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 \r
 627           Vector settingsAdded = new Vector();\r
 628           for(int ro=0; ro<renderOrder.length; ro++)\r
 629           {\r
 630             Setting setting = new Setting();\r
 631             setting.setType(renderOrder[ro]);\r
 632             setting.setColour(\r
 633                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()\r
 634                 );\r
 635 \r
 636             setting.setDisplay(\r
 637                 av.featuresDisplayed.containsKey(renderOrder[ro])\r
 638                 );\r
 639 \r
 640             fs.addSetting(setting);\r
 641             settingsAdded.addElement(renderOrder[ro]);\r
 642           }\r
 643 \r
 644           //Make sure we save none displayed feature settings\r
 645           Enumeration en =\r
 646               af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();\r
 647           while(en.hasMoreElements())\r
 648           {\r
 649             String key = en.nextElement().toString();\r
 650             if(settingsAdded.contains(key))\r
 651               continue;\r
 652 \r
 653             Setting setting = new Setting();\r
 654             setting.setType(key);\r
 655             setting.setColour(\r
 656                 af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()\r
 657                 );\r
 658 \r
 659             setting.setDisplay(false);\r
 660 \r
 661             fs.addSetting(setting);\r
 662             settingsAdded.addElement(key);\r
 663           }\r
 664 \r
 665           jms.setFeatureSettings(fs);\r
 666 \r
 667         }\r
 668 \r
 669         if(av.hasHiddenColumns)\r
 670         {\r
 671           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)\r
 672           {\r
 673             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);\r
 674             HiddenColumns hc = new HiddenColumns();\r
 675             hc.setStart(region[0]);\r
 676             hc.setEnd(region[1]);\r
 677             view.addHiddenColumns(hc);\r
 678           }\r
 679         }\r
 680 \r
 681         jms.addViewport(view);\r
 682 \r
 683 \r
 684         object.setJalviewModelSequence(jms);\r
 685         object.getVamsasModel().addSequenceSet(vamsasSet);\r
 686 \r
 687         try\r
 688         {\r
 689             if (!fileName.endsWith(".xml"))\r
 690             {\r
 691                 fileName = fileName + ".xml";\r
 692             }\r
 693 \r
 694             JarEntry entry = new JarEntry(fileName);\r
 695             jout.putNextEntry(entry);\r
 696 \r
 697             object.marshal(out);\r
 698         }\r
 699         catch (Exception ex)\r
 700         {\r
 701             ex.printStackTrace();\r
 702         }\r
 703     }\r
 704 \r
 705     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 706         Vector userColours, JalviewModelSequence jms)\r
 707     {\r
 708         String id = null;\r
 709         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
 710 \r
 711         if (!userColours.contains(ucs))\r
 712         {\r
 713             userColours.add(ucs);\r
 714 \r
 715             java.awt.Color[] colours = ucs.getColours();\r
 716             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
 717             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
 718 \r
 719             for (int i = 0; i < colours.length; i++)\r
 720             {\r
 721                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
 722                 col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 723                 jbucs.addColour(col);\r
 724             }\r
 725 \r
 726             id = "ucs" + userColours.indexOf(ucs);\r
 727             uc.setId(id);\r
 728             uc.setUserColourScheme(jbucs);\r
 729             jms.addUserColours(uc);\r
 730         }\r
 731 \r
 732         return id;\r
 733     }\r
 734 \r
 735    jalview.schemes.UserColourScheme GetUserColourScheme(\r
 736         JalviewModelSequence jms, String id)\r
 737     {\r
 738         UserColours[] uc = jms.getUserColours();\r
 739         UserColours colours = null;\r
 740 \r
 741         for (int i = 0; i < uc.length; i++)\r
 742         {\r
 743             if (uc[i].getId().equals(id))\r
 744             {\r
 745                 colours = uc[i];\r
 746 \r
 747                 break;\r
 748             }\r
 749         }\r
 750 \r
 751         int csize = colours.getUserColourScheme().getColourCount();\r
 752         java.awt.Color[] newColours = new java.awt.Color[csize];\r
 753 \r
 754         for (int i = 0; i < csize; i++)\r
 755         {\r
 756             newColours[i] = new java.awt.Color(Integer.parseInt(\r
 757                         colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 758         }\r
 759 \r
 760         return new jalview.schemes.UserColourScheme(newColours);\r
 761     }\r
 762 \r
 763     /**\r
 764      * DOCUMENT ME!\r
 765      *\r
 766      * @param file DOCUMENT ME!\r
 767      */\r
 768     public AlignFrame LoadJalviewAlign(String file)\r
 769     {\r
 770         jalview.gui.AlignFrame af = null;\r
 771         try\r
 772         {\r
 773             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 774             URL url = null;\r
 775 \r
 776             if (file.startsWith("http://"))\r
 777             {\r
 778                 url = new URL(file);\r
 779             }\r
 780 \r
 781             JarInputStream jin = null;\r
 782             JarEntry jarentry = null;\r
 783             int entryCount = 1;\r
 784 \r
 785             do\r
 786             {\r
 787                 if (url != null)\r
 788                 {\r
 789                     jin = new JarInputStream(url.openStream());\r
 790                 }\r
 791                 else\r
 792                 {\r
 793                     jin = new JarInputStream(new FileInputStream(file));\r
 794                 }\r
 795 \r
 796                 for (int i = 0; i < entryCount; i++)\r
 797                 {\r
 798                     jarentry = jin.getNextJarEntry();\r
 799                 }\r
 800 \r
 801                 if (jarentry != null && jarentry.getName().endsWith(".xml"))\r
 802                 {\r
 803                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 804                     JalviewModel object = new JalviewModel();\r
 805 \r
 806                     Unmarshaller unmar = new Unmarshaller(object);\r
 807                     unmar.setValidation(false);\r
 808                     object = (JalviewModel) unmar.unmarshal( in );\r
 809 \r
 810                     af = LoadFromObject(object, file);\r
 811                     entryCount++;\r
 812                 }\r
 813                 else if (jarentry != null)\r
 814                 {\r
 815                   //Some other file here.\r
 816                   entryCount++;\r
 817                 }\r
 818             }\r
 819             while (jarentry != null);\r
 820         }\r
 821         catch(java.net.UnknownHostException ex)\r
 822         {\r
 823           if (Desktop.instance != null)\r
 824             Desktop.instance.stopLoading();\r
 825 \r
 826           ex.printStackTrace();\r
 827           System.err.println("Couldn't locate Jalview XML file : " +\r
 828               ex + "\n");\r
 829            JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 830                                     "Couldn't locate " + file,\r
 831                                     "URL not found",\r
 832                                     JOptionPane.WARNING_MESSAGE);\r
 833 \r
 834         }\r
 835         catch (Exception ex)\r
 836         {\r
 837           if (Desktop.instance != null)\r
 838             Desktop.instance.stopLoading();\r
 839 \r
 840           //Is Version 1 Jar file?\r
 841           af =  new Jalview2XML_V1().LoadJalviewAlign(file);\r
 842 \r
 843           if(af!=null)\r
 844           {\r
 845             System.out.println("Successfully loaded archive file");\r
 846             return af;\r
 847           }\r
 848           ex.printStackTrace();\r
 849             System.err.println("Exception whilst loading jalview XML file : " +\r
 850                 ex + "\n");\r
 851              JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
 852                                       "Error loading  " + file,\r
 853                                       "Error loading Jalview file",\r
 854                                       JOptionPane.WARNING_MESSAGE);\r
 855 \r
 856         }\r
 857 \r
 858         return af;\r
 859     }\r
 860 \r
 861     String loadPDBFile(String file, String pdbId)\r
 862     {\r
 863       System.out.println("load file "+file);\r
 864       try\r
 865       {\r
 866         JarInputStream jin = null;\r
 867 \r
 868         if (file.startsWith("http://"))\r
 869         {\r
 870           jin = new JarInputStream(new URL(file).openStream());\r
 871         }\r
 872         else\r
 873         {\r
 874           jin = new JarInputStream(new FileInputStream(file));\r
 875         }\r
 876 \r
 877         JarEntry entry = null;\r
 878         do\r
 879         {\r
 880           entry = jin.getNextJarEntry();\r
 881         }\r
 882         while (!entry.getName().equals(pdbId));\r
 883 \r
 884         BufferedReader in = new BufferedReader(new InputStreamReader(jin));\r
 885         File outFile = File.createTempFile("jalview_pdb", ".txt");\r
 886         outFile.deleteOnExit();\r
 887         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
 888         String data;\r
 889 \r
 890         while ( (data = in.readLine()) != null)\r
 891         {\r
 892           out.println(data);\r
 893         }\r
 894         out.close();\r
 895         return outFile.getAbsolutePath();\r
 896 \r
 897       }\r
 898       catch (Exception ex)\r
 899       {\r
 900         ex.printStackTrace();\r
 901       }\r
 902 \r
 903       return null;\r
 904     }\r
 905 \r
 906 \r
 907     AlignFrame LoadFromObject(JalviewModel object, String file)\r
 908     {\r
 909         Vector seqids = new Vector();\r
 910         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 911         Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 912 \r
 913         JalviewModelSequence jms = object.getJalviewModelSequence();\r
 914 \r
 915         //////////////////////////////////\r
 916         //LOAD SEQUENCES\r
 917         Vector hiddenSeqs = null;\r
 918         jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
 919         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 920         for (int i = 0; i < vamsasSeq.length; i++)\r
 921         {\r
 922             jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 923                     vamsasSeq[i].getSequence());\r
 924             jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
 925 \r
 926             if(JSEQ[i].getHidden())\r
 927             {\r
 928               if(hiddenSeqs == null)\r
 929                 hiddenSeqs = new Vector();\r
 930               hiddenSeqs.addElement(jseqs[i]);\r
 931             }\r
 932             jseqs[i].setStart(JSEQ[i].getStart());\r
 933             jseqs[i].setEnd(JSEQ[i].getEnd());\r
 934             jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 935             seqids.add(jseqs[i]);\r
 936         }\r
 937 \r
 938         ///SequenceFeatures are added to the DatasetSequence,\r
 939         // so we must create the dataset before loading features\r
 940         /////////////////////////////////\r
 941         jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 942         al.setDataset(null);\r
 943         /////////////////////////////////\r
 944 \r
 945 \r
 946         Hashtable pdbloaded = new Hashtable();\r
 947         for (int i = 0; i < vamsasSeq.length; i++)\r
 948         {\r
 949           if (JSEQ[i].getFeaturesCount() > 0)\r
 950           {\r
 951             Features[] features = JSEQ[i].getFeatures();\r
 952             for (int f = 0; f < features.length; f++)\r
 953             {\r
 954               jalview.datamodel.SequenceFeature sf\r
 955                   = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
 956                   features[f].getDescription(), features[f].getStatus(),\r
 957                   features[f].getBegin(), features[f].getEnd(),\r
 958                   features[f].getFeatureGroup());\r
 959 \r
 960               sf.setScore(features[f].getScore());\r
 961               for(int od=0; od<features[f].getOtherDataCount(); od++)\r
 962               {\r
 963                 OtherData keyValue = features[f].getOtherData(od);\r
 964                 if(keyValue.getKey().startsWith("LINK"))\r
 965                   sf.addLink(keyValue.getValue());\r
 966                 else\r
 967                   sf.setValue(keyValue.getKey(), keyValue.getValue());\r
 968 \r
 969               }\r
 970 \r
 971               al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
 972             }\r
 973           }\r
 974           if (JSEQ[i].getPdbidsCount() > 0)\r
 975           {\r
 976             Pdbids[] ids = JSEQ[i].getPdbids();\r
 977             for (int p = 0; p < ids.length; p++)\r
 978             {\r
 979               jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
 980               entry.setId(ids[p].getId());\r
 981               entry.setType(ids[p].getType());\r
 982               if (ids[p].getFile() != null)\r
 983               {\r
 984                 if (!pdbloaded.containsKey(ids[p].getFile()))\r
 985                 {\r
 986                   String tmppdb = loadPDBFile(file, ids[p].getId());\r
 987                   entry.setFile(tmppdb);\r
 988                   pdbloaded.put(ids[p].getId(), tmppdb);\r
 989                 }\r
 990                 else\r
 991                   entry.setFile(pdbloaded.get(ids[p].getId()).toString());\r
 992               }\r
 993 \r
 994               al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
 995             }\r
 996           }\r
 997           if(vamsasSeq[i].getDBRefCount()>0)\r
 998           {\r
 999             for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)\r
1000             {\r
1001               jalview.datamodel.DBRefEntry entry =\r
1002                   new jalview.datamodel.DBRefEntry(\r
1003                       vamsasSeq[i].getDBRef(d).getSource(),\r
1004                       vamsasSeq[i].getDBRef(d).getVersion(),\r
1005                       vamsasSeq[i].getDBRef(d).getAccessionId()\r
1006                       );\r
1007               al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);\r
1008             }\r
1009 \r
1010           }\r
1011         }\r
1012 \r
1013 \r
1014 \r
1015          /////////////////////////////////\r
1016         //////////////////////////////////\r
1017         //LOAD ANNOTATIONS\r
1018         boolean hideQuality = true,\r
1019             hideConservation = true,\r
1020             hideConsensus = true;\r
1021 \r
1022         if (vamsasSet.getAnnotation() != null)\r
1023         {\r
1024             Annotation[] an = vamsasSet.getAnnotation();\r
1025 \r
1026             for (int i = 0; i < an.length; i++)\r
1027             {\r
1028                if (an[i].getLabel().equals("Quality"))\r
1029                 {\r
1030                  hideQuality = false;\r
1031                  continue;\r
1032                 }\r
1033                else if(an[i].getLabel().equals("Conservation"))\r
1034                {\r
1035                  hideConservation = false;\r
1036                  continue;\r
1037                }\r
1038                else if(an[i].getLabel().equals("Consensus"))\r
1039                {\r
1040                  hideConsensus = false;\r
1041                  continue;\r
1042                }\r
1043 \r
1044                 AnnotationElement[] ae = an[i].getAnnotationElement();\r
1045                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
1046 \r
1047                 for (int aa = 0; aa < ae.length; aa++)\r
1048                 {\r
1049                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
1050                             ae[aa].getDescription(),\r
1051                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
1052                             ae[aa].getValue());\r
1053                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );\r
1054                 }\r
1055 \r
1056                 jalview.datamodel.AlignmentAnnotation jaa = null;\r
1057 \r
1058                 if (an[i].getGraph())\r
1059                 {\r
1060                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
1061                       an[i].getDescription(), anot, 0, 0,\r
1062                       an[i].getGraphType());\r
1063 \r
1064                   jaa.graphGroup = an[i].getGraphGroup();\r
1065 \r
1066                   if (an[i].getThresholdLine() != null)\r
1067                   {\r
1068                     jaa.setThreshold(new jalview.datamodel.GraphLine(\r
1069                                   an[i].getThresholdLine().getValue(),\r
1070                                   an[i].getThresholdLine().getLabel(),\r
1071                                 new java.awt.Color(an[i].getThresholdLine().getColour()))\r
1072                              );\r
1073 \r
1074                   }\r
1075 \r
1076                 }\r
1077                 else\r
1078                 {\r
1079                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
1080                             an[i].getDescription(), anot);\r
1081                 }\r
1082 \r
1083                 if(an[i].getSequenceRef()!=null)\r
1084                 {\r
1085                   jaa.createSequenceMapping(\r
1086                       al.findName(an[i].getSequenceRef()), 1\r
1087                       );\r
1088                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);\r
1089                 }\r
1090 \r
1091                 al.addAnnotation(jaa);\r
1092             }\r
1093         }\r
1094 \r
1095 \r
1096         //  af.changeColour() );\r
1097         /////////////////////////\r
1098         //LOAD GROUPS\r
1099         if (jms.getJGroupCount() > 0)\r
1100         {\r
1101             JGroup[] groups = jms.getJGroup();\r
1102 \r
1103             for (int i = 0; i < groups.length; i++)\r
1104             {\r
1105                 ColourSchemeI cs = null;\r
1106 \r
1107                 if (groups[i].getColour() != null)\r
1108                 {\r
1109                     if (groups[i].getColour().startsWith("ucs"))\r
1110                     {\r
1111                         cs = GetUserColourScheme(jms, groups[i].getColour());\r
1112                     }\r
1113                     else\r
1114                     {\r
1115                         cs = ColourSchemeProperty.getColour(al,\r
1116                                 groups[i].getColour());\r
1117                     }\r
1118 \r
1119                     if(cs!=null)\r
1120                       cs.setThreshold(groups[i].getPidThreshold(), true);\r
1121                 }\r
1122 \r
1123                 Vector seqs = new Vector();\r
1124                 int[] ids = groups[i].getSeq();\r
1125 \r
1126                 for (int s = 0; s < ids.length; s++)\r
1127                 {\r
1128                     seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
1129                             ids[s]));\r
1130                 }\r
1131 \r
1132                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
1133                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
1134                         groups[i].getDisplayText(), groups[i].getColourText(),\r
1135                         groups[i].getStart(), groups[i].getEnd());\r
1136 \r
1137                 sg.setOutlineColour(new java.awt.Color(\r
1138                         groups[i].getOutlineColour()));\r
1139 \r
1140                 if (groups[i].getConsThreshold() != 0)\r
1141                 {\r
1142                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
1143                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
1144                             sg.getWidth() - 1);\r
1145                     c.calculate();\r
1146                     c.verdict(false, 25);\r
1147                     sg.cs.setConservation(c);\r
1148                 }\r
1149 \r
1150                 al.addGroup(sg);\r
1151             }\r
1152         }\r
1153 \r
1154 \r
1155         /////////////////////////////////\r
1156         // LOAD VIEWPORT\r
1157         Viewport[] views = jms.getViewport();\r
1158         Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
1159 \r
1160 \r
1161         AlignFrame af = new AlignFrame(al);\r
1162 \r
1163         if(hiddenSeqs!=null)\r
1164         {\r
1165           for(int s=0; s<JSEQ.length; s++)\r
1166           {\r
1167             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)\r
1168             {\r
1169               al.getSequenceAt(s).addHiddenSequence(\r
1170                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )\r
1171                   );\r
1172             }\r
1173           }\r
1174 \r
1175           for(int s=0; s<hiddenSeqs.size(); s++)\r
1176           {\r
1177               af.viewport.hideSequence(\r
1178                 (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));\r
1179           }\r
1180         }\r
1181 \r
1182 \r
1183         if(hideConsensus || hideQuality || hideConservation)\r
1184         {\r
1185           int hSize = al.getAlignmentAnnotation().length;\r
1186           for (int h = 0; h < hSize; h++)\r
1187           {\r
1188             if (\r
1189                 (hideConsensus &&\r
1190                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))\r
1191                 ||\r
1192                 (hideQuality &&\r
1193                  al.getAlignmentAnnotation()[h].label.equals("Quality"))\r
1194                 ||\r
1195                 (hideConservation &&\r
1196                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))\r
1197             {\r
1198               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);\r
1199               hSize--;\r
1200               h--;\r
1201             }\r
1202           }\r
1203           af.alignPanel.adjustAnnotationHeight();\r
1204         }\r
1205 \r
1206         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
1207             view.getHeight());\r
1208         af.viewport.setStartRes(view.getStartRes());\r
1209         af.viewport.setStartSeq(view.getStartSeq());\r
1210         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
1211         af.viewport.showConservation = view.getShowConservation();\r
1212         af.viewport.showQuality = view.getShowQuality();\r
1213         af.viewport.showIdentity = view.getShowIdentity();\r
1214         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
1215         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
1216         af.viewport.setColourText(view.getShowColourText());\r
1217         af.colourTextMenuItem.setSelected(view.getShowColourText());\r
1218         af.viewport.setConservationSelected(view.getConservationSelected());\r
1219         af.conservationMenuItem.setSelected(view.getConservationSelected());\r
1220 \r
1221         af.viewport.setShowJVSuffix(view.getShowFullId());\r
1222         af.seqLimits.setSelected(view.getShowFullId());\r
1223 \r
1224         af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
1225                 view.getFontStyle(), view.getFontSize()));\r
1226         af.alignPanel.fontChanged();\r
1227 \r
1228         af.viewport.setRenderGaps(view.getRenderGaps());\r
1229         af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
1230 \r
1231         af.viewport.setWrapAlignment(view.getWrapAlignment());\r
1232         af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
1233 \r
1234         af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
1235 \r
1236         af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
1237         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
1238         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
1239 \r
1240         af.viewport.setShowBoxes(view.getShowBoxes());\r
1241         af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
1242         af.viewport.setShowText(view.getShowText());\r
1243         af.viewTextMenuItem.setSelected(view.getShowText());\r
1244 \r
1245         ColourSchemeI cs = null;\r
1246 \r
1247         if (view.getBgColour() != null)\r
1248         {\r
1249             if (view.getBgColour().startsWith("ucs"))\r
1250             {\r
1251                 cs = GetUserColourScheme(jms, view.getBgColour());\r
1252             }\r
1253             else if(view.getBgColour().startsWith("Annotation"))\r
1254             {\r
1255               //int find annotation\r
1256               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
1257               {\r
1258                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
1259                     equals(view.getAnnotationColours().getAnnotation()))\r
1260                 {\r
1261                   if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
1262                       getThreshold() == null)\r
1263                   {\r
1264                     af.viewport.alignment.getAlignmentAnnotation()[i].\r
1265                         setThreshold(\r
1266                             new jalview.datamodel.GraphLine(\r
1267                                 view.getAnnotationColours().getThreshold(),\r
1268                                 "Threshold", java.awt.Color.black)\r
1269 \r
1270                         );\r
1271                   }\r
1272 \r
1273 \r
1274                   if (view.getAnnotationColours().getColourScheme().equals(\r
1275                       "None"))\r
1276                   {\r
1277                     cs = new AnnotationColourGradient(\r
1278                         af.viewport.alignment.getAlignmentAnnotation()[i],\r
1279                         new java.awt.Color(view.getAnnotationColours().\r
1280                                            getMinColour()),\r
1281                         new java.awt.Color(view.getAnnotationColours().\r
1282                                            getMaxColour()),\r
1283                         view.getAnnotationColours().getAboveThreshold());\r
1284                   }\r
1285                   else if (view.getAnnotationColours().getColourScheme().\r
1286                            startsWith("ucs"))\r
1287                   {\r
1288                      cs = new AnnotationColourGradient(\r
1289                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1290                          GetUserColourScheme(jms, view.getAnnotationColours().\r
1291                                                         getColourScheme()),\r
1292                          view.getAnnotationColours().getAboveThreshold()\r
1293                          );\r
1294                    }\r
1295                    else\r
1296                    {\r
1297                      cs = new AnnotationColourGradient(\r
1298                          af.viewport.alignment.getAlignmentAnnotation()[i],\r
1299                          ColourSchemeProperty.getColour(al,\r
1300                          view.getAnnotationColours().getColourScheme()),\r
1301                          view.getAnnotationColours().getAboveThreshold()\r
1302                          );\r
1303                    }\r
1304 \r
1305                   // Also use these settings for all the groups\r
1306                   if (al.getGroups() != null)\r
1307                     for (int g = 0; g < al.getGroups().size(); g++)\r
1308                     {\r
1309                       jalview.datamodel.SequenceGroup sg\r
1310                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
1311 \r
1312                       if(sg.cs == null)\r
1313                         continue;\r
1314 \r
1315 \r
1316                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))\r
1317                       {\r
1318                         sg.cs = new AnnotationColourGradient(\r
1319                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1320                             new java.awt.Color(view.getAnnotationColours().\r
1321                                                getMinColour()),\r
1322                             new java.awt.Color(view.getAnnotationColours().\r
1323                                                getMaxColour()),\r
1324                             view.getAnnotationColours().getAboveThreshold());\r
1325                       }\r
1326                       else*/\r
1327                       {\r
1328                         sg.cs = new AnnotationColourGradient(\r
1329                             af.viewport.alignment.getAlignmentAnnotation()[i],\r
1330                             sg.cs,\r
1331                             view.getAnnotationColours().getAboveThreshold()\r
1332                             );\r
1333                       }\r
1334 \r
1335                     }\r
1336 \r
1337 \r
1338                   break;\r
1339                 }\r
1340 \r
1341               }\r
1342             }\r
1343             else\r
1344             {\r
1345                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
1346             }\r
1347 \r
1348             if(cs!=null)\r
1349             {\r
1350               cs.setThreshold(view.getPidThreshold(), true);\r
1351               cs.setConsensus(af.viewport.vconsensus);\r
1352             }\r
1353         }\r
1354 \r
1355         af.setColourSelected(view.getBgColour());\r
1356         af.viewport.setGlobalColourScheme(cs);\r
1357         af.viewport.setColourAppliesToAllGroups(false);\r
1358         af.changeColour(cs);\r
1359         if (view.getConservationSelected() && cs!=null)\r
1360         {\r
1361           cs.setConservationInc(view.getConsThreshold());\r
1362         }\r
1363 \r
1364         af.viewport.setColourAppliesToAllGroups(true);\r
1365 \r
1366         if (view.getShowSequenceFeatures())\r
1367         {\r
1368            af.viewport.showSequenceFeatures = true;\r
1369            af.showSeqFeatures.setSelected(true);\r
1370         }\r
1371 \r
1372         if(jms.getFeatureSettings()!=null)\r
1373         {\r
1374           af.viewport.featuresDisplayed = new Hashtable();\r
1375           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
1376          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
1377          {\r
1378            Setting setting = jms.getFeatureSettings().getSetting(fs);\r
1379 \r
1380            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
1381                new java.awt.Color(setting.getColour()));\r
1382 \r
1383            renderOrder[fs] = setting.getType();\r
1384 \r
1385            if(setting.getDisplay())\r
1386              af.viewport.featuresDisplayed.put(\r
1387                  setting.getType(), new Integer(setting.getColour()));\r
1388          }\r
1389          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
1390         }\r
1391 \r
1392         if (view.getHiddenColumnsCount() > 0)\r
1393         {\r
1394           for (int c = 0; c < view.getHiddenColumnsCount(); c++)\r
1395           {\r
1396               af.viewport.hideColumns(\r
1397                 view.getHiddenColumns(c).getStart(),\r
1398                 view.getHiddenColumns(c).getEnd()+1\r
1399                 );\r
1400           }\r
1401         }\r
1402 \r
1403 \r
1404         Desktop.addInternalFrame(af, view.getTitle(),\r
1405              view.getWidth(), view.getHeight());\r
1406 \r
1407         //LOAD TREES\r
1408         ///////////////////////////////////////\r
1409         if (jms.getTreeCount() > 0)\r
1410         {\r
1411             try\r
1412             {\r
1413                 for (int t = 0; t < jms.getTreeCount(); t++)\r
1414                 {\r
1415 \r
1416                     Tree tree = jms.getTree(t);\r
1417 \r
1418                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
1419                                 tree.getNewick()), tree.getTitle(),\r
1420                                 tree.getWidth(), tree.getHeight(),\r
1421                                 tree.getXpos(), tree.getYpos());\r
1422 \r
1423                     tp.fitToWindow.setState(tree.getFitToWindow());\r
1424                     tp.fitToWindow_actionPerformed(null);\r
1425 \r
1426                     if(tree.getFontName()!=null)\r
1427                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
1428                                           tree.getFontStyle(),\r
1429                                           tree.getFontSize()));\r
1430                     else\r
1431                       tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
1432                                             view.getFontStyle(),\r
1433                                             tree.getFontSize()));\r
1434 \r
1435                     tp.showPlaceholders(tree.getMarkUnlinked());\r
1436                     tp.showBootstrap(tree.getShowBootstrap());\r
1437                     tp.showDistances(tree.getShowDistances());\r
1438 \r
1439                     tp.treeCanvas.threshold = tree.getThreshold();\r
1440 \r
1441                     if (tree.getCurrentTree())\r
1442                       af.viewport.setCurrentTree(tp.getTree());\r
1443                 }\r
1444 \r
1445             }\r
1446             catch (Exception ex)\r
1447             {\r
1448                 ex.printStackTrace();\r
1449             }\r
1450 \r
1451         }\r
1452 \r
1453         return af;\r
1454     }\r
1455 }\r
1456 \r