src/jalview/gui/Jalview2XML_V1.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
   3  * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  * \r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  * \r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  * \r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.gui;\r
  20 \r
  21 import java.io.*;\r
  22 import java.net.*;\r
  23 import java.util.*;\r
  24 import java.util.jar.*;\r
  25 \r
  26 import javax.swing.*;\r
  27 \r
  28 import org.exolab.castor.xml.*;\r
  29 import jalview.binding.*;\r
  30 import jalview.schemes.*;\r
  31 import jalview.util.jarInputStreamProvider;\r
  32 \r
  33 /**\r
  34  * DOCUMENT ME!\r
  35  * \r
  36  * @author $author$\r
  37  * @version $Revision$\r
  38  */\r
  39 public class Jalview2XML_V1\r
  40 {\r
  41   boolean raiseGUI = true;\r
  42 \r
  43   public Jalview2XML_V1()\r
  44   {\r
  45 \r
  46   };\r
  47 \r
  48   public Jalview2XML_V1(boolean raiseGUI)\r
  49   {\r
  50     this.raiseGUI = raiseGUI;\r
  51   };\r
  52 \r
  53   jalview.schemes.UserColourScheme GetUserColourScheme(\r
  54           JalviewModelSequence jms, String id)\r
  55   {\r
  56     UserColours[] uc = jms.getUserColours();\r
  57     UserColours colours = null;\r
  58 \r
  59     for (int i = 0; i < uc.length; i++)\r
  60     {\r
  61       if (uc[i].getId().equals(id))\r
  62       {\r
  63         colours = uc[i];\r
  64 \r
  65         break;\r
  66       }\r
  67     }\r
  68 \r
  69     int csize = colours.getUserColourScheme().getColourCount();\r
  70     java.awt.Color[] newColours = new java.awt.Color[csize];\r
  71 \r
  72     for (int i = 0; i < csize; i++)\r
  73     {\r
  74       newColours[i] = new java.awt.Color(Integer.parseInt(colours\r
  75               .getUserColourScheme().getColour(i).getRGB(), 16));\r
  76     }\r
  77 \r
  78     return new jalview.schemes.UserColourScheme(newColours);\r
  79   }\r
  80 \r
  81   /**\r
  82    * DOCUMENT ME!\r
  83    * \r
  84    * @param file\r
  85    *                DOCUMENT ME!\r
  86    */\r
  87   public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)\r
  88   {\r
  89     final String file  = jprovider.getFilename();\r
  90     jalview.gui.AlignFrame af = null;\r
  91 \r
  92     try\r
  93     {\r
  94       JarInputStream jin = null;\r
  95       JarEntry jarentry = null;\r
  96       int entryCount = 1;\r
  97 \r
  98       do\r
  99       {\r
 100         jin = jprovider.getJarInputStream();\r
 101 \r
 102         for (int i = 0; i < entryCount; i++)\r
 103         {\r
 104           jarentry = jin.getNextJarEntry();\r
 105         }\r
 106 \r
 107         class NoDescIDResolver implements IDResolver\r
 108         {\r
 109           public Object resolve(String idref)\r
 110           {\r
 111             System.out.println(idref + " used");\r
 112             return null;\r
 113           }\r
 114         }\r
 115 \r
 116         if (jarentry != null)\r
 117         {\r
 118           InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 119           JalviewModel object = new JalviewModel();\r
 120 \r
 121           object = (JalviewModel) object.unmarshal(in);\r
 122 \r
 123           af = LoadFromObject(object, file);\r
 124           entryCount++;\r
 125         }\r
 126       } while (jarentry != null);\r
 127     } catch (final java.net.UnknownHostException ex)\r
 128     {\r
 129       ex.printStackTrace();\r
 130       if (raiseGUI)\r
 131       {\r
 132         javax.swing.SwingUtilities.invokeLater(new Runnable()\r
 133         {\r
 134           public void run()\r
 135           {\r
 136 \r
 137             System.err.println("Couldn't locate Jalview XML file : " + ex\r
 138                     + "\n");\r
 139             JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 140                     "Couldn't locate " + file, "URL not found",\r
 141                     JOptionPane.WARNING_MESSAGE);\r
 142           }\r
 143         });\r
 144       }\r
 145       ;\r
 146     } catch (Exception ex)\r
 147     {\r
 148       System.err.println("Exception whilst loading jalview XML file : ");\r
 149       ex.printStackTrace();\r
 150       if (raiseGUI)\r
 151       {\r
 152         javax.swing.SwingUtilities.invokeLater(new Runnable()\r
 153         {\r
 154           public void run()\r
 155           {\r
 156 \r
 157             JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 158                     "Error loading  " + file, "Error loading Jalview file",\r
 159                     JOptionPane.WARNING_MESSAGE);\r
 160           }\r
 161         });\r
 162       }\r
 163     }\r
 164 \r
 165     return af;\r
 166   }\r
 167 \r
 168   AlignFrame LoadFromObject(JalviewModel object, String file)\r
 169   {\r
 170     Vector seqids = new Vector();\r
 171     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 172     Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 173 \r
 174     JalviewModelSequence jms = object.getJalviewModelSequence();\r
 175 \r
 176     // ////////////////////////////////\r
 177     // LOAD SEQUENCES\r
 178     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 179     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 180     for (int i = 0; i < vamsasSeq.length; i++)\r
 181     {\r
 182       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 183               vamsasSeq[i].getSequence());\r
 184       jseqs[i].setStart(JSEQ[i].getStart());\r
 185       jseqs[i].setEnd(JSEQ[i].getEnd());\r
 186       seqids.add(jseqs[i]);\r
 187     }\r
 188 \r
 189     // /SequenceFeatures are added to the DatasetSequence,\r
 190     // so we must create the dataset before loading features\r
 191     // ///////////////////////////////\r
 192     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 193     al.setDataset(null);\r
 194     // ///////////////////////////////\r
 195 \r
 196     for (int i = 0; i < vamsasSeq.length; i++)\r
 197     {\r
 198       if (JSEQ[i].getFeaturesCount() > 0)\r
 199       {\r
 200         Features[] features = JSEQ[i].getFeatures();\r
 201         for (int f = 0; f < features.length; f++)\r
 202         {\r
 203           jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(\r
 204                   features[f].getType(), features[f].getDescription(),\r
 205                   features[f].getStatus(), features[f].getBegin(),\r
 206                   features[f].getEnd(), null);\r
 207 \r
 208           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 209         }\r
 210       }\r
 211       if (JSEQ[i].getPdbidsCount() > 0)\r
 212       {\r
 213         Pdbids[] ids = JSEQ[i].getPdbids();\r
 214         for (int p = 0; p < ids.length; p++)\r
 215         {\r
 216           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 217           entry.setId(ids[p].getId());\r
 218           entry.setType(ids[p].getType());\r
 219           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 220         }\r
 221 \r
 222       }\r
 223     }\r
 224 \r
 225     // ///////////////////////////////\r
 226     // ////////////////////////////////\r
 227     // LOAD ANNOTATIONS\r
 228     if (vamsasSet.getAnnotation() != null)\r
 229     {\r
 230       Annotation[] an = vamsasSet.getAnnotation();\r
 231 \r
 232       for (int i = 0; i < an.length; i++)\r
 233       {\r
 234         AnnotationElement[] ae = an[i].getAnnotationElement();\r
 235         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al\r
 236                 .getWidth()];\r
 237 \r
 238         for (int aa = 0; aa < ae.length; aa++)\r
 239         {\r
 240           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(\r
 241                   ae[aa].getDisplayCharacter(), ae[aa].getDescription(),\r
 242                   ae[aa].getSecondaryStructure().charAt(0), ae[aa]\r
 243                           .getValue());\r
 244         }\r
 245 \r
 246         jalview.datamodel.AlignmentAnnotation jaa = null;\r
 247 \r
 248         if (an[i].getGraph())\r
 249         {\r
 250           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 251                   an[i].getDescription(), anot, 0, 0,\r
 252                   jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);\r
 253         }\r
 254         else\r
 255         {\r
 256           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 257                   an[i].getDescription(), anot);\r
 258         }\r
 259 \r
 260         al.addAnnotation(jaa);\r
 261       }\r
 262     }\r
 263 \r
 264     // ///////////////////////////////\r
 265     // LOAD VIEWPORT\r
 266     Viewport[] views = jms.getViewport();\r
 267     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 268 \r
 269     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
 270 \r
 271     af.setFileName(file, "Jalview");\r
 272 \r
 273     for (int i = 0; i < JSEQ.length; i++)\r
 274     {\r
 275       af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),\r
 276               new java.awt.Color(JSEQ[i].getColour()));\r
 277     }\r
 278 \r
 279     // af.changeColour() );\r
 280     // ///////////////////////\r
 281     // LOAD GROUPS\r
 282     if (jms.getJGroupCount() > 0)\r
 283     {\r
 284       JGroup[] groups = jms.getJGroup();\r
 285 \r
 286       for (int i = 0; i < groups.length; i++)\r
 287       {\r
 288         ColourSchemeI cs = null;\r
 289 \r
 290         if (groups[i].getColour() != null)\r
 291         {\r
 292           if (groups[i].getColour().startsWith("ucs"))\r
 293           {\r
 294             cs = GetUserColourScheme(jms, groups[i].getColour());\r
 295           }\r
 296           else\r
 297           {\r
 298             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());\r
 299           }\r
 300 \r
 301           if (cs != null)\r
 302           {\r
 303             cs.setThreshold(groups[i].getPidThreshold(), true);\r
 304           }\r
 305 \r
 306         }\r
 307 \r
 308         Vector seqs = new Vector();\r
 309         int[] ids = groups[i].getSeq();\r
 310 \r
 311         for (int s = 0; s < ids.length; s++)\r
 312         {\r
 313           seqs.addElement((jalview.datamodel.SequenceI) seqids\r
 314                   .elementAt(ids[s]));\r
 315         }\r
 316 \r
 317         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(\r
 318                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 319                 groups[i].getDisplayText(), groups[i].getColourText(),\r
 320                 groups[i].getStart(), groups[i].getEnd());\r
 321 \r
 322         sg\r
 323                 .setOutlineColour(new java.awt.Color(groups[i]\r
 324                         .getOutlineColour()));\r
 325 \r
 326         if (groups[i].getConsThreshold() != 0)\r
 327         {\r
 328           jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
 329                   "All", ResidueProperties.propHash, 3, sg\r
 330                           .getSequences(null), 0, sg.getWidth() - 1);\r
 331           c.calculate();\r
 332           c.verdict(false, 25);\r
 333           sg.cs.setConservation(c);\r
 334         }\r
 335 \r
 336         al.addGroup(sg);\r
 337       }\r
 338     }\r
 339 \r
 340     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view\r
 341             .getHeight());\r
 342     af.viewport.setStartRes(view.getStartRes());\r
 343     af.viewport.setStartSeq(view.getStartSeq());\r
 344     af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 345     af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 346     af.viewport.setColourText(view.getShowColourText());\r
 347     af.viewport.setConservationSelected(view.getConservationSelected());\r
 348     af.viewport.setShowJVSuffix(view.getShowFullId());\r
 349     af.viewport.setFont(new java.awt.Font(view.getFontName(), view\r
 350             .getFontStyle(), view.getFontSize()));\r
 351     af.alignPanel.fontChanged();\r
 352 \r
 353     af.viewport.setRenderGaps(view.getRenderGaps());\r
 354     af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 355     af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 356     af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 357     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 358     af.viewport.setShowBoxes(view.getShowBoxes());\r
 359     af.viewport.setShowText(view.getShowText());\r
 360 \r
 361     ColourSchemeI cs = null;\r
 362 \r
 363     if (view.getBgColour() != null)\r
 364     {\r
 365       if (view.getBgColour().startsWith("ucs"))\r
 366       {\r
 367         cs = GetUserColourScheme(jms, view.getBgColour());\r
 368       }\r
 369       else\r
 370       {\r
 371         cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 372       }\r
 373 \r
 374       if (cs != null)\r
 375       {\r
 376         cs.setThreshold(view.getPidThreshold(), true);\r
 377         cs.setConsensus(af.viewport.hconsensus);\r
 378       }\r
 379     }\r
 380 \r
 381     af.viewport.setGlobalColourScheme(cs);\r
 382     af.viewport.setColourAppliesToAllGroups(false);\r
 383     af.changeColour(cs);\r
 384     if (view.getConservationSelected() && cs != null)\r
 385     {\r
 386       cs.setConservationInc(view.getConsThreshold());\r
 387     }\r
 388 \r
 389     af.viewport.setColourAppliesToAllGroups(true);\r
 390     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();\r
 391 \r
 392     if (jms.getFeatureSettings() != null)\r
 393     {\r
 394       af.viewport.featuresDisplayed = new Hashtable();\r
 395       String[] renderOrder = new String[jms.getFeatureSettings()\r
 396               .getSettingCount()];\r
 397       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)\r
 398       {\r
 399         Setting setting = jms.getFeatureSettings().getSetting(fs);\r
 400 \r
 401         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(\r
 402                 setting.getType(), new java.awt.Color(setting.getColour()));\r
 403 \r
 404         renderOrder[fs] = setting.getType();\r
 405 \r
 406         if (setting.getDisplay())\r
 407         {\r
 408           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(\r
 409                   setting.getColour()));\r
 410         }\r
 411       }\r
 412       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
 413     }\r
 414 \r
 415     af.setMenusFromViewport(af.viewport);\r
 416 \r
 417     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view\r
 418             .getHeight());\r
 419 \r
 420     // LOAD TREES\r
 421     // /////////////////////////////////////\r
 422     if (jms.getTreeCount() > 0)\r
 423     {\r
 424       try\r
 425       {\r
 426         for (int t = 0; t < jms.getTreeCount(); t++)\r
 427         {\r
 428 \r
 429           Tree tree = jms.getTree(t);\r
 430 \r
 431           TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree\r
 432                   .getNewick()), tree.getTitle(), tree.getWidth(), tree\r
 433                   .getHeight(), tree.getXpos(), tree.getYpos());\r
 434 \r
 435           tp.fitToWindow.setState(tree.getFitToWindow());\r
 436           tp.fitToWindow_actionPerformed(null);\r
 437 \r
 438           if (tree.getFontName() != null)\r
 439           {\r
 440             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree\r
 441                     .getFontStyle(), tree.getFontSize()));\r
 442           }\r
 443           else\r
 444           {\r
 445             tp.setTreeFont(new java.awt.Font(view.getFontName(), view\r
 446                     .getFontStyle(), tree.getFontSize()));\r
 447           }\r
 448 \r
 449           tp.showPlaceholders(tree.getMarkUnlinked());\r
 450           tp.showBootstrap(tree.getShowBootstrap());\r
 451           tp.showDistances(tree.getShowDistances());\r
 452 \r
 453           tp.treeCanvas.threshold = tree.getThreshold();\r
 454 \r
 455           if (tree.getCurrentTree())\r
 456           {\r
 457             af.viewport.setCurrentTree(tp.getTree());\r
 458           }\r
 459         }\r
 460 \r
 461       } catch (Exception ex)\r
 462       {\r
 463         ex.printStackTrace();\r
 464       }\r
 465 \r
 466     }\r
 467 \r
 468     return af;\r
 469   }\r
 470 }\r