src/jalview/gui/Jalview2XML_V1.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
   3  * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
   4  * \r
   5  * This file is part of Jalview.\r
   6  * \r
   7  * Jalview is free software: you can redistribute it and/or\r
   8  * modify it under the terms of the GNU General Public License \r
   9  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
  10  * \r
  11  * Jalview is distributed in the hope that it will be useful, but \r
  12  * WITHOUT ANY WARRANTY; without even the implied warranty \r
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
  14  * PURPOSE.  See the GNU General Public License for more details.\r
  15  * \r
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.\r
  17  */\r
  18 package jalview.gui;\r
  19 \r
  20 import java.io.*;\r
  21 import java.net.*;\r
  22 import java.util.*;\r
  23 import java.util.jar.*;\r
  24 \r
  25 import javax.swing.*;\r
  26 \r
  27 import org.exolab.castor.xml.*;\r
  28 import jalview.binding.*;\r
  29 import jalview.schemes.*;\r
  30 import jalview.util.jarInputStreamProvider;\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 jarInputStreamProvider jprovider)\r
  87   {\r
  88     final String file = jprovider.getFilename();\r
  89     jalview.gui.AlignFrame af = null;\r
  90 \r
  91     try\r
  92     {\r
  93       JarInputStream jin = null;\r
  94       JarEntry jarentry = null;\r
  95       int entryCount = 1;\r
  96 \r
  97       do\r
  98       {\r
  99         jin = jprovider.getJarInputStream();\r
 100 \r
 101         for (int i = 0; i < entryCount; i++)\r
 102         {\r
 103           jarentry = jin.getNextJarEntry();\r
 104         }\r
 105 \r
 106         class NoDescIDResolver implements IDResolver\r
 107         {\r
 108           public Object resolve(String idref)\r
 109           {\r
 110             System.out.println(idref + " used");\r
 111             return null;\r
 112           }\r
 113         }\r
 114 \r
 115         if (jarentry != null)\r
 116         {\r
 117           InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 118           JalviewModel object = new JalviewModel();\r
 119 \r
 120           object = (JalviewModel) object.unmarshal(in);\r
 121 \r
 122           af = LoadFromObject(object, file);\r
 123           entryCount++;\r
 124         }\r
 125       } while (jarentry != null);\r
 126     } catch (final java.net.UnknownHostException ex)\r
 127     {\r
 128       ex.printStackTrace();\r
 129       if (raiseGUI)\r
 130       {\r
 131         javax.swing.SwingUtilities.invokeLater(new Runnable()\r
 132         {\r
 133           public void run()\r
 134           {\r
 135 \r
 136             System.err.println("Couldn't locate Jalview XML file : " + ex\r
 137                     + "\n");\r
 138             JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 139                     "Couldn't locate " + file, "URL not found",\r
 140                     JOptionPane.WARNING_MESSAGE);\r
 141           }\r
 142         });\r
 143       }\r
 144       ;\r
 145     } catch (Exception ex)\r
 146     {\r
 147       System.err.println("Exception whilst loading jalview XML file : ");\r
 148       ex.printStackTrace();\r
 149       if (raiseGUI)\r
 150       {\r
 151         javax.swing.SwingUtilities.invokeLater(new Runnable()\r
 152         {\r
 153           public void run()\r
 154           {\r
 155 \r
 156             JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 157                     "Error loading  " + file, "Error loading Jalview file",\r
 158                     JOptionPane.WARNING_MESSAGE);\r
 159           }\r
 160         });\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 = new jalview.datamodel.SequenceFeature(\r
 203                   features[f].getType(), features[f].getDescription(),\r
 204                   features[f].getStatus(), features[f].getBegin(),\r
 205                   features[f].getEnd(), null);\r
 206 \r
 207           al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 208         }\r
 209       }\r
 210       if (JSEQ[i].getPdbidsCount() > 0)\r
 211       {\r
 212         Pdbids[] ids = JSEQ[i].getPdbids();\r
 213         for (int p = 0; p < ids.length; p++)\r
 214         {\r
 215           jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 216           entry.setId(ids[p].getId());\r
 217           entry.setType(ids[p].getType());\r
 218           al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 219         }\r
 220 \r
 221       }\r
 222     }\r
 223 \r
 224     // ///////////////////////////////\r
 225     // ////////////////////////////////\r
 226     // LOAD ANNOTATIONS\r
 227     if (vamsasSet.getAnnotation() != null)\r
 228     {\r
 229       Annotation[] an = vamsasSet.getAnnotation();\r
 230 \r
 231       for (int i = 0; i < an.length; i++)\r
 232       {\r
 233         AnnotationElement[] ae = an[i].getAnnotationElement();\r
 234         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al\r
 235                 .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(\r
 240                   ae[aa].getDisplayCharacter(), 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     // LOAD VIEWPORT\r
 265     Viewport[] views = jms.getViewport();\r
 266     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 267 \r
 268     AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());\r
 269 \r
 270     af.setFileName(file, "Jalview");\r
 271 \r
 272     for (int i = 0; i < JSEQ.length; i++)\r
 273     {\r
 274       af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),\r
 275               new java.awt.Color(JSEQ[i].getColour()));\r
 276     }\r
 277 \r
 278     // af.changeColour() );\r
 279     // ///////////////////////\r
 280     // LOAD GROUPS\r
 281     if (jms.getJGroupCount() > 0)\r
 282     {\r
 283       JGroup[] groups = jms.getJGroup();\r
 284 \r
 285       for (int i = 0; i < groups.length; i++)\r
 286       {\r
 287         ColourSchemeI cs = null;\r
 288 \r
 289         if (groups[i].getColour() != null)\r
 290         {\r
 291           if (groups[i].getColour().startsWith("ucs"))\r
 292           {\r
 293             cs = GetUserColourScheme(jms, groups[i].getColour());\r
 294           }\r
 295           else\r
 296           {\r
 297             cs = ColourSchemeProperty.getColour(al, groups[i].getColour());\r
 298           }\r
 299 \r
 300           if (cs != null)\r
 301           {\r
 302             cs.setThreshold(groups[i].getPidThreshold(), true);\r
 303           }\r
 304 \r
 305         }\r
 306 \r
 307         Vector seqs = new Vector();\r
 308         int[] ids = groups[i].getSeq();\r
 309 \r
 310         for (int s = 0; s < ids.length; s++)\r
 311         {\r
 312           seqs.addElement((jalview.datamodel.SequenceI) seqids\r
 313                   .elementAt(ids[s]));\r
 314         }\r
 315 \r
 316         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(\r
 317                 seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 318                 groups[i].getDisplayText(), groups[i].getColourText(),\r
 319                 groups[i].getStart(), groups[i].getEnd());\r
 320 \r
 321         sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));\r
 322 \r
 323         if (groups[i].getConsThreshold() != 0)\r
 324         {\r
 325           jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
 326                   "All", ResidueProperties.propHash, 3,\r
 327                   sg.getSequences(null), 0, sg.getWidth() - 1);\r
 328           c.calculate();\r
 329           c.verdict(false, 25);\r
 330           sg.cs.setConservation(c);\r
 331         }\r
 332 \r
 333         al.addGroup(sg);\r
 334       }\r
 335     }\r
 336 \r
 337     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 338             view.getHeight());\r
 339     af.viewport.setStartRes(view.getStartRes());\r
 340     af.viewport.setStartSeq(view.getStartSeq());\r
 341     af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 342     af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 343     af.viewport.setColourText(view.getShowColourText());\r
 344     af.viewport.setConservationSelected(view.getConservationSelected());\r
 345     af.viewport.setShowJVSuffix(view.getShowFullId());\r
 346     af.viewport.setFont(new java.awt.Font(view.getFontName(), view\r
 347             .getFontStyle(), view.getFontSize()));\r
 348     af.alignPanel.fontChanged();\r
 349 \r
 350     af.viewport.setRenderGaps(view.getRenderGaps());\r
 351     af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 352     af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 353     af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 354     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 355     af.viewport.setShowBoxes(view.getShowBoxes());\r
 356     af.viewport.setShowText(view.getShowText());\r
 357 \r
 358     ColourSchemeI cs = null;\r
 359 \r
 360     if (view.getBgColour() != null)\r
 361     {\r
 362       if (view.getBgColour().startsWith("ucs"))\r
 363       {\r
 364         cs = GetUserColourScheme(jms, view.getBgColour());\r
 365       }\r
 366       else\r
 367       {\r
 368         cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 369       }\r
 370 \r
 371       if (cs != null)\r
 372       {\r
 373         cs.setThreshold(view.getPidThreshold(), true);\r
 374         cs.setConsensus(af.viewport.hconsensus);\r
 375       }\r
 376     }\r
 377 \r
 378     af.viewport.setGlobalColourScheme(cs);\r
 379     af.viewport.setColourAppliesToAllGroups(false);\r
 380     af.changeColour(cs);\r
 381     if (view.getConservationSelected() && cs != null)\r
 382     {\r
 383       cs.setConservationInc(view.getConsThreshold());\r
 384     }\r
 385 \r
 386     af.viewport.setColourAppliesToAllGroups(true);\r
 387     af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();\r
 388 \r
 389     if (jms.getFeatureSettings() != null)\r
 390     {\r
 391       af.viewport.featuresDisplayed = new Hashtable();\r
 392       String[] renderOrder = new String[jms.getFeatureSettings()\r
 393               .getSettingCount()];\r
 394       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)\r
 395       {\r
 396         Setting setting = jms.getFeatureSettings().getSetting(fs);\r
 397 \r
 398         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(\r
 399                 setting.getType(), new java.awt.Color(setting.getColour()));\r
 400 \r
 401         renderOrder[fs] = setting.getType();\r
 402 \r
 403         if (setting.getDisplay())\r
 404         {\r
 405           af.viewport.featuresDisplayed.put(setting.getType(), new Integer(\r
 406                   setting.getColour()));\r
 407         }\r
 408       }\r
 409       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
 410     }\r
 411 \r
 412     af.setMenusFromViewport(af.viewport);\r
 413 \r
 414     Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),\r
 415             view.getHeight());\r
 416 \r
 417     // LOAD TREES\r
 418     // /////////////////////////////////////\r
 419     if (jms.getTreeCount() > 0)\r
 420     {\r
 421       try\r
 422       {\r
 423         for (int t = 0; t < jms.getTreeCount(); t++)\r
 424         {\r
 425 \r
 426           Tree tree = jms.getTree(t);\r
 427 \r
 428           TreePanel tp = af.ShowNewickTree(\r
 429                   new jalview.io.NewickFile(tree.getNewick()),\r
 430                   tree.getTitle(), tree.getWidth(), tree.getHeight(),\r
 431                   tree.getXpos(), tree.getYpos());\r
 432 \r
 433           tp.fitToWindow.setState(tree.getFitToWindow());\r
 434           tp.fitToWindow_actionPerformed(null);\r
 435 \r
 436           if (tree.getFontName() != null)\r
 437           {\r
 438             tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree\r
 439                     .getFontStyle(), tree.getFontSize()));\r
 440           }\r
 441           else\r
 442           {\r
 443             tp.setTreeFont(new java.awt.Font(view.getFontName(), view\r
 444                     .getFontStyle(), tree.getFontSize()));\r
 445           }\r
 446 \r
 447           tp.showPlaceholders(tree.getMarkUnlinked());\r
 448           tp.showBootstrap(tree.getShowBootstrap());\r
 449           tp.showDistances(tree.getShowDistances());\r
 450 \r
 451           tp.treeCanvas.threshold = tree.getThreshold();\r
 452 \r
 453           if (tree.getCurrentTree())\r
 454           {\r
 455             af.viewport.setCurrentTree(tp.getTree());\r
 456           }\r
 457         }\r
 458 \r
 459       } catch (Exception ex)\r
 460       {\r
 461         ex.printStackTrace();\r
 462       }\r
 463 \r
 464     }\r
 465 \r
 466     return af;\r
 467   }\r
 468 }\r