src/jalview/gui/Jalview2XML_V1.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2006 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 jalview.schemes.*;\r
  22 \r
  23 import jalview.gui.*;\r
  24 \r
  25 import java.io.*;\r
  26 \r
  27 import java.net.*;\r
  28 \r
  29 import java.util.*;\r
  30 \r
  31 import java.util.jar.*;\r
  32 \r
  33 import javax.swing.*;\r
  34 \r
  35 import org.exolab.castor.xml.*;\r
  36 \r
  37 import jalview.binding.*;\r
  38 \r
  39 \r
  40 \r
  41 \r
  42 /**\r
  43  * DOCUMENT ME!\r
  44  *\r
  45  * @author $author$\r
  46  * @version $Revision$\r
  47  */\r
  48 public class Jalview2XML_V1\r
  49 {\r
  50    jalview.schemes.UserColourScheme GetUserColourScheme(\r
  51         JalviewModelSequence jms, String id)\r
  52     {\r
  53         UserColours[] uc = jms.getUserColours();\r
  54         UserColours colours = null;\r
  55 \r
  56         for (int i = 0; i < uc.length; i++)\r
  57         {\r
  58             if (uc[i].getId().equals(id))\r
  59             {\r
  60                 colours = uc[i];\r
  61 \r
  62                 break;\r
  63             }\r
  64         }\r
  65 \r
  66         int csize = colours.getUserColourScheme().getColourCount();\r
  67         java.awt.Color[] newColours = new java.awt.Color[csize];\r
  68 \r
  69         for (int i = 0; i < csize; i++)\r
  70         {\r
  71             newColours[i] = new java.awt.Color(Integer.parseInt(\r
  72                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
  73         }\r
  74 \r
  75         return new jalview.schemes.UserColourScheme(newColours);\r
  76     }\r
  77 \r
  78     /**\r
  79      * DOCUMENT ME!\r
  80      *\r
  81      * @param file DOCUMENT ME!\r
  82      */\r
  83     public AlignFrame LoadJalviewAlign(String file)\r
  84     {\r
  85 \r
  86         jalview.gui.AlignFrame af = null;\r
  87 \r
  88         try\r
  89         {\r
  90             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
  91             URL url = null;\r
  92 \r
  93             if (file.startsWith("http://"))\r
  94             {\r
  95                 url = new URL(file);\r
  96             }\r
  97 \r
  98             JarInputStream jin = null;\r
  99             JarEntry jarentry = null;\r
 100             int entryCount = 1;\r
 101 \r
 102             do\r
 103             {\r
 104                 if (url != null)\r
 105                 {\r
 106                     jin = new JarInputStream(url.openStream());\r
 107                 }\r
 108                 else\r
 109                 {\r
 110                     jin = new JarInputStream(new FileInputStream(file));\r
 111                 }\r
 112 \r
 113                 for (int i = 0; i < entryCount; i++)\r
 114                 {\r
 115                     jarentry = jin.getNextJarEntry();\r
 116                   }\r
 117 \r
 118                   class NoDescIDResolver implements IDResolver\r
 119                   {\r
 120                     public Object resolve(String idref)\r
 121                     {\r
 122                       System.out.println(idref+" used");\r
 123                       return null;\r
 124                     }\r
 125                   }\r
 126 \r
 127 \r
 128                 if (jarentry != null)\r
 129                 {\r
 130                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 131                     JalviewModel object = new JalviewModel();\r
 132 \r
 133                     object = (JalviewModel) object.unmarshal(in);\r
 134 \r
 135                     af = LoadFromObject(object, file);\r
 136                     entryCount++;\r
 137                 }\r
 138             }\r
 139             while (jarentry != null);\r
 140         }\r
 141         catch(java.net.UnknownHostException ex)\r
 142         {\r
 143           ex.printStackTrace();\r
 144           System.err.println("Couldn't locate Jalview XML file : " +\r
 145               ex + "\n");\r
 146            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 147                                     "Couldn't locate " + file,\r
 148                                     "URL not found",\r
 149                                     JOptionPane.WARNING_MESSAGE);\r
 150 \r
 151         }\r
 152         catch (Exception ex)\r
 153         {\r
 154           ex.printStackTrace();\r
 155             System.err.println("Exception whilst loading jalview XML file : " +\r
 156                 ex + "\n");\r
 157              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 158                                       "Error loading  " + file,\r
 159                                       "Error loading Jalview file",\r
 160                                       JOptionPane.WARNING_MESSAGE);\r
 161 \r
 162         }\r
 163 \r
 164         return af;\r
 165     }\r
 166 \r
 167     AlignFrame LoadFromObject(JalviewModel object, String file)\r
 168     {\r
 169         Vector seqids = new Vector();\r
 170         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 171         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 172 \r
 173         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 174 \r
 175         //////////////////////////////////\r
 176         //LOAD SEQUENCES\r
 177         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 178         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 179         for (int i = 0; i < vamsasSeq.length; i++)\r
 180         {\r
 181             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 182                     vamsasSeq[i].getSequence());\r
 183             jseqs[i].setStart(JSEQ[i].getStart());\r
 184             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 185             seqids.add(jseqs[i]);\r
 186         }\r
 187 \r
 188         ///SequenceFeatures are added to the DatasetSequence,\r
 189         // so we must create the dataset before loading features\r
 190         /////////////////////////////////\r
 191         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 192         al.setDataset(null);\r
 193         /////////////////////////////////\r
 194 \r
 195         for (int i = 0; i < vamsasSeq.length; i++)\r
 196         {\r
 197           if (JSEQ[i].getFeaturesCount() > 0)\r
 198           {\r
 199             Features[] features = JSEQ[i].getFeatures();\r
 200             for (int f = 0; f < features.length; f++)\r
 201             {\r
 202               jalview.datamodel.SequenceFeature sf\r
 203                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 204                   features[f].getDescription(), features[f].getStatus(),\r
 205                   features[f].getBegin(), features[f].getEnd(),\r
 206                   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.getWidth()];\r
 236 \r
 237                 for (int aa = 0; aa < ae.length; aa++)\r
 238                 {\r
 239                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 240                             ae[aa].getDescription(),\r
 241                             ae[aa].getSecondaryStructure().charAt(0),\r
 242                             ae[aa].getValue());\r
 243                 }\r
 244 \r
 245                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 246 \r
 247                 if (an[i].getGraph())\r
 248                 {\r
 249                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 250                             an[i].getDescription(), anot, 0, 0,\r
 251                             jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);\r
 252                 }\r
 253                 else\r
 254                 {\r
 255                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 256                             an[i].getDescription(), anot);\r
 257                 }\r
 258 \r
 259                 al.addAnnotation(jaa);\r
 260             }\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(\r
 276               af.viewport.alignment.getSequenceAt(i),\r
 277               new java.awt.Color(\r
 278                   JSEQ[i].getColour()));\r
 279         }\r
 280 \r
 281 \r
 282 \r
 283         //  af.changeColour() );\r
 284         /////////////////////////\r
 285         //LOAD GROUPS\r
 286         if (jms.getJGroupCount() > 0)\r
 287         {\r
 288             JGroup[] groups = jms.getJGroup();\r
 289 \r
 290             for (int i = 0; i < groups.length; i++)\r
 291             {\r
 292                 ColourSchemeI cs = null;\r
 293 \r
 294                 if (groups[i].getColour() != null)\r
 295                 {\r
 296                     if (groups[i].getColour().startsWith("ucs"))\r
 297                     {\r
 298                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 299                     }\r
 300                     else\r
 301                     {\r
 302                         cs = ColourSchemeProperty.getColour(al,\r
 303                                 groups[i].getColour());\r
 304                     }\r
 305 \r
 306                     if(cs!=null)\r
 307                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
 308 \r
 309                 }\r
 310 \r
 311                 Vector seqs = new Vector();\r
 312                 int[] ids = groups[i].getSeq();\r
 313 \r
 314                 for (int s = 0; s < ids.length; s++)\r
 315                 {\r
 316                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 317                             ids[s]));\r
 318                 }\r
 319 \r
 320                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 321                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 322                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 323                         groups[i].getStart(), groups[i].getEnd());\r
 324 \r
 325                 sg.setOutlineColour(new java.awt.Color(\r
 326                         groups[i].getOutlineColour()));\r
 327 \r
 328                 if (groups[i].getConsThreshold() != 0)\r
 329                 {\r
 330                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 331                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
 332                             sg.getWidth() - 1);\r
 333                     c.calculate();\r
 334                     c.verdict(false, 25);\r
 335                     sg.cs.setConservation(c);\r
 336                 }\r
 337 \r
 338                 al.addGroup(sg);\r
 339             }\r
 340         }\r
 341 \r
 342 \r
 343 \r
 344         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 345             view.getHeight());\r
 346         af.viewport.setStartRes(view.getStartRes());\r
 347         af.viewport.setStartSeq(view.getStartSeq());\r
 348         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 349         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 350         af.viewport.setColourText(view.getShowColourText());\r
 351         af.viewport.setConservationSelected(view.getConservationSelected());\r
 352         af.viewport.setShowJVSuffix(view.getShowFullId());\r
 353         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 354                 view.getFontStyle(), view.getFontSize()));\r
 355         af.alignPanel.fontChanged();\r
 356 \r
 357         af.viewport.setRenderGaps(view.getRenderGaps());\r
 358         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 359         af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 360         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 361         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 362         af.viewport.setShowBoxes(view.getShowBoxes());\r
 363         af.viewport.setShowText(view.getShowText());\r
 364 \r
 365         ColourSchemeI cs = null;\r
 366 \r
 367         if (view.getBgColour() != null)\r
 368         {\r
 369             if (view.getBgColour().startsWith("ucs"))\r
 370             {\r
 371                 cs = GetUserColourScheme(jms, view.getBgColour());\r
 372             }\r
 373             else\r
 374             {\r
 375                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 376             }\r
 377 \r
 378             if(cs!=null)\r
 379             {\r
 380               cs.setThreshold(view.getPidThreshold(), true);\r
 381               cs.setConsensus(af.viewport.hconsensus);\r
 382             }\r
 383         }\r
 384 \r
 385         af.viewport.setGlobalColourScheme(cs);\r
 386         af.viewport.setColourAppliesToAllGroups(false);\r
 387         af.changeColour(cs);\r
 388         if (view.getConservationSelected() && cs!=null)\r
 389         {\r
 390           cs.setConservationInc(view.getConsThreshold());\r
 391         }\r
 392 \r
 393         af.viewport.setColourAppliesToAllGroups(true);\r
 394         af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();\r
 395 \r
 396 \r
 397         if(jms.getFeatureSettings()!=null)\r
 398         {\r
 399           af.viewport.featuresDisplayed = new Hashtable();\r
 400           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
 401          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
 402          {\r
 403            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
 404 \r
 405            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
 406                new java.awt.Color(setting.getColour()));\r
 407 \r
 408            renderOrder[fs] = setting.getType();\r
 409 \r
 410            if(setting.getDisplay())\r
 411              af.viewport.featuresDisplayed.put(\r
 412                  setting.getType(), new Integer(setting.getColour()));\r
 413          }\r
 414          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
 415         }\r
 416 \r
 417         af.setMenusFromViewport(af.viewport);\r
 418 \r
 419         Desktop.addInternalFrame(af, view.getTitle(),\r
 420              view.getWidth(), view.getHeight());\r
 421 \r
 422         //LOAD TREES\r
 423         ///////////////////////////////////////\r
 424         if (jms.getTreeCount() > 0)\r
 425         {\r
 426             try\r
 427             {\r
 428                 for (int t = 0; t < jms.getTreeCount(); t++)\r
 429                 {\r
 430 \r
 431                     Tree tree = jms.getTree(t);\r
 432 \r
 433                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
 434                                 tree.getNewick()), tree.getTitle(),\r
 435                                 tree.getWidth(), tree.getHeight(),\r
 436                                 tree.getXpos(), tree.getYpos());\r
 437 \r
 438                     tp.fitToWindow.setState(tree.getFitToWindow());\r
 439                     tp.fitToWindow_actionPerformed(null);\r
 440 \r
 441                     if(tree.getFontName()!=null)\r
 442                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
 443                                           tree.getFontStyle(),\r
 444                                           tree.getFontSize()));\r
 445                     else\r
 446                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
 447                                             view.getFontStyle(),\r
 448                                             tree.getFontSize()));\r
 449 \r
 450                     tp.showPlaceholders(tree.getMarkUnlinked());\r
 451                     tp.showBootstrap(tree.getShowBootstrap());\r
 452                     tp.showDistances(tree.getShowDistances());\r
 453 \r
 454                     tp.treeCanvas.threshold = tree.getThreshold();\r
 455 \r
 456                     if (tree.getCurrentTree())\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
 471 \r