src/jalview/gui/Jalview2XML_V1.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2007 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   public Jalview2XML_V1() {\r
  42     \r
  43   };\r
  44   public Jalview2XML_V1(boolean raiseGUI) {\r
  45     this.raiseGUI = raiseGUI;\r
  46   };\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\r
 117             implements IDResolver\r
 118         {\r
 119           public Object resolve(String idref)\r
 120           {\r
 121             System.out.println(idref + " used");\r
 122             return null;\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       if (raiseGUI)\r
 143         {javax.swing.SwingUtilities.invokeLater(new Runnable()\r
 144       {\r
 145         public void run()\r
 146         {\r
 147 \r
 148           System.err.println("Couldn't locate Jalview XML file : " +\r
 149                              ex + "\n");\r
 150           JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 151                                                 "Couldn't locate " + file,\r
 152                                                 "URL not found",\r
 153                                                 JOptionPane.WARNING_MESSAGE);\r
 154         }\r
 155       });};\r
 156     }\r
 157     catch (Exception ex)\r
 158     {\r
 159       System.err.println("Exception whilst loading jalview XML file : ");\r
 160       ex.printStackTrace();\r
 161       if (raiseGUI)\r
 162       {  javax.swing.SwingUtilities.invokeLater(new Runnable()\r
 163       {\r
 164         public void run()\r
 165         {\r
 166 \r
 167           JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 168                                                 "Error loading  " + file,\r
 169                                                 "Error loading Jalview file",\r
 170                                                 JOptionPane.WARNING_MESSAGE);\r
 171         }\r
 172       });\r
 173       }\r
 174     }\r
 175 \r
 176     return af;\r
 177   }\r
 178 \r
 179   AlignFrame LoadFromObject(JalviewModel object, String file)\r
 180   {\r
 181     Vector seqids = new Vector();\r
 182     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 183     Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 184 \r
 185     JalviewModelSequence jms = object.getJalviewModelSequence();\r
 186 \r
 187     //////////////////////////////////\r
 188     //LOAD SEQUENCES\r
 189     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[\r
 190         vamsasSeq.length];\r
 191     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 192     for (int i = 0; i < vamsasSeq.length; i++)\r
 193     {\r
 194       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 195                                                 vamsasSeq[i].getSequence());\r
 196       jseqs[i].setStart(JSEQ[i].getStart());\r
 197       jseqs[i].setEnd(JSEQ[i].getEnd());\r
 198       seqids.add(jseqs[i]);\r
 199     }\r
 200 \r
 201     ///SequenceFeatures are added to the DatasetSequence,\r
 202     // so we must create the dataset before loading features\r
 203     /////////////////////////////////\r
 204     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 205     al.setDataset(null);\r
 206     /////////////////////////////////\r
 207 \r
 208     for (int i = 0; i < vamsasSeq.length; i++)\r
 209     {\r
 210       if (JSEQ[i].getFeaturesCount() > 0)\r
 211       {\r
 212         Features[] features = JSEQ[i].getFeatures();\r
 213         for (int f = 0; f < features.length; f++)\r
 214         {\r
 215           jalview.datamodel.SequenceFeature sf\r
 216               = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 217               features[f].getDescription(), features[f].getStatus(),\r
 218               features[f].getBegin(), features[f].getEnd(),\r
 219               null);\r
 220 \r
 221           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 222         }\r
 223       }\r
 224       if (JSEQ[i].getPdbidsCount() > 0)\r
 225       {\r
 226         Pdbids[] ids = JSEQ[i].getPdbids();\r
 227         for (int p = 0; p < ids.length; p++)\r
 228         {\r
 229           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 230           entry.setId(ids[p].getId());\r
 231           entry.setType(ids[p].getType());\r
 232           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 233         }\r
 234 \r
 235       }\r
 236     }\r
 237 \r
 238     /////////////////////////////////\r
 239     //////////////////////////////////\r
 240     //LOAD ANNOTATIONS\r
 241     if (vamsasSet.getAnnotation() != null)\r
 242     {\r
 243       Annotation[] an = vamsasSet.getAnnotation();\r
 244 \r
 245       for (int i = 0; i < an.length; i++)\r
 246       {\r
 247         AnnotationElement[] ae = an[i].getAnnotationElement();\r
 248         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[\r
 249             al.getWidth()];\r
 250 \r
 251         for (int aa = 0; aa < ae.length; aa++)\r
 252         {\r
 253           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].\r
 254               getDisplayCharacter(),\r
 255               ae[aa].getDescription(),\r
 256               ae[aa].getSecondaryStructure().charAt(0),\r
 257               ae[aa].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(\r
 290           af.viewport.alignment.getSequenceAt(i),\r
 291           new java.awt.Color(\r
 292               JSEQ[i].getColour()));\r
 293     }\r
 294 \r
 295     //  af.changeColour() );\r
 296     /////////////////////////\r
 297     //LOAD GROUPS\r
 298     if (jms.getJGroupCount() > 0)\r
 299     {\r
 300       JGroup[] groups = jms.getJGroup();\r
 301 \r
 302       for (int i = 0; i < groups.length; i++)\r
 303       {\r
 304         ColourSchemeI cs = null;\r
 305 \r
 306         if (groups[i].getColour() != null)\r
 307         {\r
 308           if (groups[i].getColour().startsWith("ucs"))\r
 309           {\r
 310             cs = GetUserColourScheme(jms, groups[i].getColour());\r
 311           }\r
 312           else\r
 313           {\r
 314             cs = ColourSchemeProperty.getColour(al,\r
 315                                                 groups[i].getColour());\r
 316           }\r
 317 \r
 318           if (cs != null)\r
 319           {\r
 320             cs.setThreshold(groups[i].getPidThreshold(), true);\r
 321           }\r
 322 \r
 323         }\r
 324 \r
 325         Vector seqs = new Vector();\r
 326         int[] ids = groups[i].getSeq();\r
 327 \r
 328         for (int s = 0; s < ids.length; s++)\r
 329         {\r
 330           seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(\r
 331               ids[s]));\r
 332         }\r
 333 \r
 334         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.\r
 335             SequenceGroup(seqs,\r
 336                           groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 337                           groups[i].getDisplayText(), groups[i].getColourText(),\r
 338                           groups[i].getStart(), groups[i].getEnd());\r
 339 \r
 340         sg.setOutlineColour(new java.awt.Color(\r
 341             groups[i].getOutlineColour()));\r
 342 \r
 343         if (groups[i].getConsThreshold() != 0)\r
 344         {\r
 345           jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
 346               "All",\r
 347               ResidueProperties.propHash, 3, sg.getSequences(null), 0,\r
 348               sg.getWidth() - 1);\r
 349           c.calculate();\r
 350           c.verdict(false, 25);\r
 351           sg.cs.setConservation(c);\r
 352         }\r
 353 \r
 354         al.addGroup(sg);\r
 355       }\r
 356     }\r
 357 \r
 358     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 359                  view.getHeight());\r
 360     af.viewport.setStartRes(view.getStartRes());\r
 361     af.viewport.setStartSeq(view.getStartSeq());\r
 362     af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 363     af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 364     af.viewport.setColourText(view.getShowColourText());\r
 365     af.viewport.setConservationSelected(view.getConservationSelected());\r
 366     af.viewport.setShowJVSuffix(view.getShowFullId());\r
 367     af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 368                                           view.getFontStyle(), view.getFontSize()));\r
 369     af.alignPanel.fontChanged();\r
 370 \r
 371     af.viewport.setRenderGaps(view.getRenderGaps());\r
 372     af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 373     af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 374     af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 375     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 376     af.viewport.setShowBoxes(view.getShowBoxes());\r
 377     af.viewport.setShowText(view.getShowText());\r
 378 \r
 379     ColourSchemeI cs = null;\r
 380 \r
 381     if (view.getBgColour() != null)\r
 382     {\r
 383       if (view.getBgColour().startsWith("ucs"))\r
 384       {\r
 385         cs = GetUserColourScheme(jms, view.getBgColour());\r
 386       }\r
 387       else\r
 388       {\r
 389         cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 390       }\r
 391 \r
 392       if (cs != null)\r
 393       {\r
 394         cs.setThreshold(view.getPidThreshold(), true);\r
 395         cs.setConsensus(af.viewport.hconsensus);\r
 396       }\r
 397     }\r
 398 \r
 399     af.viewport.setGlobalColourScheme(cs);\r
 400     af.viewport.setColourAppliesToAllGroups(false);\r
 401     af.changeColour(cs);\r
 402     if (view.getConservationSelected() && cs != null)\r
 403     {\r
 404       cs.setConservationInc(view.getConsThreshold());\r
 405     }\r
 406 \r
 407     af.viewport.setColourAppliesToAllGroups(true);\r
 408     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();\r
 409 \r
 410     if (jms.getFeatureSettings() != null)\r
 411     {\r
 412       af.viewport.featuresDisplayed = new Hashtable();\r
 413       String[] renderOrder = new String[jms.getFeatureSettings().\r
 414           getSettingCount()];\r
 415       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)\r
 416       {\r
 417         Setting setting = jms.getFeatureSettings().getSetting(fs);\r
 418 \r
 419         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.\r
 420             getType(),\r
 421             new java.awt.Color(setting.getColour()));\r
 422 \r
 423         renderOrder[fs] = setting.getType();\r
 424 \r
 425         if (setting.getDisplay())\r
 426         {\r
 427           af.viewport.featuresDisplayed.put(\r
 428               setting.getType(), new Integer(setting.getColour()));\r
 429         }\r
 430       }\r
 431       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =\r
 432           renderOrder;\r
 433     }\r
 434 \r
 435     af.setMenusFromViewport(af.viewport);\r
 436 \r
 437     Desktop.addInternalFrame(af, view.getTitle(),\r
 438                              view.getWidth(), view.getHeight());\r
 439 \r
 440     //LOAD TREES\r
 441     ///////////////////////////////////////\r
 442     if (jms.getTreeCount() > 0)\r
 443     {\r
 444       try\r
 445       {\r
 446         for (int t = 0; t < jms.getTreeCount(); t++)\r
 447         {\r
 448 \r
 449           Tree tree = jms.getTree(t);\r
 450 \r
 451           TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
 452               tree.getNewick()), tree.getTitle(),\r
 453                                            tree.getWidth(), tree.getHeight(),\r
 454                                            tree.getXpos(), tree.getYpos());\r
 455 \r
 456           tp.fitToWindow.setState(tree.getFitToWindow());\r
 457           tp.fitToWindow_actionPerformed(null);\r
 458 \r
 459           if (tree.getFontName() != null)\r
 460           {\r
 461             tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
 462                                              tree.getFontStyle(),\r
 463                                              tree.getFontSize()));\r
 464           }\r
 465           else\r
 466           {\r
 467             tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
 468                                              view.getFontStyle(),\r
 469                                              tree.getFontSize()));\r
 470           }\r
 471 \r
 472           tp.showPlaceholders(tree.getMarkUnlinked());\r
 473           tp.showBootstrap(tree.getShowBootstrap());\r
 474           tp.showDistances(tree.getShowDistances());\r
 475 \r
 476           tp.treeCanvas.threshold = tree.getThreshold();\r
 477 \r
 478           if (tree.getCurrentTree())\r
 479           {\r
 480             af.viewport.setCurrentTree(tp.getTree());\r
 481           }\r
 482         }\r
 483 \r
 484       }\r
 485       catch (Exception ex)\r
 486       {\r
 487         ex.printStackTrace();\r
 488       }\r
 489 \r
 490     }\r
 491 \r
 492     return af;\r
 493   }\r
 494 }\r