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 import java.io.*;\r
  22 import java.net.*;\r
  23 import java.util.*;\r
  24 import java.util.jar.*;\r
  25 \r
  26 import javax.swing.*;\r
  27 \r
  28 import jalview.binding.*;\r
  29 import jalview.io.*;\r
  30 import jalview.schemes.*;\r
  31 \r
  32 public class Jalview2XML\r
  33 {\r
  34   // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
  35   public static void SaveState(File statefile)\r
  36   {\r
  37     long creation = System.currentTimeMillis();\r
  38     JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
  39 \r
  40     if (frames == null)\r
  41     {\r
  42       return;\r
  43     }\r
  44 \r
  45     try\r
  46     {\r
  47       FileOutputStream fos = new FileOutputStream(statefile);\r
  48       JarOutputStream jout = new JarOutputStream(fos);\r
  49 \r
  50       //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
  51       ////////////////////////////////////////////////////\r
  52       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
  53           "UTF-8"));\r
  54 \r
  55       Vector shortNames = new Vector();\r
  56       int treeCount=1;\r
  57 \r
  58       //REVERSE ORDER\r
  59       for (int i = frames.length - 1; i > -1; i--)\r
  60       {\r
  61         if (frames[i] instanceof AlignFrame)\r
  62         {\r
  63           AlignFrame af = (AlignFrame) frames[i];\r
  64 \r
  65           String shortName = af.getTitle();\r
  66 \r
  67           if (shortName.indexOf(File.separatorChar) > -1)\r
  68           {\r
  69             shortName = shortName.substring(shortName.lastIndexOf(\r
  70                 File.separatorChar) + 1);\r
  71           }\r
  72 \r
  73           int count = 1;\r
  74 \r
  75           while (shortNames.contains(shortName))\r
  76           {\r
  77             if (shortName.endsWith("_" + (count - 1)))\r
  78             {\r
  79               shortName = shortName.substring(0,\r
  80                                               shortName.lastIndexOf("_"));\r
  81             }\r
  82 \r
  83             shortName = shortName.concat("_" + count);\r
  84             count++;\r
  85           }\r
  86 \r
  87           shortNames.addElement(shortName);\r
  88 \r
  89           if (!shortName.endsWith(".xml"))\r
  90           {\r
  91             shortName = shortName + ".xml";\r
  92           }\r
  93 \r
  94           SaveState(af, creation, shortName, jout, out);\r
  95         }\r
  96       }\r
  97 \r
  98       out.close();\r
  99       jout.close();\r
 100     }\r
 101     catch (Exception ex)\r
 102     {\r
 103       ex.printStackTrace();\r
 104     }\r
 105   }\r
 106 \r
 107 \r
 108   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
 109   public static void SaveAlignment(AlignFrame af, String jarFile, String fileName)\r
 110   {\r
 111     try\r
 112     {\r
 113       FileOutputStream fos = new FileOutputStream(jarFile);\r
 114       JarOutputStream jout = new JarOutputStream(fos);\r
 115 \r
 116       //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
 117       ////////////////////////////////////////////////////\r
 118       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
 119           "UTF-8"));\r
 120 \r
 121       SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
 122       out.close();\r
 123       jout.close();\r
 124     }\r
 125     catch (Exception ex)\r
 126     {\r
 127     }\r
 128   }\r
 129 \r
 130   public static void SaveState(AlignFrame af, long timeStamp,\r
 131                                String fileName, JarOutputStream jout,\r
 132                                PrintWriter out)\r
 133   {\r
 134     Vector seqids = new Vector();\r
 135     Vector userColours = new Vector();\r
 136 \r
 137     AlignViewport av = af.viewport;\r
 138 \r
 139     JalviewModel object = new JalviewModel();\r
 140     object.setVamsasModel(new VamsasModel());\r
 141 \r
 142     object.setCreationDate(new java.util.Date(timeStamp));\r
 143     object.setVersion(jalview.bin.Cache.VERSION);\r
 144 \r
 145     jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
 146 \r
 147     SequenceSet vamsasSet = new SequenceSet();\r
 148     Sequence vamsasSeq;\r
 149     JalviewModelSequence jms = new JalviewModelSequence();\r
 150 \r
 151     vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
 152 \r
 153     JSeq jseq;\r
 154 \r
 155     //SAVE SEQUENCES\r
 156     int id = 0;\r
 157 \r
 158     for (int i = 0; i < jal.getHeight(); i++)\r
 159     {\r
 160       seqids.add(jal.getSequenceAt(i));\r
 161 \r
 162       vamsasSeq = new Sequence();\r
 163       vamsasSeq.setId(id + "");\r
 164       vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
 165       vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
 166 \r
 167       jseq = new JSeq();\r
 168       jseq.setStart(jal.getSequenceAt(i).getStart());\r
 169       jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
 170 \r
 171       jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
 172 \r
 173       jseq.setId(id);\r
 174 \r
 175       jms.addJSeq(jseq);\r
 176       vamsasSet.addSequence(vamsasSeq);\r
 177       id++;\r
 178     }\r
 179 \r
 180     //SAVE TREES\r
 181     ///////////////////////////////////\r
 182     if (af.viewport.currentTree != null)\r
 183     {\r
 184       // FIND ANY ASSOCIATED TREES\r
 185       JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
 186       for(int t=0; t<frames.length; t++)\r
 187       {\r
 188         if (frames[t] instanceof TreePanel)\r
 189         {\r
 190           TreePanel tp = (TreePanel) frames[t];\r
 191           if(tp.treeCanvas.av.alignment==jal)\r
 192           {\r
 193             Tree tree = new Tree();\r
 194             tree.setTitle(tp.getTitle());\r
 195             tree.setCurrentTree((af.viewport.currentTree == tp.getTree()));\r
 196             tree.setNewick(tp.getTree().toString());\r
 197             tree.setThreshold(tp.treeCanvas.threshold);\r
 198 \r
 199             tree.setFitToWindow(tp.fitToWindow.getState());\r
 200             tree.setFontSize(tp.treeCanvas.fontSize);\r
 201             tree.setMarkUnlinked( tp.placeholdersMenu.getState() );\r
 202             tree.setShowBootstrap( tp.bootstrapMenu.getState() );\r
 203             tree.setShowDistances( tp.distanceMenu.getState() );\r
 204 \r
 205             tree.setHeight(tp.getHeight());\r
 206             tree.setWidth(tp.getWidth());\r
 207             tree.setXpos(tp.getX());\r
 208             tree.setYpos(tp.getY());\r
 209 \r
 210             jms.addTree(tree);\r
 211           }\r
 212         }\r
 213       }\r
 214     }\r
 215 \r
 216     //SAVE ANNOTATIONS\r
 217     if (jal.getAlignmentAnnotation() != null)\r
 218     {\r
 219       jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
 220 \r
 221       for (int i = 0; i < aa.length; i++)\r
 222       {\r
 223         if (aa[i].label.equals("Quality") ||\r
 224             aa[i].label.equals("Conservation") ||\r
 225             aa[i].label.equals("Consensus"))\r
 226         {\r
 227           continue;\r
 228         }\r
 229 \r
 230         Annotation an = new Annotation();\r
 231         an.setDescription(aa[i].description);\r
 232         an.setGraph(aa[i].isGraph);\r
 233         an.setLabel(aa[i].label);\r
 234 \r
 235         AnnotationElement ae;\r
 236 \r
 237         for (int a = 0; a < aa[i].annotations.length; a++)\r
 238         {\r
 239           if ( (aa[i] == null) || (aa[i].annotations[a] == null))\r
 240           {\r
 241             continue;\r
 242           }\r
 243 \r
 244           ae = new AnnotationElement();\r
 245           ae.setDescription(aa[i].annotations[a].description);\r
 246           ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
 247           ae.setValue(aa[i].annotations[a].value);\r
 248           ae.setPosition(a);\r
 249           ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
 250                                    "");\r
 251           an.addAnnotationElement(ae);\r
 252         }\r
 253 \r
 254         vamsasSet.addAnnotation(an);\r
 255       }\r
 256     }\r
 257 \r
 258     //SAVE GROUPS\r
 259     if (jal.getGroups() != null)\r
 260     {\r
 261       JGroup[] groups = new JGroup[jal.getGroups().size()];\r
 262 \r
 263       for (int i = 0; i < groups.length; i++)\r
 264       {\r
 265         groups[i] = new JGroup();\r
 266 \r
 267         jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)\r
 268             jal.getGroups()\r
 269             .elementAt(i);\r
 270         groups[i].setStart(sg.getStartRes());\r
 271         groups[i].setEnd(sg.getEndRes());\r
 272         groups[i].setName(sg.getName());\r
 273 \r
 274         if (sg.cs instanceof ConservationColourScheme)\r
 275         {\r
 276           groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);\r
 277         }\r
 278 \r
 279         if (sg.cs instanceof ResidueColourScheme)\r
 280         {\r
 281           groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).\r
 282                                     getThreshold());\r
 283         }\r
 284         else if (sg.cs instanceof ScoreColourScheme)\r
 285         {\r
 286           groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());\r
 287         }\r
 288 \r
 289         if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
 290         {\r
 291           groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
 292                                                   jms));\r
 293         }\r
 294         else\r
 295         {\r
 296           groups[i].setColour(ColourSchemeProperty.getColourName(\r
 297               sg.cs));\r
 298         }\r
 299 \r
 300         groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
 301         groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
 302         groups[i].setDisplayText(sg.getDisplayText());\r
 303         groups[i].setColourText(sg.getColourText());\r
 304 \r
 305         for (int s = 0; s < sg.getSize(); s++)\r
 306         {\r
 307           jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.\r
 308               getSequenceAt(s);\r
 309           int index = seqids.indexOf(seq);\r
 310           groups[i].addSeq(index);\r
 311         }\r
 312       }\r
 313 \r
 314       jms.setJGroup(groups);\r
 315     }\r
 316 \r
 317     ///////////SAVE VIEWPORT\r
 318     Viewport view = new Viewport();\r
 319     view.setTitle(af.getTitle());\r
 320     view.setXpos(af.getX());\r
 321     view.setYpos(af.getY());\r
 322     view.setWidth(af.getWidth());\r
 323     view.setHeight(af.getHeight());\r
 324     view.setStartRes(av.startRes);\r
 325     view.setStartSeq(av.startSeq);\r
 326 \r
 327     if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
 328     {\r
 329       view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
 330                                            userColours, jms));\r
 331     }\r
 332     else\r
 333     {\r
 334       view.setBgColour(ColourSchemeProperty.getColourName(\r
 335           av.getGlobalColourScheme()));\r
 336     }\r
 337 \r
 338     ColourSchemeI cs = av.getGlobalColourScheme();\r
 339 \r
 340     if (cs instanceof ConservationColourScheme)\r
 341     {\r
 342       view.setConsThreshold( ( (ConservationColourScheme) cs).inc);\r
 343     }\r
 344 \r
 345     if (cs instanceof ResidueColourScheme)\r
 346     {\r
 347       view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());\r
 348     }\r
 349     else if (cs instanceof ScoreColourScheme)\r
 350     {\r
 351       view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());\r
 352     }\r
 353 \r
 354     view.setConservationSelected(av.getConservationSelected());\r
 355     view.setPidSelected(av.getAbovePIDThreshold());\r
 356     view.setFontName(av.font.getFontName());\r
 357     view.setFontSize(av.font.getSize());\r
 358     view.setFontStyle(av.font.getStyle());\r
 359     view.setRenderGaps(av.renderGaps);\r
 360     view.setShowAnnotation(av.getShowAnnotation());\r
 361     view.setShowBoxes(av.getShowBoxes());\r
 362     view.setShowColourText(av.getColourText());\r
 363     view.setShowConservation(av.showConservation);\r
 364     view.setShowFullId(av.getShowFullId());\r
 365     view.setShowIdentity(av.showIdentity);\r
 366     view.setShowQuality(av.showQuality);\r
 367     view.setShowSequenceFeatures(av.showSequenceFeatures);\r
 368     view.setShowText(av.getShowText());\r
 369     view.setWrapAlignment(av.getWrapAlignment());\r
 370 \r
 371     jms.addViewport(view);\r
 372 \r
 373     object.setJalviewModelSequence(jms);\r
 374     object.getVamsasModel().addSequenceSet(vamsasSet);\r
 375 \r
 376     try\r
 377     {\r
 378       if (!fileName.endsWith(".xml"))\r
 379       {\r
 380         fileName = fileName + ".xml";\r
 381       }\r
 382 \r
 383       JarEntry entry = new JarEntry(fileName);\r
 384       jout.putNextEntry(entry);\r
 385 \r
 386       object.marshal(out);\r
 387     }\r
 388     catch (Exception ex)\r
 389     {\r
 390       ex.printStackTrace();\r
 391     }\r
 392   }\r
 393 \r
 394   static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
 395                                     Vector userColours,\r
 396                                     JalviewModelSequence jms)\r
 397   {\r
 398     String id = null;\r
 399     jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)\r
 400         cs;\r
 401 \r
 402     if (!userColours.contains(ucs))\r
 403     {\r
 404       userColours.add(ucs);\r
 405 \r
 406       java.awt.Color[] colours = ucs.getColours();\r
 407       jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
 408       jalview.binding.UserColourScheme jbucs = new jalview.binding.\r
 409           UserColourScheme();\r
 410 \r
 411       for (int i = 0; i < colours.length; i++)\r
 412       {\r
 413         jalview.binding.Colour col = new jalview.binding.Colour();\r
 414         col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
 415         jbucs.addColour(col);\r
 416       }\r
 417 \r
 418       id = "ucs" + userColours.indexOf(ucs);\r
 419       uc.setId(id);\r
 420       uc.setUserColourScheme(jbucs);\r
 421       jms.addUserColours(uc);\r
 422     }\r
 423 \r
 424     return id;\r
 425   }\r
 426 \r
 427   static jalview.schemes.UserColourScheme GetUserColourScheme(\r
 428       JalviewModelSequence jms, String id)\r
 429   {\r
 430     UserColours[] uc = jms.getUserColours();\r
 431     UserColours colours = null;\r
 432 \r
 433     for (int i = 0; i < uc.length; i++)\r
 434     {\r
 435       if (uc[i].getId().equals(id))\r
 436       {\r
 437         colours = uc[i];\r
 438 \r
 439         break;\r
 440       }\r
 441     }\r
 442 \r
 443     int csize = colours.getUserColourScheme().getColourCount();\r
 444     java.awt.Color[] newColours = new java.awt.Color[csize];\r
 445 \r
 446     for (int i = 0; i < csize; i++)\r
 447     {\r
 448       newColours[i] = new java.awt.Color(Integer.parseInt(\r
 449           colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
 450     }\r
 451 \r
 452     return new jalview.schemes.UserColourScheme(newColours);\r
 453   }\r
 454 \r
 455   public static void LoadJalviewAlign(String file)\r
 456   {\r
 457     JalviewModel object = new JalviewModel();\r
 458 \r
 459     try\r
 460     {\r
 461       //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
 462       URL url = null;\r
 463 \r
 464       if (file.startsWith("http://"))\r
 465       {\r
 466         url = new URL(file);\r
 467       }\r
 468 \r
 469       JarInputStream jin = null;\r
 470       JarEntry jarentry = null;\r
 471       int entryCount = 1;\r
 472 \r
 473       do\r
 474       {\r
 475         if (url != null)\r
 476         {\r
 477           jin = new JarInputStream(url.openStream());\r
 478         }\r
 479         else\r
 480         {\r
 481           jin = new JarInputStream(new FileInputStream(file));\r
 482         }\r
 483 \r
 484         for (int i = 0; i < entryCount; i++)\r
 485         {\r
 486           jarentry = jin.getNextJarEntry();\r
 487         }\r
 488 \r
 489         if (jarentry != null)\r
 490         {\r
 491           InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
 492           object = (JalviewModel) object.unmarshal(in);\r
 493           LoadFromObject(object);\r
 494           entryCount++;\r
 495         }\r
 496       }\r
 497       while (jarentry != null);\r
 498     }\r
 499     catch (Exception ex)\r
 500     {\r
 501       System.err.println("Exception whilst loading jalview XML file : " +\r
 502                          ex + "\n");\r
 503       ex.printStackTrace();\r
 504 \r
 505       return;\r
 506     }\r
 507   }\r
 508 \r
 509   static void LoadFromObject(JalviewModel object)\r
 510   {\r
 511     Vector seqids = new Vector();\r
 512     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
 513     Sequence[] vamsasSeq = vamsasSet.getSequence();\r
 514 \r
 515     JalviewModelSequence jms = object.getJalviewModelSequence();\r
 516 \r
 517     //////////////////////////////////\r
 518     //LOAD SEQUENCES\r
 519     jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[\r
 520         vamsasSeq.length];\r
 521     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
 522 \r
 523     for (int i = 0; i < vamsasSeq.length; i++)\r
 524     {\r
 525       jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
 526                                                 vamsasSeq[i].getSequence());\r
 527 \r
 528       jseqs[i].setStart(JSEQ[i].getStart());\r
 529       jseqs[i].setEnd(JSEQ[i].getEnd());\r
 530       jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
 531       seqids.add(jseqs[i]);\r
 532     }\r
 533 \r
 534     /////////////////////////////////\r
 535     jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
 536 \r
 537     /////////////////////////////////\r
 538     //////////////////////////////////\r
 539     //LOAD ANNOTATIONS\r
 540     if (vamsasSet.getAnnotation() != null)\r
 541     {\r
 542       Annotation[] an = vamsasSet.getAnnotation();\r
 543 \r
 544       for (int i = 0; i < an.length; i++)\r
 545       {\r
 546         AnnotationElement[] ae = an[i].getAnnotationElement();\r
 547         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[\r
 548             al.getWidth()];\r
 549 \r
 550         for (int aa = 0; aa < ae.length; aa++)\r
 551         {\r
 552           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].\r
 553               getDisplayCharacter(),\r
 554               ae[aa].getDescription(),\r
 555               ae[aa].getSecondaryStructure().charAt(0),\r
 556               ae[aa].getValue());\r
 557         }\r
 558 \r
 559         jalview.datamodel.AlignmentAnnotation jaa = null;\r
 560 \r
 561         if (an[i].getGraph())\r
 562         {\r
 563           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 564               an[i].getDescription(), anot, 0, 0, 1);\r
 565         }\r
 566         else\r
 567         {\r
 568           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
 569               an[i].getDescription(), anot);\r
 570         }\r
 571 \r
 572         al.addAnnotation(jaa);\r
 573       }\r
 574     }\r
 575 \r
 576     /////////////////////////////////\r
 577     // LOAD VIEWPORT\r
 578     Viewport[] views = jms.getViewport();\r
 579     Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
 580 \r
 581     AlignFrame af = new AlignFrame(al);\r
 582 \r
 583     //  af.changeColour() );\r
 584     /////////////////////////\r
 585     //LOAD GROUPS\r
 586     if (jms.getJGroupCount() > 0)\r
 587     {\r
 588       JGroup[] groups = jms.getJGroup();\r
 589 \r
 590       for (int i = 0; i < groups.length; i++)\r
 591       {\r
 592         ColourSchemeI cs = null;\r
 593 \r
 594         if (groups[i].getColour() != null)\r
 595         {\r
 596           if (groups[i].getColour().startsWith("ucs"))\r
 597           {\r
 598             cs = GetUserColourScheme(jms, groups[i].getColour());\r
 599           }\r
 600           else\r
 601           {\r
 602             cs = ColourSchemeProperty.getColour(al,\r
 603                                                 groups[i].getColour());\r
 604           }\r
 605 \r
 606           if (cs instanceof ResidueColourScheme)\r
 607           {\r
 608             ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
 609           }\r
 610           else if (cs instanceof ScoreColourScheme)\r
 611           {\r
 612             ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
 613           }\r
 614         }\r
 615 \r
 616         Vector seqs = new Vector();\r
 617         int[] ids = groups[i].getSeq();\r
 618 \r
 619         for (int s = 0; s < ids.length; s++)\r
 620         {\r
 621           seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(\r
 622               ids[s]));\r
 623         }\r
 624 \r
 625         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.\r
 626             SequenceGroup(seqs, groups[i].getName(),\r
 627                           cs, groups[i].getDisplayBoxes(),\r
 628                           groups[i].getDisplayText(), groups[i].getColourText(),\r
 629                           groups[i].getStart(), groups[i].getEnd());\r
 630 \r
 631         sg.setOutlineColour(new java.awt.Color(\r
 632             groups[i].getOutlineColour()));\r
 633 \r
 634 \r
 635         if (groups[i].getConsThreshold() != 0)\r
 636         {\r
 637           jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
 638               "All",\r
 639               ResidueProperties.propHash, 3, sg.sequences, 0,\r
 640               sg.getWidth() - 1);\r
 641           c.calculate();\r
 642           c.verdict(false, 25);\r
 643           cs = new ConservationColourScheme(c, cs);\r
 644           sg.cs = cs;\r
 645         }\r
 646 \r
 647         al.addGroup(sg);\r
 648       }\r
 649     }\r
 650 \r
 651     Desktop.addInternalFrame(af, view.getTitle(),\r
 652                              AlignFrame.NEW_WINDOW_WIDTH,\r
 653                              AlignFrame.NEW_WINDOW_HEIGHT);\r
 654     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
 655                  view.getHeight());\r
 656     af.viewport.setStartRes(view.getStartRes());\r
 657     af.viewport.setStartSeq(view.getStartSeq());\r
 658     af.viewport.showConservation = view.getShowConservation();\r
 659     af.viewport.showQuality = view.getShowQuality();\r
 660     af.viewport.showIdentity = view.getShowIdentity();\r
 661     af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
 662     af.abovePIDThreshold.setSelected(view.getPidSelected());\r
 663     af.viewport.setColourText(view.getShowColourText());\r
 664     af.colourTextMenuItem.setSelected(view.getShowColourText());\r
 665     af.viewport.setConservationSelected(view.getConservationSelected());\r
 666     af.conservationMenuItem.setSelected(view.getConservationSelected());\r
 667 \r
 668     af.viewport.setShowFullId(view.getShowFullId());\r
 669     af.fullSeqId.setSelected(view.getShowFullId());\r
 670 \r
 671     af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
 672                                           view.getFontStyle(), view.getFontSize()));\r
 673     af.alignPanel.fontChanged();\r
 674 \r
 675     af.viewport.setRenderGaps(view.getRenderGaps());\r
 676     af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
 677 \r
 678     af.viewport.setWrapAlignment(view.getWrapAlignment());\r
 679     af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
 680 \r
 681     if (view.getWrapAlignment())\r
 682     {\r
 683       af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
 684     }\r
 685     else\r
 686     {\r
 687       af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
 688       af.viewport.setShowAnnotation(view.getShowAnnotation());\r
 689       af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
 690     }\r
 691 \r
 692     af.viewport.setShowBoxes(view.getShowBoxes());\r
 693     af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
 694     af.viewport.setShowText(view.getShowText());\r
 695     af.viewTextMenuItem.setSelected(view.getShowText());\r
 696 \r
 697     ColourSchemeI cs = null;\r
 698 \r
 699     if (view.getBgColour() != null)\r
 700     {\r
 701       if (view.getBgColour().startsWith("ucs"))\r
 702       {\r
 703         cs = GetUserColourScheme(jms, view.getBgColour());\r
 704       }\r
 705       else\r
 706       {\r
 707         cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
 708       }\r
 709 \r
 710       if (cs instanceof ConservationColourScheme)\r
 711       {\r
 712         ( (ConservationColourScheme) cs).inc = view.getConsThreshold();\r
 713       }\r
 714 \r
 715       if (cs instanceof ResidueColourScheme)\r
 716       {\r
 717         ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
 718       }\r
 719       else if (cs instanceof ScoreColourScheme)\r
 720       {\r
 721         ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
 722       }\r
 723     }\r
 724 \r
 725     af.viewport.setGlobalColourScheme(cs);\r
 726 \r
 727     af.viewport.setColourAppliesToAllGroups(false);\r
 728     af.changeColour(af.viewport.getGlobalColourScheme());\r
 729     af.viewport.setColourAppliesToAllGroups(true);\r
 730 \r
 731     if (view.getShowSequenceFeatures())\r
 732     {\r
 733       af.viewport.showSequenceFeatures = true;\r
 734       af.sequenceFeatures.setSelected(true);\r
 735       new SequenceFeatureFetcher(al, af.alignPanel);\r
 736        al.featuresAdded = true;\r
 737     }\r
 738 \r
 739     //LOAD TREES\r
 740     ///////////////////////////////////////\r
 741     if (jms.getTreeCount() > 0)\r
 742     {\r
 743       try\r
 744       {\r
 745         for(int t = 0; t<jms.getTreeCount(); t++)\r
 746         {\r
 747           Tree tree = jms.getTree(t);\r
 748 \r
 749           TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
 750                   tree.getNewick()), tree.getTitle());\r
 751 \r
 752           tp.setBounds( tree.getXpos(),\r
 753                         tree.getYpos(),\r
 754                         tree.getWidth(),\r
 755                         tree.getHeight());\r
 756 \r
 757           tp.fitToWindow.setState(tree.getFitToWindow());\r
 758           tp.fitToWindow_actionPerformed(null);\r
 759           tp.treeCanvas.fontSize = tree.getFontSize();\r
 760           tp.fontSize.setText("Font Size - "+tree.getFontSize());\r
 761           tp.placeholdersMenu.setState(tree.getMarkUnlinked());\r
 762           tp.placeholdersMenu_actionPerformed(null);\r
 763           tp.bootstrapMenu.setState(tree.getShowBootstrap());\r
 764           tp.bootstrapMenu_actionPerformed(null);\r
 765           tp.distanceMenu.setState(tree.getShowDistances());\r
 766           tp.distanceMenu_actionPerformed(null);\r
 767           tp.treeCanvas.threshold = tree.getThreshold();\r
 768           if(tree.getCurrentTree());\r
 769              af.viewport.setCurrentTree(tp.getTree());\r
 770         }\r
 771       }\r
 772       catch (Exception ex)\r
 773       {\r
 774         ex.printStackTrace();\r
 775       }\r
 776     }\r
 777   }\r
 778 }\r