src/jalview/gui/Jalview2XML.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21
  22 import jalview.schemes.*;
  23
  24 import java.io.*;
  25
  26 import java.net.*;
  27
  28 import java.util.*;
  29
  30 import java.util.jar.*;
  31
  32 import javax.swing.*;
  33
  34 import org.exolab.castor.xml.*;
  35
  36 import jalview.schemabinding.version2.*;
  37
  38
  39
  40
  41 /**
  42  * DOCUMENT ME!
  43  *
  44  * @author $author$
  45  * @version $Revision$
  46  */
  47 public class Jalview2XML
  48 {
  49
  50   Hashtable seqRefIds;
  51
  52   /**
  53    * This maintains a list of viewports, the key being the
  54    * seqSetId. Important to set historyItem and redoList
  55    * for multiple views
  56    */
  57   Hashtable viewportsAdded;
  58
  59   String uniqueSetSuffix = "";
  60
  61
  62     // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
  63     public void SaveState(File statefile)
  64     {
  65         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
  66
  67         if (frames == null)
  68         {
  69             return;
  70         }
  71
  72         try
  73         {
  74             FileOutputStream fos = new FileOutputStream(statefile);
  75             JarOutputStream jout = new JarOutputStream(fos);
  76
  77             //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
  78             ////////////////////////////////////////////////////
  79             PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
  80                         "UTF-8"));
  81
  82             Vector shortNames = new Vector();
  83
  84             //REVERSE ORDER
  85             for (int i = frames.length - 1; i > -1; i--)
  86             {
  87                 if (frames[i] instanceof AlignFrame)
  88                 {
  89                     AlignFrame af = (AlignFrame) frames[i];
  90
  91                     String shortName = af.getTitle();
  92
  93                     if (shortName.indexOf(File.separatorChar) > -1)
  94                     {
  95                         shortName = shortName.substring(shortName.lastIndexOf(
  96                                     File.separatorChar) + 1);
  97                     }
  98
  99                     int count = 1;
 100
 101                     while (shortNames.contains(shortName))
 102                     {
 103                         if (shortName.endsWith("_" + (count - 1)))
 104                         {
 105                             shortName = shortName.substring(0,
 106                                     shortName.lastIndexOf("_"));
 107                         }
 108
 109                         shortName = shortName.concat("_" + count);
 110                         count++;
 111                     }
 112
 113                     shortNames.addElement(shortName);
 114
 115                     if (!shortName.endsWith(".xml"))
 116                     {
 117                         shortName = shortName + ".xml";
 118                     }
 119
 120                     int ap, apSize= af.alignPanels.size();
 121                     for (ap = 0; ap < apSize; ap++)
 122                     {
 123                       AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
 124                           elementAt(ap);
 125
 126                       SaveState(apanel,
 127                                 apSize == 1 ? shortName : ap+shortName,
 128                                 jout, out);
 129                     }
 130                 }
 131             }
 132
 133             out.close();
 134             jout.close();
 135         }
 136         catch (Exception ex)
 137         {
 138             ex.printStackTrace();
 139         }
 140     }
 141
 142     // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
 143     public boolean SaveAlignment(AlignFrame af, String jarFile,
 144         String fileName)
 145     {
 146         try
 147         {
 148           int ap, apSize= af.alignPanels.size();
 149           FileOutputStream fos = new FileOutputStream(jarFile);
 150           JarOutputStream jout = new JarOutputStream(fos);
 151           PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
 152                 "UTF-8"));
 153           for( ap=0; ap<apSize; ap++)
 154           {
 155             AlignmentPanel apanel = (AlignmentPanel)af.alignPanels.elementAt(ap);
 156
 157             SaveState(apanel,
 158                       apSize==1?fileName:fileName+ap,
 159                       jout, out);
 160           }
 161
 162           out.close();
 163           jout.close();
 164           return true;
 165         }
 166         catch (Exception ex)
 167         {
 168           ex.printStackTrace();
 169           return false;
 170         }
 171     }
 172
 173     /**
 174      * DOCUMENT ME!
 175      *
 176      * @param af DOCUMENT ME!
 177      * @param timeStamp DOCUMENT ME!
 178      * @param fileName DOCUMENT ME!
 179      * @param jout DOCUMENT ME!
 180      * @param out DOCUMENT ME!
 181      */
 182     public JalviewModel SaveState(AlignmentPanel ap,
 183                           String fileName,
 184                           JarOutputStream jout,
 185                           PrintWriter out)
 186     {
 187       if (seqRefIds == null)
 188         seqRefIds = new Hashtable();
 189
 190         Vector userColours = new Vector();
 191
 192         AlignViewport av = ap.av;
 193
 194         JalviewModel object = new JalviewModel();
 195         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 196
 197         object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
 198         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 199
 200         jalview.datamodel.AlignmentI jal = av.alignment;
 201
 202         if(av.hasHiddenRows)
 203         {
 204           jal = jal.getHiddenSequences().getFullAlignment();
 205         }
 206
 207         SequenceSet vamsasSet = new SequenceSet();
 208         Sequence vamsasSeq;
 209         JalviewModelSequence jms = new JalviewModelSequence();
 210
 211         vamsasSet.setGapChar(jal.getGapCharacter() + "");
 212
 213         JSeq jseq;
 214         Vector pdbfiles = null;
 215
 216         //SAVE SEQUENCES
 217         int id = 0;
 218         jalview.datamodel.SequenceI jds;
 219         for (int i = 0; i < jal.getHeight(); i++)
 220         {
 221             jds = jal.getSequenceAt(i);
 222             id = jds.hashCode();
 223
 224             if(seqRefIds.get(id+"")!=null)
 225             {
 226
 227             }
 228             else
 229             {
 230               vamsasSeq = new Sequence();
 231               vamsasSeq.setId(id + "");
 232               vamsasSeq.setName(jds.getName());
 233               vamsasSeq.setSequence(jds.getSequenceAsString());
 234               vamsasSeq.setDescription(jds.getDescription());
 235
 236               if (jds.getDatasetSequence().getDBRef() != null)
 237               {
 238                 jalview.datamodel.DBRefEntry[] dbrefs =
 239                     jds.getDatasetSequence().getDBRef();
 240
 241                 for (int d = 0; d < dbrefs.length; d++)
 242                 {
 243                   DBRef dbref = new DBRef();
 244                   dbref.setSource(dbrefs[d].getSource());
 245                   dbref.setVersion(dbrefs[d].getVersion());
 246                   dbref.setAccessionId(dbrefs[d].getAccessionId());
 247                   vamsasSeq.addDBRef(dbref);
 248                 }
 249               }
 250
 251               vamsasSet.addSequence(vamsasSeq);
 252               seqRefIds.put(id+"", jal.getSequenceAt(i));
 253             }
 254
 255             jseq = new JSeq();
 256             jseq.setStart(jds.getStart());
 257             jseq.setEnd(jds.getEnd());
 258             jseq.setColour( av.getSequenceColour(jds).getRGB());
 259
 260             jseq.setId(id);
 261
 262             if (av.hasHiddenRows)
 263             {
 264               jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 265
 266               if(jal.getSequenceAt(i).getHiddenSequences()!=null)
 267               {
 268                 jalview.datamodel.SequenceI [] reps =
 269                     jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
 270
 271                 for(int h=0; h<reps.length; h++)
 272                 {
 273                   jseq.addHiddenSequences(
 274                       jal.findIndex(reps[h])
 275                       );
 276                 }
 277               }
 278             }
 279
 280
 281             if(jds.getDatasetSequence().getSequenceFeatures()!=null)
 282             {
 283               jalview.datamodel.SequenceFeature[] sf
 284                   = jds.getDatasetSequence().getSequenceFeatures();
 285               int index = 0;
 286               while(index < sf.length)
 287               {
 288                 Features features = new Features();
 289
 290                 features.setBegin(sf[index].getBegin());
 291                 features.setEnd(sf[index].getEnd());
 292                 features.setDescription(sf[index].getDescription());
 293                 features.setType(sf[index].getType());
 294                 features.setFeatureGroup(sf[index].getFeatureGroup());
 295                 features.setScore(sf[index].getScore());
 296                 if(sf[index].links!=null)
 297                 {
 298                   for(int l=0; l<sf[index].links.size(); l++)
 299                   {
 300                     OtherData keyValue = new OtherData();
 301                     keyValue.setKey("LINK_"+l);
 302                     keyValue.setValue(sf[index].links.elementAt(l).toString());
 303                     features.addOtherData(keyValue);
 304                   }
 305                 }
 306                 if(sf[index].otherDetails!=null)
 307                 {
 308                   String key;
 309                   Enumeration keys = sf[index].otherDetails.keys();
 310                   while(keys.hasMoreElements())
 311                   {
 312                     key = keys.nextElement().toString();
 313                     OtherData keyValue = new OtherData();
 314                     keyValue.setKey( key );
 315                     keyValue.setValue(
 316                         sf[index].otherDetails.get(key).toString());
 317                     features.addOtherData(keyValue);
 318                   }
 319                 }
 320
 321                 jseq.addFeatures(features);
 322                 index ++;
 323               }
 324             }
 325
 326             if(jds.getDatasetSequence().getPDBId()!=null)
 327             {
 328               Enumeration en = jds.getDatasetSequence().getPDBId().elements();
 329               while(en.hasMoreElements())
 330               {
 331                 Pdbids pdb = new Pdbids();
 332                 jalview.datamodel.PDBEntry entry
 333                    = (jalview.datamodel.PDBEntry)en.nextElement();
 334
 335                 pdb.setId(entry.getId());
 336                 pdb.setType(entry.getType());
 337
 338
 339                 if(entry.getFile()!=null)
 340                 {
 341                   pdb.setFile(entry.getFile());
 342                   if(pdbfiles==null)
 343                     pdbfiles = new Vector();
 344
 345                   if(!pdbfiles.contains(entry.getId()))
 346                   {
 347                     pdbfiles.addElement(entry.getId());
 348                     try
 349                     {
 350                       File file = new File(entry.getFile());
 351                       if(file.exists() && jout!=null)
 352                       {
 353                         byte[] data = new byte[ (int) file.length()];
 354                         jout.putNextEntry(new JarEntry(entry.getId()));
 355                         DataInputStream dis = new DataInputStream(new
 356                             FileInputStream(file));
 357                         dis.readFully(data);
 358
 359                         DataOutputStream dout = new DataOutputStream(jout);
 360                         dout.write(data, 0, data.length);
 361                         jout.closeEntry();
 362                       }
 363                     }
 364                     catch (Exception ex)
 365                     {
 366                       ex.printStackTrace();
 367                     }
 368                   }
 369                 }
 370
 371
 372                 if(entry.getProperty()!=null)
 373                 {
 374                   PdbentryItem item = new PdbentryItem();
 375                   Hashtable properties = entry.getProperty();
 376                   Enumeration en2 = properties.keys();
 377                   while(en2.hasMoreElements())
 378                   {
 379                     Property prop = new Property();
 380                     String key = en2.nextElement().toString();
 381                     prop.setName(key);
 382                     prop.setValue( properties.get(key).toString() );
 383                     item.addProperty(prop);
 384                   }
 385                   pdb.addPdbentryItem(item);
 386                 }
 387
 388                 jseq.addPdbids(pdb);
 389               }
 390             }
 391
 392             jms.addJSeq(jseq);
 393         }
 394
 395         if(av.hasHiddenRows)
 396           jal = av.alignment;
 397
 398
 399         //SAVE TREES
 400         ///////////////////////////////////
 401         if (av.currentTree != null)
 402         {
 403           // FIND ANY ASSOCIATED TREES
 404           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 405           if (Desktop.desktop != null)
 406           {
 407             JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 408
 409             for (int t = 0; t < frames.length; t++)
 410             {
 411               if (frames[t] instanceof TreePanel)
 412               {
 413                 TreePanel tp = (TreePanel) frames[t];
 414
 415                 if (tp.treeCanvas.av.alignment == jal)
 416                 {
 417                   Tree tree = new Tree();
 418                   tree.setTitle(tp.getTitle());
 419                   tree.setCurrentTree( (av.currentTree == tp.getTree()));
 420                   tree.setNewick(tp.getTree().toString());
 421                   tree.setThreshold(tp.treeCanvas.threshold);
 422
 423                   tree.setFitToWindow(tp.fitToWindow.getState());
 424                   tree.setFontName(tp.getTreeFont().getName());
 425                   tree.setFontSize(tp.getTreeFont().getSize());
 426                   tree.setFontStyle(tp.getTreeFont().getStyle());
 427                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 428
 429                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
 430                   tree.setShowDistances(tp.distanceMenu.getState());
 431
 432                   tree.setHeight(tp.getHeight());
 433                   tree.setWidth(tp.getWidth());
 434                   tree.setXpos(tp.getX());
 435                   tree.setYpos(tp.getY());
 436
 437                   jms.addTree(tree);
 438                 }
 439               }
 440             }
 441           }
 442         }
 443
 444         //SAVE ANNOTATIONS
 445         if (jal.getAlignmentAnnotation() != null)
 446         {
 447             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 448
 449             for (int i = 0; i < aa.length; i++)
 450             {
 451                 Annotation an = new Annotation();
 452
 453                 if (aa[i].label.equals("Quality") ||
 454                         aa[i].label.equals("Conservation") ||
 455                         aa[i].label.equals("Consensus"))
 456                 {
 457                     an.setLabel(aa[i].label);
 458                     an.setGraph(true);
 459                     vamsasSet.addAnnotation(an);
 460                     continue;
 461                 }
 462
 463
 464                 an.setDescription(aa[i].description);
 465
 466                 if(aa[i].sequenceRef!=null)
 467                  {
 468                    an.setSequenceRef(aa[i].sequenceRef.getName());
 469                  }
 470
 471                 if(aa[i].graph>0)
 472                 {
 473                   an.setGraph(true);
 474                   an.setGraphType(aa[i].graph);
 475                   an.setGraphGroup(aa[i].graphGroup);
 476                   if(aa[i].getThreshold()!=null)
 477                   {
 478                     ThresholdLine line = new ThresholdLine();
 479                     line.setLabel(aa[i].getThreshold().label);
 480                     line.setValue(aa[i].getThreshold().value);
 481                     line.setColour(aa[i].getThreshold().colour.getRGB());
 482                     an.setThresholdLine(line);
 483                   }
 484                 }
 485                 else
 486                   an.setGraph(false);
 487
 488                 an.setLabel(aa[i].label);
 489
 490                 AnnotationElement ae;
 491
 492                 for (int a = 0; a < aa[i].annotations.length; a++)
 493                 {
 494                     if ((aa[i] == null) || (aa[i].annotations[a] == null))
 495                     {
 496                         continue;
 497                     }
 498
 499                     ae = new AnnotationElement();
 500                     ae.setDescription(aa[i].annotations[a].description);
 501                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 502                     ae.setValue(aa[i].annotations[a].value);
 503                     ae.setPosition(a);
 504                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
 505                         "");
 506
 507                     if(aa[i].annotations[a].colour!=java.awt.Color.black)
 508                       ae.setColour(aa[i].annotations[a].colour.getRGB());
 509
 510                     an.addAnnotationElement(ae);
 511                 }
 512
 513                 vamsasSet.addAnnotation(an);
 514             }
 515         }
 516
 517         //SAVE GROUPS
 518         if (jal.getGroups() != null)
 519         {
 520             JGroup[] groups = new JGroup[jal.getGroups().size()];
 521
 522             for (int i = 0; i < groups.length; i++)
 523             {
 524                 groups[i] = new JGroup();
 525
 526                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
 527                                                                                           .elementAt(i);
 528                 groups[i].setStart(sg.getStartRes());
 529                 groups[i].setEnd(sg.getEndRes());
 530                 groups[i].setName(sg.getName());
 531                 if(sg.cs!=null)
 532                 {
 533                   if (sg.cs.conservationApplied())
 534                   {
 535                     groups[i].setConsThreshold(sg.cs.getConservationInc());
 536
 537                     if (sg.cs instanceof jalview.schemes.UserColourScheme)
 538                     {
 539                       groups[i].setColour(SetUserColourScheme(sg.cs,
 540                           userColours,
 541                           jms));
 542                     }
 543                     else
 544                     {
 545                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.
 546                           cs));
 547                     }
 548                   }
 549                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 550                   {
 551                     groups[i].setColour(
 552                         ColourSchemeProperty.getColourName(
 553                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
 554                   }
 555                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 556                   {
 557                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 558                         jms));
 559                   }
 560                   else
 561                   {
 562                     groups[i].setColour(ColourSchemeProperty.getColourName(
 563                         sg.cs));
 564                   }
 565
 566                   groups[i].setPidThreshold(sg.cs.getThreshold());
 567                 }
 568
 569                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 570                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 571                 groups[i].setDisplayText(sg.getDisplayText());
 572                 groups[i].setColourText(sg.getColourText());
 573                 groups[i].setTextCol1(sg.textColour.getRGB());
 574                 groups[i].setTextCol2(sg.textColour2.getRGB());
 575                 groups[i].setTextColThreshold(sg.thresholdTextColour);
 576
 577                 for (int s = 0; s < sg.getSize(false); s++)
 578                 {
 579                     jalview.datamodel.Sequence seq =
 580                         (jalview.datamodel.Sequence) sg.getSequenceAt(s);
 581                     groups[i].addSeq(seq.hashCode());
 582                 }
 583             }
 584
 585             jms.setJGroup(groups);
 586         }
 587
 588
 589         ///////////SAVE VIEWPORT
 590         Viewport view = new Viewport();
 591         view.setTitle(ap.alignFrame.getTitle());
 592         view.setSequenceSetId(av.getSequenceSetId());
 593         view.setViewName(av.viewName);
 594         view.setGatheredViews(av.gatherViewsHere);
 595
 596
 597         if (ap.av.explodedPosition != null)
 598         {
 599           view.setXpos(av.explodedPosition.x);
 600           view.setYpos(av.explodedPosition.y);
 601           view.setWidth(av.explodedPosition.width);
 602           view.setHeight(av.explodedPosition.height);
 603         }
 604         else
 605         {
 606           view.setXpos(ap.alignFrame.getBounds().x);
 607           view.setYpos(ap.alignFrame.getBounds().y);
 608           view.setWidth(ap.alignFrame.getBounds().width);
 609           view.setHeight(ap.alignFrame.getBounds().height);
 610         }
 611
 612         view.setStartRes(av.startRes);
 613         view.setStartSeq(av.startSeq);
 614
 615         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 616         {
 617             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 618                     userColours, jms));
 619         }
 620         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 621         {
 622            jalview.schemes.AnnotationColourGradient acg
 623               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
 624
 625             AnnotationColours ac = new AnnotationColours();
 626             ac.setAboveThreshold(acg.getAboveThreshold());
 627             ac.setThreshold(acg.getAnnotationThreshold());
 628             ac.setAnnotation(acg.getAnnotation());
 629             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 630               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 631                     userColours, jms));
 632             else
 633               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 634
 635             ac.setMaxColour(acg.getMaxColour().getRGB());
 636             ac.setMinColour(acg.getMinColour().getRGB());
 637             view.setAnnotationColours(ac);
 638             view.setBgColour("AnnotationColourGradient");
 639         }
 640         else
 641         {
 642             view.setBgColour(ColourSchemeProperty.getColourName(
 643                     av.getGlobalColourScheme()));
 644         }
 645
 646         ColourSchemeI cs = av.getGlobalColourScheme();
 647
 648         if(cs!=null)
 649         {
 650           if (cs.conservationApplied())
 651           {
 652             view.setConsThreshold(cs.getConservationInc());
 653             if (cs instanceof jalview.schemes.UserColourScheme)
 654               view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 655           }
 656
 657           if (cs instanceof ResidueColourScheme)
 658           {
 659             view.setPidThreshold(cs.getThreshold());
 660           }
 661         }
 662
 663         view.setConservationSelected(av.getConservationSelected());
 664         view.setPidSelected(av.getAbovePIDThreshold());
 665         view.setFontName(av.font.getName());
 666         view.setFontSize(av.font.getSize());
 667         view.setFontStyle(av.font.getStyle());
 668         view.setRenderGaps(av.renderGaps);
 669         view.setShowAnnotation(av.getShowAnnotation());
 670         view.setShowBoxes(av.getShowBoxes());
 671         view.setShowColourText(av.getColourText());
 672         view.setShowFullId(av.getShowJVSuffix());
 673         view.setRightAlignIds(av.rightAlignIds);
 674         view.setShowSequenceFeatures(av.showSequenceFeatures);
 675         view.setShowText(av.getShowText());
 676         view.setWrapAlignment(av.getWrapAlignment());
 677         view.setTextCol1(av.textColour.getRGB());
 678         view.setTextCol2(av.textColour2.getRGB());
 679         view.setTextColThreshold(av.thresholdTextColour);
 680
 681
 682         if(av.featuresDisplayed!=null)
 683         {
 684           jalview.schemabinding.version2.FeatureSettings fs
 685               = new jalview.schemabinding.version2.FeatureSettings();
 686
 687           String [] renderOrder =
 688               ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 689
 690           Vector settingsAdded = new Vector();
 691           for(int ro=0; ro<renderOrder.length; ro++)
 692           {
 693             Setting setting = new Setting();
 694             setting.setType(renderOrder[ro]);
 695             setting.setColour(
 696                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
 697                 );
 698
 699             setting.setDisplay(
 700                 av.featuresDisplayed.containsKey(renderOrder[ro])
 701                 );
 702
 703             fs.addSetting(setting);
 704             settingsAdded.addElement(renderOrder[ro]);
 705           }
 706
 707           //Make sure we save none displayed feature settings
 708           Enumeration en =
 709               ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 710           while(en.hasMoreElements())
 711           {
 712             String key = en.nextElement().toString();
 713             if(settingsAdded.contains(key))
 714               continue;
 715
 716             Setting setting = new Setting();
 717             setting.setType(key);
 718             setting.setColour(
 719                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 720                 );
 721
 722             setting.setDisplay(false);
 723
 724             fs.addSetting(setting);
 725             settingsAdded.addElement(key);
 726           }
 727
 728           jms.setFeatureSettings(fs);
 729
 730         }
 731
 732         if(av.hasHiddenColumns)
 733         {
 734           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
 735           {
 736             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
 737             HiddenColumns hc = new HiddenColumns();
 738             hc.setStart(region[0]);
 739             hc.setEnd(region[1]);
 740             view.addHiddenColumns(hc);
 741           }
 742         }
 743
 744         jms.addViewport(view);
 745
 746
 747         object.setJalviewModelSequence(jms);
 748         object.getVamsasModel().addSequenceSet(vamsasSet);
 749
 750         if(out!=null)
 751         {
 752           //We may not want to right the object to disk,
 753           //eg we can copy the alignViewport to a new view object
 754           //using save and then load
 755           try
 756           {
 757             if (!fileName.endsWith(".xml"))
 758             {
 759               fileName = fileName + ".xml";
 760             }
 761
 762             JarEntry entry = new JarEntry(fileName);
 763             jout.putNextEntry(entry);
 764
 765             object.marshal(out);
 766           }
 767           catch (Exception ex)
 768           {
 769             ex.printStackTrace();
 770           }
 771         }
 772         return object;
 773     }
 774
 775     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 776         Vector userColours, JalviewModelSequence jms)
 777     {
 778         String id = null;
 779         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 780
 781         if (!userColours.contains(ucs))
 782         {
 783             userColours.add(ucs);
 784
 785             java.awt.Color[] colours = ucs.getColours();
 786             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
 787             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 788
 789             for (int i = 0; i < colours.length; i++)
 790             {
 791                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 792                 col.setName(ResidueProperties.aa[i]);
 793                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 794                 jbucs.addColour(col);
 795             }
 796             if(ucs.getLowerCaseColours()!=null)
 797             {
 798               colours = ucs.getLowerCaseColours();
 799               for (int i = 0; i < colours.length; i++)
 800              {
 801                  jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 802                  col.setName(ResidueProperties.aa[i].toLowerCase());
 803                  col.setRGB(jalview.util.Format.getHexString(colours[i]));
 804                  jbucs.addColour(col);
 805              }
 806             }
 807
 808             id = "ucs" + userColours.indexOf(ucs);
 809             uc.setId(id);
 810             uc.setUserColourScheme(jbucs);
 811             jms.addUserColours(uc);
 812         }
 813
 814         return id;
 815     }
 816
 817    jalview.schemes.UserColourScheme GetUserColourScheme(
 818         JalviewModelSequence jms, String id)
 819     {
 820         UserColours[] uc = jms.getUserColours();
 821         UserColours colours = null;
 822
 823         for (int i = 0; i < uc.length; i++)
 824         {
 825             if (uc[i].getId().equals(id))
 826             {
 827                 colours = uc[i];
 828
 829                 break;
 830             }
 831         }
 832
 833         java.awt.Color[] newColours = new java.awt.Color[24];
 834
 835         for (int i = 0; i < 24; i++)
 836         {
 837             newColours[i] = new java.awt.Color(Integer.parseInt(
 838                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 839         }
 840
 841         jalview.schemes.UserColourScheme ucs =
 842             new jalview.schemes.UserColourScheme(newColours);
 843
 844         if (colours.getUserColourScheme().getColourCount() > 24)
 845         {
 846           newColours = new java.awt.Color[23];
 847           for (int i = 0; i < 23; i++)
 848           {
 849             newColours[i] = new java.awt.Color(Integer.parseInt(
 850                 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
 851           }
 852           ucs.setLowerCaseColours(newColours);
 853         }
 854
 855         return ucs;
 856     }
 857
 858
 859     /**
 860      * DOCUMENT ME!
 861      *
 862      * @param file DOCUMENT ME!
 863      */
 864     public AlignFrame LoadJalviewAlign(final String file)
 865     {
 866         uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
 867
 868         jalview.gui.AlignFrame af = null;
 869
 870         seqRefIds = new Hashtable();
 871         viewportsAdded = new Hashtable();
 872
 873         Vector gatherToThisFrame= new Vector();
 874
 875         try
 876         {
 877             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 878             URL url = null;
 879
 880             if (file.startsWith("http://"))
 881             {
 882                 url = new URL(file);
 883             }
 884
 885             JarInputStream jin = null;
 886             JarEntry jarentry = null;
 887             int entryCount = 1;
 888
 889             do
 890             {
 891                 if (url != null)
 892                 {
 893                     jin = new JarInputStream(url.openStream());
 894                 }
 895                 else
 896                 {
 897                     jin = new JarInputStream(new FileInputStream(file));
 898                 }
 899
 900                 for (int i = 0; i < entryCount; i++)
 901                 {
 902                     jarentry = jin.getNextJarEntry();
 903                 }
 904
 905                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 906                 {
 907                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 908                     JalviewModel object = new JalviewModel();
 909
 910                     Unmarshaller unmar = new Unmarshaller(object);
 911                     unmar.setValidation(false);
 912                     object = (JalviewModel) unmar.unmarshal( in );
 913
 914                     af = LoadFromObject(object, file, true);
 915                     if(af.viewport.gatherViewsHere)
 916                     {
 917                       gatherToThisFrame.add(af);
 918                     }
 919                     entryCount++;
 920                 }
 921                 else if (jarentry != null)
 922                 {
 923                   //Some other file here.
 924                   entryCount++;
 925                 }
 926             }
 927             while (jarentry != null);
 928         }
 929         catch(java.net.UnknownHostException ex)
 930         {
 931           ex.printStackTrace();
 932           System.err.println("Couldn't locate Jalview XML file : " +
 933               ex + "\n");
 934
 935           javax.swing.SwingUtilities.invokeLater(new Runnable()
 936           {
 937             public void run()
 938             {
 939               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 940                   "Couldn't locate " + file,
 941                   "URL not found",
 942                   JOptionPane.WARNING_MESSAGE);
 943             }
 944           });
 945         }
 946         catch (Exception ex)
 947         {
 948           //Is Version 1 Jar file?
 949           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 950
 951           if(af!=null)
 952           {
 953             System.out.println("Successfully loaded archive file");
 954             return af;
 955           }
 956
 957             System.err.println("Exception whilst loading jalview XML file : " +
 958                 ex + "\n");
 959             javax.swing.SwingUtilities.invokeLater(new Runnable()
 960             {
 961               public void run()
 962               {
 963
 964                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 965                     "Error loading  " + file,
 966                     "Error loading Jalview file",
 967                     JOptionPane.WARNING_MESSAGE);
 968               }});
 969         }
 970
 971         if (Desktop.instance != null)
 972           Desktop.instance.stopLoading();
 973
 974         for (int i = 0; i < gatherToThisFrame.size(); i++)
 975         {
 976           Desktop.instance.gatherViews(
 977               (AlignFrame) gatherToThisFrame.elementAt(i));
 978         }
 979
 980         return af;
 981     }
 982
 983     String loadPDBFile(String file, String pdbId)
 984     {
 985       System.out.println(file +" "+pdbId);
 986       try
 987       {
 988         JarInputStream jin = null;
 989
 990         if (file.startsWith("http://"))
 991         {
 992           jin = new JarInputStream(new URL(file).openStream());
 993         }
 994         else
 995         {
 996           jin = new JarInputStream(new FileInputStream(file));
 997         }
 998
 999         JarEntry entry = null;
1000         do
1001         {
1002           entry = jin.getNextJarEntry();
1003         }
1004         while (!entry.getName().equals(pdbId));
1005
1006         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1007         File outFile = File.createTempFile("jalview_pdb", ".txt");
1008         outFile.deleteOnExit();
1009         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1010         String data;
1011
1012         while ( (data = in.readLine()) != null)
1013         {
1014           out.println(data);
1015         }
1016         out.close();
1017         return outFile.getAbsolutePath();
1018
1019       }
1020       catch (Exception ex)
1021       {
1022         ex.printStackTrace();
1023       }
1024
1025       return null;
1026     }
1027
1028
1029     AlignFrame LoadFromObject(JalviewModel object,
1030                               String file,
1031                               boolean loadTrees )
1032     {
1033         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1034         Sequence[] vamsasSeq = vamsasSet.getSequence();
1035
1036         JalviewModelSequence jms = object.getJalviewModelSequence();
1037
1038         Viewport view = jms.getViewport(0);
1039
1040         //////////////////////////////////
1041         //LOAD SEQUENCES
1042
1043         Vector hiddenSeqs = null;
1044         jalview.datamodel.Sequence jseq;
1045
1046         ArrayList tmpseqs = new ArrayList();
1047
1048         boolean multipleView = false;
1049
1050         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1051         for (int i = 0; i < JSEQ.length; i++)
1052         {
1053           String seqId = JSEQ[i].getId() + "";
1054
1055           if (seqRefIds.get(seqId) != null)
1056           {
1057             tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1058             multipleView = true;
1059           }
1060           else
1061           {
1062             jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1063                 vamsasSeq[i].getSequence());
1064             jseq.setDescription(vamsasSeq[i].getDescription());
1065             jseq.setStart(JSEQ[i].getStart());
1066             jseq.setEnd(JSEQ[i].getEnd());
1067             seqRefIds.put(vamsasSeq[i].getId(), jseq);
1068             tmpseqs.add( jseq );
1069           }
1070
1071
1072
1073           if (JSEQ[i].getHidden())
1074           {
1075             if (hiddenSeqs == null)
1076               hiddenSeqs = new Vector();
1077
1078
1079             hiddenSeqs.addElement(
1080                 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1081           }
1082
1083         }
1084
1085         ///SequenceFeatures are added to the DatasetSequence,
1086         // so we must create the dataset before loading features
1087         /////////////////////////////////
1088
1089
1090       jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1091           tmpseqs.size()];
1092
1093        tmpseqs.toArray(orderedSeqs) ;
1094
1095
1096         jalview.datamodel.Alignment al =
1097             new jalview.datamodel.Alignment(orderedSeqs);
1098
1099         al.setDataset(null);
1100         /////////////////////////////////
1101
1102
1103         Hashtable pdbloaded = new Hashtable();
1104         if(!multipleView)
1105         {
1106           for (int i = 0; i < vamsasSeq.length; i++)
1107           {
1108             if (JSEQ[i].getFeaturesCount() > 0)
1109             {
1110               Features[] features = JSEQ[i].getFeatures();
1111               for (int f = 0; f < features.length; f++)
1112               {
1113                 jalview.datamodel.SequenceFeature sf
1114                     = new jalview.datamodel.SequenceFeature(features[f].getType(),
1115                     features[f].getDescription(), features[f].getStatus(),
1116                     features[f].getBegin(), features[f].getEnd(),
1117                     features[f].getFeatureGroup());
1118
1119                 sf.setScore(features[f].getScore());
1120                 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1121                 {
1122                   OtherData keyValue = features[f].getOtherData(od);
1123                   if (keyValue.getKey().startsWith("LINK"))
1124                     sf.addLink(keyValue.getValue());
1125                   else
1126                     sf.setValue(keyValue.getKey(), keyValue.getValue());
1127
1128                 }
1129
1130                 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1131               }
1132             }
1133             if (JSEQ[i].getPdbidsCount() > 0)
1134             {
1135               Pdbids[] ids = JSEQ[i].getPdbids();
1136               for (int p = 0; p < ids.length; p++)
1137               {
1138                 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1139                     PDBEntry();
1140                 entry.setId(ids[p].getId());
1141                 entry.setType(ids[p].getType());
1142                 if (ids[p].getFile() != null)
1143                 {
1144                   if (!pdbloaded.containsKey(ids[p].getFile()))
1145                   {
1146                     String tmppdb = loadPDBFile(file, ids[p].getId());
1147                     entry.setFile(tmppdb);
1148                     pdbloaded.put(ids[p].getId(), tmppdb);
1149                   }
1150                   else
1151                     entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1152                 }
1153
1154                 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1155               }
1156             }
1157             if (vamsasSeq[i].getDBRefCount() > 0)
1158             {
1159               for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1160               {
1161                 jalview.datamodel.DBRefEntry entry =
1162                     new jalview.datamodel.DBRefEntry(
1163                         vamsasSeq[i].getDBRef(d).getSource(),
1164                         vamsasSeq[i].getDBRef(d).getVersion(),
1165                         vamsasSeq[i].getDBRef(d).getAccessionId()
1166                     );
1167                 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1168               }
1169
1170             }
1171           }
1172         }
1173
1174
1175          /////////////////////////////////
1176         //////////////////////////////////
1177         //LOAD ANNOTATIONS
1178         boolean hideQuality = true,
1179             hideConservation = true,
1180             hideConsensus = true;
1181
1182         if (vamsasSet.getAnnotationCount()>0)
1183         {
1184             Annotation[] an = vamsasSet.getAnnotation();
1185
1186             for (int i = 0; i < an.length; i++)
1187             {
1188                if (an[i].getLabel().equals("Quality"))
1189                 {
1190                  hideQuality = false;
1191                  continue;
1192                 }
1193                else if(an[i].getLabel().equals("Conservation"))
1194                {
1195                  hideConservation = false;
1196                  continue;
1197                }
1198                else if(an[i].getLabel().equals("Consensus"))
1199                {
1200                  hideConsensus = false;
1201                  continue;
1202                }
1203
1204                 AnnotationElement[] ae = an[i].getAnnotationElement();
1205                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1206
1207                 for (int aa = 0; aa < ae.length; aa++)
1208                 {
1209                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1210                             ae[aa].getDescription(),
1211                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1212                             ae[aa].getValue());
1213                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1214                 }
1215
1216                 jalview.datamodel.AlignmentAnnotation jaa = null;
1217
1218                 if (an[i].getGraph())
1219                 {
1220                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1221                       an[i].getDescription(), anot, 0, 0,
1222                       an[i].getGraphType());
1223
1224                   jaa.graphGroup = an[i].getGraphGroup();
1225
1226                   if (an[i].getThresholdLine() != null)
1227                   {
1228                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1229                                   an[i].getThresholdLine().getValue(),
1230                                   an[i].getThresholdLine().getLabel(),
1231                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1232                              );
1233
1234                   }
1235
1236                 }
1237                 else
1238                 {
1239                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1240                             an[i].getDescription(), anot);
1241                 }
1242
1243                 if(an[i].getSequenceRef()!=null)
1244                 {
1245                   jaa.createSequenceMapping(
1246                       al.findName(an[i].getSequenceRef()), 1, true
1247                       );
1248                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1249                 }
1250
1251                 al.addAnnotation(jaa);
1252             }
1253         }
1254
1255         /////////////////////////
1256         //LOAD GROUPS
1257         if (jms.getJGroupCount() > 0)
1258         {
1259             JGroup[] groups = jms.getJGroup();
1260
1261             for (int i = 0; i < groups.length; i++)
1262             {
1263                 ColourSchemeI cs = null;
1264
1265                 if (groups[i].getColour() != null)
1266                 {
1267                     if (groups[i].getColour().startsWith("ucs"))
1268                     {
1269                         cs = GetUserColourScheme(jms, groups[i].getColour());
1270                     }
1271                     else
1272                     {
1273                         cs = ColourSchemeProperty.getColour(al,
1274                                 groups[i].getColour());
1275                     }
1276
1277                     if(cs!=null)
1278                       cs.setThreshold(groups[i].getPidThreshold(), true);
1279                 }
1280
1281                 Vector seqs = new Vector();
1282
1283                 for (int s = 0; s < groups[i].getSeqCount(); s++)
1284                 {
1285                     String seqId = groups[i].getSeq(s)+"";
1286                     seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1287                 }
1288
1289                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1290                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1291                         groups[i].getDisplayText(), groups[i].getColourText(),
1292                         groups[i].getStart(), groups[i].getEnd());
1293
1294                 sg.setOutlineColour(new java.awt.Color(
1295                         groups[i].getOutlineColour()));
1296
1297                 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1298                 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1299                 sg.thresholdTextColour = groups[i].getTextColThreshold();
1300
1301                 if (groups[i].getConsThreshold() != 0)
1302                 {
1303                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1304                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1305                             sg.getWidth() - 1);
1306                     c.calculate();
1307                     c.verdict(false, 25);
1308                     sg.cs.setConservation(c);
1309                 }
1310
1311                 al.addGroup(sg);
1312             }
1313         }
1314
1315
1316         /////////////////////////////////
1317         // LOAD VIEWPORT
1318
1319         AlignFrame af = new AlignFrame(al,
1320                                        view.getWidth(),
1321                                        view.getHeight() );
1322
1323         af.setFileName(file, "Jalview");
1324
1325         for (int i = 0; i < JSEQ.length; i++)
1326         {
1327           af.viewport.setSequenceColour(
1328               af.viewport.alignment.getSequenceAt(i),
1329               new java.awt.Color(
1330                   JSEQ[i].getColour()));
1331         }
1332
1333         //If we just load in the same jar file again, the sequenceSetId
1334         //will be the same, and we end up with multiple references
1335         //to the same sequenceSet. We must modify this id on load
1336         //so that each load of the file gives a unique id
1337         String uniqueSeqSetId =  view.getSequenceSetId()+uniqueSetSuffix;
1338
1339         af.viewport.gatherViewsHere = view.getGatheredViews();
1340
1341         if (view.getSequenceSetId() != null)
1342         {
1343           jalview.gui.AlignViewport av =
1344               (jalview.gui.AlignViewport)
1345               viewportsAdded.get(uniqueSeqSetId);
1346
1347           af.viewport.sequenceSetID = uniqueSeqSetId;
1348           if(av!=null)
1349           {
1350
1351             af.viewport.historyList = av.historyList;
1352             af.viewport.redoList = av.redoList;
1353           }
1354           else
1355           {
1356             viewportsAdded.put(uniqueSeqSetId, af.viewport);
1357           }
1358
1359           PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1360         }
1361         if(hiddenSeqs!=null)
1362         {
1363           for(int s=0; s<JSEQ.length; s++)
1364           {
1365             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1366             {
1367               al.getSequenceAt(s).addHiddenSequence(
1368                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
1369                   );
1370             }
1371           }
1372
1373           jalview.datamodel.SequenceI [] hseqs = new
1374               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1375
1376           for(int s=0; s<hiddenSeqs.size(); s++)
1377             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1378
1379           af.viewport.hideSequence( hseqs );
1380
1381         }
1382
1383
1384         if((hideConsensus || hideQuality || hideConservation)
1385             && al.getAlignmentAnnotation()!=null)
1386         {
1387           int hSize = al.getAlignmentAnnotation().length;
1388           for (int h = 0; h < hSize; h++)
1389           {
1390             if (
1391                 (hideConsensus &&
1392                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1393                 ||
1394                 (hideQuality &&
1395                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1396                 ||
1397                 (hideConservation &&
1398                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1399             {
1400               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1401               hSize--;
1402               h--;
1403             }
1404           }
1405           af.alignPanel.adjustAnnotationHeight();
1406         }
1407
1408         if(view.getViewName()!=null)
1409         {
1410           af.viewport.viewName = view.getViewName();
1411           af.setInitialTabVisible();
1412         }
1413         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1414             view.getHeight());
1415
1416         af.viewport.setShowAnnotation(view.getShowAnnotation());
1417         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1418
1419         af.viewport.setColourText(view.getShowColourText());
1420
1421         af.viewport.setConservationSelected(view.getConservationSelected());
1422         af.viewport.setShowJVSuffix(view.getShowFullId());
1423         af.viewport.rightAlignIds=view.getRightAlignIds();
1424         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1425                 view.getFontStyle(), view.getFontSize()));
1426         af.alignPanel.fontChanged();
1427         af.viewport.setRenderGaps(view.getRenderGaps());
1428         af.viewport.setWrapAlignment(view.getWrapAlignment());
1429         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1430         af.viewport.setShowAnnotation(view.getShowAnnotation());
1431         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1432
1433         af.viewport.setShowBoxes(view.getShowBoxes());
1434
1435         af.viewport.setShowText(view.getShowText());
1436
1437         af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1438         af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1439         af.viewport.thresholdTextColour = view.getTextColThreshold();
1440
1441         af.viewport.setStartRes(view.getStartRes());
1442         af.viewport.setStartSeq(view.getStartSeq());
1443
1444         ColourSchemeI cs = null;
1445
1446         if (view.getBgColour() != null)
1447         {
1448             if (view.getBgColour().startsWith("ucs"))
1449             {
1450                 cs = GetUserColourScheme(jms, view.getBgColour());
1451             }
1452             else if(view.getBgColour().startsWith("Annotation"))
1453             {
1454               //int find annotation
1455               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1456               {
1457                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1458                     equals(view.getAnnotationColours().getAnnotation()))
1459                 {
1460                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1461                       getThreshold() == null)
1462                   {
1463                     af.viewport.alignment.getAlignmentAnnotation()[i].
1464                         setThreshold(
1465                             new jalview.datamodel.GraphLine(
1466                                 view.getAnnotationColours().getThreshold(),
1467                                 "Threshold", java.awt.Color.black)
1468
1469                         );
1470                   }
1471
1472
1473                   if (view.getAnnotationColours().getColourScheme().equals(
1474                       "None"))
1475                   {
1476                     cs = new AnnotationColourGradient(
1477                         af.viewport.alignment.getAlignmentAnnotation()[i],
1478                         new java.awt.Color(view.getAnnotationColours().
1479                                            getMinColour()),
1480                         new java.awt.Color(view.getAnnotationColours().
1481                                            getMaxColour()),
1482                         view.getAnnotationColours().getAboveThreshold());
1483                   }
1484                   else if (view.getAnnotationColours().getColourScheme().
1485                            startsWith("ucs"))
1486                   {
1487                      cs = new AnnotationColourGradient(
1488                          af.viewport.alignment.getAlignmentAnnotation()[i],
1489                          GetUserColourScheme(jms, view.getAnnotationColours().
1490                                                         getColourScheme()),
1491                          view.getAnnotationColours().getAboveThreshold()
1492                          );
1493                    }
1494                    else
1495                    {
1496                      cs = new AnnotationColourGradient(
1497                          af.viewport.alignment.getAlignmentAnnotation()[i],
1498                          ColourSchemeProperty.getColour(al,
1499                          view.getAnnotationColours().getColourScheme()),
1500                          view.getAnnotationColours().getAboveThreshold()
1501                          );
1502                    }
1503
1504                   // Also use these settings for all the groups
1505                   if (al.getGroups() != null)
1506                     for (int g = 0; g < al.getGroups().size(); g++)
1507                     {
1508                       jalview.datamodel.SequenceGroup sg
1509                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1510
1511                       if(sg.cs == null)
1512                         continue;
1513
1514
1515                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1516                       {
1517                         sg.cs = new AnnotationColourGradient(
1518                             af.viewport.alignment.getAlignmentAnnotation()[i],
1519                             new java.awt.Color(view.getAnnotationColours().
1520                                                getMinColour()),
1521                             new java.awt.Color(view.getAnnotationColours().
1522                                                getMaxColour()),
1523                             view.getAnnotationColours().getAboveThreshold());
1524                       }
1525                       else*/
1526                       {
1527                         sg.cs = new AnnotationColourGradient(
1528                             af.viewport.alignment.getAlignmentAnnotation()[i],
1529                             sg.cs,
1530                             view.getAnnotationColours().getAboveThreshold()
1531                             );
1532                       }
1533
1534                     }
1535
1536
1537                   break;
1538                 }
1539
1540               }
1541             }
1542             else
1543             {
1544                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1545             }
1546
1547             if(cs!=null)
1548             {
1549               cs.setThreshold(view.getPidThreshold(), true);
1550               cs.setConsensus(af.viewport.hconsensus);
1551             }
1552         }
1553
1554
1555         af.viewport.setGlobalColourScheme(cs);
1556         af.viewport.setColourAppliesToAllGroups(false);
1557
1558         if (view.getConservationSelected() && cs!=null)
1559         {
1560           cs.setConservationInc(view.getConsThreshold());
1561         }
1562
1563         af.changeColour(cs);
1564
1565         af.viewport.setColourAppliesToAllGroups(true);
1566
1567
1568
1569         if (view.getShowSequenceFeatures())
1570         {
1571            af.viewport.showSequenceFeatures = true;
1572         }
1573
1574         if(jms.getFeatureSettings()!=null)
1575         {
1576           af.viewport.featuresDisplayed = new Hashtable();
1577           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1578          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1579          {
1580            Setting setting = jms.getFeatureSettings().getSetting(fs);
1581
1582            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1583                new java.awt.Color(setting.getColour()));
1584
1585            renderOrder[fs] = setting.getType();
1586
1587            if(setting.getDisplay())
1588              af.viewport.featuresDisplayed.put(
1589                  setting.getType(), new Integer(setting.getColour()));
1590          }
1591          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1592         }
1593
1594         if (view.getHiddenColumnsCount() > 0)
1595         {
1596           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1597           {
1598               af.viewport.hideColumns(
1599                 view.getHiddenColumns(c).getStart(),
1600                 view.getHiddenColumns(c).getEnd() //+1
1601                 );
1602           }
1603         }
1604
1605         af.setMenusFromViewport(af.viewport);
1606
1607
1608         Desktop.addInternalFrame(af, view.getTitle(),
1609              view.getWidth(), view.getHeight());
1610
1611         //LOAD TREES
1612         ///////////////////////////////////////
1613         if (loadTrees && jms.getTreeCount() > 0)
1614         {
1615             try
1616             {
1617                 for (int t = 0; t < jms.getTreeCount(); t++)
1618                 {
1619
1620                     Tree tree = jms.getTree(t);
1621
1622                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1623                                 tree.getNewick()), tree.getTitle(),
1624                                 tree.getWidth(), tree.getHeight(),
1625                                 tree.getXpos(), tree.getYpos());
1626
1627                     tp.fitToWindow.setState(tree.getFitToWindow());
1628                     tp.fitToWindow_actionPerformed(null);
1629
1630                     if(tree.getFontName()!=null)
1631                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1632                                           tree.getFontStyle(),
1633                                           tree.getFontSize()));
1634                     else
1635                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1636                                             view.getFontStyle(),
1637                                             tree.getFontSize()));
1638
1639                     tp.showPlaceholders(tree.getMarkUnlinked());
1640                     tp.showBootstrap(tree.getShowBootstrap());
1641                     tp.showDistances(tree.getShowDistances());
1642
1643                     tp.treeCanvas.threshold = tree.getThreshold();
1644
1645                     if (tree.getCurrentTree())
1646                       af.viewport.setCurrentTree(tp.getTree());
1647                 }
1648
1649             }
1650             catch (Exception ex)
1651             {
1652                 ex.printStackTrace();
1653             }
1654
1655         }
1656
1657         return af;
1658     }
1659
1660     public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1661     {
1662       jalview.schemabinding.version2.JalviewModel jm
1663           = SaveState(ap, null, null, null);
1664
1665       if (!keepSeqRefs)
1666       {
1667         seqRefIds.clear();
1668         jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1669       }
1670       else
1671         uniqueSetSuffix = "";
1672
1673       viewportsAdded = new Hashtable();
1674
1675       AlignFrame af = LoadFromObject(jm, null, false);
1676       af.alignPanels.clear();
1677       af.closeMenuItem_actionPerformed(true);
1678
1679       return af.alignPanel;
1680     }
1681 }
1682