tree.setFontName(tp.getTreeFont().getName());
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383 tree.setFontSize(tp.getTreeFont().getSize());
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384 tree.setFontStyle(tp.getTreeFont().getStyle());
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385 tree.setMarkUnlinked(tp.placeholdersMenu.getState());
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387 tree.setShowBootstrap(tp.bootstrapMenu.getState());
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388 tree.setShowDistances(tp.distanceMenu.getState());
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390 tree.setHeight(tp.getHeight());
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391 tree.setWidth(tp.getWidth());
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392 tree.setXpos(tp.getX());
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393 tree.setYpos(tp.getY());
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403 if (jal.getAlignmentAnnotation() != null)
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405 jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
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407 for (int i = 0; i < aa.length; i++)
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409 Annotation an = new Annotation();
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411 if (aa[i].label.equals("Quality") ||
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412 aa[i].label.equals("Conservation") ||
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413 aa[i].label.equals("Consensus"))
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415 an.setLabel(aa[i].label);
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417 vamsasSet.addAnnotation(an);
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422 an.setDescription(aa[i].description);
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424 if(aa[i].sequenceRef!=null)
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426 an.setSequenceRef(aa[i].sequenceRef.getName());
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432 an.setGraphType(aa[i].graph);
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433 an.setGraphGroup(aa[i].graphGroup);
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434 if(aa[i].getThreshold()!=null)
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436 ThresholdLine line = new ThresholdLine();
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437 line.setLabel(aa[i].getThreshold().label);
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438 line.setValue(aa[i].getThreshold().value);
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439 line.setColour(aa[i].getThreshold().colour.getRGB());
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440 an.setThresholdLine(line);
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444 an.setGraph(false);
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446 an.setLabel(aa[i].label);
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448 AnnotationElement ae;
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450 for (int a = 0; a < aa[i].annotations.length; a++)
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452 if ((aa[i] == null) || (aa[i].annotations[a] == null))
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457 ae = new AnnotationElement();
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458 ae.setDescription(aa[i].annotations[a].description);
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459 ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
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460 ae.setValue(aa[i].annotations[a].value);
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462 ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
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465 if(aa[i].annotations[a].colour!=java.awt.Color.black)
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466 ae.setColour(aa[i].annotations[a].colour.getRGB());
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468 an.addAnnotationElement(ae);
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471 vamsasSet.addAnnotation(an);
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476 if (jal.getGroups() != null)
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478 JGroup[] groups = new JGroup[jal.getGroups().size()];
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480 for (int i = 0; i < groups.length; i++)
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482 groups[i] = new JGroup();
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484 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
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486 groups[i].setStart(sg.getStartRes());
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487 groups[i].setEnd(sg.getEndRes());
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488 groups[i].setName(sg.getName());
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491 if (sg.cs.conservationApplied())
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493 groups[i].setConsThreshold(sg.cs.getConservationInc());
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495 if (sg.cs instanceof jalview.schemes.UserColourScheme)
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497 groups[i].setColour(SetUserColourScheme(sg.cs,
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503 groups[i].setColour(ColourSchemeProperty.getColourName(sg.
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507 else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
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509 groups[i].setColour(
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510 ColourSchemeProperty.getColourName(
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511 ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
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513 else if (sg.cs instanceof jalview.schemes.UserColourScheme)
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515 groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
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520 groups[i].setColour(ColourSchemeProperty.getColourName(
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524 groups[i].setPidThreshold(sg.cs.getThreshold());
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527 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
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528 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
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529 groups[i].setDisplayText(sg.getDisplayText());
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530 groups[i].setColourText(sg.getColourText());
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532 for (int s = 0; s < sg.getSize(false); s++)
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534 jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);
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535 int index = seqids.indexOf(seq);
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536 groups[i].addSeq(index);
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540 jms.setJGroup(groups);
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544 ///////////SAVE VIEWPORT
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545 Viewport view = new Viewport();
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546 view.setTitle(af.getTitle());
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547 view.setXpos(af.getX());
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548 view.setYpos(af.getY());
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549 view.setWidth(af.getWidth());
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550 view.setHeight(af.getHeight());
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551 view.setStartRes(av.startRes);
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552 view.setStartSeq(av.startSeq);
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554 if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
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556 view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
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557 userColours, jms));
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559 else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
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561 jalview.schemes.AnnotationColourGradient acg
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562 = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
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564 AnnotationColours ac = new AnnotationColours();
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565 ac.setAboveThreshold(acg.getAboveThreshold());
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566 ac.setThreshold(acg.getAnnotationThreshold());
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567 ac.setAnnotation(acg.getAnnotation());
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568 if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
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569 ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
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570 userColours, jms));
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572 ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
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574 ac.setMaxColour(acg.getMaxColour().getRGB());
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575 ac.setMinColour(acg.getMinColour().getRGB());
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576 view.setAnnotationColours(ac);
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577 view.setBgColour("AnnotationColourGradient");
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581 view.setBgColour(ColourSchemeProperty.getColourName(
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582 av.getGlobalColourScheme()));
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585 ColourSchemeI cs = av.getGlobalColourScheme();
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589 if (cs.conservationApplied())
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591 view.setConsThreshold(cs.getConservationInc());
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592 if (cs instanceof jalview.schemes.UserColourScheme)
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593 view.setBgColour(SetUserColourScheme(cs, userColours, jms));
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596 if (cs instanceof ResidueColourScheme)
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598 view.setPidThreshold(cs.getThreshold());
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602 view.setConservationSelected(av.getConservationSelected());
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603 view.setPidSelected(av.getAbovePIDThreshold());
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604 view.setFontName(av.font.getName());
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605 view.setFontSize(av.font.getSize());
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606 view.setFontStyle(av.font.getStyle());
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607 view.setRenderGaps(av.renderGaps);
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608 view.setShowAnnotation(av.getShowAnnotation());
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609 view.setShowBoxes(av.getShowBoxes());
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610 view.setShowColourText(av.getColourText());
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611 view.setShowConservation(av.showConservation);
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612 view.setShowFullId(av.getShowJVSuffix());
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613 view.setShowIdentity(av.showIdentity);
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614 view.setShowQuality(av.showQuality);
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615 view.setShowSequenceFeatures(av.showSequenceFeatures);
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616 view.setShowText(av.getShowText());
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617 view.setWrapAlignment(av.getWrapAlignment());
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619 if(av.featuresDisplayed!=null)
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621 jalview.schemabinding.version2.FeatureSettings fs
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622 = new jalview.schemabinding.version2.FeatureSettings();
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624 String [] renderOrder =
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625 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
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626 for(int ro=0; ro<renderOrder.length; ro++)
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628 Setting setting = new Setting();
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629 setting.setType(renderOrder[ro]);
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631 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
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634 setting.setDisplay(
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635 av.featuresDisplayed.containsKey(renderOrder[ro])
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638 fs.addSetting(setting);
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641 jms.setFeatureSettings(fs);
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645 if(av.hasHiddenColumns)
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647 for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
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649 int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
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650 HiddenColumns hc = new HiddenColumns();
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651 hc.setStart(region[0]);
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652 hc.setEnd(region[1]);
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653 view.addHiddenColumns(hc);
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657 jms.addViewport(view);
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660 object.setJalviewModelSequence(jms);
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661 object.getVamsasModel().addSequenceSet(vamsasSet);
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665 if (!fileName.endsWith(".xml"))
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667 fileName = fileName + ".xml";
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670 JarEntry entry = new JarEntry(fileName);
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671 jout.putNextEntry(entry);
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673 object.marshal(out);
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675 catch (Exception ex)
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677 ex.printStackTrace();
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681 String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
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682 Vector userColours, JalviewModelSequence jms)
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685 jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
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687 if (!userColours.contains(ucs))
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689 userColours.add(ucs);
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691 java.awt.Color[] colours = ucs.getColours();
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692 jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
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693 jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
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695 for (int i = 0; i < colours.length; i++)
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697 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
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698 col.setRGB(jalview.util.Format.getHexString(colours[i]));
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699 jbucs.addColour(col);
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702 id = "ucs" + userColours.indexOf(ucs);
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704 uc.setUserColourScheme(jbucs);
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705 jms.addUserColours(uc);
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711 jalview.schemes.UserColourScheme GetUserColourScheme(
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712 JalviewModelSequence jms, String id)
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714 UserColours[] uc = jms.getUserColours();
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715 UserColours colours = null;
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717 for (int i = 0; i < uc.length; i++)
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719 if (uc[i].getId().equals(id))
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727 int csize = colours.getUserColourScheme().getColourCount();
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728 java.awt.Color[] newColours = new java.awt.Color[csize];
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730 for (int i = 0; i < csize; i++)
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732 newColours[i] = new java.awt.Color(Integer.parseInt(
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733 colours.getUserColourScheme().getColour(i).getRGB(), 16));
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736 return new jalview.schemes.UserColourScheme(newColours);
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742 * @param file DOCUMENT ME!
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744 public AlignFrame LoadJalviewAlign(String file)
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746 jalview.gui.AlignFrame af = null;
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749 //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
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752 if (file.startsWith("http://"))
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754 url = new URL(file);
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757 JarInputStream jin = null;
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758 JarEntry jarentry = null;
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759 int entryCount = 1;
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765 jin = new JarInputStream(url.openStream());
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769 jin = new JarInputStream(new FileInputStream(file));
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772 for (int i = 0; i < entryCount; i++)
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774 jarentry = jin.getNextJarEntry();
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777 if (jarentry != null && jarentry.getName().endsWith(".xml"))
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779 InputStreamReader in = new InputStreamReader(jin, "UTF-8");
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780 JalviewModel object = new JalviewModel();
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782 Unmarshaller unmar = new Unmarshaller(object);
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783 unmar.setValidation(false);
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784 object = (JalviewModel) unmar.unmarshal( in );
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786 af = LoadFromObject(object, file);
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789 else if (jarentry != null)
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791 //Some other file here.
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795 while (jarentry != null);
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797 catch(java.net.UnknownHostException ex)
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799 ex.printStackTrace();
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800 System.err.println("Couldn't locate Jalview XML file : " +
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802 JOptionPane.showInternalMessageDialog(Desktop.desktop,
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803 "Couldn't locate " + file,
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805 JOptionPane.WARNING_MESSAGE);
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808 catch (Exception ex)
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810 //Is Version 1 Jar file?
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811 af = new Jalview2XML_V1().LoadJalviewAlign(file);
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815 System.out.println("Successfully loaded archive file");
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818 ex.printStackTrace();
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819 System.err.println("Exception whilst loading jalview XML file : " +
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821 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
822 "Error loading " + file,
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823 "Error loading Jalview file",
\r
824 JOptionPane.WARNING_MESSAGE);
\r
831 String loadPDBFile(String file, String pdbId)
\r
833 System.out.println("load file "+file);
\r
836 JarInputStream jin = null;
\r
838 if (file.startsWith("http://"))
\r
840 jin = new JarInputStream(new URL(file).openStream());
\r
844 jin = new JarInputStream(new FileInputStream(file));
\r
847 JarEntry entry = null;
\r
850 entry = jin.getNextJarEntry();
\r
852 while (!entry.getName().equals(pdbId));
\r
854 BufferedReader in = new BufferedReader(new InputStreamReader(jin));
\r
855 File outFile = File.createTempFile("jalview_pdb", ".txt");
\r
856 outFile.deleteOnExit();
\r
857 PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
\r
860 while ( (data = in.readLine()) != null)
\r
865 return outFile.getAbsolutePath();
\r
868 catch (Exception ex)
\r
870 ex.printStackTrace();
\r
877 AlignFrame LoadFromObject(JalviewModel object, String file)
\r
879 Vector seqids = new Vector();
\r
880 SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
\r
881 Sequence[] vamsasSeq = vamsasSet.getSequence();
\r
883 JalviewModelSequence jms = object.getJalviewModelSequence();
\r
885 //////////////////////////////////
\r
887 Vector hiddenSeqs = null;
\r
888 jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
\r
889 JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
\r
890 for (int i = 0; i < vamsasSeq.length; i++)
\r
892 jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
\r
893 vamsasSeq[i].getSequence());
\r
894 jseqs[i].setDescription( vamsasSeq[i].getDescription() );
\r
896 if(JSEQ[i].getHidden())
\r
898 if(hiddenSeqs == null)
\r
899 hiddenSeqs = new Vector();
\r
900 hiddenSeqs.addElement(jseqs[i]);
\r
902 jseqs[i].setStart(JSEQ[i].getStart());
\r
903 jseqs[i].setEnd(JSEQ[i].getEnd());
\r
904 jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));
\r
905 seqids.add(jseqs[i]);
\r
908 ///SequenceFeatures are added to the DatasetSequence,
\r
909 // so we must create the dataset before loading features
\r
910 /////////////////////////////////
\r
911 jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
\r
912 al.setDataset(null);
\r
913 /////////////////////////////////
\r
916 Hashtable pdbloaded = new Hashtable();
\r
917 for (int i = 0; i < vamsasSeq.length; i++)
\r
919 if (JSEQ[i].getFeaturesCount() > 0)
\r
921 Features[] features = JSEQ[i].getFeatures();
\r
922 for (int f = 0; f < features.length; f++)
\r
924 jalview.datamodel.SequenceFeature sf
\r
925 = new jalview.datamodel.SequenceFeature(features[f].getType(),
\r
926 features[f].getDescription(), features[f].getStatus(),
\r
927 features[f].getBegin(), features[f].getEnd(),
\r
928 features[f].getFeatureGroup());
\r
930 sf.setScore(features[f].getScore());
\r
931 for(int od=0; od<features[f].getOtherDataCount(); od++)
\r
933 OtherData keyValue = features[f].getOtherData(od);
\r
934 if(keyValue.getKey().startsWith("LINK"))
\r
935 sf.addLink(keyValue.getValue());
\r
937 sf.setValue(keyValue.getKey(), keyValue.getValue());
\r
941 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
\r
944 if (JSEQ[i].getPdbidsCount() > 0)
\r
946 Pdbids[] ids = JSEQ[i].getPdbids();
\r
947 for (int p = 0; p < ids.length; p++)
\r
949 jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
\r
950 entry.setId(ids[p].getId());
\r
951 entry.setType(ids[p].getType());
\r
952 if (ids[p].getFile() != null)
\r
954 if (!pdbloaded.containsKey(ids[p].getFile()))
\r
956 String tmppdb = loadPDBFile(file, ids[p].getId());
\r
957 entry.setFile(tmppdb);
\r
958 pdbloaded.put(ids[p].getId(), tmppdb);
\r
961 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
\r
964 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
\r
967 if(vamsasSeq[i].getDBRefCount()>0)
\r
969 for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)
\r
971 jalview.datamodel.DBRefEntry entry =
\r
972 new jalview.datamodel.DBRefEntry(
\r
973 vamsasSeq[i].getDBRef(d).getSource(),
\r
974 vamsasSeq[i].getDBRef(d).getVersion(),
\r
975 vamsasSeq[i].getDBRef(d).getAccessionId()
\r
977 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
\r
985 /////////////////////////////////
\r
986 //////////////////////////////////
\r
988 boolean hideQuality = true,
\r
989 hideConservation = true,
\r
990 hideConsensus = true;
\r
992 if (vamsasSet.getAnnotation() != null)
\r
994 Annotation[] an = vamsasSet.getAnnotation();
\r
996 for (int i = 0; i < an.length; i++)
\r
998 if (an[i].getLabel().equals("Quality"))
\r
1000 hideQuality = false;
\r
1003 else if(an[i].getLabel().equals("Conservation"))
\r
1005 hideConservation = false;
\r
1008 else if(an[i].getLabel().equals("Consensus"))
\r
1010 hideConsensus = false;
\r
1014 AnnotationElement[] ae = an[i].getAnnotationElement();
\r
1015 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
\r
1017 for (int aa = 0; aa < ae.length; aa++)
\r
1019 anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
\r
1020 ae[aa].getDescription(),
\r
1021 ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
\r
1022 ae[aa].getValue());
\r
1023 anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
\r
1026 jalview.datamodel.AlignmentAnnotation jaa = null;
\r
1028 if (an[i].getGraph())
\r
1030 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
\r
1031 an[i].getDescription(), anot, 0, 0,
\r
1032 an[i].getGraphType());
\r
1034 jaa.graphGroup = an[i].getGraphGroup();
\r
1036 if (an[i].getThresholdLine() != null)
\r
1038 jaa.setThreshold(new jalview.datamodel.GraphLine(
\r
1039 an[i].getThresholdLine().getValue(),
\r
1040 an[i].getThresholdLine().getLabel(),
\r
1041 new java.awt.Color(an[i].getThresholdLine().getColour()))
\r
1049 jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
\r
1050 an[i].getDescription(), anot);
\r
1053 if(an[i].getSequenceRef()!=null)
\r
1055 jaa.createSequenceMapping(
\r
1056 al.findName(an[i].getSequenceRef()), 1
\r
1058 al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
\r
1061 al.addAnnotation(jaa);
\r
1066 // af.changeColour() );
\r
1067 /////////////////////////
\r
1069 if (jms.getJGroupCount() > 0)
\r
1071 JGroup[] groups = jms.getJGroup();
\r
1073 for (int i = 0; i < groups.length; i++)
\r
1075 ColourSchemeI cs = null;
\r
1077 if (groups[i].getColour() != null)
\r
1079 if (groups[i].getColour().startsWith("ucs"))
\r
1081 cs = GetUserColourScheme(jms, groups[i].getColour());
\r
1085 cs = ColourSchemeProperty.getColour(al,
\r
1086 groups[i].getColour());
\r
1090 cs.setThreshold(groups[i].getPidThreshold(), true);
\r
1093 Vector seqs = new Vector();
\r
1094 int[] ids = groups[i].getSeq();
\r
1096 for (int s = 0; s < ids.length; s++)
\r
1098 seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(
\r
1102 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
\r
1103 groups[i].getName(), cs, groups[i].getDisplayBoxes(),
\r
1104 groups[i].getDisplayText(), groups[i].getColourText(),
\r
1105 groups[i].getStart(), groups[i].getEnd());
\r
1107 sg.setOutlineColour(new java.awt.Color(
\r
1108 groups[i].getOutlineColour()));
\r
1110 if (groups[i].getConsThreshold() != 0)
\r
1112 jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
\r
1113 ResidueProperties.propHash, 3, sg.getSequences(false), 0,
\r
1114 sg.getWidth() - 1);
\r
1116 c.verdict(false, 25);
\r
1117 sg.cs.setConservation(c);
\r
1125 /////////////////////////////////
\r
1127 Viewport[] views = jms.getViewport();
\r
1128 Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
\r
1131 AlignFrame af = new AlignFrame(al);
\r
1133 if(hiddenSeqs!=null)
\r
1135 for(int s=0; s<JSEQ.length; s++)
\r
1137 for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
\r
1139 al.getSequenceAt(s).addHiddenSequence(
\r
1140 al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )
\r
1145 for(int s=0; s<hiddenSeqs.size(); s++)
\r
1147 af.viewport.hideSequence(
\r
1148 (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));
\r
1153 if(hideConsensus || hideQuality || hideConservation)
\r
1155 int hSize = al.getAlignmentAnnotation().length;
\r
1156 for (int h = 0; h < hSize; h++)
\r
1160 al.getAlignmentAnnotation()[h].label.equals("Consensus"))
\r
1163 al.getAlignmentAnnotation()[h].label.equals("Quality"))
\r
1165 (hideConservation &&
\r
1166 al.getAlignmentAnnotation()[h].label.equals("Conservation")))
\r
1168 al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
\r
1173 af.alignPanel.adjustAnnotationHeight();
\r
1176 af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
\r
1177 view.getHeight());
\r
1178 af.viewport.setStartRes(view.getStartRes());
\r
1179 af.viewport.setStartSeq(view.getStartSeq());
\r
1180 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
1181 af.viewport.showConservation = view.getShowConservation();
\r
1182 af.viewport.showQuality = view.getShowQuality();
\r
1183 af.viewport.showIdentity = view.getShowIdentity();
\r
1184 af.viewport.setAbovePIDThreshold(view.getPidSelected());
\r
1185 af.abovePIDThreshold.setSelected(view.getPidSelected());
\r
1186 af.viewport.setColourText(view.getShowColourText());
\r
1187 af.colourTextMenuItem.setSelected(view.getShowColourText());
\r
1188 af.viewport.setConservationSelected(view.getConservationSelected());
\r
1189 af.conservationMenuItem.setSelected(view.getConservationSelected());
\r
1191 af.viewport.setShowJVSuffix(view.getShowFullId());
\r
1192 af.seqLimits.setSelected(view.getShowFullId());
\r
1194 af.viewport.setFont(new java.awt.Font(view.getFontName(),
\r
1195 view.getFontStyle(), view.getFontSize()));
\r
1196 af.alignPanel.fontChanged();
\r
1198 af.viewport.setRenderGaps(view.getRenderGaps());
\r
1199 af.renderGapsMenuItem.setSelected(view.getRenderGaps());
\r
1201 af.viewport.setWrapAlignment(view.getWrapAlignment());
\r
1202 af.wrapMenuItem.setSelected(view.getWrapAlignment());
\r
1204 af.alignPanel.setWrapAlignment(view.getWrapAlignment());
\r
1206 af.annotationPanelMenuItem.setState(view.getShowAnnotation());
\r
1207 af.viewport.setShowAnnotation(view.getShowAnnotation());
\r
1208 af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
\r
1210 af.viewport.setShowBoxes(view.getShowBoxes());
\r
1211 af.viewBoxesMenuItem.setSelected(view.getShowBoxes());
\r
1212 af.viewport.setShowText(view.getShowText());
\r
1213 af.viewTextMenuItem.setSelected(view.getShowText());
\r
1215 ColourSchemeI cs = null;
\r
1217 if (view.getBgColour() != null)
\r
1219 if (view.getBgColour().startsWith("ucs"))
\r
1221 cs = GetUserColourScheme(jms, view.getBgColour());
\r
1223 else if(view.getBgColour().startsWith("Annotation"))
\r
1225 //int find annotation
\r
1226 for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
\r
1228 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
\r
1229 equals(view.getAnnotationColours().getAnnotation()))
\r
1231 if (af.viewport.alignment.getAlignmentAnnotation()[i].
\r
1232 getThreshold() == null)
\r
1234 af.viewport.alignment.getAlignmentAnnotation()[i].
\r
1236 new jalview.datamodel.GraphLine(
\r
1237 view.getAnnotationColours().getThreshold(),
\r
1238 "Threshold", java.awt.Color.black)
\r
1244 if (view.getAnnotationColours().getColourScheme().equals(
\r
1247 cs = new AnnotationColourGradient(
\r
1248 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1249 new java.awt.Color(view.getAnnotationColours().
\r
1251 new java.awt.Color(view.getAnnotationColours().
\r
1253 view.getAnnotationColours().getAboveThreshold());
\r
1255 else if (view.getAnnotationColours().getColourScheme().
\r
1256 startsWith("ucs"))
\r
1258 cs = new AnnotationColourGradient(
\r
1259 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1260 GetUserColourScheme(jms, view.getAnnotationColours().
\r
1261 getColourScheme()),
\r
1262 view.getAnnotationColours().getAboveThreshold()
\r
1267 cs = new AnnotationColourGradient(
\r
1268 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1269 ColourSchemeProperty.getColour(al,
\r
1270 view.getAnnotationColours().getColourScheme()),
\r
1271 view.getAnnotationColours().getAboveThreshold()
\r
1275 // Also use these settings for all the groups
\r
1276 if (al.getGroups() != null)
\r
1277 for (int g = 0; g < al.getGroups().size(); g++)
\r
1279 jalview.datamodel.SequenceGroup sg
\r
1280 = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
\r
1286 /* if (view.getAnnotationColours().getColourScheme().equals("None"))
\r
1288 sg.cs = new AnnotationColourGradient(
\r
1289 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1290 new java.awt.Color(view.getAnnotationColours().
\r
1292 new java.awt.Color(view.getAnnotationColours().
\r
1294 view.getAnnotationColours().getAboveThreshold());
\r
1298 sg.cs = new AnnotationColourGradient(
\r
1299 af.viewport.alignment.getAlignmentAnnotation()[i],
\r
1301 view.getAnnotationColours().getAboveThreshold()
\r
1315 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
\r
1320 cs.setThreshold(view.getPidThreshold(), true);
\r
1321 cs.setConsensus(af.viewport.vconsensus);
\r
1325 af.setColourSelected(view.getBgColour());
\r
1326 af.viewport.setGlobalColourScheme(cs);
\r
1327 af.viewport.setColourAppliesToAllGroups(false);
\r
1328 af.changeColour(cs);
\r
1329 if (view.getConservationSelected() && cs!=null)
\r
1331 cs.setConservationInc(view.getConsThreshold());
\r
1334 af.viewport.setColourAppliesToAllGroups(true);
\r
1336 if (view.getShowSequenceFeatures())
\r
1338 af.viewport.showSequenceFeatures = true;
\r
1339 af.showSeqFeatures.setSelected(true);
\r
1342 if(jms.getFeatureSettings()!=null)
\r
1344 af.viewport.featuresDisplayed = new Hashtable();
\r
1345 String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
\r
1346 for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
\r
1348 Setting setting = jms.getFeatureSettings().getSetting(fs);
\r
1350 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
\r
1351 new java.awt.Color(setting.getColour()));
\r
1353 renderOrder[fs] = setting.getType();
\r
1355 if(setting.getDisplay())
\r
1356 af.viewport.featuresDisplayed.put(
\r
1357 setting.getType(), new Integer(setting.getColour()));
\r
1359 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
\r
1362 if (view.getHiddenColumnsCount() > 0)
\r
1364 for (int c = 0; c < view.getHiddenColumnsCount(); c++)
\r
1366 af.viewport.hideColumns(
\r
1367 view.getHiddenColumns(c).getStart(),
\r
1368 view.getHiddenColumns(c).getEnd()+1
\r
1374 Desktop.addInternalFrame(af, view.getTitle(),
\r
1375 view.getWidth(), view.getHeight());
\r
1378 ///////////////////////////////////////
\r
1379 if (jms.getTreeCount() > 0)
\r
1383 for (int t = 0; t < jms.getTreeCount(); t++)
\r
1386 Tree tree = jms.getTree(t);
\r
1388 TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
\r
1389 tree.getNewick()), tree.getTitle(),
\r
1390 tree.getWidth(), tree.getHeight(),
\r
1391 tree.getXpos(), tree.getYpos());
\r
1393 tp.fitToWindow.setState(tree.getFitToWindow());
\r
1394 tp.fitToWindow_actionPerformed(null);
\r
1396 if(tree.getFontName()!=null)
\r
1397 tp.setTreeFont(new java.awt.Font(tree.getFontName(),
\r
1398 tree.getFontStyle(),
\r
1399 tree.getFontSize()));
\r
1401 tp.setTreeFont(new java.awt.Font(view.getFontName(),
\r
1402 view.getFontStyle(),
\r
1403 tree.getFontSize()));
\r
1405 tp.showPlaceholders(tree.getMarkUnlinked());
\r
1406 tp.showBootstrap(tree.getShowBootstrap());
\r
1407 tp.showDistances(tree.getShowDistances());
\r
1409 tp.treeCanvas.threshold = tree.getThreshold();
\r
1411 if (tree.getCurrentTree())
\r
1412 af.viewport.setCurrentTree(tp.getTree());
\r
1416 catch (Exception ex)
\r
1418 ex.printStackTrace();
\r