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