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