src/jalview/gui/Jalview2XML.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer
   3  * Copyright (C) 2007 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 import java.io.*;
  22 import java.net.*;
  23 import java.util.*;
  24 import java.util.jar.*;
  25
  26 import javax.swing.*;
  27
  28 import org.exolab.castor.xml.*;
  29 import jalview.schemabinding.version2.*;
  30 import jalview.schemes.*;
  31
  32 /**
  33  * DOCUMENT ME!
  34  *
  35  * @author $author$
  36  * @version $Revision$
  37  */
  38 public class Jalview2XML
  39 {
  40
  41   Hashtable seqRefIds;
  42
  43   /**
  44    * This maintains a list of viewports, the key being the
  45    * seqSetId. Important to set historyItem and redoList
  46    * for multiple views
  47    */
  48   Hashtable viewportsAdded;
  49
  50   Hashtable annotationIds = new Hashtable();
  51
  52   String uniqueSetSuffix = "";
  53
  54   // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
  55   public void SaveState(File statefile)
  56   {
  57     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
  58
  59     if (frames == null)
  60     {
  61       return;
  62     }
  63
  64     try
  65     {
  66       FileOutputStream fos = new FileOutputStream(statefile);
  67       JarOutputStream jout = new JarOutputStream(fos);
  68
  69       //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
  70       ////////////////////////////////////////////////////
  71       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
  72           "UTF-8"));
  73
  74       Vector shortNames = new Vector();
  75
  76       //REVERSE ORDER
  77       for (int i = frames.length - 1; i > -1; i--)
  78       {
  79         if (frames[i] instanceof AlignFrame)
  80         {
  81           AlignFrame af = (AlignFrame) frames[i];
  82
  83           String shortName = af.getTitle();
  84
  85           if (shortName.indexOf(File.separatorChar) > -1)
  86           {
  87             shortName = shortName.substring(shortName.lastIndexOf(
  88                 File.separatorChar) + 1);
  89           }
  90
  91           int count = 1;
  92
  93           while (shortNames.contains(shortName))
  94           {
  95             if (shortName.endsWith("_" + (count - 1)))
  96             {
  97               shortName = shortName.substring(0,
  98                                               shortName.lastIndexOf("_"));
  99             }
 100
 101             shortName = shortName.concat("_" + count);
 102             count++;
 103           }
 104
 105           shortNames.addElement(shortName);
 106
 107           if (!shortName.endsWith(".xml"))
 108           {
 109             shortName = shortName + ".xml";
 110           }
 111
 112           int ap, apSize = af.alignPanels.size();
 113           for (ap = 0; ap < apSize; ap++)
 114           {
 115             AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
 116                 elementAt(ap);
 117
 118             SaveState(apanel,
 119                       apSize == 1 ? shortName : ap + shortName,
 120                       jout, out);
 121           }
 122         }
 123       }
 124
 125       out.close();
 126       jout.close();
 127     }
 128     catch (Exception ex)
 129     {
 130       ex.printStackTrace();
 131     }
 132   }
 133
 134   // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
 135   public boolean SaveAlignment(AlignFrame af, String jarFile,
 136                                String fileName)
 137   {
 138     try
 139     {
 140       int ap, apSize = af.alignPanels.size();
 141       FileOutputStream fos = new FileOutputStream(jarFile);
 142       JarOutputStream jout = new JarOutputStream(fos);
 143       PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
 144           "UTF-8"));
 145       for (ap = 0; ap < apSize; ap++)
 146       {
 147         AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
 148
 149         SaveState(apanel,
 150                   apSize == 1 ? fileName : fileName + ap,
 151                   jout, out);
 152       }
 153
 154       out.close();
 155       jout.close();
 156       return true;
 157     }
 158     catch (Exception ex)
 159     {
 160       ex.printStackTrace();
 161       return false;
 162     }
 163   }
 164
 165   /**
 166    * DOCUMENT ME!
 167    *
 168    * @param af DOCUMENT ME!
 169    * @param timeStamp DOCUMENT ME!
 170    * @param fileName DOCUMENT ME!
 171    * @param jout DOCUMENT ME!
 172    * @param out DOCUMENT ME!
 173    */
 174   public JalviewModel SaveState(AlignmentPanel ap,
 175                                 String fileName,
 176                                 JarOutputStream jout,
 177                                 PrintWriter out)
 178   {
 179     if (seqRefIds == null)
 180     {
 181       seqRefIds = new Hashtable();
 182     }
 183
 184     Vector userColours = new Vector();
 185
 186     AlignViewport av = ap.av;
 187
 188     JalviewModel object = new JalviewModel();
 189     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
 190
 191     object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
 192     object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
 193
 194     jalview.datamodel.AlignmentI jal = av.alignment;
 195
 196     if (av.hasHiddenRows)
 197     {
 198       jal = jal.getHiddenSequences().getFullAlignment();
 199     }
 200
 201     SequenceSet vamsasSet = new SequenceSet();
 202     Sequence vamsasSeq;
 203     JalviewModelSequence jms = new JalviewModelSequence();
 204
 205     vamsasSet.setGapChar(jal.getGapCharacter() + "");
 206
 207     JSeq jseq;
 208     Vector pdbfiles = null;
 209
 210     //SAVE SEQUENCES
 211     int id = 0;
 212     jalview.datamodel.SequenceI jds;
 213     for (int i = 0; i < jal.getHeight(); i++)
 214     {
 215       jds = jal.getSequenceAt(i);
 216       id = jds.hashCode();
 217
 218       if (seqRefIds.get(id + "") != null)
 219       {
 220
 221       }
 222       else
 223       {
 224         vamsasSeq = new Sequence();
 225         vamsasSeq.setId(id + "");
 226         vamsasSeq.setName(jds.getName());
 227         vamsasSeq.setSequence(jds.getSequenceAsString());
 228         vamsasSeq.setDescription(jds.getDescription());
 229
 230         if (jds.getDatasetSequence().getDBRef() != null)
 231         {
 232           jalview.datamodel.DBRefEntry[] dbrefs =
 233               jds.getDatasetSequence().getDBRef();
 234
 235           for (int d = 0; d < dbrefs.length; d++)
 236           {
 237             DBRef dbref = new DBRef();
 238             dbref.setSource(dbrefs[d].getSource());
 239             dbref.setVersion(dbrefs[d].getVersion());
 240             dbref.setAccessionId(dbrefs[d].getAccessionId());
 241             vamsasSeq.addDBRef(dbref);
 242           }
 243         }
 244
 245         vamsasSet.addSequence(vamsasSeq);
 246         seqRefIds.put(id + "", jal.getSequenceAt(i));
 247       }
 248
 249       jseq = new JSeq();
 250       jseq.setStart(jds.getStart());
 251       jseq.setEnd(jds.getEnd());
 252       jseq.setColour(av.getSequenceColour(jds).getRGB());
 253
 254       jseq.setId(id);
 255
 256       if (av.hasHiddenRows)
 257       {
 258         jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
 259
 260         if (av.hiddenRepSequences != null
 261             && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
 262         {
 263           jalview.datamodel.SequenceI[] reps =
 264               ( (jalview.datamodel.SequenceGroup)
 265                av.hiddenRepSequences.get(
 266                    jal.getSequenceAt(i))).getSequencesInOrder(jal);
 267
 268           for (int h = 0; h < reps.length; h++)
 269           {
 270             if (reps[h] != jal.getSequenceAt(i))
 271             {
 272               jseq.addHiddenSequences(
 273                   jal.findIndex(reps[h])
 274                   );
 275             }
 276           }
 277         }
 278       }
 279
 280       if (jds.getDatasetSequence().getSequenceFeatures() != null)
 281       {
 282         jalview.datamodel.SequenceFeature[] sf
 283             = jds.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 (jds.getDatasetSequence().getPDBId() != null)
 326       {
 327         Enumeration en = jds.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             pdb.setFile(entry.getFile());
 340             if (pdbfiles == null)
 341             {
 342               pdbfiles = new Vector();
 343             }
 344
 345             if (!pdbfiles.contains(entry.getId()))
 346             {
 347               pdbfiles.addElement(entry.getId());
 348               try
 349               {
 350                 File file = new File(entry.getFile());
 351                 if (file.exists() && jout != null)
 352                 {
 353                   byte[] data = new byte[ (int) file.length()];
 354                   jout.putNextEntry(new JarEntry(entry.getId()));
 355                   DataInputStream dis = new DataInputStream(new
 356                       FileInputStream(file));
 357                   dis.readFully(data);
 358
 359                   DataOutputStream dout = new DataOutputStream(jout);
 360                   dout.write(data, 0, data.length);
 361                   jout.closeEntry();
 362                 }
 363               }
 364               catch (Exception ex)
 365               {
 366                 ex.printStackTrace();
 367               }
 368             }
 369           }
 370
 371           if (entry.getProperty() != null)
 372           {
 373             PdbentryItem item = new PdbentryItem();
 374             Hashtable properties = entry.getProperty();
 375             Enumeration en2 = properties.keys();
 376             while (en2.hasMoreElements())
 377             {
 378               Property prop = new Property();
 379               String key = en2.nextElement().toString();
 380               prop.setName(key);
 381               prop.setValue(properties.get(key).toString());
 382               item.addProperty(prop);
 383             }
 384             pdb.addPdbentryItem(item);
 385           }
 386
 387           jseq.addPdbids(pdb);
 388         }
 389       }
 390
 391       jms.addJSeq(jseq);
 392     }
 393
 394     if (av.hasHiddenRows)
 395     {
 396       jal = av.alignment;
 397     }
 398
 399     //SAVE TREES
 400     ///////////////////////////////////
 401     if (av.currentTree != null)
 402     {
 403       // FIND ANY ASSOCIATED TREES
 404       // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
 405       if (Desktop.desktop != null)
 406       {
 407         JInternalFrame[] frames = Desktop.desktop.getAllFrames();
 408
 409         for (int t = 0; t < frames.length; t++)
 410         {
 411           if (frames[t] instanceof TreePanel)
 412           {
 413             TreePanel tp = (TreePanel) frames[t];
 414
 415             if (tp.treeCanvas.av.alignment == jal)
 416             {
 417               Tree tree = new Tree();
 418               tree.setTitle(tp.getTitle());
 419               tree.setCurrentTree( (av.currentTree == tp.getTree()));
 420               tree.setNewick(tp.getTree().toString());
 421               tree.setThreshold(tp.treeCanvas.threshold);
 422
 423               tree.setFitToWindow(tp.fitToWindow.getState());
 424               tree.setFontName(tp.getTreeFont().getName());
 425               tree.setFontSize(tp.getTreeFont().getSize());
 426               tree.setFontStyle(tp.getTreeFont().getStyle());
 427               tree.setMarkUnlinked(tp.placeholdersMenu.getState());
 428
 429               tree.setShowBootstrap(tp.bootstrapMenu.getState());
 430               tree.setShowDistances(tp.distanceMenu.getState());
 431
 432               tree.setHeight(tp.getHeight());
 433               tree.setWidth(tp.getWidth());
 434               tree.setXpos(tp.getX());
 435               tree.setYpos(tp.getY());
 436
 437               jms.addTree(tree);
 438             }
 439           }
 440         }
 441       }
 442     }
 443
 444     //SAVE ANNOTATIONS
 445     if (jal.getAlignmentAnnotation() != null)
 446     {
 447       jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
 448
 449       for (int i = 0; i < aa.length; i++)
 450       {
 451         Annotation an = new Annotation();
 452
 453         if (aa[i].annotationId != null)
 454         {
 455           annotationIds.put(aa[i].annotationId, aa[i]);
 456         }
 457
 458         an.setId(aa[i].annotationId);
 459
 460         if (aa[i] == av.quality ||
 461             aa[i] == av.conservation ||
 462             aa[i] == av.consensus)
 463         {
 464           an.setLabel(aa[i].label);
 465           an.setGraph(true);
 466           vamsasSet.addAnnotation(an);
 467           continue;
 468         }
 469
 470         an.setDescription(aa[i].description);
 471
 472         if (aa[i].sequenceRef != null)
 473         {
 474           an.setSequenceRef(aa[i].sequenceRef.getName());
 475         }
 476
 477         if (aa[i].graph > 0)
 478         {
 479           an.setGraph(true);
 480           an.setGraphType(aa[i].graph);
 481           an.setGraphGroup(aa[i].graphGroup);
 482           if (aa[i].getThreshold() != null)
 483           {
 484             ThresholdLine line = new ThresholdLine();
 485             line.setLabel(aa[i].getThreshold().label);
 486             line.setValue(aa[i].getThreshold().value);
 487             line.setColour(aa[i].getThreshold().colour.getRGB());
 488             an.setThresholdLine(line);
 489           }
 490         }
 491         else
 492         {
 493           an.setGraph(false);
 494         }
 495
 496         an.setLabel(aa[i].label);
 497
 498         AnnotationElement ae;
 499
 500         for (int a = 0; a < aa[i].annotations.length; a++)
 501         {
 502           if ( (aa[i] == null) || (aa[i].annotations[a] == null))
 503           {
 504             continue;
 505           }
 506
 507           ae = new AnnotationElement();
 508           ae.setDescription(aa[i].annotations[a].description);
 509           ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
 510           ae.setValue(aa[i].annotations[a].value);
 511           ae.setPosition(a);
 512           ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
 513                                    "");
 514
 515           if (aa[i].annotations[a].colour != java.awt.Color.black)
 516           {
 517             ae.setColour(aa[i].annotations[a].colour.getRGB());
 518           }
 519
 520           an.addAnnotationElement(ae);
 521         }
 522
 523         vamsasSet.addAnnotation(an);
 524       }
 525     }
 526
 527     //SAVE GROUPS
 528     if (jal.getGroups() != null)
 529     {
 530       JGroup[] groups = new JGroup[jal.getGroups().size()];
 531
 532       for (int i = 0; i < groups.length; i++)
 533       {
 534         groups[i] = new JGroup();
 535
 536         jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
 537             jal.getGroups()
 538             .elementAt(i);
 539         groups[i].setStart(sg.getStartRes());
 540         groups[i].setEnd(sg.getEndRes());
 541         groups[i].setName(sg.getName());
 542         if (sg.cs != null)
 543         {
 544           if (sg.cs.conservationApplied())
 545           {
 546             groups[i].setConsThreshold(sg.cs.getConservationInc());
 547
 548             if (sg.cs instanceof jalview.schemes.UserColourScheme)
 549             {
 550               groups[i].setColour(SetUserColourScheme(sg.cs,
 551                   userColours,
 552                   jms));
 553             }
 554             else
 555             {
 556               groups[i].setColour(ColourSchemeProperty.getColourName(sg.
 557                   cs));
 558             }
 559           }
 560           else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
 561           {
 562             groups[i].setColour(
 563                 ColourSchemeProperty.getColourName(
 564                     ( (jalview.schemes.AnnotationColourGradient) sg.cs).
 565                     getBaseColour()));
 566           }
 567           else if (sg.cs instanceof jalview.schemes.UserColourScheme)
 568           {
 569             groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
 570                 jms));
 571           }
 572           else
 573           {
 574             groups[i].setColour(ColourSchemeProperty.getColourName(
 575                 sg.cs));
 576           }
 577
 578           groups[i].setPidThreshold(sg.cs.getThreshold());
 579         }
 580
 581         groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
 582         groups[i].setDisplayBoxes(sg.getDisplayBoxes());
 583         groups[i].setDisplayText(sg.getDisplayText());
 584         groups[i].setColourText(sg.getColourText());
 585         groups[i].setTextCol1(sg.textColour.getRGB());
 586         groups[i].setTextCol2(sg.textColour2.getRGB());
 587         groups[i].setTextColThreshold(sg.thresholdTextColour);
 588
 589         for (int s = 0; s < sg.getSize(); s++)
 590         {
 591           jalview.datamodel.Sequence seq =
 592               (jalview.datamodel.Sequence) sg.getSequenceAt(s);
 593           groups[i].addSeq(seq.hashCode());
 594         }
 595       }
 596
 597       jms.setJGroup(groups);
 598     }
 599
 600     ///////////SAVE VIEWPORT
 601     Viewport view = new Viewport();
 602     view.setTitle(ap.alignFrame.getTitle());
 603     view.setSequenceSetId(av.getSequenceSetId());
 604     view.setViewName(av.viewName);
 605     view.setGatheredViews(av.gatherViewsHere);
 606
 607     if (ap.av.explodedPosition != null)
 608     {
 609       view.setXpos(av.explodedPosition.x);
 610       view.setYpos(av.explodedPosition.y);
 611       view.setWidth(av.explodedPosition.width);
 612       view.setHeight(av.explodedPosition.height);
 613     }
 614     else
 615     {
 616       view.setXpos(ap.alignFrame.getBounds().x);
 617       view.setYpos(ap.alignFrame.getBounds().y);
 618       view.setWidth(ap.alignFrame.getBounds().width);
 619       view.setHeight(ap.alignFrame.getBounds().height);
 620     }
 621
 622     view.setStartRes(av.startRes);
 623     view.setStartSeq(av.startSeq);
 624
 625     if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
 626     {
 627       view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
 628                                            userColours, jms));
 629     }
 630     else if (av.getGlobalColourScheme() instanceof jalview.schemes.
 631              AnnotationColourGradient)
 632     {
 633       jalview.schemes.AnnotationColourGradient acg
 634           = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
 635
 636       AnnotationColours ac = new AnnotationColours();
 637       ac.setAboveThreshold(acg.getAboveThreshold());
 638       ac.setThreshold(acg.getAnnotationThreshold());
 639       ac.setAnnotation(acg.getAnnotation());
 640       if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
 641       {
 642         ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
 643                                                userColours, jms));
 644       }
 645       else
 646       {
 647         ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
 648       }
 649
 650       ac.setMaxColour(acg.getMaxColour().getRGB());
 651       ac.setMinColour(acg.getMinColour().getRGB());
 652       view.setAnnotationColours(ac);
 653       view.setBgColour("AnnotationColourGradient");
 654     }
 655     else
 656     {
 657       view.setBgColour(ColourSchemeProperty.getColourName(
 658           av.getGlobalColourScheme()));
 659     }
 660
 661     ColourSchemeI cs = av.getGlobalColourScheme();
 662
 663     if (cs != null)
 664     {
 665       if (cs.conservationApplied())
 666       {
 667         view.setConsThreshold(cs.getConservationInc());
 668         if (cs instanceof jalview.schemes.UserColourScheme)
 669         {
 670           view.setBgColour(SetUserColourScheme(cs, userColours, jms));
 671         }
 672       }
 673
 674       if (cs instanceof ResidueColourScheme)
 675       {
 676         view.setPidThreshold(cs.getThreshold());
 677       }
 678     }
 679
 680     view.setConservationSelected(av.getConservationSelected());
 681     view.setPidSelected(av.getAbovePIDThreshold());
 682     view.setFontName(av.font.getName());
 683     view.setFontSize(av.font.getSize());
 684     view.setFontStyle(av.font.getStyle());
 685     view.setRenderGaps(av.renderGaps);
 686     view.setShowAnnotation(av.getShowAnnotation());
 687     view.setShowBoxes(av.getShowBoxes());
 688     view.setShowColourText(av.getColourText());
 689     view.setShowFullId(av.getShowJVSuffix());
 690     view.setRightAlignIds(av.rightAlignIds);
 691     view.setShowSequenceFeatures(av.showSequenceFeatures);
 692     view.setShowText(av.getShowText());
 693     view.setWrapAlignment(av.getWrapAlignment());
 694     view.setTextCol1(av.textColour.getRGB());
 695     view.setTextCol2(av.textColour2.getRGB());
 696     view.setTextColThreshold(av.thresholdTextColour);
 697
 698     if (av.featuresDisplayed != null)
 699     {
 700       jalview.schemabinding.version2.FeatureSettings fs
 701           = new jalview.schemabinding.version2.FeatureSettings();
 702
 703       String[] renderOrder =
 704           ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
 705
 706       Vector settingsAdded = new Vector();
 707       for (int ro = 0; ro < renderOrder.length; ro++)
 708       {
 709         Setting setting = new Setting();
 710         setting.setType(renderOrder[ro]);
 711         setting.setColour(
 712             ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
 713             getRGB()
 714             );
 715
 716         setting.setDisplay(
 717             av.featuresDisplayed.containsKey(renderOrder[ro])
 718             );
 719
 720         fs.addSetting(setting);
 721         settingsAdded.addElement(renderOrder[ro]);
 722       }
 723
 724       //Make sure we save none displayed feature settings
 725       Enumeration en =
 726           ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
 727       while (en.hasMoreElements())
 728       {
 729         String key = en.nextElement().toString();
 730         if (settingsAdded.contains(key))
 731         {
 732           continue;
 733         }
 734
 735         Setting setting = new Setting();
 736         setting.setType(key);
 737         setting.setColour(
 738             ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
 739             );
 740
 741         setting.setDisplay(false);
 742
 743         fs.addSetting(setting);
 744         settingsAdded.addElement(key);
 745       }
 746
 747       jms.setFeatureSettings(fs);
 748
 749     }
 750
 751     if (av.hasHiddenColumns)
 752     {
 753       for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
 754       {
 755         int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
 756             elementAt(c);
 757         HiddenColumns hc = new HiddenColumns();
 758         hc.setStart(region[0]);
 759         hc.setEnd(region[1]);
 760         view.addHiddenColumns(hc);
 761       }
 762     }
 763
 764     jms.addViewport(view);
 765
 766     object.setJalviewModelSequence(jms);
 767     object.getVamsasModel().addSequenceSet(vamsasSet);
 768
 769     if (out != null)
 770     {
 771       //We may not want to right the object to disk,
 772       //eg we can copy the alignViewport to a new view object
 773       //using save and then load
 774       try
 775       {
 776         if (!fileName.endsWith(".xml"))
 777         {
 778           fileName = fileName + ".xml";
 779         }
 780
 781         JarEntry entry = new JarEntry(fileName);
 782         jout.putNextEntry(entry);
 783
 784         object.marshal(out);
 785       }
 786       catch (Exception ex)
 787       {
 788         ex.printStackTrace();
 789       }
 790     }
 791     return object;
 792   }
 793
 794   String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
 795                              Vector userColours, JalviewModelSequence jms)
 796   {
 797     String id = null;
 798     jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
 799         cs;
 800
 801     if (!userColours.contains(ucs))
 802     {
 803       userColours.add(ucs);
 804
 805       java.awt.Color[] colours = ucs.getColours();
 806       jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
 807           version2.UserColours();
 808       jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
 809           schemabinding.version2.UserColourScheme();
 810
 811       for (int i = 0; i < colours.length; i++)
 812       {
 813         jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
 814             version2.Colour();
 815         col.setName(ResidueProperties.aa[i]);
 816         col.setRGB(jalview.util.Format.getHexString(colours[i]));
 817         jbucs.addColour(col);
 818       }
 819       if (ucs.getLowerCaseColours() != null)
 820       {
 821         colours = ucs.getLowerCaseColours();
 822         for (int i = 0; i < colours.length; i++)
 823         {
 824           jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
 825               version2.Colour();
 826           col.setName(ResidueProperties.aa[i].toLowerCase());
 827           col.setRGB(jalview.util.Format.getHexString(colours[i]));
 828           jbucs.addColour(col);
 829         }
 830       }
 831
 832       id = "ucs" + userColours.indexOf(ucs);
 833       uc.setId(id);
 834       uc.setUserColourScheme(jbucs);
 835       jms.addUserColours(uc);
 836     }
 837
 838     return id;
 839   }
 840
 841   jalview.schemes.UserColourScheme GetUserColourScheme(
 842       JalviewModelSequence jms, String id)
 843   {
 844     UserColours[] uc = jms.getUserColours();
 845     UserColours colours = null;
 846
 847     for (int i = 0; i < uc.length; i++)
 848     {
 849       if (uc[i].getId().equals(id))
 850       {
 851         colours = uc[i];
 852
 853         break;
 854       }
 855     }
 856
 857     java.awt.Color[] newColours = new java.awt.Color[24];
 858
 859     for (int i = 0; i < 24; i++)
 860     {
 861       newColours[i] = new java.awt.Color(Integer.parseInt(
 862           colours.getUserColourScheme().getColour(i).getRGB(), 16));
 863     }
 864
 865     jalview.schemes.UserColourScheme ucs =
 866         new jalview.schemes.UserColourScheme(newColours);
 867
 868     if (colours.getUserColourScheme().getColourCount() > 24)
 869     {
 870       newColours = new java.awt.Color[23];
 871       for (int i = 0; i < 23; i++)
 872       {
 873         newColours[i] = new java.awt.Color(Integer.parseInt(
 874             colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
 875       }
 876       ucs.setLowerCaseColours(newColours);
 877     }
 878
 879     return ucs;
 880   }
 881
 882   /**
 883    * DOCUMENT ME!
 884    *
 885    * @param file DOCUMENT ME!
 886    */
 887   public AlignFrame LoadJalviewAlign(final String file)
 888   {
 889     uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
 890
 891     jalview.gui.AlignFrame af = null;
 892
 893     seqRefIds = new Hashtable();
 894     viewportsAdded = new Hashtable();
 895
 896     Vector gatherToThisFrame = new Vector();
 897
 898     try
 899     {
 900       //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
 901       URL url = null;
 902
 903       if (file.startsWith("http://"))
 904       {
 905         url = new URL(file);
 906       }
 907
 908       JarInputStream jin = null;
 909       JarEntry jarentry = null;
 910       int entryCount = 1;
 911
 912       do
 913       {
 914         if (url != null)
 915         {
 916           jin = new JarInputStream(url.openStream());
 917         }
 918         else
 919         {
 920           jin = new JarInputStream(new FileInputStream(file));
 921         }
 922
 923         for (int i = 0; i < entryCount; i++)
 924         {
 925           jarentry = jin.getNextJarEntry();
 926         }
 927
 928         if (jarentry != null && jarentry.getName().endsWith(".xml"))
 929         {
 930           InputStreamReader in = new InputStreamReader(jin, "UTF-8");
 931           JalviewModel object = new JalviewModel();
 932
 933           Unmarshaller unmar = new Unmarshaller(object);
 934           unmar.setValidation(false);
 935           object = (JalviewModel) unmar.unmarshal(in);
 936
 937           af = LoadFromObject(object, file, true);
 938           if (af.viewport.gatherViewsHere)
 939           {
 940             gatherToThisFrame.add(af);
 941           }
 942           entryCount++;
 943         }
 944         else if (jarentry != null)
 945         {
 946           //Some other file here.
 947           entryCount++;
 948         }
 949       }
 950       while (jarentry != null);
 951     }
 952     catch (java.net.UnknownHostException ex)
 953     {
 954       ex.printStackTrace();
 955       System.err.println("Couldn't locate Jalview XML file : " +
 956                          ex + "\n");
 957
 958       javax.swing.SwingUtilities.invokeLater(new Runnable()
 959       {
 960         public void run()
 961         {
 962           JOptionPane.showInternalMessageDialog(Desktop.desktop,
 963                                                 "Couldn't locate " + file,
 964                                                 "URL not found",
 965                                                 JOptionPane.WARNING_MESSAGE);
 966         }
 967       });
 968     }
 969     catch (Exception ex)
 970     {
 971       //Is Version 1 Jar file?
 972       af = new Jalview2XML_V1().LoadJalviewAlign(file);
 973
 974       if (af != null)
 975       {
 976         System.out.println("Successfully loaded archive file");
 977         return af;
 978       }
 979       ex.printStackTrace();
 980
 981       System.err.println("Exception whilst loading jalview XML file : " +
 982                          ex + "\n");
 983       javax.swing.SwingUtilities.invokeLater(new Runnable()
 984       {
 985         public void run()
 986         {
 987
 988           JOptionPane.showInternalMessageDialog(Desktop.desktop,
 989                                                 "Error loading  " + file,
 990                                                 "Error loading Jalview file",
 991                                                 JOptionPane.WARNING_MESSAGE);
 992         }
 993       });
 994     }
 995
 996     if (Desktop.instance != null)
 997     {
 998       Desktop.instance.stopLoading();
 999     }
1000
1001     for (int i = 0; i < gatherToThisFrame.size(); i++)
1002     {
1003       Desktop.instance.gatherViews(
1004           (AlignFrame) gatherToThisFrame.elementAt(i));
1005     }
1006
1007     return af;
1008   }
1009
1010   String loadPDBFile(String file, String pdbId)
1011   {
1012     System.out.println(file + " " + pdbId);
1013     try
1014     {
1015       JarInputStream jin = null;
1016
1017       if (file.startsWith("http://"))
1018       {
1019         jin = new JarInputStream(new URL(file).openStream());
1020       }
1021       else
1022       {
1023         jin = new JarInputStream(new FileInputStream(file));
1024       }
1025
1026       JarEntry entry = null;
1027       do
1028       {
1029         entry = jin.getNextJarEntry();
1030       }
1031       while (!entry.getName().equals(pdbId));
1032
1033       BufferedReader in = new BufferedReader(new InputStreamReader(jin));
1034       File outFile = File.createTempFile("jalview_pdb", ".txt");
1035       outFile.deleteOnExit();
1036       PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
1037       String data;
1038
1039       while ( (data = in.readLine()) != null)
1040       {
1041         out.println(data);
1042       }
1043       out.close();
1044       return outFile.getAbsolutePath();
1045
1046     }
1047     catch (Exception ex)
1048     {
1049       ex.printStackTrace();
1050     }
1051
1052     return null;
1053   }
1054
1055   AlignFrame LoadFromObject(JalviewModel object,
1056                             String file,
1057                             boolean loadTrees)
1058   {
1059     SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
1060     Sequence[] vamsasSeq = vamsasSet.getSequence();
1061
1062     JalviewModelSequence jms = object.getJalviewModelSequence();
1063
1064     Viewport view = jms.getViewport(0);
1065
1066     //////////////////////////////////
1067     //LOAD SEQUENCES
1068
1069     Vector hiddenSeqs = null;
1070     jalview.datamodel.Sequence jseq;
1071
1072     ArrayList tmpseqs = new ArrayList();
1073
1074     boolean multipleView = false;
1075
1076     JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
1077     for (int i = 0; i < JSEQ.length; i++)
1078     {
1079       String seqId = JSEQ[i].getId() + "";
1080
1081       if (seqRefIds.get(seqId) != null)
1082       {
1083         tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1084         multipleView = true;
1085       }
1086       else
1087       {
1088         jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
1089                                               vamsasSeq[i].getSequence());
1090         jseq.setDescription(vamsasSeq[i].getDescription());
1091         jseq.setStart(JSEQ[i].getStart());
1092         jseq.setEnd(JSEQ[i].getEnd());
1093         seqRefIds.put(vamsasSeq[i].getId(), jseq);
1094         tmpseqs.add(jseq);
1095       }
1096
1097       if (JSEQ[i].getHidden())
1098       {
1099         if (hiddenSeqs == null)
1100         {
1101           hiddenSeqs = new Vector();
1102         }
1103
1104         hiddenSeqs.addElement(
1105             (jalview.datamodel.Sequence) seqRefIds.get(seqId));
1106       }
1107
1108     }
1109
1110     ///SequenceFeatures are added to the DatasetSequence,
1111     // so we must create the dataset before loading features
1112     /////////////////////////////////
1113
1114
1115     jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
1116         tmpseqs.size()];
1117
1118     tmpseqs.toArray(orderedSeqs);
1119
1120     jalview.datamodel.Alignment al =
1121         new jalview.datamodel.Alignment(orderedSeqs);
1122
1123     al.setDataset(null);
1124     /////////////////////////////////
1125
1126
1127     Hashtable pdbloaded = new Hashtable();
1128     if (!multipleView)
1129     {
1130       for (int i = 0; i < vamsasSeq.length; i++)
1131       {
1132         if (JSEQ[i].getFeaturesCount() > 0)
1133         {
1134           Features[] features = JSEQ[i].getFeatures();
1135           for (int f = 0; f < features.length; f++)
1136           {
1137             jalview.datamodel.SequenceFeature sf
1138                 = new jalview.datamodel.SequenceFeature(features[f].getType(),
1139                 features[f].getDescription(), features[f].getStatus(),
1140                 features[f].getBegin(), features[f].getEnd(),
1141                 features[f].getFeatureGroup());
1142
1143             sf.setScore(features[f].getScore());
1144             for (int od = 0; od < features[f].getOtherDataCount(); od++)
1145             {
1146               OtherData keyValue = features[f].getOtherData(od);
1147               if (keyValue.getKey().startsWith("LINK"))
1148               {
1149                 sf.addLink(keyValue.getValue());
1150               }
1151               else
1152               {
1153                 sf.setValue(keyValue.getKey(), keyValue.getValue());
1154               }
1155
1156             }
1157
1158             al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
1159           }
1160         }
1161         if (JSEQ[i].getPdbidsCount() > 0)
1162         {
1163           Pdbids[] ids = JSEQ[i].getPdbids();
1164           for (int p = 0; p < ids.length; p++)
1165           {
1166             jalview.datamodel.PDBEntry entry = new jalview.datamodel.
1167                 PDBEntry();
1168             entry.setId(ids[p].getId());
1169             entry.setType(ids[p].getType());
1170             if (ids[p].getFile() != null)
1171             {
1172               if (!pdbloaded.containsKey(ids[p].getFile()))
1173               {
1174                 String tmppdb = loadPDBFile(file, ids[p].getId());
1175                 entry.setFile(tmppdb);
1176                 pdbloaded.put(ids[p].getId(), tmppdb);
1177               }
1178               else
1179               {
1180                 entry.setFile(pdbloaded.get(ids[p].getId()).toString());
1181               }
1182             }
1183
1184             al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
1185           }
1186         }
1187         if (vamsasSeq[i].getDBRefCount() > 0)
1188         {
1189           for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
1190           {
1191             jalview.datamodel.DBRefEntry entry =
1192                 new jalview.datamodel.DBRefEntry(
1193                     vamsasSeq[i].getDBRef(d).getSource(),
1194                     vamsasSeq[i].getDBRef(d).getVersion(),
1195                     vamsasSeq[i].getDBRef(d).getAccessionId()
1196                 );
1197             al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
1198           }
1199
1200         }
1201       }
1202     }
1203
1204     /////////////////////////////////
1205     //////////////////////////////////
1206     //LOAD ANNOTATIONS
1207     boolean hideQuality = true,
1208         hideConservation = true,
1209         hideConsensus = true;
1210
1211     if (vamsasSet.getAnnotationCount() > 0)
1212     {
1213       Annotation[] an = vamsasSet.getAnnotation();
1214
1215       for (int i = 0; i < an.length; i++)
1216       {
1217         if (an[i].getLabel().equals("Quality"))
1218         {
1219           hideQuality = false;
1220           continue;
1221         }
1222         else if (an[i].getLabel().equals("Conservation"))
1223         {
1224           hideConservation = false;
1225           continue;
1226         }
1227         else if (an[i].getLabel().equals("Consensus"))
1228         {
1229           hideConsensus = false;
1230           continue;
1231         }
1232
1233         if (an[i].getId() != null
1234             && annotationIds.containsKey(an[i].getId()))
1235         {
1236           al.addAnnotation(
1237               (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
1238               getId())
1239               );
1240
1241           continue;
1242         }
1243
1244         AnnotationElement[] ae = an[i].getAnnotationElement();
1245         jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[
1246             al.getWidth()];
1247
1248         for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
1249         {
1250           anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
1251               getDisplayCharacter(),
1252               ae[aa].getDescription(),
1253               ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
1254               ae[aa].getSecondaryStructure().charAt(0),
1255                    ae[aa].getValue());
1256           anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
1257               getColour());
1258         }
1259
1260         jalview.datamodel.AlignmentAnnotation jaa = null;
1261
1262         if (an[i].getGraph())
1263         {
1264           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1265               an[i].getDescription(), anot, 0, 0,
1266               an[i].getGraphType());
1267
1268           jaa.graphGroup = an[i].getGraphGroup();
1269
1270           if (an[i].getThresholdLine() != null)
1271           {
1272             jaa.setThreshold(new jalview.datamodel.GraphLine(
1273                 an[i].getThresholdLine().getValue(),
1274                 an[i].getThresholdLine().getLabel(),
1275                 new java.awt.Color(an[i].getThresholdLine().getColour()))
1276                 );
1277
1278           }
1279
1280         }
1281         else
1282         {
1283           jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
1284               an[i].getDescription(), anot);
1285         }
1286
1287         if (an[i].getId() != null)
1288         {
1289           annotationIds.put(an[i].getId(), jaa);
1290           jaa.annotationId = an[i].getId();
1291         }
1292
1293         if (an[i].getSequenceRef() != null)
1294         {
1295           jaa.createSequenceMapping(
1296               al.findName(an[i].getSequenceRef()), 1, true
1297               );
1298           al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
1299         }
1300
1301         al.addAnnotation(jaa);
1302       }
1303     }
1304
1305     /////////////////////////
1306     //LOAD GROUPS
1307     if (jms.getJGroupCount() > 0)
1308     {
1309       JGroup[] groups = jms.getJGroup();
1310
1311       for (int i = 0; i < groups.length; i++)
1312       {
1313         ColourSchemeI cs = null;
1314
1315         if (groups[i].getColour() != null)
1316         {
1317           if (groups[i].getColour().startsWith("ucs"))
1318           {
1319             cs = GetUserColourScheme(jms, groups[i].getColour());
1320           }
1321           else
1322           {
1323             cs = ColourSchemeProperty.getColour(al,
1324                                                 groups[i].getColour());
1325           }
1326
1327           if (cs != null)
1328           {
1329             cs.setThreshold(groups[i].getPidThreshold(), true);
1330           }
1331         }
1332
1333         Vector seqs = new Vector();
1334
1335         for (int s = 0; s < groups[i].getSeqCount(); s++)
1336         {
1337           String seqId = groups[i].getSeq(s) + "";
1338           jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
1339               seqRefIds.get(seqId);
1340
1341           if (ts != null)
1342           {
1343             seqs.addElement(ts);
1344           }
1345         }
1346
1347         if (seqs.size() < 1)
1348         {
1349           continue;
1350         }
1351
1352         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
1353             SequenceGroup(seqs,
1354                           groups[i].getName(), cs, groups[i].getDisplayBoxes(),
1355                           groups[i].getDisplayText(), groups[i].getColourText(),
1356                           groups[i].getStart(), groups[i].getEnd());
1357
1358         sg.setOutlineColour(new java.awt.Color(
1359             groups[i].getOutlineColour()));
1360
1361         sg.textColour = new java.awt.Color(groups[i].getTextCol1());
1362         sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
1363         sg.thresholdTextColour = groups[i].getTextColThreshold();
1364
1365         if (groups[i].getConsThreshold() != 0)
1366         {
1367           jalview.analysis.Conservation c = new jalview.analysis.Conservation(
1368               "All",
1369               ResidueProperties.propHash, 3, sg.getSequences(null), 0,
1370               sg.getWidth() - 1);
1371           c.calculate();
1372           c.verdict(false, 25);
1373           sg.cs.setConservation(c);
1374         }
1375
1376         al.addGroup(sg);
1377       }
1378     }
1379
1380     /////////////////////////////////
1381     // LOAD VIEWPORT
1382
1383     AlignFrame af = new AlignFrame(al,
1384                                    view.getWidth(),
1385                                    view.getHeight());
1386
1387     af.setFileName(file, "Jalview");
1388
1389     for (int i = 0; i < JSEQ.length; i++)
1390     {
1391       af.viewport.setSequenceColour(
1392           af.viewport.alignment.getSequenceAt(i),
1393           new java.awt.Color(
1394               JSEQ[i].getColour()));
1395     }
1396
1397     //If we just load in the same jar file again, the sequenceSetId
1398     //will be the same, and we end up with multiple references
1399     //to the same sequenceSet. We must modify this id on load
1400     //so that each load of the file gives a unique id
1401     String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
1402
1403     af.viewport.gatherViewsHere = view.getGatheredViews();
1404
1405     if (view.getSequenceSetId() != null)
1406     {
1407       jalview.gui.AlignViewport av =
1408           (jalview.gui.AlignViewport)
1409           viewportsAdded.get(uniqueSeqSetId);
1410
1411       af.viewport.sequenceSetID = uniqueSeqSetId;
1412       if (av != null)
1413       {
1414
1415         af.viewport.historyList = av.historyList;
1416         af.viewport.redoList = av.redoList;
1417       }
1418       else
1419       {
1420         viewportsAdded.put(uniqueSeqSetId, af.viewport);
1421       }
1422
1423       PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
1424     }
1425     if (hiddenSeqs != null)
1426     {
1427       for (int s = 0; s < JSEQ.length; s++)
1428       {
1429         jalview.datamodel.SequenceGroup hidden =
1430             new jalview.datamodel.SequenceGroup();
1431
1432         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
1433         {
1434           hidden.addSequence(
1435               al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
1436               , false
1437               );
1438         }
1439         af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
1440       }
1441
1442       jalview.datamodel.SequenceI[] hseqs = new
1443           jalview.datamodel.SequenceI[hiddenSeqs.size()];
1444
1445       for (int s = 0; s < hiddenSeqs.size(); s++)
1446       {
1447         hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
1448       }
1449
1450       af.viewport.hideSequence(hseqs);
1451
1452     }
1453
1454     if ( (hideConsensus || hideQuality || hideConservation)
1455         && al.getAlignmentAnnotation() != null)
1456     {
1457       int hSize = al.getAlignmentAnnotation().length;
1458       for (int h = 0; h < hSize; h++)
1459       {
1460         if (
1461             (hideConsensus &&
1462              al.getAlignmentAnnotation()[h].label.equals("Consensus"))
1463             ||
1464             (hideQuality &&
1465              al.getAlignmentAnnotation()[h].label.equals("Quality"))
1466             ||
1467             (hideConservation &&
1468              al.getAlignmentAnnotation()[h].label.equals("Conservation")))
1469         {
1470           al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
1471           hSize--;
1472           h--;
1473         }
1474       }
1475       af.alignPanel.adjustAnnotationHeight();
1476     }
1477
1478     if (view.getViewName() != null)
1479     {
1480       af.viewport.viewName = view.getViewName();
1481       af.setInitialTabVisible();
1482     }
1483     af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
1484                  view.getHeight());
1485
1486     af.viewport.setShowAnnotation(view.getShowAnnotation());
1487     af.viewport.setAbovePIDThreshold(view.getPidSelected());
1488
1489     af.viewport.setColourText(view.getShowColourText());
1490
1491     af.viewport.setConservationSelected(view.getConservationSelected());
1492     af.viewport.setShowJVSuffix(view.getShowFullId());
1493     af.viewport.rightAlignIds = view.getRightAlignIds();
1494     af.viewport.setFont(new java.awt.Font(view.getFontName(),
1495                                           view.getFontStyle(), view.getFontSize()));
1496     af.alignPanel.fontChanged();
1497     af.viewport.setRenderGaps(view.getRenderGaps());
1498     af.viewport.setWrapAlignment(view.getWrapAlignment());
1499     af.alignPanel.setWrapAlignment(view.getWrapAlignment());
1500     af.viewport.setShowAnnotation(view.getShowAnnotation());
1501     af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
1502
1503     af.viewport.setShowBoxes(view.getShowBoxes());
1504
1505     af.viewport.setShowText(view.getShowText());
1506
1507     af.viewport.textColour = new java.awt.Color(view.getTextCol1());
1508     af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
1509     af.viewport.thresholdTextColour = view.getTextColThreshold();
1510
1511     af.viewport.setStartRes(view.getStartRes());
1512     af.viewport.setStartSeq(view.getStartSeq());
1513
1514     ColourSchemeI cs = null;
1515
1516     if (view.getBgColour() != null)
1517     {
1518       if (view.getBgColour().startsWith("ucs"))
1519       {
1520         cs = GetUserColourScheme(jms, view.getBgColour());
1521       }
1522       else if (view.getBgColour().startsWith("Annotation"))
1523       {
1524         //int find annotation
1525         for (int i = 0;
1526              i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
1527         {
1528           if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
1529               equals(view.getAnnotationColours().getAnnotation()))
1530           {
1531             if (af.viewport.alignment.getAlignmentAnnotation()[i].
1532                 getThreshold() == null)
1533             {
1534               af.viewport.alignment.getAlignmentAnnotation()[i].
1535                   setThreshold(
1536                       new jalview.datamodel.GraphLine(
1537                           view.getAnnotationColours().getThreshold(),
1538                           "Threshold", java.awt.Color.black)
1539
1540                   );
1541             }
1542
1543             if (view.getAnnotationColours().getColourScheme().equals(
1544                 "None"))
1545             {
1546               cs = new AnnotationColourGradient(
1547                   af.viewport.alignment.getAlignmentAnnotation()[i],
1548                   new java.awt.Color(view.getAnnotationColours().
1549                                      getMinColour()),
1550                   new java.awt.Color(view.getAnnotationColours().
1551                                      getMaxColour()),
1552                   view.getAnnotationColours().getAboveThreshold());
1553             }
1554             else if (view.getAnnotationColours().getColourScheme().
1555                      startsWith("ucs"))
1556             {
1557               cs = new AnnotationColourGradient(
1558                   af.viewport.alignment.getAlignmentAnnotation()[i],
1559                   GetUserColourScheme(jms, view.getAnnotationColours().
1560                                       getColourScheme()),
1561                   view.getAnnotationColours().getAboveThreshold()
1562                   );
1563             }
1564             else
1565             {
1566               cs = new AnnotationColourGradient(
1567                   af.viewport.alignment.getAlignmentAnnotation()[i],
1568                   ColourSchemeProperty.getColour(al,
1569                                                  view.getAnnotationColours().
1570                                                  getColourScheme()),
1571                   view.getAnnotationColours().getAboveThreshold()
1572                   );
1573             }
1574
1575             // Also use these settings for all the groups
1576             if (al.getGroups() != null)
1577             {
1578               for (int g = 0; g < al.getGroups().size(); g++)
1579               {
1580                 jalview.datamodel.SequenceGroup sg
1581                     = (jalview.datamodel.SequenceGroup) al.getGroups().
1582                     elementAt(g);
1583
1584                 if (sg.cs == null)
1585                 {
1586                   continue;
1587                 }
1588
1589                 /*    if (view.getAnnotationColours().getColourScheme().equals("None"))
1590                     {
1591                       sg.cs = new AnnotationColourGradient(
1592                           af.viewport.alignment.getAlignmentAnnotation()[i],
1593                           new java.awt.Color(view.getAnnotationColours().
1594                                              getMinColour()),
1595                           new java.awt.Color(view.getAnnotationColours().
1596                                              getMaxColour()),
1597                           view.getAnnotationColours().getAboveThreshold());
1598                     }
1599                     else*/
1600                 {
1601                   sg.cs = new AnnotationColourGradient(
1602                       af.viewport.alignment.getAlignmentAnnotation()[i],
1603                       sg.cs,
1604                       view.getAnnotationColours().getAboveThreshold()
1605                       );
1606                 }
1607
1608               }
1609             }
1610
1611             break;
1612           }
1613
1614         }
1615       }
1616       else
1617       {
1618         cs = ColourSchemeProperty.getColour(al, view.getBgColour());
1619       }
1620
1621       if (cs != null)
1622       {
1623         cs.setThreshold(view.getPidThreshold(), true);
1624         cs.setConsensus(af.viewport.hconsensus);
1625       }
1626     }
1627
1628     af.viewport.setGlobalColourScheme(cs);
1629     af.viewport.setColourAppliesToAllGroups(false);
1630
1631     if (view.getConservationSelected() && cs != null)
1632     {
1633       cs.setConservationInc(view.getConsThreshold());
1634     }
1635
1636     af.changeColour(cs);
1637
1638     af.viewport.setColourAppliesToAllGroups(true);
1639
1640     if (view.getShowSequenceFeatures())
1641     {
1642       af.viewport.showSequenceFeatures = true;
1643     }
1644
1645     if (jms.getFeatureSettings() != null)
1646     {
1647       af.viewport.featuresDisplayed = new Hashtable();
1648       String[] renderOrder = new String[jms.getFeatureSettings().
1649           getSettingCount()];
1650       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
1651       {
1652         Setting setting = jms.getFeatureSettings().getSetting(fs);
1653
1654         af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
1655             getType(),
1656             new java.awt.Color(setting.getColour()));
1657
1658         renderOrder[fs] = setting.getType();
1659
1660         if (setting.getDisplay())
1661         {
1662           af.viewport.featuresDisplayed.put(
1663               setting.getType(), new Integer(setting.getColour()));
1664         }
1665       }
1666       af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
1667           renderOrder;
1668     }
1669
1670     if (view.getHiddenColumnsCount() > 0)
1671     {
1672       for (int c = 0; c < view.getHiddenColumnsCount(); c++)
1673       {
1674         af.viewport.hideColumns(
1675             view.getHiddenColumns(c).getStart(),
1676             view.getHiddenColumns(c).getEnd() //+1
1677             );
1678       }
1679     }
1680
1681     af.setMenusFromViewport(af.viewport);
1682
1683     Desktop.addInternalFrame(af, view.getTitle(),
1684                              view.getWidth(), view.getHeight());
1685
1686     //LOAD TREES
1687     ///////////////////////////////////////
1688     if (loadTrees && jms.getTreeCount() > 0)
1689     {
1690       try
1691       {
1692         for (int t = 0; t < jms.getTreeCount(); t++)
1693         {
1694
1695           Tree tree = jms.getTree(t);
1696
1697           TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
1698               tree.getNewick()), tree.getTitle(),
1699                                            tree.getWidth(), tree.getHeight(),
1700                                            tree.getXpos(), tree.getYpos());
1701
1702           tp.fitToWindow.setState(tree.getFitToWindow());
1703           tp.fitToWindow_actionPerformed(null);
1704
1705           if (tree.getFontName() != null)
1706           {
1707             tp.setTreeFont(new java.awt.Font(tree.getFontName(),
1708                                              tree.getFontStyle(),
1709                                              tree.getFontSize()));
1710           }
1711           else
1712           {
1713             tp.setTreeFont(new java.awt.Font(view.getFontName(),
1714                                              view.getFontStyle(),
1715                                              tree.getFontSize()));
1716           }
1717
1718           tp.showPlaceholders(tree.getMarkUnlinked());
1719           tp.showBootstrap(tree.getShowBootstrap());
1720           tp.showDistances(tree.getShowDistances());
1721
1722           tp.treeCanvas.threshold = tree.getThreshold();
1723
1724           if (tree.getCurrentTree())
1725           {
1726             af.viewport.setCurrentTree(tp.getTree());
1727           }
1728         }
1729
1730       }
1731       catch (Exception ex)
1732       {
1733         ex.printStackTrace();
1734       }
1735
1736     }
1737
1738     return af;
1739   }
1740
1741   public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
1742       boolean keepSeqRefs)
1743   {
1744     jalview.schemabinding.version2.JalviewModel jm
1745         = SaveState(ap, null, null, null);
1746
1747     if (!keepSeqRefs)
1748     {
1749       seqRefIds.clear();
1750       jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
1751     }
1752     else
1753     {
1754       uniqueSetSuffix = "";
1755     }
1756
1757     viewportsAdded = new Hashtable();
1758
1759     AlignFrame af = LoadFromObject(jm, null, false);
1760     af.alignPanels.clear();
1761     af.closeMenuItem_actionPerformed(true);
1762
1763     /*  if(ap.av.alignment.getAlignmentAnnotation()!=null)
1764       {
1765         for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length; i++)
1766         {
1767           if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated)
1768           {
1769             af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
1770                 ap.av.alignment.getAlignmentAnnotation()[i];
1771           }
1772         }
1773       }   */
1774
1775     return af.alignPanel;
1776   }
1777 }