src/jalview/gui/Jalview2XML.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
   4  *
   5  * This program is free software; you can redistribute it and/or
   6  * modify it under the terms of the GNU General Public License
   7  * as published by the Free Software Foundation; either version 2
   8  * of the License, or (at your option) any later version.
   9  *
  10  * This program is distributed in the hope that it will be useful,
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  13  * GNU General Public License for more details.
  14  *
  15  * You should have received a copy of the GNU General Public License
  16  * along with this program; if not, write to the Free Software
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  18  */
  19 package jalview.gui;
  20
  21
  22 import jalview.schemes.*;
  23
  24 import java.io.*;
  25
  26 import java.net.*;
  27
  28 import java.util.*;
  29
  30 import java.util.jar.*;
  31
  32 import javax.swing.*;
  33
  34 import org.exolab.castor.xml.*;
  35
  36 import jalview.schemabinding.version2.*;
  37
  38
  39
  40
  41 /**
  42  * DOCUMENT ME!
  43  *
  44  * @author $author$
  45  * @version $Revision$
  46  */
  47 public class Jalview2XML
  48 {
  49
  50   Hashtable seqRefIds;
  51
  52   /**
  53    * This maintains a list of viewports, the key being the
  54    * seqSetId. Important to set historyItem and redoList
  55    * for multiple views
  56    */
  57   Hashtable viewportsAdded;
  58
  59   Hashtable annotationIds = new Hashtable();
  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(av.hiddenRepSequences!=null
 269               && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
 270               {
 271                 jalview.datamodel.SequenceI[] reps =
 272                     ( (jalview.datamodel.SequenceGroup)
 273                      av.hiddenRepSequences.get(
 274                          jal.getSequenceAt(i))).getSequencesInOrder(jal);
 275
 276                 for(int h=0; h<reps.length; h++)
 277                 {
 278                   if (reps[h] != jal.getSequenceAt(i))
 279                     jseq.addHiddenSequences(
 280                         jal.findIndex(reps[h])
 281                         );
 282                 }
 283               }
 284             }
 285
 286
 287             if(jds.getDatasetSequence().getSequenceFeatures()!=null)
 288             {
 289               jalview.datamodel.SequenceFeature[] sf
 290                   = jds.getDatasetSequence().getSequenceFeatures();
 291               int index = 0;
 292               while(index < sf.length)
 293               {
 294                 Features features = new Features();
 295
 296                 features.setBegin(sf[index].getBegin());
 297                 features.setEnd(sf[index].getEnd());
 298                 features.setDescription(sf[index].getDescription());
 299                 features.setType(sf[index].getType());
 300                 features.setFeatureGroup(sf[index].getFeatureGroup());
 301                 features.setScore(sf[index].getScore());
 302                 if(sf[index].links!=null)
 303                 {
 304                   for(int l=0; l<sf[index].links.size(); l++)
 305                   {
 306                     OtherData keyValue = new OtherData();
 307                     keyValue.setKey("LINK_"+l);
 308                     keyValue.setValue(sf[index].links.elementAt(l).toString());
 309                     features.addOtherData(keyValue);
 310                   }
 311                 }
 312                 if(sf[index].otherDetails!=null)
 313                 {
 314                   String key;
 315                   Enumeration keys = sf[index].otherDetails.keys();
 316                   while(keys.hasMoreElements())
 317                   {
 318                     key = keys.nextElement().toString();
 319                     OtherData keyValue = new OtherData();
 320                     keyValue.setKey( key );
 321                     keyValue.setValue(
 322                         sf[index].otherDetails.get(key).toString());
 323                     features.addOtherData(keyValue);
 324                   }
 325                 }
 326
 327                 jseq.addFeatures(features);
 328                 index ++;
 329               }
 330             }
 331
 332             if(jds.getDatasetSequence().getPDBId()!=null)
 333             {
 334               Enumeration en = jds.getDatasetSequence().getPDBId().elements();
 335               while(en.hasMoreElements())
 336               {
 337                 Pdbids pdb = new Pdbids();
 338                 jalview.datamodel.PDBEntry entry
 339                    = (jalview.datamodel.PDBEntry)en.nextElement();
 340
 341                 pdb.setId(entry.getId());
 342                 pdb.setType(entry.getType());
 343
 344
 345                 if(entry.getFile()!=null)
 346                 {
 347                   pdb.setFile(entry.getFile());
 348                   if(pdbfiles==null)
 349                     pdbfiles = new Vector();
 350
 351                   if(!pdbfiles.contains(entry.getId()))
 352                   {
 353                     pdbfiles.addElement(entry.getId());
 354                     try
 355                     {
 356                       File file = new File(entry.getFile());
 357                       if(file.exists() && jout!=null)
 358                       {
 359                         byte[] data = new byte[ (int) file.length()];
 360                         jout.putNextEntry(new JarEntry(entry.getId()));
 361                         DataInputStream dis = new DataInputStream(new
 362                             FileInputStream(file));
 363                         dis.readFully(data);
 364
 365                         DataOutputStream dout = new DataOutputStream(jout);
 366                         dout.write(data, 0, data.length);
 367                         jout.closeEntry();
 368                       }
 369                     }
 370                     catch (Exception ex)
 371                     {
 372                       ex.printStackTrace();
 373                     }
 374                   }
 375                 }
 376
 377
 378                 if(entry.getProperty()!=null)
 379                 {
 380                   PdbentryItem item = new PdbentryItem();
 381                   Hashtable properties = entry.getProperty();
 382                   Enumeration en2 = properties.keys();
 383                   while(en2.hasMoreElements())
 384                   {
 385                     Property prop = new Property();
 386                     String key = en2.nextElement().toString();
 387                     prop.setName(key);
 388                     prop.setValue( properties.get(key).toString() );
 389                     item.addProperty(prop);
 390                   }
 391                   pdb.addPdbentryItem(item);
 392                 }
 393
 394                 jseq.addPdbids(pdb);
 395               }
 396             }
 397
 398             jms.addJSeq(jseq);
 399         }
 400
 401         if(av.hasHiddenRows)
 402           jal = av.alignment;
 403
 404
 405         //SAVE TREES
 406         ///////////////////////////////////
 407         if (av.currentTree != null)
 408         {
 409           // FIND ANY ASSOCIATED TREES
 410           // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 411           if (Desktop.desktop != null)
 412           {
 413             JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 414
 415             for (int t = 0; t < frames.length; t++)
 416             {
 417               if (frames[t] instanceof TreePanel)
 418               {
 419                 TreePanel tp = (TreePanel) frames[t];
 420
 421                 if (tp.treeCanvas.av.alignment == jal)
 422                 {
 423                   Tree tree = new Tree();
 424                   tree.setTitle(tp.getTitle());
 425                   tree.setCurrentTree( (av.currentTree == tp.getTree()));
 426                   tree.setNewick(tp.getTree().toString());
 427                   tree.setThreshold(tp.treeCanvas.threshold);
 428
 429                   tree.setFitToWindow(tp.fitToWindow.getState());
 430                   tree.setFontName(tp.getTreeFont().getName());
 431                   tree.setFontSize(tp.getTreeFont().getSize());
 432                   tree.setFontStyle(tp.getTreeFont().getStyle());
 433                   tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 434
 435                   tree.setShowBootstrap(tp.bootstrapMenu.getState());
 436                   tree.setShowDistances(tp.distanceMenu.getState());
 437
 438                   tree.setHeight(tp.getHeight());
 439                   tree.setWidth(tp.getWidth());
 440                   tree.setXpos(tp.getX());
 441                   tree.setYpos(tp.getY());
 442
 443                   jms.addTree(tree);
 444                 }
 445               }
 446             }
 447           }
 448         }
 449
 450         //SAVE ANNOTATIONS
 451         if (jal.getAlignmentAnnotation() != null)
 452         {
 453             jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 454
 455             for (int i = 0; i < aa.length; i++)
 456             {
 457                 Annotation an = new Annotation();
 458
 459                 if(aa[i].annotationId!=null)
 460                 {
 461                   annotationIds.put(aa[i].annotationId, aa[i]);
 462                 }
 463
 464                 an.setId(aa[i].annotationId);
 465
 466                 if (aa[i]==av.quality ||
 467                         aa[i]==av.conservation ||
 468                         aa[i]==av.consensus)
 469                 {
 470                     an.setLabel(aa[i].label);
 471                     an.setGraph(true);
 472                     vamsasSet.addAnnotation(an);
 473                     continue;
 474                 }
 475
 476
 477                 an.setDescription(aa[i].description);
 478
 479                 if(aa[i].sequenceRef!=null)
 480                  {
 481                    an.setSequenceRef(aa[i].sequenceRef.getName());
 482                  }
 483
 484                 if(aa[i].graph>0)
 485                 {
 486                   an.setGraph(true);
 487                   an.setGraphType(aa[i].graph);
 488                   an.setGraphGroup(aa[i].graphGroup);
 489                   if(aa[i].getThreshold()!=null)
 490                   {
 491                     ThresholdLine line = new ThresholdLine();
 492                     line.setLabel(aa[i].getThreshold().label);
 493                     line.setValue(aa[i].getThreshold().value);
 494                     line.setColour(aa[i].getThreshold().colour.getRGB());
 495                     an.setThresholdLine(line);
 496                   }
 497                 }
 498                 else
 499                   an.setGraph(false);
 500
 501                 an.setLabel(aa[i].label);
 502
 503                 AnnotationElement ae;
 504
 505                 for (int a = 0; a < aa[i].annotations.length; a++)
 506                 {
 507                     if ((aa[i] == null) || (aa[i].annotations[a] == null))
 508                     {
 509                         continue;
 510                     }
 511
 512                     ae = new AnnotationElement();
 513                     ae.setDescription(aa[i].annotations[a].description);
 514                     ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 515                     ae.setValue(aa[i].annotations[a].value);
 516                     ae.setPosition(a);
 517                     ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
 518                         "");
 519
 520                     if(aa[i].annotations[a].colour!=java.awt.Color.black)
 521                       ae.setColour(aa[i].annotations[a].colour.getRGB());
 522
 523                     an.addAnnotationElement(ae);
 524                 }
 525
 526                 vamsasSet.addAnnotation(an);
 527             }
 528         }
 529
 530         //SAVE GROUPS
 531         if (jal.getGroups() != null)
 532         {
 533             JGroup[] groups = new JGroup[jal.getGroups().size()];
 534
 535             for (int i = 0; i < groups.length; i++)
 536             {
 537                 groups[i] = new JGroup();
 538
 539                 jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()
 540                                                                                           .elementAt(i);
 541                 groups[i].setStart(sg.getStartRes());
 542                 groups[i].setEnd(sg.getEndRes());
 543                 groups[i].setName(sg.getName());
 544                 if(sg.cs!=null)
 545                 {
 546                   if (sg.cs.conservationApplied())
 547                   {
 548                     groups[i].setConsThreshold(sg.cs.getConservationInc());
 549
 550                     if (sg.cs instanceof jalview.schemes.UserColourScheme)
 551                     {
 552                       groups[i].setColour(SetUserColourScheme(sg.cs,
 553                           userColours,
 554                           jms));
 555                     }
 556                     else
 557                     {
 558                       groups[i].setColour(ColourSchemeProperty.getColourName(sg.
 559                           cs));
 560                     }
 561                   }
 562                   else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 563                   {
 564                     groups[i].setColour(
 565                         ColourSchemeProperty.getColourName(
 566                       ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));
 567                   }
 568                   else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 569                   {
 570                     groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 571                         jms));
 572                   }
 573                   else
 574                   {
 575                     groups[i].setColour(ColourSchemeProperty.getColourName(
 576                         sg.cs));
 577                   }
 578
 579                   groups[i].setPidThreshold(sg.cs.getThreshold());
 580                 }
 581
 582                 groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 583                 groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 584                 groups[i].setDisplayText(sg.getDisplayText());
 585                 groups[i].setColourText(sg.getColourText());
 586                 groups[i].setTextCol1(sg.textColour.getRGB());
 587                 groups[i].setTextCol2(sg.textColour2.getRGB());
 588                 groups[i].setTextColThreshold(sg.thresholdTextColour);
 589
 590                 for (int s = 0; s < sg.getSize(); s++)
 591                 {
 592                     jalview.datamodel.Sequence seq =
 593                         (jalview.datamodel.Sequence) sg.getSequenceAt(s);
 594                     groups[i].addSeq(seq.hashCode());
 595                 }
 596             }
 597
 598             jms.setJGroup(groups);
 599         }
 600
 601
 602         ///////////SAVE VIEWPORT
 603         Viewport view = new Viewport();
 604         view.setTitle(ap.alignFrame.getTitle());
 605         view.setSequenceSetId(av.getSequenceSetId());
 606         view.setViewName(av.viewName);
 607         view.setGatheredViews(av.gatherViewsHere);
 608
 609
 610         if (ap.av.explodedPosition != null)
 611         {
 612           view.setXpos(av.explodedPosition.x);
 613           view.setYpos(av.explodedPosition.y);
 614           view.setWidth(av.explodedPosition.width);
 615           view.setHeight(av.explodedPosition.height);
 616         }
 617         else
 618         {
 619           view.setXpos(ap.alignFrame.getBounds().x);
 620           view.setYpos(ap.alignFrame.getBounds().y);
 621           view.setWidth(ap.alignFrame.getBounds().width);
 622           view.setHeight(ap.alignFrame.getBounds().height);
 623         }
 624
 625         view.setStartRes(av.startRes);
 626         view.setStartSeq(av.startSeq);
 627
 628         if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 629         {
 630             view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 631                     userColours, jms));
 632         }
 633         else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
 634         {
 635            jalview.schemes.AnnotationColourGradient acg
 636               = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();
 637
 638             AnnotationColours ac = new AnnotationColours();
 639             ac.setAboveThreshold(acg.getAboveThreshold());
 640             ac.setThreshold(acg.getAnnotationThreshold());
 641             ac.setAnnotation(acg.getAnnotation());
 642             if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 643               ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 644                     userColours, jms));
 645             else
 646               ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 647
 648             ac.setMaxColour(acg.getMaxColour().getRGB());
 649             ac.setMinColour(acg.getMinColour().getRGB());
 650             view.setAnnotationColours(ac);
 651             view.setBgColour("AnnotationColourGradient");
 652         }
 653         else
 654         {
 655             view.setBgColour(ColourSchemeProperty.getColourName(
 656                     av.getGlobalColourScheme()));
 657         }
 658
 659         ColourSchemeI cs = av.getGlobalColourScheme();
 660
 661         if(cs!=null)
 662         {
 663           if (cs.conservationApplied())
 664           {
 665             view.setConsThreshold(cs.getConservationInc());
 666             if (cs instanceof jalview.schemes.UserColourScheme)
 667               view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 668           }
 669
 670           if (cs instanceof ResidueColourScheme)
 671           {
 672             view.setPidThreshold(cs.getThreshold());
 673           }
 674         }
 675
 676         view.setConservationSelected(av.getConservationSelected());
 677         view.setPidSelected(av.getAbovePIDThreshold());
 678         view.setFontName(av.font.getName());
 679         view.setFontSize(av.font.getSize());
 680         view.setFontStyle(av.font.getStyle());
 681         view.setRenderGaps(av.renderGaps);
 682         view.setShowAnnotation(av.getShowAnnotation());
 683         view.setShowBoxes(av.getShowBoxes());
 684         view.setShowColourText(av.getColourText());
 685         view.setShowFullId(av.getShowJVSuffix());
 686         view.setRightAlignIds(av.rightAlignIds);
 687         view.setShowSequenceFeatures(av.showSequenceFeatures);
 688         view.setShowText(av.getShowText());
 689         view.setWrapAlignment(av.getWrapAlignment());
 690         view.setTextCol1(av.textColour.getRGB());
 691         view.setTextCol2(av.textColour2.getRGB());
 692         view.setTextColThreshold(av.thresholdTextColour);
 693
 694
 695         if(av.featuresDisplayed!=null)
 696         {
 697           jalview.schemabinding.version2.FeatureSettings fs
 698               = new jalview.schemabinding.version2.FeatureSettings();
 699
 700           String [] renderOrder =
 701               ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 702
 703           Vector settingsAdded = new Vector();
 704           for(int ro=0; ro<renderOrder.length; ro++)
 705           {
 706             Setting setting = new Setting();
 707             setting.setType(renderOrder[ro]);
 708             setting.setColour(
 709                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()
 710                 );
 711
 712             setting.setDisplay(
 713                 av.featuresDisplayed.containsKey(renderOrder[ro])
 714                 );
 715
 716             fs.addSetting(setting);
 717             settingsAdded.addElement(renderOrder[ro]);
 718           }
 719
 720           //Make sure we save none displayed feature settings
 721           Enumeration en =
 722               ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 723           while(en.hasMoreElements())
 724           {
 725             String key = en.nextElement().toString();
 726             if(settingsAdded.contains(key))
 727               continue;
 728
 729             Setting setting = new Setting();
 730             setting.setType(key);
 731             setting.setColour(
 732                 ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 733                 );
 734
 735             setting.setDisplay(false);
 736
 737             fs.addSetting(setting);
 738             settingsAdded.addElement(key);
 739           }
 740
 741           jms.setFeatureSettings(fs);
 742
 743         }
 744
 745         if(av.hasHiddenColumns)
 746         {
 747           for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)
 748           {
 749             int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);
 750             HiddenColumns hc = new HiddenColumns();
 751             hc.setStart(region[0]);
 752             hc.setEnd(region[1]);
 753             view.addHiddenColumns(hc);
 754           }
 755         }
 756
 757         jms.addViewport(view);
 758
 759
 760         object.setJalviewModelSequence(jms);
 761         object.getVamsasModel().addSequenceSet(vamsasSet);
 762
 763         if(out!=null)
 764         {
 765           //We may not want to right the object to disk,
 766           //eg we can copy the alignViewport to a new view object
 767           //using save and then load
 768           try
 769           {
 770             if (!fileName.endsWith(".xml"))
 771             {
 772               fileName = fileName + ".xml";
 773             }
 774
 775             JarEntry entry = new JarEntry(fileName);
 776             jout.putNextEntry(entry);
 777
 778             object.marshal(out);
 779           }
 780           catch (Exception ex)
 781           {
 782             ex.printStackTrace();
 783           }
 784         }
 785         return object;
 786     }
 787
 788     String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 789         Vector userColours, JalviewModelSequence jms)
 790     {
 791         String id = null;
 792         jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
 793
 794         if (!userColours.contains(ucs))
 795         {
 796             userColours.add(ucs);
 797
 798             java.awt.Color[] colours = ucs.getColours();
 799             jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
 800             jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
 801
 802             for (int i = 0; i < colours.length; i++)
 803             {
 804                 jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 805                 col.setName(ResidueProperties.aa[i]);
 806                 col.setRGB(jalview.util.Format.getHexString(colours[i]));
 807                 jbucs.addColour(col);
 808             }
 809             if(ucs.getLowerCaseColours()!=null)
 810             {
 811               colours = ucs.getLowerCaseColours();
 812               for (int i = 0; i < colours.length; i++)
 813              {
 814                  jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
 815                  col.setName(ResidueProperties.aa[i].toLowerCase());
 816                  col.setRGB(jalview.util.Format.getHexString(colours[i]));
 817                  jbucs.addColour(col);
 818              }
 819             }
 820
 821             id = "ucs" + userColours.indexOf(ucs);
 822             uc.setId(id);
 823             uc.setUserColourScheme(jbucs);
 824             jms.addUserColours(uc);
 825         }
 826
 827         return id;
 828     }
 829
 830    jalview.schemes.UserColourScheme GetUserColourScheme(
 831         JalviewModelSequence jms, String id)
 832     {
 833         UserColours[] uc = jms.getUserColours();
 834         UserColours colours = null;
 835
 836         for (int i = 0; i < uc.length; i++)
 837         {
 838             if (uc[i].getId().equals(id))
 839             {
 840                 colours = uc[i];
 841
 842                 break;
 843             }
 844         }
 845
 846         java.awt.Color[] newColours = new java.awt.Color[24];
 847
 848         for (int i = 0; i < 24; i++)
 849         {
 850             newColours[i] = new java.awt.Color(Integer.parseInt(
 851                         colours.getUserColourScheme().getColour(i).getRGB(), 16));
 852         }
 853
 854         jalview.schemes.UserColourScheme ucs =
 855             new jalview.schemes.UserColourScheme(newColours);
 856
 857         if (colours.getUserColourScheme().getColourCount() > 24)
 858         {
 859           newColours = new java.awt.Color[23];
 860           for (int i = 0; i < 23; i++)
 861           {
 862             newColours[i] = new java.awt.Color(Integer.parseInt(
 863                 colours.getUserColourScheme().getColour(i+24).getRGB(), 16));
 864           }
 865           ucs.setLowerCaseColours(newColours);
 866         }
 867
 868         return ucs;
 869     }
 870
 871
 872     /**
 873      * DOCUMENT ME!
 874      *
 875      * @param file DOCUMENT ME!
 876      */
 877     public AlignFrame LoadJalviewAlign(final String file)
 878     {
 879         uniqueSetSuffix = System.currentTimeMillis()%100000 +"";
 880
 881         jalview.gui.AlignFrame af = null;
 882
 883         seqRefIds = new Hashtable();
 884         viewportsAdded = new Hashtable();
 885
 886         Vector gatherToThisFrame= new Vector();
 887
 888         try
 889         {
 890             //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 891             URL url = null;
 892
 893             if (file.startsWith("http://"))
 894             {
 895                 url = new URL(file);
 896             }
 897
 898             JarInputStream jin = null;
 899             JarEntry jarentry = null;
 900             int entryCount = 1;
 901
 902             do
 903             {
 904                 if (url != null)
 905                 {
 906                     jin = new JarInputStream(url.openStream());
 907                 }
 908                 else
 909                 {
 910                     jin = new JarInputStream(new FileInputStream(file));
 911                 }
 912
 913                 for (int i = 0; i < entryCount; i++)
 914                 {
 915                     jarentry = jin.getNextJarEntry();
 916                 }
 917
 918                 if (jarentry != null && jarentry.getName().endsWith(".xml"))
 919                 {
 920                     InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 921                     JalviewModel object = new JalviewModel();
 922
 923                     Unmarshaller unmar = new Unmarshaller(object);
 924                     unmar.setValidation(false);
 925                     object = (JalviewModel) unmar.unmarshal( in );
 926
 927                     af = LoadFromObject(object, file, true);
 928                     if(af.viewport.gatherViewsHere)
 929                     {
 930                       gatherToThisFrame.add(af);
 931                     }
 932                     entryCount++;
 933                 }
 934                 else if (jarentry != null)
 935                 {
 936                   //Some other file here.
 937                   entryCount++;
 938                 }
 939             }
 940             while (jarentry != null);
 941         }
 942         catch(java.net.UnknownHostException ex)
 943         {
 944           ex.printStackTrace();
 945           System.err.println("Couldn't locate Jalview XML file : " +
 946               ex + "\n");
 947
 948           javax.swing.SwingUtilities.invokeLater(new Runnable()
 949           {
 950             public void run()
 951             {
 952               JOptionPane.showInternalMessageDialog(Desktop.desktop,
 953                   "Couldn't locate " + file,
 954                   "URL not found",
 955                   JOptionPane.WARNING_MESSAGE);
 956             }
 957           });
 958         }
 959         catch (Exception ex)
 960         {
 961           //Is Version 1 Jar file?
 962           af =  new Jalview2XML_V1().LoadJalviewAlign(file);
 963
 964           if(af!=null)
 965           {
 966             System.out.println("Successfully loaded archive file");
 967             return af;
 968           }
 969           ex.printStackTrace();
 970
 971             System.err.println("Exception whilst loading jalview XML file : " +
 972                 ex + "\n");
 973             javax.swing.SwingUtilities.invokeLater(new Runnable()
 974             {
 975               public void run()
 976               {
 977
 978                 JOptionPane.showInternalMessageDialog(Desktop.desktop,
 979                     "Error loading  " + file,
 980                     "Error loading Jalview file",
 981                     JOptionPane.WARNING_MESSAGE);
 982               }});
 983         }
 984
 985         if (Desktop.instance != null)
 986           Desktop.instance.stopLoading();
 987
 988         for (int i = 0; i < gatherToThisFrame.size(); i++)
 989         {
 990           Desktop.instance.gatherViews(
 991               (AlignFrame) gatherToThisFrame.elementAt(i));
 992         }
 993
 994         return af;
 995     }
 996
 997     String loadPDBFile(String file, String pdbId)
 998     {
 999       System.out.println(file +" "+pdbId);
1000       try
1001       {
1002         JarInputStream jin = null;
1003
1004         if (file.startsWith("http://"))
1005         {
1006           jin = new JarInputStream(new URL(file).openStream());
1007         }
1008         else
1009         {
1010           jin = new JarInputStream(new FileInputStream(file));
1011         }
1012
1013         JarEntry entry = null;
1014         do
1015         {
1016           entry = jin.getNextJarEntry();
1017         }
1018         while (!entry.getName().equals(pdbId));
1019
1020         BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1021         File outFile = File.createTempFile("jalview_pdb", ".txt");
1022         outFile.deleteOnExit();
1023         PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1024         String data;
1025
1026         while ( (data = in.readLine()) != null)
1027         {
1028           out.println(data);
1029         }
1030         out.close();
1031         return outFile.getAbsolutePath();
1032
1033       }
1034       catch (Exception ex)
1035       {
1036         ex.printStackTrace();
1037       }
1038
1039       return null;
1040     }
1041
1042
1043     AlignFrame LoadFromObject(JalviewModel object,
1044                               String file,
1045                               boolean loadTrees )
1046     {
1047         SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1048         Sequence[] vamsasSeq = vamsasSet.getSequence();
1049
1050         JalviewModelSequence jms = object.getJalviewModelSequence();
1051
1052         Viewport view = jms.getViewport(0);
1053
1054         //////////////////////////////////
1055         //LOAD SEQUENCES
1056
1057         Vector hiddenSeqs = null;
1058         jalview.datamodel.Sequence jseq;
1059
1060         ArrayList tmpseqs = new ArrayList();
1061
1062         boolean multipleView = false;
1063
1064         JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1065         for (int i = 0; i < JSEQ.length; i++)
1066         {
1067           String seqId = JSEQ[i].getId() + "";
1068
1069           if (seqRefIds.get(seqId) != null)
1070           {
1071             tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1072             multipleView = true;
1073           }
1074           else
1075           {
1076             jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1077                 vamsasSeq[i].getSequence());
1078             jseq.setDescription(vamsasSeq[i].getDescription());
1079             jseq.setStart(JSEQ[i].getStart());
1080             jseq.setEnd(JSEQ[i].getEnd());
1081             seqRefIds.put(vamsasSeq[i].getId(), jseq);
1082             tmpseqs.add( jseq );
1083           }
1084
1085
1086
1087           if (JSEQ[i].getHidden())
1088           {
1089             if (hiddenSeqs == null)
1090               hiddenSeqs = new Vector();
1091
1092
1093             hiddenSeqs.addElement(
1094                 (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1095           }
1096
1097         }
1098
1099         ///SequenceFeatures are added to the DatasetSequence,
1100         // so we must create the dataset before loading features
1101         /////////////////////////////////
1102
1103
1104       jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1105           tmpseqs.size()];
1106
1107        tmpseqs.toArray(orderedSeqs) ;
1108
1109
1110         jalview.datamodel.Alignment al =
1111             new jalview.datamodel.Alignment(orderedSeqs);
1112
1113         al.setDataset(null);
1114         /////////////////////////////////
1115
1116
1117         Hashtable pdbloaded = new Hashtable();
1118         if(!multipleView)
1119         {
1120           for (int i = 0; i < vamsasSeq.length; i++)
1121           {
1122             if (JSEQ[i].getFeaturesCount() > 0)
1123             {
1124               Features[] features = JSEQ[i].getFeatures();
1125               for (int f = 0; f < features.length; f++)
1126               {
1127                 jalview.datamodel.SequenceFeature sf
1128                     = new jalview.datamodel.SequenceFeature(features[f].getType(),
1129                     features[f].getDescription(), features[f].getStatus(),
1130                     features[f].getBegin(), features[f].getEnd(),
1131                     features[f].getFeatureGroup());
1132
1133                 sf.setScore(features[f].getScore());
1134                 for (int od = 0; od < features[f].getOtherDataCount(); od++)
1135                 {
1136                   OtherData keyValue = features[f].getOtherData(od);
1137                   if (keyValue.getKey().startsWith("LINK"))
1138                     sf.addLink(keyValue.getValue());
1139                   else
1140                     sf.setValue(keyValue.getKey(), keyValue.getValue());
1141
1142                 }
1143
1144                 al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1145               }
1146             }
1147             if (JSEQ[i].getPdbidsCount() > 0)
1148             {
1149               Pdbids[] ids = JSEQ[i].getPdbids();
1150               for (int p = 0; p < ids.length; p++)
1151               {
1152                 jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1153                     PDBEntry();
1154                 entry.setId(ids[p].getId());
1155                 entry.setType(ids[p].getType());
1156                 if (ids[p].getFile() != null)
1157                 {
1158                   if (!pdbloaded.containsKey(ids[p].getFile()))
1159                   {
1160                     String tmppdb = loadPDBFile(file, ids[p].getId());
1161                     entry.setFile(tmppdb);
1162                     pdbloaded.put(ids[p].getId(), tmppdb);
1163                   }
1164                   else
1165                     entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1166                 }
1167
1168                 al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1169               }
1170             }
1171             if (vamsasSeq[i].getDBRefCount() > 0)
1172             {
1173               for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1174               {
1175                 jalview.datamodel.DBRefEntry entry =
1176                     new jalview.datamodel.DBRefEntry(
1177                         vamsasSeq[i].getDBRef(d).getSource(),
1178                         vamsasSeq[i].getDBRef(d).getVersion(),
1179                         vamsasSeq[i].getDBRef(d).getAccessionId()
1180                     );
1181                 al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1182               }
1183
1184             }
1185           }
1186         }
1187
1188
1189          /////////////////////////////////
1190         //////////////////////////////////
1191         //LOAD ANNOTATIONS
1192         boolean hideQuality = true,
1193             hideConservation = true,
1194             hideConsensus = true;
1195
1196         if (vamsasSet.getAnnotationCount()>0)
1197         {
1198             Annotation[] an = vamsasSet.getAnnotation();
1199
1200             for (int i = 0; i < an.length; i++)
1201             {
1202                if (an[i].getLabel().equals("Quality"))
1203                 {
1204                  hideQuality = false;
1205                  continue;
1206                 }
1207                else if(an[i].getLabel().equals("Conservation"))
1208                {
1209                  hideConservation = false;
1210                  continue;
1211                }
1212                else if(an[i].getLabel().equals("Consensus"))
1213                {
1214                  hideConsensus = false;
1215                  continue;
1216                }
1217
1218                if (an[i].getId() != null
1219                    && annotationIds.containsKey(an[i].getId()))
1220                {
1221                  al.addAnnotation(
1222                      (jalview.datamodel.AlignmentAnnotation)annotationIds.get(an[i].getId())
1223                      );
1224
1225                  continue;
1226               }
1227
1228                 AnnotationElement[] ae = an[i].getAnnotationElement();
1229                 jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
1230
1231                 for (int aa = 0; aa < ae.length && aa<anot.length; aa++)
1232                 {
1233                     anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
1234                             ae[aa].getDescription(),
1235                             ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),
1236                             ae[aa].getValue());
1237                     anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );
1238                 }
1239
1240                 jalview.datamodel.AlignmentAnnotation jaa = null;
1241
1242                 if (an[i].getGraph())
1243                 {
1244                   jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1245                       an[i].getDescription(), anot, 0, 0,
1246                       an[i].getGraphType());
1247
1248                   jaa.graphGroup = an[i].getGraphGroup();
1249
1250                   if (an[i].getThresholdLine() != null)
1251                   {
1252                     jaa.setThreshold(new jalview.datamodel.GraphLine(
1253                                   an[i].getThresholdLine().getValue(),
1254                                   an[i].getThresholdLine().getLabel(),
1255                                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1256                              );
1257
1258                   }
1259
1260                 }
1261                 else
1262                 {
1263                     jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1264                             an[i].getDescription(), anot);
1265                 }
1266
1267                 if(an[i].getId()!=null)
1268                 {
1269                   annotationIds.put(an[i].getId(), jaa);
1270                   jaa.annotationId = an[i].getId();
1271                 }
1272
1273                 if(an[i].getSequenceRef()!=null)
1274                 {
1275                   jaa.createSequenceMapping(
1276                       al.findName(an[i].getSequenceRef()), 1, true
1277                       );
1278                   al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1279                 }
1280
1281                 al.addAnnotation(jaa);
1282             }
1283         }
1284
1285         /////////////////////////
1286         //LOAD GROUPS
1287         if (jms.getJGroupCount() > 0)
1288         {
1289             JGroup[] groups = jms.getJGroup();
1290
1291             for (int i = 0; i < groups.length; i++)
1292             {
1293                 ColourSchemeI cs = null;
1294
1295                 if (groups[i].getColour() != null)
1296                 {
1297                     if (groups[i].getColour().startsWith("ucs"))
1298                     {
1299                         cs = GetUserColourScheme(jms, groups[i].getColour());
1300                     }
1301                     else
1302                     {
1303                         cs = ColourSchemeProperty.getColour(al,
1304                                 groups[i].getColour());
1305                     }
1306
1307                     if(cs!=null)
1308                       cs.setThreshold(groups[i].getPidThreshold(), true);
1309                 }
1310
1311                 Vector seqs = new Vector();
1312
1313                 for (int s = 0; s < groups[i].getSeqCount(); s++)
1314                 {
1315                     String seqId = groups[i].getSeq(s)+"";
1316                     jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
1317                         seqRefIds.get(seqId);
1318
1319                     if (ts != null)
1320                       seqs.addElement(ts);
1321                 }
1322
1323                 if(seqs.size()<1)
1324                   continue;
1325
1326                 jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,
1327                         groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1328                         groups[i].getDisplayText(), groups[i].getColourText(),
1329                         groups[i].getStart(), groups[i].getEnd());
1330
1331                 sg.setOutlineColour(new java.awt.Color(
1332                         groups[i].getOutlineColour()));
1333
1334                 sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1335                 sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1336                 sg.thresholdTextColour = groups[i].getTextColThreshold();
1337
1338                 if (groups[i].getConsThreshold() != 0)
1339                 {
1340                     jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",
1341                             ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1342                             sg.getWidth() - 1);
1343                     c.calculate();
1344                     c.verdict(false, 25);
1345                     sg.cs.setConservation(c);
1346                 }
1347
1348                 al.addGroup(sg);
1349             }
1350         }
1351
1352
1353         /////////////////////////////////
1354         // LOAD VIEWPORT
1355
1356         AlignFrame af = new AlignFrame(al,
1357                                        view.getWidth(),
1358                                        view.getHeight() );
1359
1360         af.setFileName(file, "Jalview");
1361
1362         for (int i = 0; i < JSEQ.length; i++)
1363         {
1364           af.viewport.setSequenceColour(
1365               af.viewport.alignment.getSequenceAt(i),
1366               new java.awt.Color(
1367                   JSEQ[i].getColour()));
1368         }
1369
1370         //If we just load in the same jar file again, the sequenceSetId
1371         //will be the same, and we end up with multiple references
1372         //to the same sequenceSet. We must modify this id on load
1373         //so that each load of the file gives a unique id
1374         String uniqueSeqSetId =  view.getSequenceSetId()+uniqueSetSuffix;
1375
1376         af.viewport.gatherViewsHere = view.getGatheredViews();
1377
1378         if (view.getSequenceSetId() != null)
1379         {
1380           jalview.gui.AlignViewport av =
1381               (jalview.gui.AlignViewport)
1382               viewportsAdded.get(uniqueSeqSetId);
1383
1384           af.viewport.sequenceSetID = uniqueSeqSetId;
1385           if(av!=null)
1386           {
1387
1388             af.viewport.historyList = av.historyList;
1389             af.viewport.redoList = av.redoList;
1390           }
1391           else
1392           {
1393             viewportsAdded.put(uniqueSeqSetId, af.viewport);
1394           }
1395
1396           PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1397         }
1398         if(hiddenSeqs!=null)
1399         {
1400           for(int s=0; s<JSEQ.length; s++)
1401           {
1402             jalview.datamodel.SequenceGroup hidden =
1403                 new jalview.datamodel.SequenceGroup();
1404
1405             for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
1406             {
1407               hidden.addSequence(
1408                   al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1409                   , false
1410                   );
1411             }
1412             af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1413           }
1414
1415           jalview.datamodel.SequenceI [] hseqs = new
1416               jalview.datamodel.SequenceI[hiddenSeqs.size()];
1417
1418           for(int s=0; s<hiddenSeqs.size(); s++)
1419             hseqs[s] = (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s);
1420
1421           af.viewport.hideSequence( hseqs );
1422
1423         }
1424
1425
1426         if((hideConsensus || hideQuality || hideConservation)
1427             && al.getAlignmentAnnotation()!=null)
1428         {
1429           int hSize = al.getAlignmentAnnotation().length;
1430           for (int h = 0; h < hSize; h++)
1431           {
1432             if (
1433                 (hideConsensus &&
1434                  al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1435                 ||
1436                 (hideQuality &&
1437                  al.getAlignmentAnnotation()[h].label.equals("Quality"))
1438                 ||
1439                 (hideConservation &&
1440                  al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1441             {
1442               al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1443               hSize--;
1444               h--;
1445             }
1446           }
1447           af.alignPanel.adjustAnnotationHeight();
1448         }
1449
1450         if(view.getViewName()!=null)
1451         {
1452           af.viewport.viewName = view.getViewName();
1453           af.setInitialTabVisible();
1454         }
1455         af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1456             view.getHeight());
1457
1458         af.viewport.setShowAnnotation(view.getShowAnnotation());
1459         af.viewport.setAbovePIDThreshold(view.getPidSelected());
1460
1461         af.viewport.setColourText(view.getShowColourText());
1462
1463         af.viewport.setConservationSelected(view.getConservationSelected());
1464         af.viewport.setShowJVSuffix(view.getShowFullId());
1465         af.viewport.rightAlignIds=view.getRightAlignIds();
1466         af.viewport.setFont(new java.awt.Font(view.getFontName(),
1467                 view.getFontStyle(), view.getFontSize()));
1468         af.alignPanel.fontChanged();
1469         af.viewport.setRenderGaps(view.getRenderGaps());
1470         af.viewport.setWrapAlignment(view.getWrapAlignment());
1471         af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1472         af.viewport.setShowAnnotation(view.getShowAnnotation());
1473         af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1474
1475         af.viewport.setShowBoxes(view.getShowBoxes());
1476
1477         af.viewport.setShowText(view.getShowText());
1478
1479         af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1480         af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1481         af.viewport.thresholdTextColour = view.getTextColThreshold();
1482
1483         af.viewport.setStartRes(view.getStartRes());
1484         af.viewport.setStartSeq(view.getStartSeq());
1485
1486         ColourSchemeI cs = null;
1487
1488         if (view.getBgColour() != null)
1489         {
1490             if (view.getBgColour().startsWith("ucs"))
1491             {
1492                 cs = GetUserColourScheme(jms, view.getBgColour());
1493             }
1494             else if(view.getBgColour().startsWith("Annotation"))
1495             {
1496               //int find annotation
1497               for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1498               {
1499                 if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1500                     equals(view.getAnnotationColours().getAnnotation()))
1501                 {
1502                   if (af.viewport.alignment.getAlignmentAnnotation()[i].
1503                       getThreshold() == null)
1504                   {
1505                     af.viewport.alignment.getAlignmentAnnotation()[i].
1506                         setThreshold(
1507                             new jalview.datamodel.GraphLine(
1508                                 view.getAnnotationColours().getThreshold(),
1509                                 "Threshold", java.awt.Color.black)
1510
1511                         );
1512                   }
1513
1514
1515                   if (view.getAnnotationColours().getColourScheme().equals(
1516                       "None"))
1517                   {
1518                     cs = new AnnotationColourGradient(
1519                         af.viewport.alignment.getAlignmentAnnotation()[i],
1520                         new java.awt.Color(view.getAnnotationColours().
1521                                            getMinColour()),
1522                         new java.awt.Color(view.getAnnotationColours().
1523                                            getMaxColour()),
1524                         view.getAnnotationColours().getAboveThreshold());
1525                   }
1526                   else if (view.getAnnotationColours().getColourScheme().
1527                            startsWith("ucs"))
1528                   {
1529                      cs = new AnnotationColourGradient(
1530                          af.viewport.alignment.getAlignmentAnnotation()[i],
1531                          GetUserColourScheme(jms, view.getAnnotationColours().
1532                                                         getColourScheme()),
1533                          view.getAnnotationColours().getAboveThreshold()
1534                          );
1535                    }
1536                    else
1537                    {
1538                      cs = new AnnotationColourGradient(
1539                          af.viewport.alignment.getAlignmentAnnotation()[i],
1540                          ColourSchemeProperty.getColour(al,
1541                          view.getAnnotationColours().getColourScheme()),
1542                          view.getAnnotationColours().getAboveThreshold()
1543                          );
1544                    }
1545
1546                   // Also use these settings for all the groups
1547                   if (al.getGroups() != null)
1548                     for (int g = 0; g < al.getGroups().size(); g++)
1549                     {
1550                       jalview.datamodel.SequenceGroup sg
1551                           = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);
1552
1553                       if(sg.cs == null)
1554                         continue;
1555
1556
1557                   /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1558                       {
1559                         sg.cs = new AnnotationColourGradient(
1560                             af.viewport.alignment.getAlignmentAnnotation()[i],
1561                             new java.awt.Color(view.getAnnotationColours().
1562                                                getMinColour()),
1563                             new java.awt.Color(view.getAnnotationColours().
1564                                                getMaxColour()),
1565                             view.getAnnotationColours().getAboveThreshold());
1566                       }
1567                       else*/
1568                       {
1569                         sg.cs = new AnnotationColourGradient(
1570                             af.viewport.alignment.getAlignmentAnnotation()[i],
1571                             sg.cs,
1572                             view.getAnnotationColours().getAboveThreshold()
1573                             );
1574                       }
1575
1576                     }
1577
1578
1579                   break;
1580                 }
1581
1582               }
1583             }
1584             else
1585             {
1586                 cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1587             }
1588
1589             if(cs!=null)
1590             {
1591               cs.setThreshold(view.getPidThreshold(), true);
1592               cs.setConsensus(af.viewport.hconsensus);
1593             }
1594         }
1595
1596
1597         af.viewport.setGlobalColourScheme(cs);
1598         af.viewport.setColourAppliesToAllGroups(false);
1599
1600         if (view.getConservationSelected() && cs!=null)
1601         {
1602           cs.setConservationInc(view.getConsThreshold());
1603         }
1604
1605         af.changeColour(cs);
1606
1607         af.viewport.setColourAppliesToAllGroups(true);
1608
1609
1610
1611         if (view.getShowSequenceFeatures())
1612         {
1613            af.viewport.showSequenceFeatures = true;
1614         }
1615
1616         if(jms.getFeatureSettings()!=null)
1617         {
1618           af.viewport.featuresDisplayed = new Hashtable();
1619           String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];
1620          for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)
1621          {
1622            Setting setting = jms.getFeatureSettings().getSetting(fs);
1623
1624            af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),
1625                new java.awt.Color(setting.getColour()));
1626
1627            renderOrder[fs] = setting.getType();
1628
1629            if(setting.getDisplay())
1630              af.viewport.featuresDisplayed.put(
1631                  setting.getType(), new Integer(setting.getColour()));
1632          }
1633          af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
1634         }
1635
1636         if (view.getHiddenColumnsCount() > 0)
1637         {
1638           for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1639           {
1640               af.viewport.hideColumns(
1641                 view.getHiddenColumns(c).getStart(),
1642                 view.getHiddenColumns(c).getEnd() //+1
1643                 );
1644           }
1645         }
1646
1647         af.setMenusFromViewport(af.viewport);
1648
1649
1650         Desktop.addInternalFrame(af, view.getTitle(),
1651              view.getWidth(), view.getHeight());
1652
1653         //LOAD TREES
1654         ///////////////////////////////////////
1655         if (loadTrees && jms.getTreeCount() > 0)
1656         {
1657             try
1658             {
1659                 for (int t = 0; t < jms.getTreeCount(); t++)
1660                 {
1661
1662                     Tree tree = jms.getTree(t);
1663
1664                     TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1665                                 tree.getNewick()), tree.getTitle(),
1666                                 tree.getWidth(), tree.getHeight(),
1667                                 tree.getXpos(), tree.getYpos());
1668
1669                     tp.fitToWindow.setState(tree.getFitToWindow());
1670                     tp.fitToWindow_actionPerformed(null);
1671
1672                     if(tree.getFontName()!=null)
1673                       tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1674                                           tree.getFontStyle(),
1675                                           tree.getFontSize()));
1676                     else
1677                       tp.setTreeFont(new java.awt.Font(view.getFontName(),
1678                                             view.getFontStyle(),
1679                                             tree.getFontSize()));
1680
1681                     tp.showPlaceholders(tree.getMarkUnlinked());
1682                     tp.showBootstrap(tree.getShowBootstrap());
1683                     tp.showDistances(tree.getShowDistances());
1684
1685                     tp.treeCanvas.threshold = tree.getThreshold();
1686
1687                     if (tree.getCurrentTree())
1688                       af.viewport.setCurrentTree(tp.getTree());
1689                 }
1690
1691             }
1692             catch (Exception ex)
1693             {
1694                 ex.printStackTrace();
1695             }
1696
1697         }
1698
1699         return af;
1700     }
1701
1702     public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, boolean keepSeqRefs )
1703     {
1704       jalview.schemabinding.version2.JalviewModel jm
1705           = SaveState(ap, null, null, null);
1706
1707       if (!keepSeqRefs)
1708       {
1709         seqRefIds.clear();
1710         jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1711       }
1712       else
1713         uniqueSetSuffix = "";
1714
1715       viewportsAdded = new Hashtable();
1716
1717       AlignFrame af = LoadFromObject(jm, null, false);
1718       af.alignPanels.clear();
1719       af.closeMenuItem_actionPerformed(true);
1720
1721     /*  if(ap.av.alignment.getAlignmentAnnotation()!=null)
1722       {
1723         for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
1724         {
1725           if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
1726           {
1727             af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
1728                 ap.av.alignment.getAlignmentAnnotation()[i];
1729           }
1730         }
1731       }   */
1732
1733       return af.alignPanel;
1734     }
1735 }
1736