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