src/org/vamsas/objects/core/SequenceSet.java

   1 /*
   2  * This class was automatically generated with
   3  * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
   4  * Schema.
   5  * $Id$
   6  */
   7
   8 package org.vamsas.objects.core;
   9
  10   //---------------------------------/
  11  //- Imported classes and packages -/
  12 //---------------------------------/
  13
  14 import java.io.IOException;
  15 import java.io.Reader;
  16 import java.io.Serializable;
  17 import java.io.Writer;
  18 import java.util.Enumeration;
  19 import java.util.Vector;
  20 import org.exolab.castor.xml.MarshalException;
  21 import org.exolab.castor.xml.Marshaller;
  22 import org.exolab.castor.xml.Unmarshaller;
  23 import org.exolab.castor.xml.ValidationException;
  24 import org.xml.sax.ContentHandler;
  25
  26 /**
  27  * Class SequenceSet.
  28  *
  29  * @version $Revision$ $Date$
  30  */
  31 public class SequenceSet extends org.vamsas.client.object
  32 implements java.io.Serializable
  33 {
  34
  35
  36       //--------------------------/
  37      //- Class/Member Variables -/
  38     //--------------------------/
  39
  40     /**
  41      * Field _gapChar
  42      */
  43     private java.lang.String _gapChar;
  44
  45     /**
  46      * Field _aligned
  47      */
  48     private boolean _aligned;
  49
  50     /**
  51      * keeps track of state for field: _aligned
  52      */
  53     private boolean _has_aligned;
  54
  55     /**
  56      * Field _id
  57      */
  58     private java.lang.String _id;
  59
  60     /**
  61      * Field _sequenceList
  62      */
  63     private java.util.Vector _sequenceList;
  64
  65     /**
  66      * Field _sequenceSetAnnotationsList
  67      */
  68     private java.util.Vector _sequenceSetAnnotationsList;
  69
  70     /**
  71      * Field _alignmentList
  72      */
  73     private java.util.Vector _alignmentList;
  74
  75     /**
  76      * Field _tree
  77      */
  78     private org.vamsas.objects.core.Tree _tree;
  79
  80     /**
  81      * Field _provenance
  82      */
  83     private org.vamsas.objects.core.Provenance _provenance;
  84
  85
  86       //----------------/
  87      //- Constructors -/
  88     //----------------/
  89
  90     public SequenceSet()
  91      {
  92         super();
  93         _sequenceList = new Vector();
  94         _sequenceSetAnnotationsList = new Vector();
  95         _alignmentList = new Vector();
  96     } //-- org.vamsas.objects.core.SequenceSet()
  97
  98
  99       //-----------/
 100      //- Methods -/
 101     //-----------/
 102
 103     /**
 104      * Method addAlignment
 105      *
 106      *
 107      *
 108      * @param vAlignment
 109      */
 110     public void addAlignment(org.vamsas.objects.core.Alignment vAlignment)
 111         throws java.lang.IndexOutOfBoundsException
 112     {
 113         _alignmentList.addElement(vAlignment);
 114     } //-- void addAlignment(org.vamsas.objects.core.Alignment)
 115
 116     /**
 117      * Method addAlignment
 118      *
 119      *
 120      *
 121      * @param index
 122      * @param vAlignment
 123      */
 124     public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
 125         throws java.lang.IndexOutOfBoundsException
 126     {
 127         _alignmentList.insertElementAt(vAlignment, index);
 128     } //-- void addAlignment(int, org.vamsas.objects.core.Alignment)
 129
 130     /**
 131      * Method addSequence
 132      *
 133      *
 134      *
 135      * @param vSequence
 136      */
 137     public void addSequence(org.vamsas.objects.core.Sequence vSequence)
 138         throws java.lang.IndexOutOfBoundsException
 139     {
 140         _sequenceList.addElement(vSequence);
 141     } //-- void addSequence(org.vamsas.objects.core.Sequence)
 142
 143     /**
 144      * Method addSequence
 145      *
 146      *
 147      *
 148      * @param index
 149      * @param vSequence
 150      */
 151     public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence)
 152         throws java.lang.IndexOutOfBoundsException
 153     {
 154         _sequenceList.insertElementAt(vSequence, index);
 155     } //-- void addSequence(int, org.vamsas.objects.core.Sequence)
 156
 157     /**
 158      * Method addSequenceSetAnnotations
 159      *
 160      *
 161      *
 162      * @param vSequenceSetAnnotations
 163      */
 164     public void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 165         throws java.lang.IndexOutOfBoundsException
 166     {
 167         _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
 168     } //-- void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
 169
 170     /**
 171      * Method addSequenceSetAnnotations
 172      *
 173      *
 174      *
 175      * @param index
 176      * @param vSequenceSetAnnotations
 177      */
 178     public void addSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 179         throws java.lang.IndexOutOfBoundsException
 180     {
 181         _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
 182     } //-- void addSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
 183
 184     /**
 185      * Method deleteAligned
 186      *
 187      */
 188     public void deleteAligned()
 189     {
 190         this._has_aligned= false;
 191     } //-- void deleteAligned()
 192
 193     /**
 194      * Method enumerateAlignment
 195      *
 196      *
 197      *
 198      * @return Enumeration
 199      */
 200     public java.util.Enumeration enumerateAlignment()
 201     {
 202         return _alignmentList.elements();
 203     } //-- java.util.Enumeration enumerateAlignment()
 204
 205     /**
 206      * Method enumerateSequence
 207      *
 208      *
 209      *
 210      * @return Enumeration
 211      */
 212     public java.util.Enumeration enumerateSequence()
 213     {
 214         return _sequenceList.elements();
 215     } //-- java.util.Enumeration enumerateSequence()
 216
 217     /**
 218      * Method enumerateSequenceSetAnnotations
 219      *
 220      *
 221      *
 222      * @return Enumeration
 223      */
 224     public java.util.Enumeration enumerateSequenceSetAnnotations()
 225     {
 226         return _sequenceSetAnnotationsList.elements();
 227     } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
 228
 229     /**
 230      * Note: hashCode() has not been overriden
 231      *
 232      * @param obj
 233      * @return boolean
 234      */
 235     public boolean equals(java.lang.Object obj)
 236     {
 237         if ( this == obj )
 238             return true;
 239
 240         if (super.equals(obj)==false)
 241             return false;
 242
 243         if (obj instanceof SequenceSet) {
 244
 245             SequenceSet temp = (SequenceSet)obj;
 246             if (this._gapChar != null) {
 247                 if (temp._gapChar == null) return false;
 248                 else if (!(this._gapChar.equals(temp._gapChar)))
 249                     return false;
 250             }
 251             else if (temp._gapChar != null)
 252                 return false;
 253             if (this._aligned != temp._aligned)
 254                 return false;
 255             if (this._has_aligned != temp._has_aligned)
 256                 return false;
 257             if (this._id != null) {
 258                 if (temp._id == null) return false;
 259                 else if (!(this._id.equals(temp._id)))
 260                     return false;
 261             }
 262             else if (temp._id != null)
 263                 return false;
 264             if (this._sequenceList != null) {
 265                 if (temp._sequenceList == null) return false;
 266                 else if (!(this._sequenceList.equals(temp._sequenceList)))
 267                     return false;
 268             }
 269             else if (temp._sequenceList != null)
 270                 return false;
 271             if (this._sequenceSetAnnotationsList != null) {
 272                 if (temp._sequenceSetAnnotationsList == null) return false;
 273                 else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
 274                     return false;
 275             }
 276             else if (temp._sequenceSetAnnotationsList != null)
 277                 return false;
 278             if (this._alignmentList != null) {
 279                 if (temp._alignmentList == null) return false;
 280                 else if (!(this._alignmentList.equals(temp._alignmentList)))
 281                     return false;
 282             }
 283             else if (temp._alignmentList != null)
 284                 return false;
 285             if (this._tree != null) {
 286                 if (temp._tree == null) return false;
 287                 else if (!(this._tree.equals(temp._tree)))
 288                     return false;
 289             }
 290             else if (temp._tree != null)
 291                 return false;
 292             if (this._provenance != null) {
 293                 if (temp._provenance == null) return false;
 294                 else if (!(this._provenance.equals(temp._provenance)))
 295                     return false;
 296             }
 297             else if (temp._provenance != null)
 298                 return false;
 299             return true;
 300         }
 301         return false;
 302     } //-- boolean equals(java.lang.Object)
 303
 304     /**
 305      * Returns the value of field 'aligned'.
 306      *
 307      * @return boolean
 308      * @return the value of field 'aligned'.
 309      */
 310     public boolean getAligned()
 311     {
 312         return this._aligned;
 313     } //-- boolean getAligned()
 314
 315     /**
 316      * Method getAlignment
 317      *
 318      *
 319      *
 320      * @param index
 321      * @return Alignment
 322      */
 323     public org.vamsas.objects.core.Alignment getAlignment(int index)
 324         throws java.lang.IndexOutOfBoundsException
 325     {
 326         //-- check bounds for index
 327         if ((index < 0) || (index > _alignmentList.size())) {
 328             throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 329         }
 330
 331         return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 332     } //-- org.vamsas.objects.core.Alignment getAlignment(int)
 333
 334     /**
 335      * Method getAlignment
 336      *
 337      *
 338      *
 339      * @return Alignment
 340      */
 341     public org.vamsas.objects.core.Alignment[] getAlignment()
 342     {
 343         int size = _alignmentList.size();
 344         org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size];
 345         for (int index = 0; index < size; index++) {
 346             mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 347         }
 348         return mArray;
 349     } //-- org.vamsas.objects.core.Alignment[] getAlignment()
 350
 351     /**
 352      * Method getAlignmentCount
 353      *
 354      *
 355      *
 356      * @return int
 357      */
 358     public int getAlignmentCount()
 359     {
 360         return _alignmentList.size();
 361     } //-- int getAlignmentCount()
 362
 363     /**
 364      * Returns the value of field 'gapChar'.
 365      *
 366      * @return String
 367      * @return the value of field 'gapChar'.
 368      */
 369     public java.lang.String getGapChar()
 370     {
 371         return this._gapChar;
 372     } //-- java.lang.String getGapChar()
 373
 374     /**
 375      * Returns the value of field 'id'.
 376      *
 377      * @return String
 378      * @return the value of field 'id'.
 379      */
 380     public java.lang.String getId()
 381     {
 382         return this._id;
 383     } //-- java.lang.String getId()
 384
 385     /**
 386      * Returns the value of field 'provenance'.
 387      *
 388      * @return Provenance
 389      * @return the value of field 'provenance'.
 390      */
 391     public org.vamsas.objects.core.Provenance getProvenance()
 392     {
 393         return this._provenance;
 394     } //-- org.vamsas.objects.core.Provenance getProvenance()
 395
 396     /**
 397      * Method getSequence
 398      *
 399      *
 400      *
 401      * @param index
 402      * @return Sequence
 403      */
 404     public org.vamsas.objects.core.Sequence getSequence(int index)
 405         throws java.lang.IndexOutOfBoundsException
 406     {
 407         //-- check bounds for index
 408         if ((index < 0) || (index > _sequenceList.size())) {
 409             throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 410         }
 411
 412         return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 413     } //-- org.vamsas.objects.core.Sequence getSequence(int)
 414
 415     /**
 416      * Method getSequence
 417      *
 418      *
 419      *
 420      * @return Sequence
 421      */
 422     public org.vamsas.objects.core.Sequence[] getSequence()
 423     {
 424         int size = _sequenceList.size();
 425         org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size];
 426         for (int index = 0; index < size; index++) {
 427             mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 428         }
 429         return mArray;
 430     } //-- org.vamsas.objects.core.Sequence[] getSequence()
 431
 432     /**
 433      * Method getSequenceCount
 434      *
 435      *
 436      *
 437      * @return int
 438      */
 439     public int getSequenceCount()
 440     {
 441         return _sequenceList.size();
 442     } //-- int getSequenceCount()
 443
 444     /**
 445      * Method getSequenceSetAnnotations
 446      *
 447      *
 448      *
 449      * @param index
 450      * @return SequenceSetAnnotations
 451      */
 452     public org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int index)
 453         throws java.lang.IndexOutOfBoundsException
 454     {
 455         //-- check bounds for index
 456         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 457             throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 458         }
 459
 460         return (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 461     } //-- org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int)
 462
 463     /**
 464      * Method getSequenceSetAnnotations
 465      *
 466      *
 467      *
 468      * @return SequenceSetAnnotations
 469      */
 470     public org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
 471     {
 472         int size = _sequenceSetAnnotationsList.size();
 473         org.vamsas.objects.core.SequenceSetAnnotations[] mArray = new org.vamsas.objects.core.SequenceSetAnnotations[size];
 474         for (int index = 0; index < size; index++) {
 475             mArray[index] = (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 476         }
 477         return mArray;
 478     } //-- org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
 479
 480     /**
 481      * Method getSequenceSetAnnotationsCount
 482      *
 483      *
 484      *
 485      * @return int
 486      */
 487     public int getSequenceSetAnnotationsCount()
 488     {
 489         return _sequenceSetAnnotationsList.size();
 490     } //-- int getSequenceSetAnnotationsCount()
 491
 492     /**
 493      * Returns the value of field 'tree'.
 494      *
 495      * @return Tree
 496      * @return the value of field 'tree'.
 497      */
 498     public org.vamsas.objects.core.Tree getTree()
 499     {
 500         return this._tree;
 501     } //-- org.vamsas.objects.core.Tree getTree()
 502
 503     /**
 504      * Method hasAligned
 505      *
 506      *
 507      *
 508      * @return boolean
 509      */
 510     public boolean hasAligned()
 511     {
 512         return this._has_aligned;
 513     } //-- boolean hasAligned()
 514
 515     /**
 516      * Method isValid
 517      *
 518      *
 519      *
 520      * @return boolean
 521      */
 522     public boolean isValid()
 523     {
 524         try {
 525             validate();
 526         }
 527         catch (org.exolab.castor.xml.ValidationException vex) {
 528             return false;
 529         }
 530         return true;
 531     } //-- boolean isValid()
 532
 533     /**
 534      * Method marshal
 535      *
 536      *
 537      *
 538      * @param out
 539      */
 540     public void marshal(java.io.Writer out)
 541         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 542     {
 543
 544         Marshaller.marshal(this, out);
 545     } //-- void marshal(java.io.Writer)
 546
 547     /**
 548      * Method marshal
 549      *
 550      *
 551      *
 552      * @param handler
 553      */
 554     public void marshal(org.xml.sax.ContentHandler handler)
 555         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 556     {
 557
 558         Marshaller.marshal(this, handler);
 559     } //-- void marshal(org.xml.sax.ContentHandler)
 560
 561     /**
 562      * Method removeAlignment
 563      *
 564      *
 565      *
 566      * @param index
 567      * @return Alignment
 568      */
 569     public org.vamsas.objects.core.Alignment removeAlignment(int index)
 570     {
 571         java.lang.Object obj = _alignmentList.elementAt(index);
 572         _alignmentList.removeElementAt(index);
 573         return (org.vamsas.objects.core.Alignment) obj;
 574     } //-- org.vamsas.objects.core.Alignment removeAlignment(int)
 575
 576     /**
 577      * Method removeAllAlignment
 578      *
 579      */
 580     public void removeAllAlignment()
 581     {
 582         _alignmentList.removeAllElements();
 583     } //-- void removeAllAlignment()
 584
 585     /**
 586      * Method removeAllSequence
 587      *
 588      */
 589     public void removeAllSequence()
 590     {
 591         _sequenceList.removeAllElements();
 592     } //-- void removeAllSequence()
 593
 594     /**
 595      * Method removeAllSequenceSetAnnotations
 596      *
 597      */
 598     public void removeAllSequenceSetAnnotations()
 599     {
 600         _sequenceSetAnnotationsList.removeAllElements();
 601     } //-- void removeAllSequenceSetAnnotations()
 602
 603     /**
 604      * Method removeSequence
 605      *
 606      *
 607      *
 608      * @param index
 609      * @return Sequence
 610      */
 611     public org.vamsas.objects.core.Sequence removeSequence(int index)
 612     {
 613         java.lang.Object obj = _sequenceList.elementAt(index);
 614         _sequenceList.removeElementAt(index);
 615         return (org.vamsas.objects.core.Sequence) obj;
 616     } //-- org.vamsas.objects.core.Sequence removeSequence(int)
 617
 618     /**
 619      * Method removeSequenceSetAnnotations
 620      *
 621      *
 622      *
 623      * @param index
 624      * @return SequenceSetAnnotations
 625      */
 626     public org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
 627     {
 628         java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
 629         _sequenceSetAnnotationsList.removeElementAt(index);
 630         return (org.vamsas.objects.core.SequenceSetAnnotations) obj;
 631     } //-- org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int)
 632
 633     /**
 634      * Sets the value of field 'aligned'.
 635      *
 636      * @param aligned the value of field 'aligned'.
 637      */
 638     public void setAligned(boolean aligned)
 639     {
 640         this._aligned = aligned;
 641         this._has_aligned = true;
 642     } //-- void setAligned(boolean)
 643
 644     /**
 645      * Method setAlignment
 646      *
 647      *
 648      *
 649      * @param index
 650      * @param vAlignment
 651      */
 652     public void setAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
 653         throws java.lang.IndexOutOfBoundsException
 654     {
 655         //-- check bounds for index
 656         if ((index < 0) || (index > _alignmentList.size())) {
 657             throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 658         }
 659         _alignmentList.setElementAt(vAlignment, index);
 660     } //-- void setAlignment(int, org.vamsas.objects.core.Alignment)
 661
 662     /**
 663      * Method setAlignment
 664      *
 665      *
 666      *
 667      * @param alignmentArray
 668      */
 669     public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray)
 670     {
 671         //-- copy array
 672         _alignmentList.removeAllElements();
 673         for (int i = 0; i < alignmentArray.length; i++) {
 674             _alignmentList.addElement(alignmentArray[i]);
 675         }
 676     } //-- void setAlignment(org.vamsas.objects.core.Alignment)
 677
 678     /**
 679      * Sets the value of field 'gapChar'.
 680      *
 681      * @param gapChar the value of field 'gapChar'.
 682      */
 683     public void setGapChar(java.lang.String gapChar)
 684     {
 685         this._gapChar = gapChar;
 686     } //-- void setGapChar(java.lang.String)
 687
 688     /**
 689      * Sets the value of field 'id'.
 690      *
 691      * @param id the value of field 'id'.
 692      */
 693     public void setId(java.lang.String id)
 694     {
 695         this._id = id;
 696     } //-- void setId(java.lang.String)
 697
 698     /**
 699      * Sets the value of field 'provenance'.
 700      *
 701      * @param provenance the value of field 'provenance'.
 702      */
 703     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 704     {
 705         this._provenance = provenance;
 706     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 707
 708     /**
 709      * Method setSequence
 710      *
 711      *
 712      *
 713      * @param index
 714      * @param vSequence
 715      */
 716     public void setSequence(int index, org.vamsas.objects.core.Sequence vSequence)
 717         throws java.lang.IndexOutOfBoundsException
 718     {
 719         //-- check bounds for index
 720         if ((index < 0) || (index > _sequenceList.size())) {
 721             throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 722         }
 723         _sequenceList.setElementAt(vSequence, index);
 724     } //-- void setSequence(int, org.vamsas.objects.core.Sequence)
 725
 726     /**
 727      * Method setSequence
 728      *
 729      *
 730      *
 731      * @param sequenceArray
 732      */
 733     public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray)
 734     {
 735         //-- copy array
 736         _sequenceList.removeAllElements();
 737         for (int i = 0; i < sequenceArray.length; i++) {
 738             _sequenceList.addElement(sequenceArray[i]);
 739         }
 740     } //-- void setSequence(org.vamsas.objects.core.Sequence)
 741
 742     /**
 743      * Method setSequenceSetAnnotations
 744      *
 745      *
 746      *
 747      * @param index
 748      * @param vSequenceSetAnnotations
 749      */
 750     public void setSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 751         throws java.lang.IndexOutOfBoundsException
 752     {
 753         //-- check bounds for index
 754         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 755             throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 756         }
 757         _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index);
 758     } //-- void setSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
 759
 760     /**
 761      * Method setSequenceSetAnnotations
 762      *
 763      *
 764      *
 765      * @param sequenceSetAnnotationsArray
 766      */
 767     public void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
 768     {
 769         //-- copy array
 770         _sequenceSetAnnotationsList.removeAllElements();
 771         for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
 772             _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
 773         }
 774     } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
 775
 776     /**
 777      * Sets the value of field 'tree'.
 778      *
 779      * @param tree the value of field 'tree'.
 780      */
 781     public void setTree(org.vamsas.objects.core.Tree tree)
 782     {
 783         this._tree = tree;
 784     } //-- void setTree(org.vamsas.objects.core.Tree)
 785
 786     /**
 787      * Method unmarshal
 788      *
 789      *
 790      *
 791      * @param reader
 792      * @return SequenceSet
 793      */
 794     public static org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader reader)
 795         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 796     {
 797         return (org.vamsas.objects.core.SequenceSet) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSet.class, reader);
 798     } //-- org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader)
 799
 800     /**
 801      * Method validate
 802      *
 803      */
 804     public void validate()
 805         throws org.exolab.castor.xml.ValidationException
 806     {
 807         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 808         validator.validate(this);
 809     } //-- void validate()
 810
 811 }