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