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