src/jalview/gui/Jalview2XML.java

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