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