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         jalview.datamodel.AlignmentI jalhidden = null;\r
 172 \r
 173         if(av.hasHiddenRows)\r
 174         {\r
 175           jalhidden = jal;\r
 176           jal = jal.getHiddenSequences().getFullAlignment();\r
 177         }\r
 178 \r
 179 \r
 180         SequenceSet vamsasSet = new SequenceSet();\r
 181         Sequence vamsasSeq;\r
 182         JalviewModelSequence jms = new JalviewModelSequence();\r
 183 \r
 184         vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 185 \r
 186         JSeq jseq;\r
 187         Vector pdbfiles = null;\r
 188 \r
 189         //SAVE SEQUENCES\r
 190         int id = 0;\r
 191         for (int i = 0; i < jal.getHeight(); i++)\r
 192         {\r
 193             seqids.add(jal.getSequenceAt(i));\r
 194             vamsasSeq = new Sequence();\r
 195             vamsasSeq.setId(id + "");\r
 196             vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 197             vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 198             vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
 199 \r
 200             if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)\r
 201             {\r
 202               jalview.datamodel.DBRefEntry [] dbrefs =\r
 203                   jal.getSequenceAt(i).getDatasetSequence().getDBRef();\r
 204 \r
 205               for(int d=0; d<dbrefs.length; d++)\r
 206               {\r
 207                 DBRef dbref = new DBRef();\r
 208                 dbref.setSource( dbrefs[d].getSource() );\r
 209                 dbref.setVersion( dbrefs[d].getVersion());\r
 210                 dbref.setAccessionId(dbrefs[d].getAccessionId());\r
 211                 vamsasSeq.addDBRef(dbref);\r
 212               }\r
 213             }\r
 214 \r
 215             jseq = new JSeq();\r
 216             jseq.setStart(jal.getSequenceAt(i).getStart());\r
 217             jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 218             jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 219 \r
 220             jseq.setId(id);\r
 221 \r
 222             if (av.hasHiddenRows)\r
 223             {\r
 224               jseq.setHidden(jalhidden.getHiddenSequences().isHidden(\r
 225                   jal.getSequenceAt(i)));\r
 226 \r
 227               if(jal.getSequenceAt(i).getHiddenSequences()!=null)\r
 228               {\r
 229                 jalview.datamodel.SequenceI [] reps =\r
 230                     jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);\r
 231 \r
 232                 for(int h=0; h<reps.length; h++)\r
 233                 {\r
 234                   jseq.addHiddenSequences(\r
 235                       jal.findIndex(reps[h])\r
 236                       );\r
 237                 }\r
 238               }\r
 239             }\r
 240 \r
 241 \r
 242             if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
 243             {\r
 244               jalview.datamodel.SequenceFeature[] sf\r
 245                   = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
 246               int index = 0;\r
 247               while(index < sf.length)\r
 248               {\r
 249                 Features features = new Features();\r
 250 \r
 251                 features.setBegin(sf[index].getBegin());\r
 252                 features.setEnd(sf[index].getEnd());\r
 253                 features.setDescription(sf[index].getDescription());\r
 254                 features.setType(sf[index].getType());\r
 255                 features.setFeatureGroup(sf[index].getFeatureGroup());\r
 256                 features.setScore(sf[index].getScore());\r
 257                 if(sf[index].links!=null)\r
 258                 {\r
 259                   for(int l=0; l<sf[index].links.size(); l++)\r
 260                   {\r
 261                     OtherData keyValue = new OtherData();\r
 262                     keyValue.setKey("LINK_"+l);\r
 263                     keyValue.setValue(sf[index].links.elementAt(l).toString());\r
 264                     features.addOtherData(keyValue);\r
 265                   }\r
 266                 }\r
 267                 if(sf[index].otherDetails!=null)\r
 268                 {\r
 269                   String key;\r
 270                   Enumeration keys = sf[index].otherDetails.keys();\r
 271                   while(keys.hasMoreElements())\r
 272                   {\r
 273                     key = keys.nextElement().toString();\r
 274                     OtherData keyValue = new OtherData();\r
 275                     keyValue.setKey( key );\r
 276                     keyValue.setValue(\r
 277                         sf[index].otherDetails.get(key).toString());\r
 278                     features.addOtherData(keyValue);\r
 279                   }\r
 280                 }\r
 281 \r
 282                 jseq.addFeatures(features);\r
 283                 index ++;\r
 284               }\r
 285             }\r
 286 \r
 287             if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
 288             {\r
 289               Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
 290               while(en.hasMoreElements())\r
 291               {\r
 292                 Pdbids pdb = new Pdbids();\r
 293                 jalview.datamodel.PDBEntry entry\r
 294                    = (jalview.datamodel.PDBEntry)en.nextElement();\r
 295 \r
 296                 pdb.setId(entry.getId());\r
 297                 pdb.setType(entry.getType());\r
 298 \r
 299                 if(entry.getFile()!=null)\r
 300                 {\r
 301                   if(pdbfiles==null)\r
 302                     pdbfiles = new Vector();\r
 303 \r
 304 \r
 305                   if(!pdbfiles.contains(entry.getId()))\r
 306                   {\r
 307                     pdbfiles.addElement(entry.getId());\r
 308                     try\r
 309                     {\r
 310                       File file = new File(entry.getFile());\r
 311                       if(file.exists())\r
 312                       {\r
 313                         byte[] data = new byte[ (int) file.length()];\r
 314                         jout.putNextEntry(new JarEntry(entry.getId()));\r
 315                         DataInputStream dis = new DataInputStream(new\r
 316                             FileInputStream(file));\r
 317                         dis.readFully(data);\r
 318 \r
 319                         DataOutputStream dout = new DataOutputStream(jout);\r
 320                         dout.write(data, 0, data.length);\r
 321                         jout.closeEntry();\r
 322                       }\r
 323                     }\r
 324                     catch (Exception ex)\r
 325                     {\r
 326                       ex.printStackTrace();\r
 327                     }\r
 328                   }\r
 329                 }\r
 330 \r
 331 \r
 332                 if(entry.getProperty()!=null)\r
 333                 {\r
 334                   PdbentryItem item = new PdbentryItem();\r
 335                   Hashtable properties = entry.getProperty();\r
 336                   Enumeration en2 = properties.keys();\r
 337                   while(en2.hasMoreElements())\r
 338                   {\r
 339                     Property prop = new Property();\r
 340                     String key = en2.nextElement().toString();\r
 341                     prop.setName(key);\r
 342                     prop.setValue( properties.get(key).toString() );\r
 343                     item.addProperty(prop);\r
 344                   }\r
 345                   pdb.addPdbentryItem(item);\r
 346                 }\r
 347 \r
 348                 jseq.addPdbids(pdb);\r
 349               }\r
 350             }\r
 351 \r
 352             jms.addJSeq(jseq);\r
 353             vamsasSet.addSequence(vamsasSeq);\r
 354             id++;\r
 355         }\r
 356 \r
 357         //SAVE TREES\r
 358         ///////////////////////////////////\r
 359         if (af.viewport.currentTree != null)\r
 360         {\r
 361           // FIND ANY ASSOCIATED TREES\r
 362           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
 363           if (Desktop.desktop != null)\r
 364           {\r
 365             JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 366 \r
 367             for (int t = 0; t < frames.length; t++)\r
 368             {\r
 369               if (frames[t] instanceof TreePanel)\r
 370               {\r
 371                 TreePanel tp = (TreePanel) frames[t];\r
 372 \r
 373                 if (tp.treeCanvas.av.alignment == jal)\r
 374                 {\r
 375                   Tree tree = new Tree();\r
 376                   tree.setTitle(tp.getTitle());\r
 377                   tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
 378                   tree.setNewick(tp.getTree().toString());\r
 379                   tree.setThreshold(tp.treeCanvas.threshold);\r
 380 \r
 381                   tree.setFitToWindow(tp.fitToWindow.getState());\r
 382                   tree.setFontName(tp.getTreeFont().getName());\r
 383                   tree.setFontSize(tp.getTreeFont().getSize());\r
 384                   tree.setFontStyle(tp.getTreeFont().getStyle());\r
 385                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
 386 \r
 387                   tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
 388                   tree.setShowDistances(tp.distanceMenu.getState());\r
 389 \r
 390                   tree.setHeight(tp.getHeight());\r
 391                   tree.setWidth(tp.getWidth());\r
 392                   tree.setXpos(tp.getX());\r
 393                   tree.setYpos(tp.getY());\r
 394 \r
 395                   jms.addTree(tree);\r
 396                 }\r
 397               }\r
 398             }\r
 399           }\r
 400         }\r
 401 \r
 402         //SAVE ANNOTATIONS\r
 403         if (jal.getAlignmentAnnotation() != null)\r
 404         {\r
 405             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 406 \r
 407             for (int i = 0; i < aa.length; i++)\r
 408             {\r
 409                 Annotation an = new Annotation();\r
 410 \r
 411                 if (aa[i].label.equals("Quality") ||\r
 412                         aa[i].label.equals("Conservation") ||\r
 413                         aa[i].label.equals("Consensus"))\r
 414                 {\r
 415                     an.setLabel(aa[i].label);\r
 416                     an.setGraph(true);\r
 417                     vamsasSet.addAnnotation(an);\r
 418                     continue;\r
 419                 }\r
 420 \r
 421 \r
 422                 an.setDescription(aa[i].description);\r
 423 \r
 424                 if(aa[i].sequenceRef!=null)\r
 425                  {\r
 426                    an.setSequenceRef(aa[i].sequenceRef.getName());\r
 427                  }\r
 428 \r
 429                 if(aa[i].graph>0)\r
 430                 {\r
 431                   an.setGraph(true);\r
 432                   an.setGraphType(aa[i].graph);\r
 433                   an.setGraphGroup(aa[i].graphGroup);\r
 434                   if(aa[i].getThreshold()!=null)\r
 435                   {\r
 436                     ThresholdLine line = new ThresholdLine();\r
 437                     line.setLabel(aa[i].getThreshold().label);\r
 438                     line.setValue(aa[i].getThreshold().value);\r
 439                     line.setColour(aa[i].getThreshold().colour.getRGB());\r
 440                     an.setThresholdLine(line);\r
 441                   }\r
 442                 }\r
 443                 else\r
 444                   an.setGraph(false);\r
 445 \r
 446                 an.setLabel(aa[i].label);\r
 447 \r
 448                 AnnotationElement ae;\r
 449 \r
 450                 for (int a = 0; a < aa[i].annotations.length; a++)\r
 451                 {\r
 452                     if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
 453                     {\r
 454                         continue;\r
 455                     }\r
 456 \r
 457                     ae = new AnnotationElement();\r
 458                     ae.setDescription(aa[i].annotations[a].description);\r
 459                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 460                     ae.setValue(aa[i].annotations[a].value);\r
 461                     ae.setPosition(a);\r
 462                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 463                         "");\r
 464 \r
 465                     if(aa[i].annotations[a].colour!=java.awt.Color.black)\r
 466                       ae.setColour(aa[i].annotations[a].colour.getRGB());\r
 467 \r
 468                     an.addAnnotationElement(ae);\r
 469                 }\r
 470 \r
 471                 vamsasSet.addAnnotation(an);\r
 472             }\r
 473         }\r
 474 \r
 475         //SAVE GROUPS\r
 476         if (jal.getGroups() != null)\r
 477         {\r
 478             JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 479 \r
 480             for (int i = 0; i < groups.length; i++)\r
 481             {\r
 482                 groups[i] = new JGroup();\r
 483 \r
 484                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
 485                                                                                           .elementAt(i);\r
 486                 groups[i].setStart(sg.getStartRes());\r
 487                 groups[i].setEnd(sg.getEndRes());\r
 488                 groups[i].setName(sg.getName());\r
 489                 if(sg.cs!=null)\r
 490                 {\r
 491                   if (sg.cs.conservationApplied())\r
 492                   {\r
 493                     groups[i].setConsThreshold(sg.cs.getConservationInc());\r
 494 \r
 495                     if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 496                     {\r
 497                       groups[i].setColour(SetUserColourScheme(sg.cs,\r
 498                           userColours,\r
 499                           jms));\r
 500                     }\r
 501                     else\r
 502                     {\r
 503                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
 504                           cs));\r
 505                     }\r
 506                   }\r
 507                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
 508                   {\r
 509                     groups[i].setColour(\r
 510                         ColourSchemeProperty.getColourName(\r
 511                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
 512                   }\r
 513                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 514                   {\r
 515                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 516                         jms));\r
 517                   }\r
 518                   else\r
 519                   {\r
 520                     groups[i].setColour(ColourSchemeProperty.getColourName(\r
 521                         sg.cs));\r
 522                   }\r
 523 \r
 524                   groups[i].setPidThreshold(sg.cs.getThreshold());\r
 525                 }\r
 526 \r
 527                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 528                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 529                 groups[i].setDisplayText(sg.getDisplayText());\r
 530                 groups[i].setColourText(sg.getColourText());\r
 531 \r
 532                 for (int s = 0; s < sg.getSize(false); s++)\r
 533                 {\r
 534                     jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
 535                     int index = seqids.indexOf(seq);\r
 536                     groups[i].addSeq(index);\r
 537                 }\r
 538             }\r
 539 \r
 540             jms.setJGroup(groups);\r
 541         }\r
 542 \r
 543 \r
 544         ///////////SAVE VIEWPORT\r
 545         Viewport view = new Viewport();\r
 546         view.setTitle(af.getTitle());\r
 547         view.setXpos(af.getX());\r
 548         view.setYpos(af.getY());\r
 549         view.setWidth(af.getWidth());\r
 550         view.setHeight(af.getHeight());\r
 551         view.setStartRes(av.startRes);\r
 552         view.setStartSeq(av.startSeq);\r
 553 \r
 554         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 555         {\r
 556             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 557                     userColours, jms));\r
 558         }\r
 559         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)\r
 560         {\r
 561            jalview.schemes.AnnotationColourGradient acg\r
 562               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();\r
 563 \r
 564             AnnotationColours ac = new AnnotationColours();\r
 565             ac.setAboveThreshold(acg.getAboveThreshold());\r
 566             ac.setThreshold(acg.getAnnotationThreshold());\r
 567             ac.setAnnotation(acg.getAnnotation());\r
 568             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)\r
 569               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),\r
 570                     userColours, jms));\r
 571             else\r
 572               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));\r
 573 \r
 574             ac.setMaxColour(acg.getMaxColour().getRGB());\r
 575             ac.setMinColour(acg.getMinColour().getRGB());\r
 576             view.setAnnotationColours(ac);\r
 577             view.setBgColour("AnnotationColourGradient");\r
 578         }\r
 579         else\r
 580         {\r
 581             view.setBgColour(ColourSchemeProperty.getColourName(\r
 582                     av.getGlobalColourScheme()));\r
 583         }\r
 584 \r
 585         ColourSchemeI cs = av.getGlobalColourScheme();\r
 586 \r
 587         if(cs!=null)\r
 588         {\r
 589           if (cs.conservationApplied())\r
 590           {\r
 591             view.setConsThreshold(cs.getConservationInc());\r
 592             if (cs instanceof jalview.schemes.UserColourScheme)\r
 593               view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
 594           }\r
 595 \r
 596           if (cs instanceof ResidueColourScheme)\r
 597           {\r
 598             view.setPidThreshold(cs.getThreshold());\r
 599           }\r
 600         }\r
 601 \r
 602         view.setConservationSelected(av.getConservationSelected());\r
 603         view.setPidSelected(av.getAbovePIDThreshold());\r
 604         view.setFontName(av.font.getName());\r
 605         view.setFontSize(av.font.getSize());\r
 606         view.setFontStyle(av.font.getStyle());\r
 607         view.setRenderGaps(av.renderGaps);\r
 608         view.setShowAnnotation(av.getShowAnnotation());\r
 609         view.setShowBoxes(av.getShowBoxes());\r
 610         view.setShowColourText(av.getColourText());\r
 611         view.setShowConservation(av.showConservation);\r
 612         view.setShowFullId(av.getShowJVSuffix());\r
 613         view.setShowIdentity(av.showIdentity);\r
 614         view.setShowQuality(av.showQuality);\r
 615         view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 616         view.setShowText(av.getShowText());\r
 617         view.setWrapAlignment(av.getWrapAlignment());\r
 618 \r
 619         if(av.featuresDisplayed!=null)\r
 620         {\r
 621           jalview.schemabinding.version2.FeatureSettings fs\r
 622               = new jalview.schemabinding.version2.FeatureSettings();\r
 623 \r
 624           String [] renderOrder =\r
 625               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
 626           for(int ro=0; ro<renderOrder.length; ro++)\r
 627           {\r
 628             Setting setting = new Setting();\r
 629             setting.setType(renderOrder[ro]);\r
 630             setting.setColour(\r
 631                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()\r
 632                 );\r
 633 \r
 634             setting.setDisplay(\r
 635                 av.featuresDisplayed.containsKey(renderOrder[ro])\r
 636                 );\r
 637 \r
 638             fs.addSetting(setting);\r
 639 \r
 640           }\r
 641           jms.setFeatureSettings(fs);\r
 642 \r
 643         }\r
 644 \r
 645         if(av.hasHiddenColumns)\r
 646         {\r
 647           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)\r
 648           {\r
 649             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);\r
 650             HiddenColumns hc = new HiddenColumns();\r
 651             hc.setStart(region[0]);\r
 652             hc.setEnd(region[1]);\r
 653             view.addHiddenColumns(hc);\r
 654           }\r
 655         }\r
 656 \r
 657         jms.addViewport(view);\r
 658 \r
 659 \r
 660         object.setJalviewModelSequence(jms);\r
 661         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 662 \r
 663         try\r
 664         {\r
 665             if (!fileName.endsWith(".xml"))\r
 666             {\r
 667                 fileName = fileName + ".xml";\r
 668             }\r
 669 \r
 670             JarEntry entry = new JarEntry(fileName);\r
 671             jout.putNextEntry(entry);\r
 672 \r
 673             object.marshal(out);\r
 674         }\r
 675         catch (Exception ex)\r
 676         {\r
 677             ex.printStackTrace();\r
 678         }\r
 679     }\r
 680 \r
 681     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 682         Vector userColours, JalviewModelSequence jms)\r
 683     {\r
 684         String id = null;\r
 685         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 686 \r
 687         if (!userColours.contains(ucs))\r
 688         {\r
 689             userColours.add(ucs);\r
 690 \r
 691             java.awt.Color[] colours = ucs.getColours();\r
 692             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
 693             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
 694 \r
 695             for (int i = 0; i < colours.length; i++)\r
 696             {\r
 697                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
 698                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 699                 jbucs.addColour(col);\r
 700             }\r
 701 \r
 702             id = "ucs" + userColours.indexOf(ucs);\r
 703             uc.setId(id);\r
 704             uc.setUserColourScheme(jbucs);\r
 705             jms.addUserColours(uc);\r
 706         }\r
 707 \r
 708         return id;\r
 709     }\r
 710 \r
 711    jalview.schemes.UserColourScheme GetUserColourScheme(\r
 712         JalviewModelSequence jms, String id)\r
 713     {\r
 714         UserColours[] uc = jms.getUserColours();\r
 715         UserColours colours = null;\r
 716 \r
 717         for (int i = 0; i < uc.length; i++)\r
 718         {\r
 719             if (uc[i].getId().equals(id))\r
 720             {\r
 721                 colours = uc[i];\r
 722 \r
 723                 break;\r
 724             }\r
 725         }\r
 726 \r
 727         int csize = colours.getUserColourScheme().getColourCount();\r
 728         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 729 \r
 730         for (int i = 0; i < csize; i++)\r
 731         {\r
 732             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 733                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 734         }\r
 735 \r
 736         return new jalview.schemes.UserColourScheme(newColours);\r
 737     }\r
 738 \r
 739     /**\r
 740      * DOCUMENT ME!\r
 741      *\r
 742      * @param file DOCUMENT ME!\r
 743      */\r
 744     public AlignFrame LoadJalviewAlign(String file)\r
 745     {\r
 746         jalview.gui.AlignFrame af = null;\r
 747         try\r
 748         {\r
 749             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 750             URL url = null;\r
 751 \r
 752             if (file.startsWith("http://"))\r
 753             {\r
 754                 url = new URL(file);\r
 755             }\r
 756 \r
 757             JarInputStream jin = null;\r
 758             JarEntry jarentry = null;\r
 759             int entryCount = 1;\r
 760 \r
 761             do\r
 762             {\r
 763                 if (url != null)\r
 764                 {\r
 765                     jin = new JarInputStream(url.openStream());\r
 766                 }\r
 767                 else\r
 768                 {\r
 769                     jin = new JarInputStream(new FileInputStream(file));\r
 770                 }\r
 771 \r
 772                 for (int i = 0; i < entryCount; i++)\r
 773                 {\r
 774                     jarentry = jin.getNextJarEntry();\r
 775                 }\r
 776 \r
 777                 if (jarentry != null && jarentry.getName().endsWith(".xml"))\r
 778                 {\r
 779                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 780                     JalviewModel object = new JalviewModel();\r
 781 \r
 782                     Unmarshaller unmar = new Unmarshaller(object);\r
 783                     unmar.setValidation(false);\r
 784                     object = (JalviewModel) unmar.unmarshal( in );\r
 785 \r
 786                     af = LoadFromObject(object, file);\r
 787                     entryCount++;\r
 788                 }\r
 789                 else if (jarentry != null)\r
 790                 {\r
 791                   //Some other file here.\r
 792                   entryCount++;\r
 793                 }\r
 794             }\r
 795             while (jarentry != null);\r
 796         }\r
 797         catch(java.net.UnknownHostException ex)\r
 798         {\r
 799           ex.printStackTrace();\r
 800           System.err.println("Couldn't locate Jalview XML file : " +\r
 801               ex + "\n");\r
 802            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 803                                     "Couldn't locate " + file,\r
 804                                     "URL not found",\r
 805                                     JOptionPane.WARNING_MESSAGE);\r
 806 \r
 807         }\r
 808         catch (Exception ex)\r
 809         {\r
 810           //Is Version 1 Jar file?\r
 811           af =  new Jalview2XML_V1().LoadJalviewAlign(file);\r
 812 \r
 813           if(af!=null)\r
 814           {\r
 815             System.out.println("Successfully loaded archive file");\r
 816             return af;\r
 817           }\r
 818           ex.printStackTrace();\r
 819             System.err.println("Exception whilst loading jalview XML file : " +\r
 820                 ex + "\n");\r
 821              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 822                                       "Error loading  " + file,\r
 823                                       "Error loading Jalview file",\r
 824                                       JOptionPane.WARNING_MESSAGE);\r
 825 \r
 826         }\r
 827 \r
 828         return af;\r
 829     }\r
 830 \r
 831     String loadPDBFile(String file, String pdbId)\r
 832     {\r
 833       System.out.println("load file "+file);\r
 834       try\r
 835       {\r
 836         JarInputStream jin = null;\r
 837 \r
 838         if (file.startsWith("http://"))\r
 839         {\r
 840           jin = new JarInputStream(new URL(file).openStream());\r
 841         }\r
 842         else\r
 843         {\r
 844           jin = new JarInputStream(new FileInputStream(file));\r
 845         }\r
 846 \r
 847         JarEntry entry = null;\r
 848         do\r
 849         {\r
 850           entry = jin.getNextJarEntry();\r
 851         }\r
 852         while (!entry.getName().equals(pdbId));\r
 853 \r
 854         BufferedReader in = new BufferedReader(new InputStreamReader(jin));\r
 855         File outFile = File.createTempFile("jalview_pdb", ".txt");\r
 856         outFile.deleteOnExit();\r
 857         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
 858         String data;\r
 859 \r
 860         while ( (data = in.readLine()) != null)\r
 861         {\r
 862           out.println(data);\r
 863         }\r
 864         out.close();\r
 865         return outFile.getAbsolutePath();\r
 866 \r
 867       }\r
 868       catch (Exception ex)\r
 869       {\r
 870         ex.printStackTrace();\r
 871       }\r
 872 \r
 873       return null;\r
 874     }\r
 875 \r
 876 \r
 877     AlignFrame LoadFromObject(JalviewModel object, String file)\r
 878     {\r
 879         Vector seqids = new Vector();\r
 880         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 881         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 882 \r
 883         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 884 \r
 885         //////////////////////////////////\r
 886         //LOAD SEQUENCES\r
 887         Vector hiddenSeqs = null;\r
 888         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 889         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 890         for (int i = 0; i < vamsasSeq.length; i++)\r
 891         {\r
 892             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 893                     vamsasSeq[i].getSequence());\r
 894             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 895 \r
 896             if(JSEQ[i].getHidden())\r
 897             {\r
 898               if(hiddenSeqs == null)\r
 899                 hiddenSeqs = new Vector();\r
 900               hiddenSeqs.addElement(jseqs[i]);\r
 901             }\r
 902             jseqs[i].setStart(JSEQ[i].getStart());\r
 903             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 904             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 905             seqids.add(jseqs[i]);\r
 906         }\r
 907 \r
 908         ///SequenceFeatures are added to the DatasetSequence,\r
 909         // so we must create the dataset before loading features\r
 910         /////////////////////////////////\r
 911         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 912         al.setDataset(null);\r
 913         /////////////////////////////////\r
 914 \r
 915 \r
 916         Hashtable pdbloaded = new Hashtable();\r
 917         for (int i = 0; i < vamsasSeq.length; i++)\r
 918         {\r
 919           if (JSEQ[i].getFeaturesCount() > 0)\r
 920           {\r
 921             Features[] features = JSEQ[i].getFeatures();\r
 922             for (int f = 0; f < features.length; f++)\r
 923             {\r
 924               jalview.datamodel.SequenceFeature sf\r
 925                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 926                   features[f].getDescription(), features[f].getStatus(),\r
 927                   features[f].getBegin(), features[f].getEnd(),\r
 928                   features[f].getFeatureGroup());\r
 929 \r
 930               sf.setScore(features[f].getScore());\r
 931               for(int od=0; od<features[f].getOtherDataCount(); od++)\r
 932               {\r
 933                 OtherData keyValue = features[f].getOtherData(od);\r
 934                 if(keyValue.getKey().startsWith("LINK"))\r
 935                   sf.addLink(keyValue.getValue());\r
 936                 else\r
 937                   sf.setValue(keyValue.getKey(), keyValue.getValue());\r
 938 \r
 939               }\r
 940 \r
 941               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 942             }\r
 943           }\r
 944           if (JSEQ[i].getPdbidsCount() > 0)\r
 945           {\r
 946             Pdbids[] ids = JSEQ[i].getPdbids();\r
 947             for (int p = 0; p < ids.length; p++)\r
 948             {\r
 949               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 950               entry.setId(ids[p].getId());\r
 951               entry.setType(ids[p].getType());\r
 952               if (ids[p].getFile() != null)\r
 953               {\r
 954                 if (!pdbloaded.containsKey(ids[p].getFile()))\r
 955                 {\r
 956                   String tmppdb = loadPDBFile(file, ids[p].getId());\r
 957                   entry.setFile(tmppdb);\r
 958                   pdbloaded.put(ids[p].getId(), tmppdb);\r
 959                 }\r
 960                 else\r
 961                   entry.setFile(pdbloaded.get(ids[p].getId()).toString());\r
 962               }\r
 963 \r
 964               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 965             }\r
 966           }\r
 967           if(vamsasSeq[i].getDBRefCount()>0)\r
 968           {\r
 969             for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)\r
 970             {\r
 971               jalview.datamodel.DBRefEntry entry =\r
 972                   new jalview.datamodel.DBRefEntry(\r
 973                       vamsasSeq[i].getDBRef(d).getSource(),\r
 974                       vamsasSeq[i].getDBRef(d).getVersion(),\r
 975                       vamsasSeq[i].getDBRef(d).getAccessionId()\r
 976                       );\r
 977               al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);\r
 978             }\r
 979 \r
 980           }\r
 981         }\r
 982 \r
 983 \r
 984 \r
 985          /////////////////////////////////\r
 986         //////////////////////////////////\r
 987         //LOAD ANNOTATIONS\r
 988         boolean hideQuality = true,\r
 989             hideConservation = true,\r
 990             hideConsensus = true;\r
 991 \r
 992         if (vamsasSet.getAnnotation() != null)\r
 993         {\r
 994             Annotation[] an = vamsasSet.getAnnotation();\r
 995 \r
 996             for (int i = 0; i < an.length; i++)\r
 997             {\r
 998                if (an[i].getLabel().equals("Quality"))\r
 999                 {\r
1000                  hideQuality = false;\r
1001                  continue;\r
1002                 }\r
1003                else if(an[i].getLabel().equals("Conservation"))\r
1004                {\r
1005                  hideConservation = false;\r
1006                  continue;\r
1007                }\r
1008                else if(an[i].getLabel().equals("Consensus"))\r
1009                {\r
1010                  hideConsensus = false;\r
1011                  continue;\r
1012                }\r
1013 \r
1014                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
1015                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
1016 \r
1017                 for (int aa = 0; aa < ae.length; aa++)\r
1018                 {\r
1019                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
1020                             ae[aa].getDescription(),\r
1021                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
1022                             ae[aa].getValue());\r
1023                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );\r
1024                 }\r
1025 \r
1026                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
1027 \r
1028                 if (an[i].getGraph())\r
1029                 {\r
1030                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
1031                       an[i].getDescription(), anot, 0, 0,\r
1032                       an[i].getGraphType());\r
1033 \r
1034                   jaa.graphGroup = an[i].getGraphGroup();\r
1035 \r
1036                   if (an[i].getThresholdLine() != null)\r
1037                   {\r
1038                     jaa.setThreshold(new jalview.datamodel.GraphLine(\r
1039                                   an[i].getThresholdLine().getValue(),\r
1040                                   an[i].getThresholdLine().getLabel(),\r
1041                                 new java.awt.Color(an[i].getThresholdLine().getColour()))\r
1042                              );\r
1043 \r
1044                   }\r
1045 \r
1046                 }\r
1047                 else\r
1048                 {\r
1049                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
1050                             an[i].getDescription(), anot);\r
1051                 }\r
1052 \r
1053                 if(an[i].getSequenceRef()!=null)\r
1054                 {\r
1055                   jaa.createSequenceMapping(\r
1056                       al.findName(an[i].getSequenceRef()), 1\r
1057                       );\r
1058                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);\r
1059                 }\r
1060 \r
1061                 al.addAnnotation(jaa);\r
1062             }\r
1063         }\r
1064 \r
1065 \r
1066         //  af.changeColour() );\r
1067         /////////////////////////\r
1068         //LOAD GROUPS\r
1069         if (jms.getJGroupCount() > 0)\r
1070         {\r
1071             JGroup[] groups = jms.getJGroup();\r
1072 \r
1073             for (int i = 0; i < groups.length; i++)\r
1074             {\r
1075                 ColourSchemeI cs = null;\r
1076 \r
1077                 if (groups[i].getColour() != null)\r
1078                 {\r
1079                     if (groups[i].getColour().startsWith("ucs"))\r
1080                     {\r
1081                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
1082                     }\r
1083                     else\r
1084                     {\r
1085                         cs = ColourSchemeProperty.getColour(al,\r
1086                                 groups[i].getColour());\r
1087                     }\r
1088 \r
1089                     if(cs!=null)\r
1090                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
1091                 }\r
1092 \r
1093                 Vector seqs = new Vector();\r
1094                 int[] ids = groups[i].getSeq();\r
1095 \r
1096                 for (int s = 0; s < ids.length; s++)\r
1097                 {\r
1098                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
1099                             ids[s]));\r
1100                 }\r
1101 \r
1102                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
1103                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
1104                         groups[i].getDisplayText(), groups[i].getColourText(),\r
1105                         groups[i].getStart(), groups[i].getEnd());\r
1106 \r
1107                 sg.setOutlineColour(new java.awt.Color(\r
1108                         groups[i].getOutlineColour()));\r
1109 \r
1110                 if (groups[i].getConsThreshold() != 0)\r
1111                 {\r
1112                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
1113                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
1114                             sg.getWidth() - 1);\r
1115                     c.calculate();\r
1116                     c.verdict(false, 25);\r
1117                     sg.cs.setConservation(c);\r
1118                 }\r
1119 \r
1120                 al.addGroup(sg);\r
1121             }\r
1122         }\r
1123 \r
1124 \r
1125         /////////////////////////////////\r
1126         // LOAD VIEWPORT\r
1127         Viewport[] views = jms.getViewport();\r
1128         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
1129 \r
1130 \r
1131         AlignFrame af = new AlignFrame(al);\r
1132 \r
1133         if(hiddenSeqs!=null)\r
1134         {\r
1135           for(int s=0; s<JSEQ.length; s++)\r
1136           {\r
1137             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)\r
1138             {\r
1139               al.getSequenceAt(s).addHiddenSequence(\r
1140                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )\r
1141                   );\r
1142             }\r
1143           }\r
1144 \r
1145           for(int s=0; s<hiddenSeqs.size(); s++)\r
1146           {\r
1147               af.viewport.hideSequence(\r
1148                 (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));\r
1149           }\r
1150         }\r
1151 \r
1152 \r
1153         if(hideConsensus || hideQuality || hideConservation)\r
1154         {\r
1155           int hSize = al.getAlignmentAnnotation().length;\r
1156           for (int h = 0; h < hSize; h++)\r
1157           {\r
1158             if (\r
1159                 (hideConsensus &&\r
1160                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))\r
1161                 ||\r
1162                 (hideQuality &&\r
1163                  al.getAlignmentAnnotation()[h].label.equals("Quality"))\r
1164                 ||\r
1165                 (hideConservation &&\r
1166                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))\r
1167             {\r
1168               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);\r
1169               hSize--;\r
1170               h--;\r
1171             }\r
1172           }\r
1173           af.alignPanel.adjustAnnotationHeight();\r
1174         }\r
1175 \r
1176         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
1177             view.getHeight());\r
1178         af.viewport.setStartRes(view.getStartRes());\r
1179         af.viewport.setStartSeq(view.getStartSeq());\r
1180         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
1181         af.viewport.showConservation = view.getShowConservation();\r
1182         af.viewport.showQuality = view.getShowQuality();\r
1183         af.viewport.showIdentity = view.getShowIdentity();\r
1184         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
1185         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
1186         af.viewport.setColourText(view.getShowColourText());\r
1187         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
1188         af.viewport.setConservationSelected(view.getConservationSelected());\r
1189         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
1190 \r
1191         af.viewport.setShowJVSuffix(view.getShowFullId());\r
1192         af.seqLimits.setSelected(view.getShowFullId());\r
1193 \r
1194         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
1195                 view.getFontStyle(), view.getFontSize()));\r
1196         af.alignPanel.fontChanged();\r
1197 \r
1198         af.viewport.setRenderGaps(view.getRenderGaps());\r
1199         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
1200 \r
1201         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
1202         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
1203 \r
1204         af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
1205 \r
1206         af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
1207         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
1208         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
1209 \r
1210         af.viewport.setShowBoxes(view.getShowBoxes());\r
1211         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
1212         af.viewport.setShowText(view.getShowText());\r
1213         af.viewTextMenuItem.setSelected(view.getShowText());\r
1214 \r
1215         ColourSchemeI cs = null;\r
1216 \r
1217         if (view.getBgColour() != null)\r
1218         {\r
1219             if (view.getBgColour().startsWith("ucs"))\r
1220             {\r
1221                 cs = GetUserColourScheme(jms, view.getBgColour());\r
1222             }\r
1223             else if(view.getBgColour().startsWith("Annotation"))\r
1224             {\r
1225               //int find annotation\r
1226               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
1227               {\r
1228                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
1229                     equals(view.getAnnotationColours().getAnnotation()))\r
1230                 {\r
1231                   if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
1232                       getThreshold() == null)\r
1233                   {\r
1234                     af.viewport.alignment.getAlignmentAnnotation()[i].\r
1235                         setThreshold(\r
1236                             new jalview.datamodel.GraphLine(\r
1237                                 view.getAnnotationColours().getThreshold(),\r
1238                                 "Threshold", java.awt.Color.black)\r
1239 \r
1240                         );\r
1241                   }\r
1242 \r
1243 \r
1244                   if (view.getAnnotationColours().getColourScheme().equals(\r
1245                       "None"))\r
1246                   {\r
1247                     cs = new AnnotationColourGradient(\r
1248                         af.viewport.alignment.getAlignmentAnnotation()[i],\r
1249                         new java.awt.Color(view.getAnnotationColours().\r
1250                                            getMinColour()),\r
1251                         new java.awt.Color(view.getAnnotationColours().\r
1252                                            getMaxColour()),\r
1253                         view.getAnnotationColours().getAboveThreshold());\r
1254                   }\r
1255                   else if (view.getAnnotationColours().getColourScheme().\r
1256                            startsWith("ucs"))\r
1257                   {\r
1258                      cs = new AnnotationColourGradient(\r
1259                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1260                          GetUserColourScheme(jms, view.getAnnotationColours().\r
1261                                                         getColourScheme()),\r
1262                          view.getAnnotationColours().getAboveThreshold()\r
1263                          );\r
1264                    }\r
1265                    else\r
1266                    {\r
1267                      cs = new AnnotationColourGradient(\r
1268                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1269                          ColourSchemeProperty.getColour(al,\r
1270                          view.getAnnotationColours().getColourScheme()),\r
1271                          view.getAnnotationColours().getAboveThreshold()\r
1272                          );\r
1273                    }\r
1274 \r
1275                   // Also use these settings for all the groups\r
1276                   if (al.getGroups() != null)\r
1277                     for (int g = 0; g < al.getGroups().size(); g++)\r
1278                     {\r
1279                       jalview.datamodel.SequenceGroup sg\r
1280                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
1281 \r
1282                       if(sg.cs == null)\r
1283                         continue;\r
1284 \r
1285 \r
1286                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))\r
1287                       {\r
1288                         sg.cs = new AnnotationColourGradient(\r
1289                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1290                             new java.awt.Color(view.getAnnotationColours().\r
1291                                                getMinColour()),\r
1292                             new java.awt.Color(view.getAnnotationColours().\r
1293                                                getMaxColour()),\r
1294                             view.getAnnotationColours().getAboveThreshold());\r
1295                       }\r
1296                       else*/\r
1297                       {\r
1298                         sg.cs = new AnnotationColourGradient(\r
1299                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1300                             sg.cs,\r
1301                             view.getAnnotationColours().getAboveThreshold()\r
1302                             );\r
1303                       }\r
1304 \r
1305                     }\r
1306 \r
1307 \r
1308                   break;\r
1309                 }\r
1310 \r
1311               }\r
1312             }\r
1313             else\r
1314             {\r
1315                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
1316             }\r
1317 \r
1318             if(cs!=null)\r
1319             {\r
1320               cs.setThreshold(view.getPidThreshold(), true);\r
1321               cs.setConsensus(af.viewport.vconsensus);\r
1322             }\r
1323         }\r
1324 \r
1325         af.setColourSelected(view.getBgColour());\r
1326         af.viewport.setGlobalColourScheme(cs);\r
1327         af.viewport.setColourAppliesToAllGroups(false);\r
1328         af.changeColour(cs);\r
1329         if (view.getConservationSelected() && cs!=null)\r
1330         {\r
1331           cs.setConservationInc(view.getConsThreshold());\r
1332         }\r
1333 \r
1334         af.viewport.setColourAppliesToAllGroups(true);\r
1335 \r
1336         if (view.getShowSequenceFeatures())\r
1337         {\r
1338            af.viewport.showSequenceFeatures = true;\r
1339            af.showSeqFeatures.setSelected(true);\r
1340         }\r
1341 \r
1342         if(jms.getFeatureSettings()!=null)\r
1343         {\r
1344           af.viewport.featuresDisplayed = new Hashtable();\r
1345           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
1346          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
1347          {\r
1348            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
1349 \r
1350            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
1351                new java.awt.Color(setting.getColour()));\r
1352 \r
1353            renderOrder[fs] = setting.getType();\r
1354 \r
1355            if(setting.getDisplay())\r
1356              af.viewport.featuresDisplayed.put(\r
1357                  setting.getType(), new Integer(setting.getColour()));\r
1358          }\r
1359          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
1360         }\r
1361 \r
1362         if (view.getHiddenColumnsCount() > 0)\r
1363         {\r
1364           for (int c = 0; c < view.getHiddenColumnsCount(); c++)\r
1365           {\r
1366               af.viewport.hideColumns(\r
1367                 view.getHiddenColumns(c).getStart(),\r
1368                 view.getHiddenColumns(c).getEnd()+1\r
1369                 );\r
1370           }\r
1371         }\r
1372 \r
1373 \r
1374         Desktop.addInternalFrame(af, view.getTitle(),\r
1375              view.getWidth(), view.getHeight());\r
1376 \r
1377         //LOAD TREES\r
1378         ///////////////////////////////////////\r
1379         if (jms.getTreeCount() > 0)\r
1380         {\r
1381             try\r
1382             {\r
1383                 for (int t = 0; t < jms.getTreeCount(); t++)\r
1384                 {\r
1385 \r
1386                     Tree tree = jms.getTree(t);\r
1387 \r
1388                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
1389                                 tree.getNewick()), tree.getTitle(),\r
1390                                 tree.getWidth(), tree.getHeight(),\r
1391                                 tree.getXpos(), tree.getYpos());\r
1392 \r
1393                     tp.fitToWindow.setState(tree.getFitToWindow());\r
1394                     tp.fitToWindow_actionPerformed(null);\r
1395 \r
1396                     if(tree.getFontName()!=null)\r
1397                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
1398                                           tree.getFontStyle(),\r
1399                                           tree.getFontSize()));\r
1400                     else\r
1401                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
1402                                             view.getFontStyle(),\r
1403                                             tree.getFontSize()));\r
1404 \r
1405                     tp.showPlaceholders(tree.getMarkUnlinked());\r
1406                     tp.showBootstrap(tree.getShowBootstrap());\r
1407                     tp.showDistances(tree.getShowDistances());\r
1408 \r
1409                     tp.treeCanvas.threshold = tree.getThreshold();\r
1410 \r
1411                     if (tree.getCurrentTree())\r
1412                       af.viewport.setCurrentTree(tp.getTree());\r
1413                 }\r
1414 \r
1415             }\r
1416             catch (Exception ex)\r
1417             {\r
1418                 ex.printStackTrace();\r
1419             }\r
1420 \r
1421         }\r
1422 \r
1423         return af;\r
1424     }\r
1425 }\r
1426 \r