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 _id
  42      */
  43     private java.lang.String _id;
  44
  45     /**
  46      * Field _sequenceList
  47      */
  48     private java.util.Vector _sequenceList;
  49
  50     /**
  51      * Field _sequenceSetAnnotationsList
  52      */
  53     private java.util.Vector _sequenceSetAnnotationsList;
  54
  55     /**
  56      * Field _alignmentList
  57      */
  58     private java.util.Vector _alignmentList;
  59
  60     /**
  61      * Field _treeList
  62      */
  63     private java.util.Vector _treeList;
  64
  65     /**
  66      * Field _provenance
  67      */
  68     private org.vamsas.objects.core.Provenance _provenance;
  69
  70
  71       //----------------/
  72      //- Constructors -/
  73     //----------------/
  74
  75     public SequenceSet()
  76      {
  77         super();
  78         _sequenceList = new Vector();
  79         _sequenceSetAnnotationsList = new Vector();
  80         _alignmentList = new Vector();
  81         _treeList = new Vector();
  82     } //-- org.vamsas.objects.core.SequenceSet()
  83
  84
  85       //-----------/
  86      //- Methods -/
  87     //-----------/
  88
  89     /**
  90      * Method addAlignment
  91      *
  92      *
  93      *
  94      * @param vAlignment
  95      */
  96     public void addAlignment(org.vamsas.objects.core.Alignment vAlignment)
  97         throws java.lang.IndexOutOfBoundsException
  98     {
  99         _alignmentList.addElement(vAlignment);
 100     } //-- void addAlignment(org.vamsas.objects.core.Alignment)
 101
 102     /**
 103      * Method addAlignment
 104      *
 105      *
 106      *
 107      * @param index
 108      * @param vAlignment
 109      */
 110     public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
 111         throws java.lang.IndexOutOfBoundsException
 112     {
 113         _alignmentList.insertElementAt(vAlignment, index);
 114     } //-- void addAlignment(int, org.vamsas.objects.core.Alignment)
 115
 116     /**
 117      * Method addSequence
 118      *
 119      *
 120      *
 121      * @param vSequence
 122      */
 123     public void addSequence(org.vamsas.objects.core.Sequence vSequence)
 124         throws java.lang.IndexOutOfBoundsException
 125     {
 126         _sequenceList.addElement(vSequence);
 127     } //-- void addSequence(org.vamsas.objects.core.Sequence)
 128
 129     /**
 130      * Method addSequence
 131      *
 132      *
 133      *
 134      * @param index
 135      * @param vSequence
 136      */
 137     public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence)
 138         throws java.lang.IndexOutOfBoundsException
 139     {
 140         _sequenceList.insertElementAt(vSequence, index);
 141     } //-- void addSequence(int, org.vamsas.objects.core.Sequence)
 142
 143     /**
 144      * Method addSequenceSetAnnotations
 145      *
 146      *
 147      *
 148      * @param vSequenceSetAnnotations
 149      */
 150     public void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 151         throws java.lang.IndexOutOfBoundsException
 152     {
 153         _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
 154     } //-- void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
 155
 156     /**
 157      * Method addSequenceSetAnnotations
 158      *
 159      *
 160      *
 161      * @param index
 162      * @param vSequenceSetAnnotations
 163      */
 164     public void addSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 165         throws java.lang.IndexOutOfBoundsException
 166     {
 167         _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
 168     } //-- void addSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
 169
 170     /**
 171      * Method addTree
 172      *
 173      *
 174      *
 175      * @param vTree
 176      */
 177     public void addTree(org.vamsas.objects.core.Tree vTree)
 178         throws java.lang.IndexOutOfBoundsException
 179     {
 180         _treeList.addElement(vTree);
 181     } //-- void addTree(org.vamsas.objects.core.Tree)
 182
 183     /**
 184      * Method addTree
 185      *
 186      *
 187      *
 188      * @param index
 189      * @param vTree
 190      */
 191     public void addTree(int index, org.vamsas.objects.core.Tree vTree)
 192         throws java.lang.IndexOutOfBoundsException
 193     {
 194         _treeList.insertElementAt(vTree, index);
 195     } //-- void addTree(int, org.vamsas.objects.core.Tree)
 196
 197     /**
 198      * Method enumerateAlignment
 199      *
 200      *
 201      *
 202      * @return Enumeration
 203      */
 204     public java.util.Enumeration enumerateAlignment()
 205     {
 206         return _alignmentList.elements();
 207     } //-- java.util.Enumeration enumerateAlignment()
 208
 209     /**
 210      * Method enumerateSequence
 211      *
 212      *
 213      *
 214      * @return Enumeration
 215      */
 216     public java.util.Enumeration enumerateSequence()
 217     {
 218         return _sequenceList.elements();
 219     } //-- java.util.Enumeration enumerateSequence()
 220
 221     /**
 222      * Method enumerateSequenceSetAnnotations
 223      *
 224      *
 225      *
 226      * @return Enumeration
 227      */
 228     public java.util.Enumeration enumerateSequenceSetAnnotations()
 229     {
 230         return _sequenceSetAnnotationsList.elements();
 231     } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
 232
 233     /**
 234      * Method enumerateTree
 235      *
 236      *
 237      *
 238      * @return Enumeration
 239      */
 240     public java.util.Enumeration enumerateTree()
 241     {
 242         return _treeList.elements();
 243     } //-- java.util.Enumeration enumerateTree()
 244
 245     /**
 246      * Note: hashCode() has not been overriden
 247      *
 248      * @param obj
 249      * @return boolean
 250      */
 251     public boolean equals(java.lang.Object obj)
 252     {
 253         if ( this == obj )
 254             return true;
 255
 256         if (super.equals(obj)==false)
 257             return false;
 258
 259         if (obj instanceof SequenceSet) {
 260
 261             SequenceSet temp = (SequenceSet)obj;
 262             if (this._id != null) {
 263                 if (temp._id == null) return false;
 264                 else if (!(this._id.equals(temp._id)))
 265                     return false;
 266             }
 267             else if (temp._id != null)
 268                 return false;
 269             if (this._sequenceList != null) {
 270                 if (temp._sequenceList == null) return false;
 271                 else if (!(this._sequenceList.equals(temp._sequenceList)))
 272                     return false;
 273             }
 274             else if (temp._sequenceList != null)
 275                 return false;
 276             if (this._sequenceSetAnnotationsList != null) {
 277                 if (temp._sequenceSetAnnotationsList == null) return false;
 278                 else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
 279                     return false;
 280             }
 281             else if (temp._sequenceSetAnnotationsList != null)
 282                 return false;
 283             if (this._alignmentList != null) {
 284                 if (temp._alignmentList == null) return false;
 285                 else if (!(this._alignmentList.equals(temp._alignmentList)))
 286                     return false;
 287             }
 288             else if (temp._alignmentList != null)
 289                 return false;
 290             if (this._treeList != null) {
 291                 if (temp._treeList == null) return false;
 292                 else if (!(this._treeList.equals(temp._treeList)))
 293                     return false;
 294             }
 295             else if (temp._treeList != null)
 296                 return false;
 297             if (this._provenance != null) {
 298                 if (temp._provenance == null) return false;
 299                 else if (!(this._provenance.equals(temp._provenance)))
 300                     return false;
 301             }
 302             else if (temp._provenance != null)
 303                 return false;
 304             return true;
 305         }
 306         return false;
 307     } //-- boolean equals(java.lang.Object)
 308
 309     /**
 310      * Method getAlignment
 311      *
 312      *
 313      *
 314      * @param index
 315      * @return Alignment
 316      */
 317     public org.vamsas.objects.core.Alignment getAlignment(int index)
 318         throws java.lang.IndexOutOfBoundsException
 319     {
 320         //-- check bounds for index
 321         if ((index < 0) || (index > _alignmentList.size())) {
 322             throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 323         }
 324
 325         return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 326     } //-- org.vamsas.objects.core.Alignment getAlignment(int)
 327
 328     /**
 329      * Method getAlignment
 330      *
 331      *
 332      *
 333      * @return Alignment
 334      */
 335     public org.vamsas.objects.core.Alignment[] getAlignment()
 336     {
 337         int size = _alignmentList.size();
 338         org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size];
 339         for (int index = 0; index < size; index++) {
 340             mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 341         }
 342         return mArray;
 343     } //-- org.vamsas.objects.core.Alignment[] getAlignment()
 344
 345     /**
 346      * Method getAlignmentCount
 347      *
 348      *
 349      *
 350      * @return int
 351      */
 352     public int getAlignmentCount()
 353     {
 354         return _alignmentList.size();
 355     } //-- int getAlignmentCount()
 356
 357     /**
 358      * Returns the value of field 'id'.
 359      *
 360      * @return String
 361      * @return the value of field 'id'.
 362      */
 363     public java.lang.String getId()
 364     {
 365         return this._id;
 366     } //-- java.lang.String getId()
 367
 368     /**
 369      * Returns the value of field 'provenance'.
 370      *
 371      * @return Provenance
 372      * @return the value of field 'provenance'.
 373      */
 374     public org.vamsas.objects.core.Provenance getProvenance()
 375     {
 376         return this._provenance;
 377     } //-- org.vamsas.objects.core.Provenance getProvenance()
 378
 379     /**
 380      * Method getSequence
 381      *
 382      *
 383      *
 384      * @param index
 385      * @return Sequence
 386      */
 387     public org.vamsas.objects.core.Sequence getSequence(int index)
 388         throws java.lang.IndexOutOfBoundsException
 389     {
 390         //-- check bounds for index
 391         if ((index < 0) || (index > _sequenceList.size())) {
 392             throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 393         }
 394
 395         return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 396     } //-- org.vamsas.objects.core.Sequence getSequence(int)
 397
 398     /**
 399      * Method getSequence
 400      *
 401      *
 402      *
 403      * @return Sequence
 404      */
 405     public org.vamsas.objects.core.Sequence[] getSequence()
 406     {
 407         int size = _sequenceList.size();
 408         org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size];
 409         for (int index = 0; index < size; index++) {
 410             mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 411         }
 412         return mArray;
 413     } //-- org.vamsas.objects.core.Sequence[] getSequence()
 414
 415     /**
 416      * Method getSequenceCount
 417      *
 418      *
 419      *
 420      * @return int
 421      */
 422     public int getSequenceCount()
 423     {
 424         return _sequenceList.size();
 425     } //-- int getSequenceCount()
 426
 427     /**
 428      * Method getSequenceSetAnnotations
 429      *
 430      *
 431      *
 432      * @param index
 433      * @return SequenceSetAnnotations
 434      */
 435     public org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int index)
 436         throws java.lang.IndexOutOfBoundsException
 437     {
 438         //-- check bounds for index
 439         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 440             throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 441         }
 442
 443         return (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 444     } //-- org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int)
 445
 446     /**
 447      * Method getSequenceSetAnnotations
 448      *
 449      *
 450      *
 451      * @return SequenceSetAnnotations
 452      */
 453     public org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
 454     {
 455         int size = _sequenceSetAnnotationsList.size();
 456         org.vamsas.objects.core.SequenceSetAnnotations[] mArray = new org.vamsas.objects.core.SequenceSetAnnotations[size];
 457         for (int index = 0; index < size; index++) {
 458             mArray[index] = (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 459         }
 460         return mArray;
 461     } //-- org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
 462
 463     /**
 464      * Method getSequenceSetAnnotationsCount
 465      *
 466      *
 467      *
 468      * @return int
 469      */
 470     public int getSequenceSetAnnotationsCount()
 471     {
 472         return _sequenceSetAnnotationsList.size();
 473     } //-- int getSequenceSetAnnotationsCount()
 474
 475     /**
 476      * Method getTree
 477      *
 478      *
 479      *
 480      * @param index
 481      * @return Tree
 482      */
 483     public org.vamsas.objects.core.Tree getTree(int index)
 484         throws java.lang.IndexOutOfBoundsException
 485     {
 486         //-- check bounds for index
 487         if ((index < 0) || (index > _treeList.size())) {
 488             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 489         }
 490
 491         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 492     } //-- org.vamsas.objects.core.Tree getTree(int)
 493
 494     /**
 495      * Method getTree
 496      *
 497      *
 498      *
 499      * @return Tree
 500      */
 501     public org.vamsas.objects.core.Tree[] getTree()
 502     {
 503         int size = _treeList.size();
 504         org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
 505         for (int index = 0; index < size; index++) {
 506             mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 507         }
 508         return mArray;
 509     } //-- org.vamsas.objects.core.Tree[] getTree()
 510
 511     /**
 512      * Method getTreeCount
 513      *
 514      *
 515      *
 516      * @return int
 517      */
 518     public int getTreeCount()
 519     {
 520         return _treeList.size();
 521     } //-- int getTreeCount()
 522
 523     /**
 524      * Method isValid
 525      *
 526      *
 527      *
 528      * @return boolean
 529      */
 530     public boolean isValid()
 531     {
 532         try {
 533             validate();
 534         }
 535         catch (org.exolab.castor.xml.ValidationException vex) {
 536             return false;
 537         }
 538         return true;
 539     } //-- boolean isValid()
 540
 541     /**
 542      * Method marshal
 543      *
 544      *
 545      *
 546      * @param out
 547      */
 548     public void marshal(java.io.Writer out)
 549         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 550     {
 551
 552         Marshaller.marshal(this, out);
 553     } //-- void marshal(java.io.Writer)
 554
 555     /**
 556      * Method marshal
 557      *
 558      *
 559      *
 560      * @param handler
 561      */
 562     public void marshal(org.xml.sax.ContentHandler handler)
 563         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 564     {
 565
 566         Marshaller.marshal(this, handler);
 567     } //-- void marshal(org.xml.sax.ContentHandler)
 568
 569     /**
 570      * Method removeAlignment
 571      *
 572      *
 573      *
 574      * @param index
 575      * @return Alignment
 576      */
 577     public org.vamsas.objects.core.Alignment removeAlignment(int index)
 578     {
 579         java.lang.Object obj = _alignmentList.elementAt(index);
 580         _alignmentList.removeElementAt(index);
 581         return (org.vamsas.objects.core.Alignment) obj;
 582     } //-- org.vamsas.objects.core.Alignment removeAlignment(int)
 583
 584     /**
 585      * Method removeAllAlignment
 586      *
 587      */
 588     public void removeAllAlignment()
 589     {
 590         _alignmentList.removeAllElements();
 591     } //-- void removeAllAlignment()
 592
 593     /**
 594      * Method removeAllSequence
 595      *
 596      */
 597     public void removeAllSequence()
 598     {
 599         _sequenceList.removeAllElements();
 600     } //-- void removeAllSequence()
 601
 602     /**
 603      * Method removeAllSequenceSetAnnotations
 604      *
 605      */
 606     public void removeAllSequenceSetAnnotations()
 607     {
 608         _sequenceSetAnnotationsList.removeAllElements();
 609     } //-- void removeAllSequenceSetAnnotations()
 610
 611     /**
 612      * Method removeAllTree
 613      *
 614      */
 615     public void removeAllTree()
 616     {
 617         _treeList.removeAllElements();
 618     } //-- void removeAllTree()
 619
 620     /**
 621      * Method removeSequence
 622      *
 623      *
 624      *
 625      * @param index
 626      * @return Sequence
 627      */
 628     public org.vamsas.objects.core.Sequence removeSequence(int index)
 629     {
 630         java.lang.Object obj = _sequenceList.elementAt(index);
 631         _sequenceList.removeElementAt(index);
 632         return (org.vamsas.objects.core.Sequence) obj;
 633     } //-- org.vamsas.objects.core.Sequence removeSequence(int)
 634
 635     /**
 636      * Method removeSequenceSetAnnotations
 637      *
 638      *
 639      *
 640      * @param index
 641      * @return SequenceSetAnnotations
 642      */
 643     public org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
 644     {
 645         java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
 646         _sequenceSetAnnotationsList.removeElementAt(index);
 647         return (org.vamsas.objects.core.SequenceSetAnnotations) obj;
 648     } //-- org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int)
 649
 650     /**
 651      * Method removeTree
 652      *
 653      *
 654      *
 655      * @param index
 656      * @return Tree
 657      */
 658     public org.vamsas.objects.core.Tree removeTree(int index)
 659     {
 660         java.lang.Object obj = _treeList.elementAt(index);
 661         _treeList.removeElementAt(index);
 662         return (org.vamsas.objects.core.Tree) obj;
 663     } //-- org.vamsas.objects.core.Tree removeTree(int)
 664
 665     /**
 666      * Method setAlignment
 667      *
 668      *
 669      *
 670      * @param index
 671      * @param vAlignment
 672      */
 673     public void setAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
 674         throws java.lang.IndexOutOfBoundsException
 675     {
 676         //-- check bounds for index
 677         if ((index < 0) || (index > _alignmentList.size())) {
 678             throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 679         }
 680         _alignmentList.setElementAt(vAlignment, index);
 681     } //-- void setAlignment(int, org.vamsas.objects.core.Alignment)
 682
 683     /**
 684      * Method setAlignment
 685      *
 686      *
 687      *
 688      * @param alignmentArray
 689      */
 690     public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray)
 691     {
 692         //-- copy array
 693         _alignmentList.removeAllElements();
 694         for (int i = 0; i < alignmentArray.length; i++) {
 695             _alignmentList.addElement(alignmentArray[i]);
 696         }
 697     } //-- void setAlignment(org.vamsas.objects.core.Alignment)
 698
 699     /**
 700      * Sets the value of field 'id'.
 701      *
 702      * @param id the value of field 'id'.
 703      */
 704     public void setId(java.lang.String id)
 705     {
 706         this._id = id;
 707     } //-- void setId(java.lang.String)
 708
 709     /**
 710      * Sets the value of field 'provenance'.
 711      *
 712      * @param provenance the value of field 'provenance'.
 713      */
 714     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 715     {
 716         this._provenance = provenance;
 717     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 718
 719     /**
 720      * Method setSequence
 721      *
 722      *
 723      *
 724      * @param index
 725      * @param vSequence
 726      */
 727     public void setSequence(int index, org.vamsas.objects.core.Sequence vSequence)
 728         throws java.lang.IndexOutOfBoundsException
 729     {
 730         //-- check bounds for index
 731         if ((index < 0) || (index > _sequenceList.size())) {
 732             throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 733         }
 734         _sequenceList.setElementAt(vSequence, index);
 735     } //-- void setSequence(int, org.vamsas.objects.core.Sequence)
 736
 737     /**
 738      * Method setSequence
 739      *
 740      *
 741      *
 742      * @param sequenceArray
 743      */
 744     public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray)
 745     {
 746         //-- copy array
 747         _sequenceList.removeAllElements();
 748         for (int i = 0; i < sequenceArray.length; i++) {
 749             _sequenceList.addElement(sequenceArray[i]);
 750         }
 751     } //-- void setSequence(org.vamsas.objects.core.Sequence)
 752
 753     /**
 754      * Method setSequenceSetAnnotations
 755      *
 756      *
 757      *
 758      * @param index
 759      * @param vSequenceSetAnnotations
 760      */
 761     public void setSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 762         throws java.lang.IndexOutOfBoundsException
 763     {
 764         //-- check bounds for index
 765         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 766             throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 767         }
 768         _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index);
 769     } //-- void setSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
 770
 771     /**
 772      * Method setSequenceSetAnnotations
 773      *
 774      *
 775      *
 776      * @param sequenceSetAnnotationsArray
 777      */
 778     public void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
 779     {
 780         //-- copy array
 781         _sequenceSetAnnotationsList.removeAllElements();
 782         for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
 783             _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
 784         }
 785     } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
 786
 787     /**
 788      * Method setTree
 789      *
 790      *
 791      *
 792      * @param index
 793      * @param vTree
 794      */
 795     public void setTree(int index, org.vamsas.objects.core.Tree vTree)
 796         throws java.lang.IndexOutOfBoundsException
 797     {
 798         //-- check bounds for index
 799         if ((index < 0) || (index > _treeList.size())) {
 800             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 801         }
 802         _treeList.setElementAt(vTree, index);
 803     } //-- void setTree(int, org.vamsas.objects.core.Tree)
 804
 805     /**
 806      * Method setTree
 807      *
 808      *
 809      *
 810      * @param treeArray
 811      */
 812     public void setTree(org.vamsas.objects.core.Tree[] treeArray)
 813     {
 814         //-- copy array
 815         _treeList.removeAllElements();
 816         for (int i = 0; i < treeArray.length; i++) {
 817             _treeList.addElement(treeArray[i]);
 818         }
 819     } //-- void setTree(org.vamsas.objects.core.Tree)
 820
 821     /**
 822      * Method unmarshal
 823      *
 824      *
 825      *
 826      * @param reader
 827      * @return SequenceSet
 828      */
 829     public static org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader reader)
 830         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 831     {
 832         return (org.vamsas.objects.core.SequenceSet) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSet.class, reader);
 833     } //-- org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader)
 834
 835     /**
 836      * Method validate
 837      *
 838      */
 839     public void validate()
 840         throws org.exolab.castor.xml.ValidationException
 841     {
 842         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 843         validator.validate(this);
 844     } //-- void validate()
 845
 846 }