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 boolean 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           return true;
 167         }
 168         catch (Exception ex)
 169         {
 170           ex.printStackTrace();
 171           return false;
 172         }
 173     }
 174
 175     /**
 176      * DOCUMENT ME!
 177      *
 178      * @param af DOCUMENT ME!
 179      * @param timeStamp DOCUMENT ME!
 180      * @param fileName DOCUMENT ME!
 181      * @param jout DOCUMENT ME!
 182      * @param out DOCUMENT ME!
 183      */
 184     public JalviewModel SaveState(AlignmentPanel ap,
 185                           String fileName,
 186                           JarOutputStream jout,
 187                           PrintWriter out)
 188     {
 189       if (seqRefIds == null)
 190         seqRefIds = new Hashtable();
 191
 192         Vector userColours = new Vector();
 193
 194         AlignViewport av = ap.av;
 195
 196         JalviewModel object = new JalviewModel();
 197         object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 198
 199         object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
 200         object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 201
 202         jalview.datamodel.AlignmentI jal = av.alignment;
 203
 204         if(av.hasHiddenRows)
 205         {
 206           jal = jal.getHiddenSequences().getFullAlignment();
 207         }
 208
 209         SequenceSet vamsasSet = new SequenceSet();
 210         Sequence vamsasSeq;
 211         JalviewModelSequence jms = new JalviewModelSequence();
 212
 213         vamsasSet.setGapChar(jal.getGapCharacter() + "");
 214
 215         JSeq jseq;
 216         Vector pdbfiles = null;
 217
 218         //SAVE SEQUENCES
 219         int id = 0;
 220         jalview.datamodel.SequenceI jds;
 221         for (int i = 0; i < jal.getHeight(); i++)
 222         {
 223             jds = jal.getSequenceAt(i);
 224             id = jds.hashCode();
 225
 226             if(seqRefIds.get(id+"")!=null)
 227             {
 228
 229             }
 230             else
 231             {
 232               vamsasSeq = new Sequence();
 233               vamsasSeq.setId(id + "");
 234               vamsasSeq.setName(jds.getName());
 235               vamsasSeq.setSequence(jds.getSequenceAsString());
 236               vamsasSeq.setDescription(jds.getDescription());
 237
 238               if (jds.getDatasetSequence().getDBRef() != null)
 239               {
 240                 jalview.datamodel.DBRefEntry[] dbrefs =
 241                     jds.getDatasetSequence().getDBRef();
 242
 243                 for (int d = 0; d < dbrefs.length; d++)
 244                 {
 245                   DBRef dbref = new DBRef();
 246                   dbref.setSource(dbrefs[d].getSource());
 247                   dbref.setVersion(dbrefs[d].getVersion());
 248                   dbref.setAccessionId(dbrefs[d].getAccessionId());
 249                   vamsasSeq.addDBRef(dbref);
 250                 }
 251               }
 252
 253               vamsasSet.addSequence(vamsasSeq);
 254               seqRefIds.put(id+"", jal.getSequenceAt(i));
 255             }
 256
 257             jseq = new JSeq();
 258             jseq.setStart(jds.getStart());
 259             jseq.setEnd(jds.getEnd());
 260             jseq.setColour( av.getSequenceColour(jds).getRGB());
 261
 262             jseq.setId(id);
 263
 264             if (av.hasHiddenRows)
 265             {
 266               jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 267
 268               if(jal.getSequenceAt(i).getHiddenSequences()!=null)
 269               {
 270                 jalview.datamodel.SequenceI [] reps =
 271                     jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
 272
 273                 for(int h=0; h<reps.length; h++)
 274                 {
 275                   jseq.addHiddenSequences(
 276                       jal.findIndex(reps[h])
 277                       );
 278                 }
 279               }
 280             }
 281
 282
 283             if(jds.getDatasetSequence().getSequenceFeatures()!=null)
 284             {
 285               jalview.datamodel.SequenceFeature[] sf
 286                   = jds.getDatasetSequence().getSequenceFeatures();
 287               int index = 0;
 288               while(index < sf.length)
 289               {
 290                 Features features = new Features();
 291
 292                 features.setBegin(sf[index].getBegin());
 293                 features.setEnd(sf[index].getEnd());
 294                 features.setDescription(sf[index].getDescription());
 295                 features.setType(sf[index].getType());
 296                 features.setFeatureGroup(sf[index].getFeatureGroup());
 297                 features.setScore(sf[index].getScore());
 298                 if(sf[index].links!=null)
 299                 {
 300                   for(int l=0; l<sf[index].links.size(); l++)
 301                   {
 302                     OtherData keyValue = new OtherData();
 303                     keyValue.setKey("LINK_"+l);
 304                     keyValue.setValue(sf[index].links.elementAt(l).toString());
 305                     features.addOtherData(keyValue);
 306                   }
 307                 }
 308                 if(sf[index].otherDetails!=null)
 309                 {
 310                   String key;
 311                   Enumeration keys = sf[index].otherDetails.keys();
 312                   while(keys.hasMoreElements())
 313                   {
 314                     key = keys.nextElement().toString();
 315                     OtherData keyValue = new OtherData();
 316                     keyValue.setKey( key );
 317                     keyValue.setValue(
 318                         sf[index].otherDetails.get(key).toString());
 319                     features.addOtherData(keyValue);
 320                   }
 321                 }
 322
 323                 jseq.addFeatures(features);
 324                 index ++;
 325               }
 326             }
 327
 328             if(jds.getDatasetSequence().getPDBId()!=null)
 329             {
 330               Enumeration en = jds.getDatasetSequence().getPDBId().elements();
 331               while(en.hasMoreElements())
 332               {
 333                 Pdbids pdb = new Pdbids();
 334                 jalview.datamodel.PDBEntry entry
 335                    = (jalview.datamodel.PDBEntry)en.nextElement();
 336
 337                 pdb.setId(entry.getId());
 338                 pdb.setType(entry.getType());
 339
 340
 341                 if(entry.getFile()!=null)
 342                 {
 343                   pdb.setFile(entry.getFile());
 344                   if(pdbfiles==null)
 345                     pdbfiles = new Vector();
 346
 347                   if(!pdbfiles.contains(entry.getId()))
 348                   {
 349                     pdbfiles.addElement(entry.getId());
 350                     try
 351                     {
 352                       File file = new File(entry.getFile());
 353                       if(file.exists() && jout!=null)
 354                       {
 355                         byte[] data = new byte[ (int) file.length()];
 356                         jout.putNextEntry(new JarEntry(entry.getId()));
 357                         DataInputStream dis = new DataInputStream(new
 358                             FileInputStream(file));
 359                         dis.readFully(data);
 360
 361                         DataOutputStream dout = new DataOutputStream(jout);
 362                         dout.write(data, 0, data.length);
 363                         jout.closeEntry();
 364                       }
 365                     }
 366                     catch (Exception ex)
 367                     {
 368                       ex.printStackTrace();
 369                     }
 370                   }
 371                 }
 372
 373
 374                 if(entry.getProperty()!=null)
 375                 {
 376                   PdbentryItem item = new PdbentryItem();
 377                   Hashtable properties = entry.getProperty();
 378                   Enumeration en2 = properties.keys();
 379                   while(en2.hasMoreElements())
 380                   {
 381                     Property prop = new Property();
 382                     String key = en2.nextElement().toString();
 383                     prop.setName(key);
 384                     prop.setValue( properties.get(key).toString() );
 385                     item.addProperty(prop);
 386                   }
 387                   pdb.addPdbentryItem(item);
 388                 }
 389
 390                 jseq.addPdbids(pdb);
 391               }
 392             }
 393
 394             jms.addJSeq(jseq);
 395         }
 396
 397         if(av.hasHiddenRows)
 398           jal = av.alignment;
 399
 400
 401         //SAVE TREES
 402         ///////////////////////////////////
 403         if (av.currentTree != null)
 404         {
 405           // FIND ANY ASSOCIATED TREES
 406           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 407           if (Desktop.desktop != null)
 408           {
 409             JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 410
 411             for (int t = 0; t < frames.length; t++)
 412             {
 413               if (frames[t] instanceof TreePanel)
 414               {
 415                 TreePanel tp = (TreePanel) frames[t];
 416
 417                 if (tp.treeCanvas.av.alignment == jal)
 418                 {
 419                   Tree tree = new Tree();
 420                   tree.setTitle(tp.getTitle());
 421                   tree.setCurrentTree( (av.currentTree == tp.getTree()));
 422                   tree.setNewick(tp.getTree().toString());
 423                   tree.setThreshold(tp.treeCanvas.threshold);
 424
 425                   tree.setFitToWindow(tp.fitToWindow.getState());
 426                   tree.setFontName(tp.getTreeFont().getName());
 427                   tree.setFontSize(tp.getTreeFont().getSize());
 428                   tree.setFontStyle(tp.getTreeFont().getStyle());
 429                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 430
 431                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
 432                   tree.setShowDistances(tp.distanceMenu.getState());
 433
 434                   tree.setHeight(tp.getHeight());
 435                   tree.setWidth(tp.getWidth());
 436                   tree.setXpos(tp.getX());
 437                   tree.setYpos(tp.getY());
 438
 439                   jms.addTree(tree);
 440                 }
 441               }
 442             }
 443           }
 444         }
 445
 446         //SAVE ANNOTATIONS
 447         if (jal.getAlignmentAnnotation() != null)
 448         {
 449             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 450
 451             for (int i = 0; i < aa.length; i++)
 452             {
 453                 Annotation an = new Annotation();
 454
 455                 if (aa[i].label.equals("Quality") ||
 456                         aa[i].label.equals("Conservation") ||
 457                         aa[i].label.equals("Consensus"))
 458                 {
 459                     an.setLabel(aa[i].label);
 460                     an.setGraph(true);
 461                     vamsasSet.addAnnotation(an);
 462                     continue;
 463                 }
 464
 465
 466                 an.setDescription(aa[i].description);
 467
 468                 if(aa[i].sequenceRef!=null)
 469                  {
 470                    an.setSequenceRef(aa[i].sequenceRef.getName());
 471                  }
 472
 473                 if(aa[i].graph>0)
 474                 {
 475                   an.setGraph(true);
 476                   an.setGraphType(aa[i].graph);
 477                   an.setGraphGroup(aa[i].graphGroup);
 478                   if(aa[i].getThreshold()!=null)
 479                   {
 480                     ThresholdLine line = new ThresholdLine();
 481                     line.setLabel(aa[i].getThreshold().label);
 482                     line.setValue(aa[i].getThreshold().value);
 483                     line.setColour(aa[i].getThreshold().colour.getRGB());
 484                     an.setThresholdLine(line);
 485                   }
 486                 }
 487                 else
 488                   an.setGraph(false);
 489
 490                 an.setLabel(aa[i].label);
 491
 492                 AnnotationElement ae;
 493
 494                 for (int a = 0; a < aa[i].annotations.length; a++)
 495                 {
 496                     if ((aa[i] == null) || (aa[i].annotations[a] == null))
 497                     {
 498                         continue;
 499                     }
 500
 501                     ae = new AnnotationElement();
 502                     ae.setDescription(aa[i].annotations[a].description);
 503                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 504                     ae.setValue(aa[i].annotations[a].value);
 505                     ae.setPosition(a);
 506                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
 507                         "");
 508
 509                     if(aa[i].annotations[a].colour!=java.awt.Color.black)
 510                       ae.setColour(aa[i].annotations[a].colour.getRGB());
 511
 512                     an.addAnnotationElement(ae);
 513                 }
 514
 515                 vamsasSet.addAnnotation(an);
 516             }
 517         }
 518
 519         //SAVE GROUPS
 520         if (jal.getGroups() != null)
 521         {
 522             JGroup[] groups = new JGroup[jal.getGroups().size()];
 523
 524             for (int i = 0; i < groups.length; i++)
 525             {
 526                 groups[i] = new JGroup();
 527
 528                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
 529                                                                                           .elementAt(i);
 530                 groups[i].setStart(sg.getStartRes());
 531                 groups[i].setEnd(sg.getEndRes());
 532                 groups[i].setName(sg.getName());
 533                 if(sg.cs!=null)
 534                 {
 535                   if (sg.cs.conservationApplied())
 536                   {
 537                     groups[i].setConsThreshold(sg.cs.getConservationInc());
 538
 539                     if (sg.cs instanceof jalview.schemes.UserColourScheme)
 540                     {
 541                       groups[i].setColour(SetUserColourScheme(sg.cs,
 542                           userColours,
 543                           jms));
 544                     }
 545                     else
 546                     {
 547                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.
 548                           cs));
 549                     }
 550                   }
 551                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 552                   {
 553                     groups[i].setColour(
 554                         ColourSchemeProperty.getColourName(
 555                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
 556                   }
 557                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 558                   {
 559                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 560                         jms));
 561                   }
 562                   else
 563                   {
 564                     groups[i].setColour(ColourSchemeProperty.getColourName(
 565                         sg.cs));
 566                   }
 567
 568                   groups[i].setPidThreshold(sg.cs.getThreshold());
 569                 }
 570
 571                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 572                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 573                 groups[i].setDisplayText(sg.getDisplayText());
 574                 groups[i].setColourText(sg.getColourText());
 575                 groups[i].setTextCol1(sg.textColour.getRGB());
 576                 groups[i].setTextCol2(sg.textColour2.getRGB());
 577                 groups[i].setTextColThreshold(sg.thresholdTextColour);
 578
 579                 for (int s = 0; s < sg.getSize(false); s++)
 580                 {
 581                     jalview.datamodel.Sequence seq =
 582                         (jalview.datamodel.Sequence) sg.getSequenceAt(s);
 583                     groups[i].addSeq(seq.hashCode());
 584                 }
 585             }
 586
 587             jms.setJGroup(groups);
 588         }
 589
 590
 591         ///////////SAVE VIEWPORT
 592         Viewport view = new Viewport();
 593         view.setTitle(ap.alignFrame.getTitle());
 594         view.setSequenceSetId(av.getSequenceSetId());
 595         view.setViewName(av.viewName);
 596         view.setGatheredViews(av.gatherViewsHere);
 597
 598
 599         if (ap.av.explodedPosition != null)
 600         {
 601           view.setXpos(av.explodedPosition.x);
 602           view.setYpos(av.explodedPosition.y);
 603           view.setWidth(av.explodedPosition.width);
 604           view.setHeight(av.explodedPosition.height);
 605         }
 606         else
 607         {
 608           view.setXpos(ap.alignFrame.getBounds().x);
 609           view.setYpos(ap.alignFrame.getBounds().y);
 610           view.setWidth(ap.alignFrame.getBounds().width);
 611           view.setHeight(ap.alignFrame.getBounds().height);
 612         }
 613
 614         view.setStartRes(av.startRes);
 615         view.setStartSeq(av.startSeq);
 616
 617         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 618         {
 619             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 620                     userColours, jms));
 621         }
 622         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 623         {
 624            jalview.schemes.AnnotationColourGradient acg
 625               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
 626
 627             AnnotationColours ac = new AnnotationColours();
 628             ac.setAboveThreshold(acg.getAboveThreshold());
 629             ac.setThreshold(acg.getAnnotationThreshold());
 630             ac.setAnnotation(acg.getAnnotation());
 631             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 632               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 633                     userColours, jms));
 634             else
 635               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 636
 637             ac.setMaxColour(acg.getMaxColour().getRGB());
 638             ac.setMinColour(acg.getMinColour().getRGB());
 639             view.setAnnotationColours(ac);
 640             view.setBgColour("AnnotationColourGradient");
 641         }
 642         else
 643         {
 644             view.setBgColour(ColourSchemeProperty.getColourName(
 645                     av.getGlobalColourScheme()));
 646         }
 647
 648         ColourSchemeI cs = av.getGlobalColourScheme();
 649
 650         if(cs!=null)
 651         {
 652           if (cs.conservationApplied())
 653           {
 654             view.setConsThreshold(cs.getConservationInc());
 655             if (cs instanceof jalview.schemes.UserColourScheme)
 656               view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 657           }
 658
 659           if (cs instanceof ResidueColourScheme)
 660           {
 661             view.setPidThreshold(cs.getThreshold());
 662           }
 663         }
 664
 665         view.setConservationSelected(av.getConservationSelected());
 666         view.setPidSelected(av.getAbovePIDThreshold());
 667         view.setFontName(av.font.getName());
 668         view.setFontSize(av.font.getSize());
 669         view.setFontStyle(av.font.getStyle());
 670         view.setRenderGaps(av.renderGaps);
 671         view.setShowAnnotation(av.getShowAnnotation());
 672         view.setShowBoxes(av.getShowBoxes());
 673         view.setShowColourText(av.getColourText());
 674         view.setShowFullId(av.getShowJVSuffix());
 675         view.setRightAlignIds(av.rightAlignIds);
 676         view.setShowSequenceFeatures(av.showSequenceFeatures);
 677         view.setShowText(av.getShowText());
 678         view.setWrapAlignment(av.getWrapAlignment());
 679         view.setTextCol1(av.textColour.getRGB());
 680         view.setTextCol2(av.textColour2.getRGB());
 681         view.setTextColThreshold(av.thresholdTextColour);
 682
 683
 684         if(av.featuresDisplayed!=null)
 685         {
 686           jalview.schemabinding.version2.FeatureSettings fs
 687               = new jalview.schemabinding.version2.FeatureSettings();
 688
 689           String [] renderOrder =
 690               ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 691
 692           Vector settingsAdded = new Vector();
 693           for(int ro=0; ro<renderOrder.length; ro++)
 694           {
 695             Setting setting = new Setting();
 696             setting.setType(renderOrder[ro]);
 697             setting.setColour(
 698                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
 699                 );
 700
 701             setting.setDisplay(
 702                 av.featuresDisplayed.containsKey(renderOrder[ro])
 703                 );
 704
 705             fs.addSetting(setting);
 706             settingsAdded.addElement(renderOrder[ro]);
 707           }
 708
 709           //Make sure we save none displayed feature settings
 710           Enumeration en =
 711               ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 712           while(en.hasMoreElements())
 713           {
 714             String key = en.nextElement().toString();
 715             if(settingsAdded.contains(key))
 716               continue;
 717
 718             Setting setting = new Setting();
 719             setting.setType(key);
 720             setting.setColour(
 721                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 722                 );
 723
 724             setting.setDisplay(false);
 725
 726             fs.addSetting(setting);
 727             settingsAdded.addElement(key);
 728           }
 729
 730           jms.setFeatureSettings(fs);
 731
 732         }
 733
 734         if(av.hasHiddenColumns)
 735         {
 736           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
 737           {
 738             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
 739             HiddenColumns hc = new HiddenColumns();
 740             hc.setStart(region[0]);
 741             hc.setEnd(region[1]);
 742             view.addHiddenColumns(hc);
 743           }
 744         }
 745
 746         jms.addViewport(view);
 747
 748
 749         object.setJalviewModelSequence(jms);
 750         object.getVamsasModel().addSequenceSet(vamsasSet);
 751
 752         if(out!=null)
 753         {
 754           //We may not want to right the object to disk,
 755           //eg we can copy the alignViewport to a new view object
 756           //using save and then load
 757           try
 758           {
 759             if (!fileName.endsWith(".xml"))
 760             {
 761               fileName = fileName + ".xml";
 762             }
 763
 764             JarEntry entry = new JarEntry(fileName);
 765             jout.putNextEntry(entry);
 766
 767             object.marshal(out);
 768           }
 769           catch (Exception ex)
 770           {
 771             ex.printStackTrace();
 772           }
 773         }
 774         return object;
 775     }
 776
 777     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 778         Vector userColours, JalviewModelSequence jms)
 779     {
 780         String id = null;
 781         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 782
 783         if (!userColours.contains(ucs))
 784         {
 785             userColours.add(ucs);
 786
 787             java.awt.Color[] colours = ucs.getColours();
 788             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
 789             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 790
 791             for (int i = 0; i < colours.length; i++)
 792             {
 793                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 794                 col.setName(ResidueProperties.aa[i]);
 795                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 796                 jbucs.addColour(col);
 797             }
 798             if(ucs.getLowerCaseColours()!=null)
 799             {
 800               colours = ucs.getLowerCaseColours();
 801               for (int i = 0; i < colours.length; i++)
 802              {
 803                  jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 804                  col.setName(ResidueProperties.aa[i].toLowerCase());
 805                  col.setRGB(jalview.util.Format.getHexString(colours[i]));
 806                  jbucs.addColour(col);
 807              }
 808             }
 809
 810             id = "ucs" + userColours.indexOf(ucs);
 811             uc.setId(id);
 812             uc.setUserColourScheme(jbucs);
 813             jms.addUserColours(uc);
 814         }
 815
 816         return id;
 817     }
 818
 819    jalview.schemes.UserColourScheme GetUserColourScheme(
 820         JalviewModelSequence jms, String id)
 821     {
 822         UserColours[] uc = jms.getUserColours();
 823         UserColours colours = null;
 824
 825         for (int i = 0; i < uc.length; i++)
 826         {
 827             if (uc[i].getId().equals(id))
 828             {
 829                 colours = uc[i];
 830
 831                 break;
 832             }
 833         }
 834
 835         java.awt.Color[] newColours = new java.awt.Color[24];
 836
 837         for (int i = 0; i < 24; i++)
 838         {
 839             newColours[i] = new java.awt.Color(Integer.parseInt(
 840                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 841         }
 842
 843         jalview.schemes.UserColourScheme ucs =
 844             new jalview.schemes.UserColourScheme(newColours);
 845
 846         if (colours.getUserColourScheme().getColourCount() > 24)
 847         {
 848           newColours = new java.awt.Color[23];
 849           for (int i = 0; i < 23; i++)
 850           {
 851             newColours[i] = new java.awt.Color(Integer.parseInt(
 852                 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
 853           }
 854           ucs.setLowerCaseColours(newColours);
 855         }
 856
 857         return ucs;
 858     }
 859
 860
 861     /**
 862      * DOCUMENT ME!
 863      *
 864      * @param file DOCUMENT ME!
 865      */
 866     public AlignFrame LoadJalviewAlign(final String file)
 867     {
 868         uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
 869
 870         jalview.gui.AlignFrame af = null;
 871
 872         seqRefIds = new Hashtable();
 873         viewportsAdded = new Hashtable();
 874
 875         Vector gatherToThisFrame= new Vector();
 876
 877         try
 878         {
 879             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 880             URL url = null;
 881
 882             if (file.startsWith("http://"))
 883             {
 884                 url = new URL(file);
 885             }
 886
 887             JarInputStream jin = null;
 888             JarEntry jarentry = null;
 889             int entryCount = 1;
 890
 891             do
 892             {
 893                 if (url != null)
 894                 {
 895                     jin = new JarInputStream(url.openStream());
 896                 }
 897                 else
 898                 {
 899                     jin = new JarInputStream(new FileInputStream(file));
 900                 }
 901
 902                 for (int i = 0; i < entryCount; i++)
 903                 {
 904                     jarentry = jin.getNextJarEntry();
 905                 }
 906
 907                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 908                 {
 909                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 910                     JalviewModel object = new JalviewModel();
 911
 912                     Unmarshaller unmar = new Unmarshaller(object);
 913                     unmar.setValidation(false);
 914                     object = (JalviewModel) unmar.unmarshal( in );
 915
 916                     af = LoadFromObject(object, file, true);
 917                     if(af.viewport.gatherViewsHere)
 918                     {
 919                       gatherToThisFrame.add(af);
 920                     }
 921                     entryCount++;
 922                 }
 923                 else if (jarentry != null)
 924                 {
 925                   //Some other file here.
 926                   entryCount++;
 927                 }
 928             }
 929             while (jarentry != null);
 930         }
 931         catch(java.net.UnknownHostException ex)
 932         {
 933           ex.printStackTrace();
 934           System.err.println("Couldn't locate Jalview XML file : " +
 935               ex + "\n");
 936
 937           javax.swing.SwingUtilities.invokeLater(new Runnable()
 938           {
 939             public void run()
 940             {
 941               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 942                   "Couldn't locate " + file,
 943                   "URL not found",
 944                   JOptionPane.WARNING_MESSAGE);
 945             }
 946           });
 947         }
 948         catch (Exception ex)
 949         {
 950           //Is Version 1 Jar file?
 951           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 952
 953           if(af!=null)
 954           {
 955             System.out.println("Successfully loaded archive file");
 956             return af;
 957           }
 958
 959             System.err.println("Exception whilst loading jalview XML file : " +
 960                 ex + "\n");
 961             javax.swing.SwingUtilities.invokeLater(new Runnable()
 962             {
 963               public void run()
 964               {
 965
 966                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 967                     "Error loading  " + file,
 968                     "Error loading Jalview file",
 969                     JOptionPane.WARNING_MESSAGE);
 970               }});
 971         }
 972
 973         if (Desktop.instance != null)
 974           Desktop.instance.stopLoading();
 975
 976         for (int i = 0; i < gatherToThisFrame.size(); i++)
 977         {
 978           Desktop.instance.gatherViews(
 979               (AlignFrame) gatherToThisFrame.elementAt(i));
 980         }
 981
 982         return af;
 983     }
 984
 985     String loadPDBFile(String file, String pdbId)
 986     {
 987       System.out.println(file +" "+pdbId);
 988       try
 989       {
 990         JarInputStream jin = null;
 991
 992         if (file.startsWith("http://"))
 993         {
 994           jin = new JarInputStream(new URL(file).openStream());
 995         }
 996         else
 997         {
 998           jin = new JarInputStream(new FileInputStream(file));
 999         }
1000
1001         JarEntry entry = null;
1002         do
1003         {
1004           entry = jin.getNextJarEntry();
1005         }
1006         while (!entry.getName().equals(pdbId));
1007
1008         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1009         File outFile = File.createTempFile("jalview_pdb", ".txt");
1010         outFile.deleteOnExit();
1011         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1012         String data;
1013
1014         while ( (data = in.readLine()) != null)
1015         {
1016           out.println(data);
1017         }
1018         out.close();
1019         return outFile.getAbsolutePath();
1020
1021       }
1022       catch (Exception ex)
1023       {
1024         ex.printStackTrace();
1025       }
1026
1027       return null;
1028     }
1029
1030
1031     AlignFrame LoadFromObject(JalviewModel object,
1032                               String file,
1033                               boolean loadTrees )
1034     {
1035         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1036         Sequence[] vamsasSeq = vamsasSet.getSequence();
1037
1038         JalviewModelSequence jms = object.getJalviewModelSequence();
1039
1040         Viewport view = jms.getViewport(0);
1041
1042         //////////////////////////////////
1043         //LOAD SEQUENCES
1044
1045         Vector hiddenSeqs = null;
1046         jalview.datamodel.Sequence jseq;
1047
1048         ArrayList tmpseqs = new ArrayList();
1049
1050         boolean multipleView = false;
1051
1052         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1053         for (int i = 0; i < JSEQ.length; i++)
1054         {
1055           String seqId = JSEQ[i].getId() + "";
1056
1057           if (seqRefIds.get(seqId) != null)
1058           {
1059             tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1060             multipleView = true;
1061           }
1062           else
1063           {
1064             jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1065                 vamsasSeq[i].getSequence());
1066             jseq.setDescription(vamsasSeq[i].getDescription());
1067             jseq.setStart(JSEQ[i].getStart());
1068             jseq.setEnd(JSEQ[i].getEnd());
1069             seqRefIds.put(vamsasSeq[i].getId(), jseq);
1070             tmpseqs.add( jseq );
1071           }
1072
1073
1074
1075           if (JSEQ[i].getHidden())
1076           {
1077             if (hiddenSeqs == null)
1078               hiddenSeqs = new Vector();
1079
1080
1081             hiddenSeqs.addElement(
1082                 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1083           }
1084
1085         }
1086
1087         ///SequenceFeatures are added to the DatasetSequence,
1088         // so we must create the dataset before loading features
1089         /////////////////////////////////
1090
1091
1092       jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1093           tmpseqs.size()];
1094
1095        tmpseqs.toArray(orderedSeqs) ;
1096
1097
1098         jalview.datamodel.Alignment al =
1099             new jalview.datamodel.Alignment(orderedSeqs);
1100
1101         al.setDataset(null);
1102         /////////////////////////////////
1103
1104
1105         Hashtable pdbloaded = new Hashtable();
1106         if(!multipleView)
1107         {
1108           for (int i = 0; i < vamsasSeq.length; i++)
1109           {
1110             if (JSEQ[i].getFeaturesCount() > 0)
1111             {
1112               Features[] features = JSEQ[i].getFeatures();
1113               for (int f = 0; f < features.length; f++)
1114               {
1115                 jalview.datamodel.SequenceFeature sf
1116                     = new jalview.datamodel.SequenceFeature(features[f].getType(),
1117                     features[f].getDescription(), features[f].getStatus(),
1118                     features[f].getBegin(), features[f].getEnd(),
1119                     features[f].getFeatureGroup());
1120
1121                 sf.setScore(features[f].getScore());
1122                 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1123                 {
1124                   OtherData keyValue = features[f].getOtherData(od);
1125                   if (keyValue.getKey().startsWith("LINK"))
1126                     sf.addLink(keyValue.getValue());
1127                   else
1128                     sf.setValue(keyValue.getKey(), keyValue.getValue());
1129
1130                 }
1131
1132                 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1133               }
1134             }
1135             if (JSEQ[i].getPdbidsCount() > 0)
1136             {
1137               Pdbids[] ids = JSEQ[i].getPdbids();
1138               for (int p = 0; p < ids.length; p++)
1139               {
1140                 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1141                     PDBEntry();
1142                 entry.setId(ids[p].getId());
1143                 entry.setType(ids[p].getType());
1144                 if (ids[p].getFile() != null)
1145                 {
1146                   if (!pdbloaded.containsKey(ids[p].getFile()))
1147                   {
1148                     String tmppdb = loadPDBFile(file, ids[p].getId());
1149                     entry.setFile(tmppdb);
1150                     pdbloaded.put(ids[p].getId(), tmppdb);
1151                   }
1152                   else
1153                     entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1154                 }
1155
1156                 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1157               }
1158             }
1159             if (vamsasSeq[i].getDBRefCount() > 0)
1160             {
1161               for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1162               {
1163                 jalview.datamodel.DBRefEntry entry =
1164                     new jalview.datamodel.DBRefEntry(
1165                         vamsasSeq[i].getDBRef(d).getSource(),
1166                         vamsasSeq[i].getDBRef(d).getVersion(),
1167                         vamsasSeq[i].getDBRef(d).getAccessionId()
1168                     );
1169                 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1170               }
1171
1172             }
1173           }
1174         }
1175
1176
1177          /////////////////////////////////
1178         //////////////////////////////////
1179         //LOAD ANNOTATIONS
1180         boolean hideQuality = true,
1181             hideConservation = true,
1182             hideConsensus = true;
1183
1184         if (vamsasSet.getAnnotationCount()>0)
1185         {
1186             Annotation[] an = vamsasSet.getAnnotation();
1187
1188             for (int i = 0; i < an.length; i++)
1189             {
1190                if (an[i].getLabel().equals("Quality"))
1191                 {
1192                  hideQuality = false;
1193                  continue;
1194                 }
1195                else if(an[i].getLabel().equals("Conservation"))
1196                {
1197                  hideConservation = false;
1198                  continue;
1199                }
1200                else if(an[i].getLabel().equals("Consensus"))
1201                {
1202                  hideConsensus = false;
1203                  continue;
1204                }
1205
1206                 AnnotationElement[] ae = an[i].getAnnotationElement();
1207                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1208
1209                 for (int aa = 0; aa < ae.length; aa++)
1210                 {
1211                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1212                             ae[aa].getDescription(),
1213                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1214                             ae[aa].getValue());
1215                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1216                 }
1217
1218                 jalview.datamodel.AlignmentAnnotation jaa = null;
1219
1220                 if (an[i].getGraph())
1221                 {
1222                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1223                       an[i].getDescription(), anot, 0, 0,
1224                       an[i].getGraphType());
1225
1226                   jaa.graphGroup = an[i].getGraphGroup();
1227
1228                   if (an[i].getThresholdLine() != null)
1229                   {
1230                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1231                                   an[i].getThresholdLine().getValue(),
1232                                   an[i].getThresholdLine().getLabel(),
1233                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1234                              );
1235
1236                   }
1237
1238                 }
1239                 else
1240                 {
1241                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1242                             an[i].getDescription(), anot);
1243                 }
1244
1245                 if(an[i].getSequenceRef()!=null)
1246                 {
1247                   jaa.createSequenceMapping(
1248                       al.findName(an[i].getSequenceRef()), 1, true
1249                       );
1250                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1251                 }
1252
1253                 al.addAnnotation(jaa);
1254             }
1255         }
1256
1257         /////////////////////////
1258         //LOAD GROUPS
1259         if (jms.getJGroupCount() > 0)
1260         {
1261             JGroup[] groups = jms.getJGroup();
1262
1263             for (int i = 0; i < groups.length; i++)
1264             {
1265                 ColourSchemeI cs = null;
1266
1267                 if (groups[i].getColour() != null)
1268                 {
1269                     if (groups[i].getColour().startsWith("ucs"))
1270                     {
1271                         cs = GetUserColourScheme(jms, groups[i].getColour());
1272                     }
1273                     else
1274                     {
1275                         cs = ColourSchemeProperty.getColour(al,
1276                                 groups[i].getColour());
1277                     }
1278
1279                     if(cs!=null)
1280                       cs.setThreshold(groups[i].getPidThreshold(), true);
1281                 }
1282
1283                 Vector seqs = new Vector();
1284
1285                 for (int s = 0; s < groups[i].getSeqCount(); s++)
1286                 {
1287                     String seqId = groups[i].getSeq(s)+"";
1288                     seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
1289                 }
1290
1291                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1292                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1293                         groups[i].getDisplayText(), groups[i].getColourText(),
1294                         groups[i].getStart(), groups[i].getEnd());
1295
1296                 sg.setOutlineColour(new java.awt.Color(
1297                         groups[i].getOutlineColour()));
1298
1299                 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1300                 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1301                 sg.thresholdTextColour = groups[i].getTextColThreshold();
1302
1303                 if (groups[i].getConsThreshold() != 0)
1304                 {
1305                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1306                             ResidueProperties.propHash, 3, sg.getSequences(false), 0,
1307                             sg.getWidth() - 1);
1308                     c.calculate();
1309                     c.verdict(false, 25);
1310                     sg.cs.setConservation(c);
1311                 }
1312
1313                 al.addGroup(sg);
1314             }
1315         }
1316
1317
1318         /////////////////////////////////
1319         // LOAD VIEWPORT
1320
1321         AlignFrame af = new AlignFrame(al,
1322                                        view.getWidth(),
1323                                        view.getHeight() );
1324
1325         af.setFileName(file, "Jalview");
1326
1327         for (int i = 0; i < JSEQ.length; i++)
1328         {
1329           af.viewport.setSequenceColour(
1330               af.viewport.alignment.getSequenceAt(i),
1331               new java.awt.Color(
1332                   JSEQ[i].getColour()));
1333         }
1334
1335         //If we just load in the same jar file again, the sequenceSetId
1336         //will be the same, and we end up with multiple references
1337         //to the same sequenceSet. We must modify this id on load
1338         //so that each load of the file gives a unique id
1339         String uniqueSeqSetId =  view.getSequenceSetId()+uniqueSetSuffix;
1340
1341         af.viewport.gatherViewsHere = view.getGatheredViews();
1342
1343         if (view.getSequenceSetId() != null)
1344         {
1345           jalview.gui.AlignViewport av =
1346               (jalview.gui.AlignViewport)
1347               viewportsAdded.get(uniqueSeqSetId);
1348
1349           af.viewport.sequenceSetID = uniqueSeqSetId;
1350           if(av!=null)
1351           {
1352
1353             af.viewport.historyList = av.historyList;
1354             af.viewport.redoList = av.redoList;
1355           }
1356           else
1357           {
1358             viewportsAdded.put(uniqueSeqSetId, af.viewport);
1359           }
1360
1361           PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1362         }
1363         if(hiddenSeqs!=null)
1364         {
1365           for(int s=0; s<JSEQ.length; s++)
1366           {
1367             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1368             {
1369               al.getSequenceAt(s).addHiddenSequence(
1370                   al.getSequenceAt( JSEQ[s].getHiddenSequences(r)  )
1371                   );
1372             }
1373           }
1374
1375           jalview.datamodel.SequenceI [] hseqs = new
1376               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1377
1378           for(int s=0; s<hiddenSeqs.size(); s++)
1379             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1380
1381           af.viewport.hideSequence( hseqs );
1382
1383         }
1384
1385
1386         if((hideConsensus || hideQuality || hideConservation)
1387             && al.getAlignmentAnnotation()!=null)
1388         {
1389           int hSize = al.getAlignmentAnnotation().length;
1390           for (int h = 0; h < hSize; h++)
1391           {
1392             if (
1393                 (hideConsensus &&
1394                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1395                 ||
1396                 (hideQuality &&
1397                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1398                 ||
1399                 (hideConservation &&
1400                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1401             {
1402               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1403               hSize--;
1404               h--;
1405             }
1406           }
1407           af.alignPanel.adjustAnnotationHeight();
1408         }
1409
1410         if(view.getViewName()!=null)
1411         {
1412           af.viewport.viewName = view.getViewName();
1413           af.setInitialTabVisible();
1414         }
1415         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1416             view.getHeight());
1417
1418         af.viewport.setShowAnnotation(view.getShowAnnotation());
1419         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1420
1421         af.viewport.setColourText(view.getShowColourText());
1422
1423         af.viewport.setConservationSelected(view.getConservationSelected());
1424         af.viewport.setShowJVSuffix(view.getShowFullId());
1425         af.viewport.rightAlignIds=view.getRightAlignIds();
1426         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1427                 view.getFontStyle(), view.getFontSize()));
1428         af.alignPanel.fontChanged();
1429         af.viewport.setRenderGaps(view.getRenderGaps());
1430         af.viewport.setWrapAlignment(view.getWrapAlignment());
1431         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1432         af.viewport.setShowAnnotation(view.getShowAnnotation());
1433         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1434
1435         af.viewport.setShowBoxes(view.getShowBoxes());
1436
1437         af.viewport.setShowText(view.getShowText());
1438
1439         af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1440         af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1441         af.viewport.thresholdTextColour = view.getTextColThreshold();
1442
1443         af.viewport.setStartRes(view.getStartRes());
1444         af.viewport.setStartSeq(view.getStartSeq());
1445
1446         ColourSchemeI cs = null;
1447
1448         if (view.getBgColour() != null)
1449         {
1450             if (view.getBgColour().startsWith("ucs"))
1451             {
1452                 cs = GetUserColourScheme(jms, view.getBgColour());
1453             }
1454             else if(view.getBgColour().startsWith("Annotation"))
1455             {
1456               //int find annotation
1457               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1458               {
1459                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1460                     equals(view.getAnnotationColours().getAnnotation()))
1461                 {
1462                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1463                       getThreshold() == null)
1464                   {
1465                     af.viewport.alignment.getAlignmentAnnotation()[i].
1466                         setThreshold(
1467                             new jalview.datamodel.GraphLine(
1468                                 view.getAnnotationColours().getThreshold(),
1469                                 "Threshold", java.awt.Color.black)
1470
1471                         );
1472                   }
1473
1474
1475                   if (view.getAnnotationColours().getColourScheme().equals(
1476                       "None"))
1477                   {
1478                     cs = new AnnotationColourGradient(
1479                         af.viewport.alignment.getAlignmentAnnotation()[i],
1480                         new java.awt.Color(view.getAnnotationColours().
1481                                            getMinColour()),
1482                         new java.awt.Color(view.getAnnotationColours().
1483                                            getMaxColour()),
1484                         view.getAnnotationColours().getAboveThreshold());
1485                   }
1486                   else if (view.getAnnotationColours().getColourScheme().
1487                            startsWith("ucs"))
1488                   {
1489                      cs = new AnnotationColourGradient(
1490                          af.viewport.alignment.getAlignmentAnnotation()[i],
1491                          GetUserColourScheme(jms, view.getAnnotationColours().
1492                                                         getColourScheme()),
1493                          view.getAnnotationColours().getAboveThreshold()
1494                          );
1495                    }
1496                    else
1497                    {
1498                      cs = new AnnotationColourGradient(
1499                          af.viewport.alignment.getAlignmentAnnotation()[i],
1500                          ColourSchemeProperty.getColour(al,
1501                          view.getAnnotationColours().getColourScheme()),
1502                          view.getAnnotationColours().getAboveThreshold()
1503                          );
1504                    }
1505
1506                   // Also use these settings for all the groups
1507                   if (al.getGroups() != null)
1508                     for (int g = 0; g < al.getGroups().size(); g++)
1509                     {
1510                       jalview.datamodel.SequenceGroup sg
1511                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1512
1513                       if(sg.cs == null)
1514                         continue;
1515
1516
1517                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1518                       {
1519                         sg.cs = new AnnotationColourGradient(
1520                             af.viewport.alignment.getAlignmentAnnotation()[i],
1521                             new java.awt.Color(view.getAnnotationColours().
1522                                                getMinColour()),
1523                             new java.awt.Color(view.getAnnotationColours().
1524                                                getMaxColour()),
1525                             view.getAnnotationColours().getAboveThreshold());
1526                       }
1527                       else*/
1528                       {
1529                         sg.cs = new AnnotationColourGradient(
1530                             af.viewport.alignment.getAlignmentAnnotation()[i],
1531                             sg.cs,
1532                             view.getAnnotationColours().getAboveThreshold()
1533                             );
1534                       }
1535
1536                     }
1537
1538
1539                   break;
1540                 }
1541
1542               }
1543             }
1544             else
1545             {
1546                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1547             }
1548
1549             if(cs!=null)
1550             {
1551               cs.setThreshold(view.getPidThreshold(), true);
1552               cs.setConsensus(af.viewport.hconsensus);
1553             }
1554         }
1555
1556
1557         af.viewport.setGlobalColourScheme(cs);
1558         af.viewport.setColourAppliesToAllGroups(false);
1559
1560         if (view.getConservationSelected() && cs!=null)
1561         {
1562           cs.setConservationInc(view.getConsThreshold());
1563         }
1564
1565         af.changeColour(cs);
1566
1567         af.viewport.setColourAppliesToAllGroups(true);
1568
1569
1570
1571         if (view.getShowSequenceFeatures())
1572         {
1573            af.viewport.showSequenceFeatures = true;
1574         }
1575
1576         if(jms.getFeatureSettings()!=null)
1577         {
1578           af.viewport.featuresDisplayed = new Hashtable();
1579           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1580          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1581          {
1582            Setting setting = jms.getFeatureSettings().getSetting(fs);
1583
1584            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1585                new java.awt.Color(setting.getColour()));
1586
1587            renderOrder[fs] = setting.getType();
1588
1589            if(setting.getDisplay())
1590              af.viewport.featuresDisplayed.put(
1591                  setting.getType(), new Integer(setting.getColour()));
1592          }
1593          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1594         }
1595
1596         if (view.getHiddenColumnsCount() > 0)
1597         {
1598           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1599           {
1600               af.viewport.hideColumns(
1601                 view.getHiddenColumns(c).getStart(),
1602                 view.getHiddenColumns(c).getEnd() //+1
1603                 );
1604           }
1605         }
1606
1607         af.setMenusFromViewport(af.viewport);
1608
1609
1610         Desktop.addInternalFrame(af, view.getTitle(),
1611              view.getWidth(), view.getHeight());
1612
1613         //LOAD TREES
1614         ///////////////////////////////////////
1615         if (loadTrees && jms.getTreeCount() > 0)
1616         {
1617             try
1618             {
1619                 for (int t = 0; t < jms.getTreeCount(); t++)
1620                 {
1621
1622                     Tree tree = jms.getTree(t);
1623
1624                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1625                                 tree.getNewick()), tree.getTitle(),
1626                                 tree.getWidth(), tree.getHeight(),
1627                                 tree.getXpos(), tree.getYpos());
1628
1629                     tp.fitToWindow.setState(tree.getFitToWindow());
1630                     tp.fitToWindow_actionPerformed(null);
1631
1632                     if(tree.getFontName()!=null)
1633                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1634                                           tree.getFontStyle(),
1635                                           tree.getFontSize()));
1636                     else
1637                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1638                                             view.getFontStyle(),
1639                                             tree.getFontSize()));
1640
1641                     tp.showPlaceholders(tree.getMarkUnlinked());
1642                     tp.showBootstrap(tree.getShowBootstrap());
1643                     tp.showDistances(tree.getShowDistances());
1644
1645                     tp.treeCanvas.threshold = tree.getThreshold();
1646
1647                     if (tree.getCurrentTree())
1648                       af.viewport.setCurrentTree(tp.getTree());
1649                 }
1650
1651             }
1652             catch (Exception ex)
1653             {
1654                 ex.printStackTrace();
1655             }
1656
1657         }
1658
1659         return af;
1660     }
1661
1662     public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1663     {
1664       jalview.schemabinding.version2.JalviewModel jm
1665           = SaveState(ap, null, null, null);
1666
1667       if (!keepSeqRefs)
1668       {
1669         seqRefIds.clear();
1670         jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1671       }
1672       else
1673         uniqueSetSuffix = "";
1674
1675       viewportsAdded = new Hashtable();
1676
1677       AlignFrame af = LoadFromObject(jm, null, false);
1678       af.alignPanels.clear();
1679       af.closeMenuItem_actionPerformed(true);
1680
1681       return af.alignPanel;
1682     }
1683 }
1684