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 _provenanceList
  67      */
  68     private java.util.Vector _provenanceList;
  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         _provenanceList = new Vector();
  83     } //-- org.vamsas.objects.core.SequenceSet()
  84
  85
  86       //-----------/
  87      //- Methods -/
  88     //-----------/
  89
  90     /**
  91      * Method addAlignment
  92      *
  93      *
  94      *
  95      * @param vAlignment
  96      */
  97     public void addAlignment(org.vamsas.objects.core.Alignment vAlignment)
  98         throws java.lang.IndexOutOfBoundsException
  99     {
 100         _alignmentList.addElement(vAlignment);
 101     } //-- void addAlignment(org.vamsas.objects.core.Alignment)
 102
 103     /**
 104      * Method addAlignment
 105      *
 106      *
 107      *
 108      * @param index
 109      * @param vAlignment
 110      */
 111     public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
 112         throws java.lang.IndexOutOfBoundsException
 113     {
 114         _alignmentList.insertElementAt(vAlignment, index);
 115     } //-- void addAlignment(int, org.vamsas.objects.core.Alignment)
 116
 117     /**
 118      * Method addProvenance
 119      *
 120      *
 121      *
 122      * @param vProvenance
 123      */
 124     public void addProvenance(org.vamsas.objects.core.Provenance vProvenance)
 125         throws java.lang.IndexOutOfBoundsException
 126     {
 127         _provenanceList.addElement(vProvenance);
 128     } //-- void addProvenance(org.vamsas.objects.core.Provenance)
 129
 130     /**
 131      * Method addProvenance
 132      *
 133      *
 134      *
 135      * @param index
 136      * @param vProvenance
 137      */
 138     public void addProvenance(int index, org.vamsas.objects.core.Provenance vProvenance)
 139         throws java.lang.IndexOutOfBoundsException
 140     {
 141         _provenanceList.insertElementAt(vProvenance, index);
 142     } //-- void addProvenance(int, org.vamsas.objects.core.Provenance)
 143
 144     /**
 145      * Method addSequence
 146      *
 147      *
 148      *
 149      * @param vSequence
 150      */
 151     public void addSequence(org.vamsas.objects.core.Sequence vSequence)
 152         throws java.lang.IndexOutOfBoundsException
 153     {
 154         _sequenceList.addElement(vSequence);
 155     } //-- void addSequence(org.vamsas.objects.core.Sequence)
 156
 157     /**
 158      * Method addSequence
 159      *
 160      *
 161      *
 162      * @param index
 163      * @param vSequence
 164      */
 165     public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence)
 166         throws java.lang.IndexOutOfBoundsException
 167     {
 168         _sequenceList.insertElementAt(vSequence, index);
 169     } //-- void addSequence(int, org.vamsas.objects.core.Sequence)
 170
 171     /**
 172      * Method addSequenceSetAnnotations
 173      *
 174      *
 175      *
 176      * @param vSequenceSetAnnotations
 177      */
 178     public void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 179         throws java.lang.IndexOutOfBoundsException
 180     {
 181         _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
 182     } //-- void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
 183
 184     /**
 185      * Method addSequenceSetAnnotations
 186      *
 187      *
 188      *
 189      * @param index
 190      * @param vSequenceSetAnnotations
 191      */
 192     public void addSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 193         throws java.lang.IndexOutOfBoundsException
 194     {
 195         _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
 196     } //-- void addSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
 197
 198     /**
 199      * Method addTree
 200      *
 201      *
 202      *
 203      * @param vTree
 204      */
 205     public void addTree(org.vamsas.objects.core.Tree vTree)
 206         throws java.lang.IndexOutOfBoundsException
 207     {
 208         _treeList.addElement(vTree);
 209     } //-- void addTree(org.vamsas.objects.core.Tree)
 210
 211     /**
 212      * Method addTree
 213      *
 214      *
 215      *
 216      * @param index
 217      * @param vTree
 218      */
 219     public void addTree(int index, org.vamsas.objects.core.Tree vTree)
 220         throws java.lang.IndexOutOfBoundsException
 221     {
 222         _treeList.insertElementAt(vTree, index);
 223     } //-- void addTree(int, org.vamsas.objects.core.Tree)
 224
 225     /**
 226      * Method enumerateAlignment
 227      *
 228      *
 229      *
 230      * @return Enumeration
 231      */
 232     public java.util.Enumeration enumerateAlignment()
 233     {
 234         return _alignmentList.elements();
 235     } //-- java.util.Enumeration enumerateAlignment()
 236
 237     /**
 238      * Method enumerateProvenance
 239      *
 240      *
 241      *
 242      * @return Enumeration
 243      */
 244     public java.util.Enumeration enumerateProvenance()
 245     {
 246         return _provenanceList.elements();
 247     } //-- java.util.Enumeration enumerateProvenance()
 248
 249     /**
 250      * Method enumerateSequence
 251      *
 252      *
 253      *
 254      * @return Enumeration
 255      */
 256     public java.util.Enumeration enumerateSequence()
 257     {
 258         return _sequenceList.elements();
 259     } //-- java.util.Enumeration enumerateSequence()
 260
 261     /**
 262      * Method enumerateSequenceSetAnnotations
 263      *
 264      *
 265      *
 266      * @return Enumeration
 267      */
 268     public java.util.Enumeration enumerateSequenceSetAnnotations()
 269     {
 270         return _sequenceSetAnnotationsList.elements();
 271     } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
 272
 273     /**
 274      * Method enumerateTree
 275      *
 276      *
 277      *
 278      * @return Enumeration
 279      */
 280     public java.util.Enumeration enumerateTree()
 281     {
 282         return _treeList.elements();
 283     } //-- java.util.Enumeration enumerateTree()
 284
 285     /**
 286      * Note: hashCode() has not been overriden
 287      *
 288      * @param obj
 289      * @return boolean
 290      */
 291     public boolean equals(java.lang.Object obj)
 292     {
 293         if ( this == obj )
 294             return true;
 295
 296         if (super.equals(obj)==false)
 297             return false;
 298
 299         if (obj instanceof SequenceSet) {
 300
 301             SequenceSet temp = (SequenceSet)obj;
 302             if (this._id != null) {
 303                 if (temp._id == null) return false;
 304                 else if (!(this._id.equals(temp._id)))
 305                     return false;
 306             }
 307             else if (temp._id != null)
 308                 return false;
 309             if (this._sequenceList != null) {
 310                 if (temp._sequenceList == null) return false;
 311                 else if (!(this._sequenceList.equals(temp._sequenceList)))
 312                     return false;
 313             }
 314             else if (temp._sequenceList != null)
 315                 return false;
 316             if (this._sequenceSetAnnotationsList != null) {
 317                 if (temp._sequenceSetAnnotationsList == null) return false;
 318                 else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
 319                     return false;
 320             }
 321             else if (temp._sequenceSetAnnotationsList != null)
 322                 return false;
 323             if (this._alignmentList != null) {
 324                 if (temp._alignmentList == null) return false;
 325                 else if (!(this._alignmentList.equals(temp._alignmentList)))
 326                     return false;
 327             }
 328             else if (temp._alignmentList != null)
 329                 return false;
 330             if (this._treeList != null) {
 331                 if (temp._treeList == null) return false;
 332                 else if (!(this._treeList.equals(temp._treeList)))
 333                     return false;
 334             }
 335             else if (temp._treeList != null)
 336                 return false;
 337             if (this._provenanceList != null) {
 338                 if (temp._provenanceList == null) return false;
 339                 else if (!(this._provenanceList.equals(temp._provenanceList)))
 340                     return false;
 341             }
 342             else if (temp._provenanceList != null)
 343                 return false;
 344             return true;
 345         }
 346         return false;
 347     } //-- boolean equals(java.lang.Object)
 348
 349     /**
 350      * Method getAlignment
 351      *
 352      *
 353      *
 354      * @param index
 355      * @return Alignment
 356      */
 357     public org.vamsas.objects.core.Alignment getAlignment(int index)
 358         throws java.lang.IndexOutOfBoundsException
 359     {
 360         //-- check bounds for index
 361         if ((index < 0) || (index > _alignmentList.size())) {
 362             throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 363         }
 364
 365         return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 366     } //-- org.vamsas.objects.core.Alignment getAlignment(int)
 367
 368     /**
 369      * Method getAlignment
 370      *
 371      *
 372      *
 373      * @return Alignment
 374      */
 375     public org.vamsas.objects.core.Alignment[] getAlignment()
 376     {
 377         int size = _alignmentList.size();
 378         org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size];
 379         for (int index = 0; index < size; index++) {
 380             mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 381         }
 382         return mArray;
 383     } //-- org.vamsas.objects.core.Alignment[] getAlignment()
 384
 385     /**
 386      * Method getAlignmentCount
 387      *
 388      *
 389      *
 390      * @return int
 391      */
 392     public int getAlignmentCount()
 393     {
 394         return _alignmentList.size();
 395     } //-- int getAlignmentCount()
 396
 397     /**
 398      * Returns the value of field 'id'.
 399      *
 400      * @return String
 401      * @return the value of field 'id'.
 402      */
 403     public java.lang.String getId()
 404     {
 405         return this._id;
 406     } //-- java.lang.String getId()
 407
 408     /**
 409      * Method getProvenance
 410      *
 411      *
 412      *
 413      * @param index
 414      * @return Provenance
 415      */
 416     public org.vamsas.objects.core.Provenance getProvenance(int index)
 417         throws java.lang.IndexOutOfBoundsException
 418     {
 419         //-- check bounds for index
 420         if ((index < 0) || (index > _provenanceList.size())) {
 421             throw new IndexOutOfBoundsException("getProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");
 422         }
 423
 424         return (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);
 425     } //-- org.vamsas.objects.core.Provenance getProvenance(int)
 426
 427     /**
 428      * Method getProvenance
 429      *
 430      *
 431      *
 432      * @return Provenance
 433      */
 434     public org.vamsas.objects.core.Provenance[] getProvenance()
 435     {
 436         int size = _provenanceList.size();
 437         org.vamsas.objects.core.Provenance[] mArray = new org.vamsas.objects.core.Provenance[size];
 438         for (int index = 0; index < size; index++) {
 439             mArray[index] = (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);
 440         }
 441         return mArray;
 442     } //-- org.vamsas.objects.core.Provenance[] getProvenance()
 443
 444     /**
 445      * Method getProvenanceCount
 446      *
 447      *
 448      *
 449      * @return int
 450      */
 451     public int getProvenanceCount()
 452     {
 453         return _provenanceList.size();
 454     } //-- int getProvenanceCount()
 455
 456     /**
 457      * Method getSequence
 458      *
 459      *
 460      *
 461      * @param index
 462      * @return Sequence
 463      */
 464     public org.vamsas.objects.core.Sequence getSequence(int index)
 465         throws java.lang.IndexOutOfBoundsException
 466     {
 467         //-- check bounds for index
 468         if ((index < 0) || (index > _sequenceList.size())) {
 469             throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 470         }
 471
 472         return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 473     } //-- org.vamsas.objects.core.Sequence getSequence(int)
 474
 475     /**
 476      * Method getSequence
 477      *
 478      *
 479      *
 480      * @return Sequence
 481      */
 482     public org.vamsas.objects.core.Sequence[] getSequence()
 483     {
 484         int size = _sequenceList.size();
 485         org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size];
 486         for (int index = 0; index < size; index++) {
 487             mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 488         }
 489         return mArray;
 490     } //-- org.vamsas.objects.core.Sequence[] getSequence()
 491
 492     /**
 493      * Method getSequenceCount
 494      *
 495      *
 496      *
 497      * @return int
 498      */
 499     public int getSequenceCount()
 500     {
 501         return _sequenceList.size();
 502     } //-- int getSequenceCount()
 503
 504     /**
 505      * Method getSequenceSetAnnotations
 506      *
 507      *
 508      *
 509      * @param index
 510      * @return SequenceSetAnnotations
 511      */
 512     public org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int index)
 513         throws java.lang.IndexOutOfBoundsException
 514     {
 515         //-- check bounds for index
 516         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 517             throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 518         }
 519
 520         return (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 521     } //-- org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int)
 522
 523     /**
 524      * Method getSequenceSetAnnotations
 525      *
 526      *
 527      *
 528      * @return SequenceSetAnnotations
 529      */
 530     public org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
 531     {
 532         int size = _sequenceSetAnnotationsList.size();
 533         org.vamsas.objects.core.SequenceSetAnnotations[] mArray = new org.vamsas.objects.core.SequenceSetAnnotations[size];
 534         for (int index = 0; index < size; index++) {
 535             mArray[index] = (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 536         }
 537         return mArray;
 538     } //-- org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
 539
 540     /**
 541      * Method getSequenceSetAnnotationsCount
 542      *
 543      *
 544      *
 545      * @return int
 546      */
 547     public int getSequenceSetAnnotationsCount()
 548     {
 549         return _sequenceSetAnnotationsList.size();
 550     } //-- int getSequenceSetAnnotationsCount()
 551
 552     /**
 553      * Method getTree
 554      *
 555      *
 556      *
 557      * @param index
 558      * @return Tree
 559      */
 560     public org.vamsas.objects.core.Tree getTree(int index)
 561         throws java.lang.IndexOutOfBoundsException
 562     {
 563         //-- check bounds for index
 564         if ((index < 0) || (index > _treeList.size())) {
 565             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 566         }
 567
 568         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 569     } //-- org.vamsas.objects.core.Tree getTree(int)
 570
 571     /**
 572      * Method getTree
 573      *
 574      *
 575      *
 576      * @return Tree
 577      */
 578     public org.vamsas.objects.core.Tree[] getTree()
 579     {
 580         int size = _treeList.size();
 581         org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
 582         for (int index = 0; index < size; index++) {
 583             mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 584         }
 585         return mArray;
 586     } //-- org.vamsas.objects.core.Tree[] getTree()
 587
 588     /**
 589      * Method getTreeCount
 590      *
 591      *
 592      *
 593      * @return int
 594      */
 595     public int getTreeCount()
 596     {
 597         return _treeList.size();
 598     } //-- int getTreeCount()
 599
 600     /**
 601      * Method isValid
 602      *
 603      *
 604      *
 605      * @return boolean
 606      */
 607     public boolean isValid()
 608     {
 609         try {
 610             validate();
 611         }
 612         catch (org.exolab.castor.xml.ValidationException vex) {
 613             return false;
 614         }
 615         return true;
 616     } //-- boolean isValid()
 617
 618     /**
 619      * Method marshal
 620      *
 621      *
 622      *
 623      * @param out
 624      */
 625     public void marshal(java.io.Writer out)
 626         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 627     {
 628
 629         Marshaller.marshal(this, out);
 630     } //-- void marshal(java.io.Writer)
 631
 632     /**
 633      * Method marshal
 634      *
 635      *
 636      *
 637      * @param handler
 638      */
 639     public void marshal(org.xml.sax.ContentHandler handler)
 640         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 641     {
 642
 643         Marshaller.marshal(this, handler);
 644     } //-- void marshal(org.xml.sax.ContentHandler)
 645
 646     /**
 647      * Method removeAlignment
 648      *
 649      *
 650      *
 651      * @param index
 652      * @return Alignment
 653      */
 654     public org.vamsas.objects.core.Alignment removeAlignment(int index)
 655     {
 656         java.lang.Object obj = _alignmentList.elementAt(index);
 657         _alignmentList.removeElementAt(index);
 658         return (org.vamsas.objects.core.Alignment) obj;
 659     } //-- org.vamsas.objects.core.Alignment removeAlignment(int)
 660
 661     /**
 662      * Method removeAllAlignment
 663      *
 664      */
 665     public void removeAllAlignment()
 666     {
 667         _alignmentList.removeAllElements();
 668     } //-- void removeAllAlignment()
 669
 670     /**
 671      * Method removeAllProvenance
 672      *
 673      */
 674     public void removeAllProvenance()
 675     {
 676         _provenanceList.removeAllElements();
 677     } //-- void removeAllProvenance()
 678
 679     /**
 680      * Method removeAllSequence
 681      *
 682      */
 683     public void removeAllSequence()
 684     {
 685         _sequenceList.removeAllElements();
 686     } //-- void removeAllSequence()
 687
 688     /**
 689      * Method removeAllSequenceSetAnnotations
 690      *
 691      */
 692     public void removeAllSequenceSetAnnotations()
 693     {
 694         _sequenceSetAnnotationsList.removeAllElements();
 695     } //-- void removeAllSequenceSetAnnotations()
 696
 697     /**
 698      * Method removeAllTree
 699      *
 700      */
 701     public void removeAllTree()
 702     {
 703         _treeList.removeAllElements();
 704     } //-- void removeAllTree()
 705
 706     /**
 707      * Method removeProvenance
 708      *
 709      *
 710      *
 711      * @param index
 712      * @return Provenance
 713      */
 714     public org.vamsas.objects.core.Provenance removeProvenance(int index)
 715     {
 716         java.lang.Object obj = _provenanceList.elementAt(index);
 717         _provenanceList.removeElementAt(index);
 718         return (org.vamsas.objects.core.Provenance) obj;
 719     } //-- org.vamsas.objects.core.Provenance removeProvenance(int)
 720
 721     /**
 722      * Method removeSequence
 723      *
 724      *
 725      *
 726      * @param index
 727      * @return Sequence
 728      */
 729     public org.vamsas.objects.core.Sequence removeSequence(int index)
 730     {
 731         java.lang.Object obj = _sequenceList.elementAt(index);
 732         _sequenceList.removeElementAt(index);
 733         return (org.vamsas.objects.core.Sequence) obj;
 734     } //-- org.vamsas.objects.core.Sequence removeSequence(int)
 735
 736     /**
 737      * Method removeSequenceSetAnnotations
 738      *
 739      *
 740      *
 741      * @param index
 742      * @return SequenceSetAnnotations
 743      */
 744     public org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
 745     {
 746         java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
 747         _sequenceSetAnnotationsList.removeElementAt(index);
 748         return (org.vamsas.objects.core.SequenceSetAnnotations) obj;
 749     } //-- org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int)
 750
 751     /**
 752      * Method removeTree
 753      *
 754      *
 755      *
 756      * @param index
 757      * @return Tree
 758      */
 759     public org.vamsas.objects.core.Tree removeTree(int index)
 760     {
 761         java.lang.Object obj = _treeList.elementAt(index);
 762         _treeList.removeElementAt(index);
 763         return (org.vamsas.objects.core.Tree) obj;
 764     } //-- org.vamsas.objects.core.Tree removeTree(int)
 765
 766     /**
 767      * Method setAlignment
 768      *
 769      *
 770      *
 771      * @param index
 772      * @param vAlignment
 773      */
 774     public void setAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
 775         throws java.lang.IndexOutOfBoundsException
 776     {
 777         //-- check bounds for index
 778         if ((index < 0) || (index > _alignmentList.size())) {
 779             throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 780         }
 781         _alignmentList.setElementAt(vAlignment, index);
 782     } //-- void setAlignment(int, org.vamsas.objects.core.Alignment)
 783
 784     /**
 785      * Method setAlignment
 786      *
 787      *
 788      *
 789      * @param alignmentArray
 790      */
 791     public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray)
 792     {
 793         //-- copy array
 794         _alignmentList.removeAllElements();
 795         for (int i = 0; i < alignmentArray.length; i++) {
 796             _alignmentList.addElement(alignmentArray[i]);
 797         }
 798     } //-- void setAlignment(org.vamsas.objects.core.Alignment)
 799
 800     /**
 801      * Sets the value of field 'id'.
 802      *
 803      * @param id the value of field 'id'.
 804      */
 805     public void setId(java.lang.String id)
 806     {
 807         this._id = id;
 808     } //-- void setId(java.lang.String)
 809
 810     /**
 811      * Method setProvenance
 812      *
 813      *
 814      *
 815      * @param index
 816      * @param vProvenance
 817      */
 818     public void setProvenance(int index, org.vamsas.objects.core.Provenance vProvenance)
 819         throws java.lang.IndexOutOfBoundsException
 820     {
 821         //-- check bounds for index
 822         if ((index < 0) || (index > _provenanceList.size())) {
 823             throw new IndexOutOfBoundsException("setProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");
 824         }
 825         _provenanceList.setElementAt(vProvenance, index);
 826     } //-- void setProvenance(int, org.vamsas.objects.core.Provenance)
 827
 828     /**
 829      * Method setProvenance
 830      *
 831      *
 832      *
 833      * @param provenanceArray
 834      */
 835     public void setProvenance(org.vamsas.objects.core.Provenance[] provenanceArray)
 836     {
 837         //-- copy array
 838         _provenanceList.removeAllElements();
 839         for (int i = 0; i < provenanceArray.length; i++) {
 840             _provenanceList.addElement(provenanceArray[i]);
 841         }
 842     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 843
 844     /**
 845      * Method setSequence
 846      *
 847      *
 848      *
 849      * @param index
 850      * @param vSequence
 851      */
 852     public void setSequence(int index, org.vamsas.objects.core.Sequence vSequence)
 853         throws java.lang.IndexOutOfBoundsException
 854     {
 855         //-- check bounds for index
 856         if ((index < 0) || (index > _sequenceList.size())) {
 857             throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 858         }
 859         _sequenceList.setElementAt(vSequence, index);
 860     } //-- void setSequence(int, org.vamsas.objects.core.Sequence)
 861
 862     /**
 863      * Method setSequence
 864      *
 865      *
 866      *
 867      * @param sequenceArray
 868      */
 869     public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray)
 870     {
 871         //-- copy array
 872         _sequenceList.removeAllElements();
 873         for (int i = 0; i < sequenceArray.length; i++) {
 874             _sequenceList.addElement(sequenceArray[i]);
 875         }
 876     } //-- void setSequence(org.vamsas.objects.core.Sequence)
 877
 878     /**
 879      * Method setSequenceSetAnnotations
 880      *
 881      *
 882      *
 883      * @param index
 884      * @param vSequenceSetAnnotations
 885      */
 886     public void setSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 887         throws java.lang.IndexOutOfBoundsException
 888     {
 889         //-- check bounds for index
 890         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 891             throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 892         }
 893         _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index);
 894     } //-- void setSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
 895
 896     /**
 897      * Method setSequenceSetAnnotations
 898      *
 899      *
 900      *
 901      * @param sequenceSetAnnotationsArray
 902      */
 903     public void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
 904     {
 905         //-- copy array
 906         _sequenceSetAnnotationsList.removeAllElements();
 907         for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
 908             _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
 909         }
 910     } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
 911
 912     /**
 913      * Method setTree
 914      *
 915      *
 916      *
 917      * @param index
 918      * @param vTree
 919      */
 920     public void setTree(int index, org.vamsas.objects.core.Tree vTree)
 921         throws java.lang.IndexOutOfBoundsException
 922     {
 923         //-- check bounds for index
 924         if ((index < 0) || (index > _treeList.size())) {
 925             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 926         }
 927         _treeList.setElementAt(vTree, index);
 928     } //-- void setTree(int, org.vamsas.objects.core.Tree)
 929
 930     /**
 931      * Method setTree
 932      *
 933      *
 934      *
 935      * @param treeArray
 936      */
 937     public void setTree(org.vamsas.objects.core.Tree[] treeArray)
 938     {
 939         //-- copy array
 940         _treeList.removeAllElements();
 941         for (int i = 0; i < treeArray.length; i++) {
 942             _treeList.addElement(treeArray[i]);
 943         }
 944     } //-- void setTree(org.vamsas.objects.core.Tree)
 945
 946     /**
 947      * Method unmarshal
 948      *
 949      *
 950      *
 951      * @param reader
 952      * @return SequenceSet
 953      */
 954     public static org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader reader)
 955         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 956     {
 957         return (org.vamsas.objects.core.SequenceSet) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSet.class, reader);
 958     } //-- org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader)
 959
 960     /**
 961      * Method validate
 962      *
 963      */
 964     public void validate()
 965         throws org.exolab.castor.xml.ValidationException
 966     {
 967         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 968         validator.validate(this);
 969     } //-- void validate()
 970
 971 }