src/jalview/gui/Jalview2XML.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer\r
   3  * Copyright (C) 2005 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 \r
  22 import jalview.schemes.*;\r
  23 \r
  24 import jalview.gui.*;\r
  25 \r
  26 import java.io.*;\r
  27 \r
  28 import java.net.*;\r
  29 \r
  30 import java.util.*;\r
  31 \r
  32 import java.util.jar.*;\r
  33 \r
  34 import javax.swing.*;\r
  35 \r
  36 import org.exolab.castor.xml.*;\r
  37 \r
  38 import jalview.schemabinding.version2.*;\r
  39 \r
  40 \r
  41 \r
  42 \r
  43 /**\r
  44  * DOCUMENT ME!\r
  45  *\r
  46  * @author $author$\r
  47  * @version $Revision$\r
  48  */\r
  49 public class Jalview2XML\r
  50 {\r
  51     // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
  52     public void SaveState(File statefile)\r
  53     {\r
  54         long creation = System.currentTimeMillis();\r
  55         JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
  56 \r
  57         if (frames == null)\r
  58         {\r
  59             return;\r
  60         }\r
  61 \r
  62         try\r
  63         {\r
  64             FileOutputStream fos = new FileOutputStream(statefile);\r
  65             JarOutputStream jout = new JarOutputStream(fos);\r
  66 \r
  67             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  68             ////////////////////////////////////////////////////\r
  69             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
  70                         "UTF-8"));\r
  71 \r
  72             Vector shortNames = new Vector();\r
  73 \r
  74             //REVERSE ORDER\r
  75             for (int i = frames.length - 1; i > -1; i--)\r
  76             {\r
  77                 if (frames[i] instanceof AlignFrame)\r
  78                 {\r
  79                     AlignFrame af = (AlignFrame) frames[i];\r
  80 \r
  81                     String shortName = af.getTitle();\r
  82 \r
  83                     if (shortName.indexOf(File.separatorChar) > -1)\r
  84                     {\r
  85                         shortName = shortName.substring(shortName.lastIndexOf(\r
  86                                     File.separatorChar) + 1);\r
  87                     }\r
  88 \r
  89                     int count = 1;\r
  90 \r
  91                     while (shortNames.contains(shortName))\r
  92                     {\r
  93                         if (shortName.endsWith("_" + (count - 1)))\r
  94                         {\r
  95                             shortName = shortName.substring(0,\r
  96                                     shortName.lastIndexOf("_"));\r
  97                         }\r
  98 \r
  99                         shortName = shortName.concat("_" + count);\r
 100                         count++;\r
 101                     }\r
 102 \r
 103                     shortNames.addElement(shortName);\r
 104 \r
 105                     if (!shortName.endsWith(".xml"))\r
 106                     {\r
 107                         shortName = shortName + ".xml";\r
 108                     }\r
 109 \r
 110                     SaveState(af, creation, shortName, jout, out);\r
 111                 }\r
 112             }\r
 113 \r
 114             out.close();\r
 115             jout.close();\r
 116         }\r
 117         catch (Exception ex)\r
 118         {\r
 119             ex.printStackTrace();\r
 120         }\r
 121     }\r
 122 \r
 123     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
 124     public void SaveAlignment(AlignFrame af, String jarFile,\r
 125         String fileName)\r
 126     {\r
 127         try\r
 128         {\r
 129             FileOutputStream fos = new FileOutputStream(jarFile);\r
 130             JarOutputStream jout = new JarOutputStream(fos);\r
 131 \r
 132             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 133             ////////////////////////////////////////////////////\r
 134             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
 135                         "UTF-8"));\r
 136 \r
 137             SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
 138             out.close();\r
 139             jout.close();\r
 140         }\r
 141         catch (Exception ex)\r
 142         {\r
 143           ex.printStackTrace();\r
 144         }\r
 145     }\r
 146 \r
 147     /**\r
 148      * DOCUMENT ME!\r
 149      *\r
 150      * @param af DOCUMENT ME!\r
 151      * @param timeStamp DOCUMENT ME!\r
 152      * @param fileName DOCUMENT ME!\r
 153      * @param jout DOCUMENT ME!\r
 154      * @param out DOCUMENT ME!\r
 155      */\r
 156     public void SaveState(AlignFrame af, long timeStamp,\r
 157         String fileName, JarOutputStream jout, PrintWriter out)\r
 158     {\r
 159         Vector seqids = new Vector();\r
 160         Vector userColours = new Vector();\r
 161 \r
 162         AlignViewport av = af.viewport;\r
 163 \r
 164         JalviewModel object = new JalviewModel();\r
 165         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());\r
 166 \r
 167         object.setCreationDate(new java.util.Date(timeStamp));\r
 168         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
 169 \r
 170         jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
 171 \r
 172         SequenceSet vamsasSet = new SequenceSet();\r
 173         Sequence vamsasSeq;\r
 174         JalviewModelSequence jms = new JalviewModelSequence();\r
 175 \r
 176         vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 177 \r
 178         JSeq jseq;\r
 179 \r
 180         //SAVE SEQUENCES\r
 181         int id = 0;\r
 182 \r
 183         for (int i = 0; i < jal.getHeight(); i++)\r
 184         {\r
 185             seqids.add(jal.getSequenceAt(i));\r
 186 \r
 187             vamsasSeq = new Sequence();\r
 188             vamsasSeq.setId(id + "");\r
 189             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 190             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 191             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
 192 \r
 193             jseq = new JSeq();\r
 194             jseq.setStart(jal.getSequenceAt(i).getStart());\r
 195             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 196 \r
 197             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 198 \r
 199             jseq.setId(id);\r
 200 \r
 201             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
 202             {\r
 203               jalview.datamodel.SequenceFeature[] sf\r
 204                   = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 205               int index = 0;\r
 206               while(index < sf.length)\r
 207               {\r
 208                 Features features = new Features();\r
 209 \r
 210                 features.setBegin(sf[index].getBegin());\r
 211                 features.setEnd(sf[index].getEnd());\r
 212                 features.setDescription(sf[index].getDescription());\r
 213                 features.setStatus(sf[index].getStatus());\r
 214                 features.setType(sf[index].getType());\r
 215                 features.setFeatureGroup(sf[index].getFeatureGroup());\r
 216                 jseq.addFeatures(features);\r
 217                 index ++;\r
 218               }\r
 219             }\r
 220 \r
 221             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
 222             {\r
 223               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
 224               while(en.hasMoreElements())\r
 225               {\r
 226                 Pdbids pdb = new Pdbids();\r
 227                 jalview.datamodel.PDBEntry entry\r
 228                    = (jalview.datamodel.PDBEntry)en.nextElement();\r
 229 \r
 230                 pdb.setId(entry.getId());\r
 231                 pdb.setType(entry.getType());\r
 232 \r
 233                 if(entry.getProperty()!=null)\r
 234                 {\r
 235                   PdbentryItem item = new PdbentryItem();\r
 236                   Hashtable properties = entry.getProperty();\r
 237                   Enumeration en2 = properties.keys();\r
 238                   while(en2.hasMoreElements())\r
 239                   {\r
 240                     Property prop = new Property();\r
 241                     String key = en2.nextElement().toString();\r
 242                     prop.setName(key);\r
 243                     prop.setValue( properties.get(key).toString() );\r
 244                     item.addProperty(prop);\r
 245                   }\r
 246                   pdb.addPdbentryItem(item);\r
 247                 }\r
 248 \r
 249                 jseq.addPdbids(pdb);\r
 250               }\r
 251             }\r
 252 \r
 253             jms.addJSeq(jseq);\r
 254             vamsasSet.addSequence(vamsasSeq);\r
 255             id++;\r
 256         }\r
 257 \r
 258         //SAVE TREES\r
 259         ///////////////////////////////////\r
 260         if (af.viewport.currentTree != null)\r
 261         {\r
 262           // FIND ANY ASSOCIATED TREES\r
 263           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
 264           if (Desktop.desktop != null)\r
 265           {\r
 266             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 267 \r
 268             for (int t = 0; t < frames.length; t++)\r
 269             {\r
 270               if (frames[t] instanceof TreePanel)\r
 271               {\r
 272                 TreePanel tp = (TreePanel) frames[t];\r
 273 \r
 274                 if (tp.treeCanvas.av.alignment == jal)\r
 275                 {\r
 276                   Tree tree = new Tree();\r
 277                   tree.setTitle(tp.getTitle());\r
 278                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
 279                   tree.setNewick(tp.getTree().toString());\r
 280                   tree.setThreshold(tp.treeCanvas.threshold);\r
 281 \r
 282                   tree.setFitToWindow(tp.fitToWindow.getState());\r
 283                   tree.setFontName(tp.getTreeFont().getName());\r
 284                   tree.setFontSize(tp.getTreeFont().getSize());\r
 285                   tree.setFontStyle(tp.getTreeFont().getStyle());\r
 286                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 287 \r
 288                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 289                   tree.setShowDistances(tp.distanceMenu.getState());\r
 290 \r
 291                   tree.setHeight(tp.getHeight());\r
 292                   tree.setWidth(tp.getWidth());\r
 293                   tree.setXpos(tp.getX());\r
 294                   tree.setYpos(tp.getY());\r
 295 \r
 296                   jms.addTree(tree);\r
 297                 }\r
 298               }\r
 299             }\r
 300           }\r
 301         }\r
 302 \r
 303         //SAVE ANNOTATIONS\r
 304         if (jal.getAlignmentAnnotation() != null)\r
 305         {\r
 306             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 307 \r
 308             for (int i = 0; i < aa.length; i++)\r
 309             {\r
 310                 if (aa[i].label.equals("Quality") ||\r
 311                         aa[i].label.equals("Conservation") ||\r
 312                         aa[i].label.equals("Consensus"))\r
 313                 {\r
 314                     continue;\r
 315                 }\r
 316 \r
 317                 Annotation an = new Annotation();\r
 318                 an.setDescription(aa[i].description);\r
 319                 if(aa[i].graph>0)\r
 320                 {\r
 321                   an.setGraph(true);\r
 322                   an.setGraphType(aa[i].graph);\r
 323                   if(aa[i].getThreshold()!=null)\r
 324                   {\r
 325                     ThresholdLine line = new ThresholdLine();\r
 326                     line.setLabel(aa[i].getThreshold().label);\r
 327                     line.setValue(aa[i].getThreshold().value);\r
 328                     line.setColour(aa[i].getThreshold().colour.getRGB());\r
 329                     an.setThresholdLine(line);\r
 330                   }\r
 331                 }\r
 332                 else\r
 333                   an.setGraph(false);\r
 334 \r
 335                 an.setLabel(aa[i].label);\r
 336 \r
 337                 AnnotationElement ae;\r
 338 \r
 339                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 340                 {\r
 341                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 342                     {\r
 343                         continue;\r
 344                     }\r
 345 \r
 346                     ae = new AnnotationElement();\r
 347                     ae.setDescription(aa[i].annotations[a].description);\r
 348                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 349                     ae.setValue(aa[i].annotations[a].value);\r
 350                     ae.setPosition(a);\r
 351                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 352                         "");\r
 353                     an.addAnnotationElement(ae);\r
 354                 }\r
 355 \r
 356                 vamsasSet.addAnnotation(an);\r
 357             }\r
 358         }\r
 359 \r
 360         //SAVE GROUPS\r
 361         if (jal.getGroups() != null)\r
 362         {\r
 363             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 364 \r
 365             for (int i = 0; i < groups.length; i++)\r
 366             {\r
 367                 groups[i] = new JGroup();\r
 368 \r
 369                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 370                                                                                           .elementAt(i);\r
 371                 groups[i].setStart(sg.getStartRes());\r
 372                 groups[i].setEnd(sg.getEndRes());\r
 373                 groups[i].setName(sg.getName());\r
 374                 if(sg.cs!=null)\r
 375                 {\r
 376                   if (sg.cs.conservationApplied())\r
 377                   {\r
 378                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 379 \r
 380                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 381                     {\r
 382                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 383                           userColours,\r
 384                           jms));\r
 385                     }\r
 386                     else\r
 387                     {\r
 388                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 389                           cs));\r
 390                     }\r
 391                   }\r
 392                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
 393                   {\r
 394                     groups[i].setColour(\r
 395                         ColourSchemeProperty.getColourName(\r
 396                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
 397                   }\r
 398                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 399                   {\r
 400                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 401                         jms));\r
 402                   }\r
 403                   else\r
 404                   {\r
 405                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 406                         sg.cs));\r
 407                   }\r
 408 \r
 409                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 410                 }\r
 411 \r
 412                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 413                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 414                 groups[i].setDisplayText(sg.getDisplayText());\r
 415                 groups[i].setColourText(sg.getColourText());\r
 416 \r
 417                 for (int s = 0; s < sg.getSize(); s++)\r
 418                 {\r
 419                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 420                     int index = seqids.indexOf(seq);\r
 421                     groups[i].addSeq(index);\r
 422                 }\r
 423             }\r
 424 \r
 425             jms.setJGroup(groups);\r
 426         }\r
 427 \r
 428 \r
 429         ///////////SAVE VIEWPORT\r
 430         Viewport view = new Viewport();\r
 431         view.setTitle(af.getTitle());\r
 432         view.setXpos(af.getX());\r
 433         view.setYpos(af.getY());\r
 434         view.setWidth(af.getWidth());\r
 435         view.setHeight(af.getHeight());\r
 436         view.setStartRes(av.startRes);\r
 437         view.setStartSeq(av.startSeq);\r
 438 \r
 439         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 440         {\r
 441             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 442                     userColours, jms));\r
 443         }\r
 444         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)\r
 445         {\r
 446            jalview.schemes.AnnotationColourGradient acg\r
 447               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();\r
 448 \r
 449             AnnotationColours ac = new AnnotationColours();\r
 450             ac.setAboveThreshold(acg.getAboveThreshold());\r
 451             ac.setThreshold(acg.getAnnotationThreshold());\r
 452             ac.setAnnotation(acg.getAnnotation());\r
 453             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)\r
 454               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),\r
 455                     userColours, jms));\r
 456             else\r
 457               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));\r
 458 \r
 459             ac.setMaxColour(acg.getMaxColour().getRGB());\r
 460             ac.setMinColour(acg.getMinColour().getRGB());\r
 461             view.setAnnotationColours(ac);\r
 462             view.setBgColour("AnnotationColourGradient");\r
 463         }\r
 464         else\r
 465         {\r
 466             view.setBgColour(ColourSchemeProperty.getColourName(\r
 467                     av.getGlobalColourScheme()));\r
 468         }\r
 469 \r
 470         ColourSchemeI cs = av.getGlobalColourScheme();\r
 471 \r
 472         if(cs!=null)\r
 473         {\r
 474           if (cs.conservationApplied())\r
 475           {\r
 476             view.setConsThreshold(cs.getConservationInc());\r
 477             if (cs instanceof jalview.schemes.UserColourScheme)\r
 478               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 479           }\r
 480 \r
 481           if (cs instanceof ResidueColourScheme)\r
 482           {\r
 483             view.setPidThreshold(cs.getThreshold());\r
 484           }\r
 485         }\r
 486 \r
 487         view.setConservationSelected(av.getConservationSelected());\r
 488         view.setPidSelected(av.getAbovePIDThreshold());\r
 489         view.setFontName(av.font.getName());\r
 490         view.setFontSize(av.font.getSize());\r
 491         view.setFontStyle(av.font.getStyle());\r
 492         view.setRenderGaps(av.renderGaps);\r
 493         view.setShowAnnotation(av.getShowAnnotation());\r
 494         view.setShowBoxes(av.getShowBoxes());\r
 495         view.setShowColourText(av.getColourText());\r
 496         view.setShowConservation(av.showConservation);\r
 497         view.setShowFullId(av.getShowJVSuffix());\r
 498         view.setShowIdentity(av.showIdentity);\r
 499         view.setShowQuality(av.showQuality);\r
 500         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 501         view.setShowText(av.getShowText());\r
 502         view.setWrapAlignment(av.getWrapAlignment());\r
 503 \r
 504         if(av.featuresDisplayed!=null)\r
 505         {\r
 506           jalview.schemabinding.version2.FeatureSettings fs\r
 507               = new jalview.schemabinding.version2.FeatureSettings();\r
 508 \r
 509           Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();\r
 510           while (e.hasMoreElements())\r
 511           {\r
 512             String type = e.nextElement().toString();\r
 513             Setting setting = new Setting();\r
 514             setting.setType(type);\r
 515             setting.setColour(\r
 516                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()\r
 517                 );\r
 518 \r
 519             setting.setDisplay(\r
 520                 av.featuresDisplayed.containsKey(type)\r
 521                 );\r
 522 \r
 523             fs.addSetting(setting);\r
 524 \r
 525           }\r
 526           jms.setFeatureSettings(fs);\r
 527 \r
 528         }\r
 529 \r
 530         jms.addViewport(view);\r
 531 \r
 532 \r
 533         object.setJalviewModelSequence(jms);\r
 534         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 535 \r
 536         try\r
 537         {\r
 538             if (!fileName.endsWith(".xml"))\r
 539             {\r
 540                 fileName = fileName + ".xml";\r
 541             }\r
 542 \r
 543             JarEntry entry = new JarEntry(fileName);\r
 544             jout.putNextEntry(entry);\r
 545 \r
 546             object.marshal(out);\r
 547         }\r
 548         catch (Exception ex)\r
 549         {\r
 550             ex.printStackTrace();\r
 551         }\r
 552     }\r
 553 \r
 554     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 555         Vector userColours, JalviewModelSequence jms)\r
 556     {\r
 557         String id = null;\r
 558         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 559 \r
 560         if (!userColours.contains(ucs))\r
 561         {\r
 562             userColours.add(ucs);\r
 563 \r
 564             java.awt.Color[] colours = ucs.getColours();\r
 565             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
 566             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
 567 \r
 568             for (int i = 0; i < colours.length; i++)\r
 569             {\r
 570                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
 571                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 572                 jbucs.addColour(col);\r
 573             }\r
 574 \r
 575             id = "ucs" + userColours.indexOf(ucs);\r
 576             uc.setId(id);\r
 577             uc.setUserColourScheme(jbucs);\r
 578             jms.addUserColours(uc);\r
 579         }\r
 580 \r
 581         return id;\r
 582     }\r
 583 \r
 584    jalview.schemes.UserColourScheme GetUserColourScheme(\r
 585         JalviewModelSequence jms, String id)\r
 586     {\r
 587         UserColours[] uc = jms.getUserColours();\r
 588         UserColours colours = null;\r
 589 \r
 590         for (int i = 0; i < uc.length; i++)\r
 591         {\r
 592             if (uc[i].getId().equals(id))\r
 593             {\r
 594                 colours = uc[i];\r
 595 \r
 596                 break;\r
 597             }\r
 598         }\r
 599 \r
 600         int csize = colours.getUserColourScheme().getColourCount();\r
 601         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 602 \r
 603         for (int i = 0; i < csize; i++)\r
 604         {\r
 605             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 606                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 607         }\r
 608 \r
 609         return new jalview.schemes.UserColourScheme(newColours);\r
 610     }\r
 611 \r
 612     /**\r
 613      * DOCUMENT ME!\r
 614      *\r
 615      * @param file DOCUMENT ME!\r
 616      */\r
 617     public AlignFrame LoadJalviewAlign(String file)\r
 618     {\r
 619 \r
 620         jalview.gui.AlignFrame af = null;\r
 621 \r
 622         try\r
 623         {\r
 624             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 625             URL url = null;\r
 626 \r
 627             if (file.startsWith("http://"))\r
 628             {\r
 629                 url = new URL(file);\r
 630             }\r
 631 \r
 632             JarInputStream jin = null;\r
 633             JarEntry jarentry = null;\r
 634             int entryCount = 1;\r
 635 \r
 636             do\r
 637             {\r
 638                 if (url != null)\r
 639                 {\r
 640                     jin = new JarInputStream(url.openStream());\r
 641                 }\r
 642                 else\r
 643                 {\r
 644                     jin = new JarInputStream(new FileInputStream(file));\r
 645                 }\r
 646 \r
 647                 for (int i = 0; i < entryCount; i++)\r
 648                 {\r
 649                     jarentry = jin.getNextJarEntry();\r
 650 \r
 651                   }\r
 652 \r
 653 \r
 654                   class NoDescIDResolver implements IDResolver\r
 655                   {\r
 656                     public Object resolve(String idref)\r
 657                     {\r
 658                       System.out.println(idref+" used");\r
 659                       return null;\r
 660                     }\r
 661                   }\r
 662 \r
 663 \r
 664                 if (jarentry != null)\r
 665                 {\r
 666                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 667                     JalviewModel object = new JalviewModel();\r
 668 \r
 669                     Unmarshaller unmar = new Unmarshaller(object);\r
 670                     unmar.setValidation(false);\r
 671                     object = (JalviewModel) unmar.unmarshal( in );\r
 672 \r
 673                     af = LoadFromObject(object);\r
 674                     entryCount++;\r
 675                 }\r
 676             }\r
 677             while (jarentry != null);\r
 678         }\r
 679         catch(java.net.UnknownHostException ex)\r
 680         {\r
 681           ex.printStackTrace();\r
 682           System.err.println("Couldn't locate Jalview XML file : " +\r
 683               ex + "\n");\r
 684            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 685                                     "Couldn't locate " + file,\r
 686                                     "URL not found",\r
 687                                     JOptionPane.WARNING_MESSAGE);\r
 688 \r
 689         }\r
 690         catch (Exception ex)\r
 691         {\r
 692           //Is Version 1 Jar file?\r
 693           af =  new Jalview2XML_V1().LoadJalviewAlign(file);\r
 694 \r
 695           if(af!=null)\r
 696           {\r
 697             System.out.println("Successfuly loaded archive file");\r
 698             return af;\r
 699           }\r
 700           ex.printStackTrace();\r
 701             System.err.println("Exception whilst loading jalview XML file : " +\r
 702                 ex + "\n");\r
 703              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 704                                       "Error loading  " + file,\r
 705                                       "Error loading Jalview file",\r
 706                                       JOptionPane.WARNING_MESSAGE);\r
 707 \r
 708         }\r
 709 \r
 710         return af;\r
 711     }\r
 712 \r
 713     AlignFrame LoadFromObject(JalviewModel object)\r
 714     {\r
 715         Vector seqids = new Vector();\r
 716         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 717         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 718 \r
 719         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 720 \r
 721         //////////////////////////////////\r
 722         //LOAD SEQUENCES\r
 723         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 724         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 725         for (int i = 0; i < vamsasSeq.length; i++)\r
 726         {\r
 727             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 728                     vamsasSeq[i].getSequence());\r
 729             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 730 \r
 731             jseqs[i].setStart(JSEQ[i].getStart());\r
 732             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 733             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 734             seqids.add(jseqs[i]);\r
 735         }\r
 736 \r
 737         ///SequenceFeatures are added to the DatasetSequence,\r
 738         // so we must create the dataset before loading features\r
 739         /////////////////////////////////\r
 740         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 741         al.setDataset(null);\r
 742         /////////////////////////////////\r
 743 \r
 744         for (int i = 0; i < vamsasSeq.length; i++)\r
 745         {\r
 746           if (JSEQ[i].getFeaturesCount() > 0)\r
 747           {\r
 748             Features[] features = JSEQ[i].getFeatures();\r
 749             for (int f = 0; f < features.length; f++)\r
 750             {\r
 751               jalview.datamodel.SequenceFeature sf\r
 752                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 753                   features[f].getDescription(), features[f].getStatus(),\r
 754                   features[f].getBegin(), features[f].getEnd(),\r
 755                   features[f].getFeatureGroup());\r
 756 \r
 757               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 758             }\r
 759           }\r
 760           if (JSEQ[i].getPdbidsCount() > 0)\r
 761           {\r
 762             Pdbids[] ids = JSEQ[i].getPdbids();\r
 763             for (int p = 0; p < ids.length; p++)\r
 764             {\r
 765               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 766               entry.setId(ids[p].getId());\r
 767               entry.setType(ids[p].getType());\r
 768               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 769             }\r
 770 \r
 771           }\r
 772         }\r
 773 \r
 774          /////////////////////////////////\r
 775         //////////////////////////////////\r
 776         //LOAD ANNOTATIONS\r
 777         if (vamsasSet.getAnnotation() != null)\r
 778         {\r
 779             Annotation[] an = vamsasSet.getAnnotation();\r
 780 \r
 781             for (int i = 0; i < an.length; i++)\r
 782             {\r
 783                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
 784                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
 785 \r
 786                 for (int aa = 0; aa < ae.length; aa++)\r
 787                 {\r
 788                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
 789                             ae[aa].getDescription(),\r
 790                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
 791                             ae[aa].getValue());\r
 792                 }\r
 793 \r
 794                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
 795 \r
 796                 if (an[i].getGraph())\r
 797                 {\r
 798                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 799                       an[i].getDescription(), anot, 0, 0,\r
 800                       an[i].getGraphType());\r
 801 \r
 802                   if (an[i].getThresholdLine() != null)\r
 803                   {\r
 804                     jaa.setThreshold(new jalview.datamodel.GraphLine(\r
 805                                   an[i].getThresholdLine().getValue(),\r
 806                                   an[i].getThresholdLine().getLabel(),\r
 807                                 new java.awt.Color(an[i].getThresholdLine().getColour()))\r
 808                              );\r
 809 \r
 810                   }\r
 811 \r
 812                 }\r
 813                 else\r
 814                 {\r
 815                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 816                             an[i].getDescription(), anot);\r
 817                 }\r
 818 \r
 819                 al.addAnnotation(jaa);\r
 820             }\r
 821         }\r
 822 \r
 823 \r
 824         /////////////////////////////////\r
 825         // LOAD VIEWPORT\r
 826         Viewport[] views = jms.getViewport();\r
 827         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 828 \r
 829         AlignFrame af = new AlignFrame(al);\r
 830 \r
 831 \r
 832         //  af.changeColour() );\r
 833         /////////////////////////\r
 834         //LOAD GROUPS\r
 835         if (jms.getJGroupCount() > 0)\r
 836         {\r
 837             JGroup[] groups = jms.getJGroup();\r
 838 \r
 839             for (int i = 0; i < groups.length; i++)\r
 840             {\r
 841                 ColourSchemeI cs = null;\r
 842 \r
 843                 if (groups[i].getColour() != null)\r
 844                 {\r
 845                     if (groups[i].getColour().startsWith("ucs"))\r
 846                     {\r
 847                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
 848                     }\r
 849                     else\r
 850                     {\r
 851                         cs = ColourSchemeProperty.getColour(al,\r
 852                                 groups[i].getColour());\r
 853                     }\r
 854 \r
 855                     if(cs!=null)\r
 856                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
 857                 }\r
 858 \r
 859                 Vector seqs = new Vector();\r
 860                 int[] ids = groups[i].getSeq();\r
 861 \r
 862                 for (int s = 0; s < ids.length; s++)\r
 863                 {\r
 864                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
 865                             ids[s]));\r
 866                 }\r
 867 \r
 868                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
 869                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
 870                         groups[i].getDisplayText(), groups[i].getColourText(),\r
 871                         groups[i].getStart(), groups[i].getEnd());\r
 872 \r
 873                 sg.setOutlineColour(new java.awt.Color(\r
 874                         groups[i].getOutlineColour()));\r
 875 \r
 876                 if (groups[i].getConsThreshold() != 0)\r
 877                 {\r
 878                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
 879                             ResidueProperties.propHash, 3, sg.sequences, 0,\r
 880                             sg.getWidth() - 1);\r
 881                     c.calculate();\r
 882                     c.verdict(false, 25);\r
 883                     sg.cs.setConservation(c);\r
 884                 }\r
 885 \r
 886                 al.addGroup(sg);\r
 887             }\r
 888         }\r
 889 \r
 890 \r
 891 \r
 892         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 893             view.getHeight());\r
 894         af.viewport.setStartRes(view.getStartRes());\r
 895         af.viewport.setStartSeq(view.getStartSeq());\r
 896         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 897         af.viewport.showConservation = view.getShowConservation();\r
 898         af.viewport.showQuality = view.getShowQuality();\r
 899         af.viewport.showIdentity = view.getShowIdentity();\r
 900         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 901         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 902         af.viewport.setColourText(view.getShowColourText());\r
 903         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 904         af.viewport.setConservationSelected(view.getConservationSelected());\r
 905         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 906 \r
 907         af.viewport.setShowJVSuffix(view.getShowFullId());\r
 908         af.seqLimits.setSelected(view.getShowFullId());\r
 909 \r
 910         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 911                 view.getFontStyle(), view.getFontSize()));\r
 912         af.alignPanel.fontChanged();\r
 913 \r
 914         af.viewport.setRenderGaps(view.getRenderGaps());\r
 915         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 916 \r
 917         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 918         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 919 \r
 920         if (view.getWrapAlignment())\r
 921         {\r
 922             af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 923         }\r
 924         else\r
 925         {\r
 926             af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 927             af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 928             af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 929         }\r
 930 \r
 931         af.viewport.setShowBoxes(view.getShowBoxes());\r
 932         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
 933         af.viewport.setShowText(view.getShowText());\r
 934         af.viewTextMenuItem.setSelected(view.getShowText());\r
 935 \r
 936         ColourSchemeI cs = null;\r
 937 \r
 938         if (view.getBgColour() != null)\r
 939         {\r
 940             if (view.getBgColour().startsWith("ucs"))\r
 941             {\r
 942                 cs = GetUserColourScheme(jms, view.getBgColour());\r
 943             }\r
 944             else if(view.getBgColour().startsWith("Annotation"))\r
 945             {\r
 946               //int find annotation\r
 947               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
 948               {\r
 949                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
 950                     equals(view.getAnnotationColours().getAnnotation()))\r
 951                 {\r
 952                   if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
 953                       getThreshold() == null)\r
 954                   {\r
 955                     af.viewport.alignment.getAlignmentAnnotation()[i].\r
 956                         setThreshold(\r
 957                             new jalview.datamodel.GraphLine(\r
 958                                 view.getAnnotationColours().getThreshold(),\r
 959                                 "Threshold", java.awt.Color.black)\r
 960 \r
 961                         );\r
 962                   }\r
 963 \r
 964 \r
 965                   if (view.getAnnotationColours().getColourScheme().equals(\r
 966                       "None"))\r
 967                   {\r
 968                     cs = new AnnotationColourGradient(\r
 969                         af.viewport.alignment.getAlignmentAnnotation()[i],\r
 970                         new java.awt.Color(view.getAnnotationColours().\r
 971                                            getMinColour()),\r
 972                         new java.awt.Color(view.getAnnotationColours().\r
 973                                            getMaxColour()),\r
 974                         view.getAnnotationColours().getAboveThreshold());\r
 975                   }\r
 976                   else if (view.getAnnotationColours().getColourScheme().\r
 977                            startsWith("ucs"))\r
 978                   {\r
 979                      cs = new AnnotationColourGradient(\r
 980                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
 981                          GetUserColourScheme(jms, view.getAnnotationColours().\r
 982                                                         getColourScheme()),\r
 983                          view.getAnnotationColours().getAboveThreshold()\r
 984                          );\r
 985                    }\r
 986                    else\r
 987                    {\r
 988                      cs = new AnnotationColourGradient(\r
 989                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
 990                          ColourSchemeProperty.getColour(al,\r
 991                          view.getAnnotationColours().getColourScheme()),\r
 992                          view.getAnnotationColours().getAboveThreshold()\r
 993                          );\r
 994                    }\r
 995 \r
 996                   // Also use these settings for all the groups\r
 997                   if (al.getGroups() != null)\r
 998                     for (int g = 0; g < al.getGroups().size(); g++)\r
 999                     {\r
1000                       jalview.datamodel.SequenceGroup sg\r
1001                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
1002 \r
1003                       if(sg.cs == null)\r
1004                         continue;\r
1005 \r
1006 \r
1007                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))\r
1008                       {\r
1009                         sg.cs = new AnnotationColourGradient(\r
1010                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1011                             new java.awt.Color(view.getAnnotationColours().\r
1012                                                getMinColour()),\r
1013                             new java.awt.Color(view.getAnnotationColours().\r
1014                                                getMaxColour()),\r
1015                             view.getAnnotationColours().getAboveThreshold());\r
1016                       }\r
1017                       else*/\r
1018                       {\r
1019                         sg.cs = new AnnotationColourGradient(\r
1020                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1021                             sg.cs,\r
1022                             view.getAnnotationColours().getAboveThreshold()\r
1023                             );\r
1024                       }\r
1025 \r
1026                     }\r
1027 \r
1028 \r
1029                   break;\r
1030                 }\r
1031 \r
1032               }\r
1033             }\r
1034             else\r
1035             {\r
1036                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
1037             }\r
1038 \r
1039             if(cs!=null)\r
1040             {\r
1041               cs.setThreshold(view.getPidThreshold(), true);\r
1042               cs.setConsensus(af.viewport.vconsensus);\r
1043             }\r
1044         }\r
1045 \r
1046         af.setColourSelected(view.getBgColour());\r
1047         af.viewport.setGlobalColourScheme(cs);\r
1048         af.viewport.setColourAppliesToAllGroups(false);\r
1049         af.changeColour(cs);\r
1050         if (view.getConservationSelected() && cs!=null)\r
1051         {\r
1052           cs.setConservationInc(view.getConsThreshold());\r
1053         }\r
1054 \r
1055         af.viewport.setColourAppliesToAllGroups(true);\r
1056 \r
1057         if (view.getShowSequenceFeatures())\r
1058         {\r
1059            af.viewport.showSequenceFeatures = true;\r
1060            af.showSeqFeatures.setSelected(true);\r
1061         }\r
1062 \r
1063         if(jms.getFeatureSettings()!=null)\r
1064         {\r
1065           af.viewport.featuresDisplayed = new Hashtable();\r
1066           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
1067          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
1068          {\r
1069            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
1070 \r
1071            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
1072                new java.awt.Color(setting.getColour()));\r
1073 \r
1074            renderOrder[fs] = setting.getType();\r
1075 \r
1076            if(setting.getDisplay())\r
1077              af.viewport.featuresDisplayed.put(\r
1078                  setting.getType(), new Integer(setting.getColour()));\r
1079          }\r
1080          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
1081         }\r
1082 \r
1083 \r
1084         Desktop.addInternalFrame(af, view.getTitle(),\r
1085              view.getWidth(), view.getHeight());\r
1086 \r
1087         //LOAD TREES\r
1088         ///////////////////////////////////////\r
1089         if (jms.getTreeCount() > 0)\r
1090         {\r
1091             try\r
1092             {\r
1093                 for (int t = 0; t < jms.getTreeCount(); t++)\r
1094                 {\r
1095 \r
1096                     Tree tree = jms.getTree(t);\r
1097 \r
1098                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
1099                                 tree.getNewick()), tree.getTitle(),\r
1100                                 tree.getWidth(), tree.getHeight(),\r
1101                                 tree.getXpos(), tree.getYpos());\r
1102 \r
1103                     tp.fitToWindow.setState(tree.getFitToWindow());\r
1104                     tp.fitToWindow_actionPerformed(null);\r
1105 \r
1106                     if(tree.getFontName()!=null)\r
1107                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
1108                                           tree.getFontStyle(),\r
1109                                           tree.getFontSize()));\r
1110                     else\r
1111                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
1112                                             view.getFontStyle(),\r
1113                                             tree.getFontSize()));\r
1114 \r
1115                     tp.showPlaceholders(tree.getMarkUnlinked());\r
1116                     tp.showBootstrap(tree.getShowBootstrap());\r
1117                     tp.showDistances(tree.getShowDistances());\r
1118 \r
1119                     tp.treeCanvas.threshold = tree.getThreshold();\r
1120 \r
1121                     if (tree.getCurrentTree())\r
1122                       af.viewport.setCurrentTree(tp.getTree());\r
1123                 }\r
1124 \r
1125             }\r
1126             catch (Exception ex)\r
1127             {\r
1128                 ex.printStackTrace();\r
1129             }\r
1130 \r
1131         }\r
1132 \r
1133         return af;\r
1134     }\r
1135 }\r
1136 \r