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 _treeList
  77      */
  78     private java.util.Vector _treeList;
  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         _treeList = new Vector();
  97     } //-- org.vamsas.objects.core.SequenceSet()
  98
  99
 100       //-----------/
 101      //- Methods -/
 102     //-----------/
 103
 104     /**
 105      * Method addAlignment
 106      *
 107      *
 108      *
 109      * @param vAlignment
 110      */
 111     public void addAlignment(org.vamsas.objects.core.Alignment vAlignment)
 112         throws java.lang.IndexOutOfBoundsException
 113     {
 114         _alignmentList.addElement(vAlignment);
 115     } //-- void addAlignment(org.vamsas.objects.core.Alignment)
 116
 117     /**
 118      * Method addAlignment
 119      *
 120      *
 121      *
 122      * @param index
 123      * @param vAlignment
 124      */
 125     public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
 126         throws java.lang.IndexOutOfBoundsException
 127     {
 128         _alignmentList.insertElementAt(vAlignment, index);
 129     } //-- void addAlignment(int, org.vamsas.objects.core.Alignment)
 130
 131     /**
 132      * Method addSequence
 133      *
 134      *
 135      *
 136      * @param vSequence
 137      */
 138     public void addSequence(org.vamsas.objects.core.Sequence vSequence)
 139         throws java.lang.IndexOutOfBoundsException
 140     {
 141         _sequenceList.addElement(vSequence);
 142     } //-- void addSequence(org.vamsas.objects.core.Sequence)
 143
 144     /**
 145      * Method addSequence
 146      *
 147      *
 148      *
 149      * @param index
 150      * @param vSequence
 151      */
 152     public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence)
 153         throws java.lang.IndexOutOfBoundsException
 154     {
 155         _sequenceList.insertElementAt(vSequence, index);
 156     } //-- void addSequence(int, org.vamsas.objects.core.Sequence)
 157
 158     /**
 159      * Method addSequenceSetAnnotations
 160      *
 161      *
 162      *
 163      * @param vSequenceSetAnnotations
 164      */
 165     public void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 166         throws java.lang.IndexOutOfBoundsException
 167     {
 168         _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
 169     } //-- void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
 170
 171     /**
 172      * Method addSequenceSetAnnotations
 173      *
 174      *
 175      *
 176      * @param index
 177      * @param vSequenceSetAnnotations
 178      */
 179     public void addSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 180         throws java.lang.IndexOutOfBoundsException
 181     {
 182         _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
 183     } //-- void addSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
 184
 185     /**
 186      * Method addTree
 187      *
 188      *
 189      *
 190      * @param vTree
 191      */
 192     public void addTree(org.vamsas.objects.core.Tree vTree)
 193         throws java.lang.IndexOutOfBoundsException
 194     {
 195         _treeList.addElement(vTree);
 196     } //-- void addTree(org.vamsas.objects.core.Tree)
 197
 198     /**
 199      * Method addTree
 200      *
 201      *
 202      *
 203      * @param index
 204      * @param vTree
 205      */
 206     public void addTree(int index, org.vamsas.objects.core.Tree vTree)
 207         throws java.lang.IndexOutOfBoundsException
 208     {
 209         _treeList.insertElementAt(vTree, index);
 210     } //-- void addTree(int, org.vamsas.objects.core.Tree)
 211
 212     /**
 213      * Method deleteAligned
 214      *
 215      */
 216     public void deleteAligned()
 217     {
 218         this._has_aligned= false;
 219     } //-- void deleteAligned()
 220
 221     /**
 222      * Method enumerateAlignment
 223      *
 224      *
 225      *
 226      * @return Enumeration
 227      */
 228     public java.util.Enumeration enumerateAlignment()
 229     {
 230         return _alignmentList.elements();
 231     } //-- java.util.Enumeration enumerateAlignment()
 232
 233     /**
 234      * Method enumerateSequence
 235      *
 236      *
 237      *
 238      * @return Enumeration
 239      */
 240     public java.util.Enumeration enumerateSequence()
 241     {
 242         return _sequenceList.elements();
 243     } //-- java.util.Enumeration enumerateSequence()
 244
 245     /**
 246      * Method enumerateSequenceSetAnnotations
 247      *
 248      *
 249      *
 250      * @return Enumeration
 251      */
 252     public java.util.Enumeration enumerateSequenceSetAnnotations()
 253     {
 254         return _sequenceSetAnnotationsList.elements();
 255     } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
 256
 257     /**
 258      * Method enumerateTree
 259      *
 260      *
 261      *
 262      * @return Enumeration
 263      */
 264     public java.util.Enumeration enumerateTree()
 265     {
 266         return _treeList.elements();
 267     } //-- java.util.Enumeration enumerateTree()
 268
 269     /**
 270      * Note: hashCode() has not been overriden
 271      *
 272      * @param obj
 273      * @return boolean
 274      */
 275     public boolean equals(java.lang.Object obj)
 276     {
 277         if ( this == obj )
 278             return true;
 279
 280         if (super.equals(obj)==false)
 281             return false;
 282
 283         if (obj instanceof SequenceSet) {
 284
 285             SequenceSet temp = (SequenceSet)obj;
 286             if (this._gapChar != null) {
 287                 if (temp._gapChar == null) return false;
 288                 else if (!(this._gapChar.equals(temp._gapChar)))
 289                     return false;
 290             }
 291             else if (temp._gapChar != null)
 292                 return false;
 293             if (this._aligned != temp._aligned)
 294                 return false;
 295             if (this._has_aligned != temp._has_aligned)
 296                 return false;
 297             if (this._id != null) {
 298                 if (temp._id == null) return false;
 299                 else if (!(this._id.equals(temp._id)))
 300                     return false;
 301             }
 302             else if (temp._id != null)
 303                 return false;
 304             if (this._sequenceList != null) {
 305                 if (temp._sequenceList == null) return false;
 306                 else if (!(this._sequenceList.equals(temp._sequenceList)))
 307                     return false;
 308             }
 309             else if (temp._sequenceList != null)
 310                 return false;
 311             if (this._sequenceSetAnnotationsList != null) {
 312                 if (temp._sequenceSetAnnotationsList == null) return false;
 313                 else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
 314                     return false;
 315             }
 316             else if (temp._sequenceSetAnnotationsList != null)
 317                 return false;
 318             if (this._alignmentList != null) {
 319                 if (temp._alignmentList == null) return false;
 320                 else if (!(this._alignmentList.equals(temp._alignmentList)))
 321                     return false;
 322             }
 323             else if (temp._alignmentList != null)
 324                 return false;
 325             if (this._treeList != null) {
 326                 if (temp._treeList == null) return false;
 327                 else if (!(this._treeList.equals(temp._treeList)))
 328                     return false;
 329             }
 330             else if (temp._treeList != null)
 331                 return false;
 332             if (this._provenance != null) {
 333                 if (temp._provenance == null) return false;
 334                 else if (!(this._provenance.equals(temp._provenance)))
 335                     return false;
 336             }
 337             else if (temp._provenance != null)
 338                 return false;
 339             return true;
 340         }
 341         return false;
 342     } //-- boolean equals(java.lang.Object)
 343
 344     /**
 345      * Returns the value of field 'aligned'.
 346      *
 347      * @return boolean
 348      * @return the value of field 'aligned'.
 349      */
 350     public boolean getAligned()
 351     {
 352         return this._aligned;
 353     } //-- boolean getAligned()
 354
 355     /**
 356      * Method getAlignment
 357      *
 358      *
 359      *
 360      * @param index
 361      * @return Alignment
 362      */
 363     public org.vamsas.objects.core.Alignment getAlignment(int index)
 364         throws java.lang.IndexOutOfBoundsException
 365     {
 366         //-- check bounds for index
 367         if ((index < 0) || (index > _alignmentList.size())) {
 368             throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 369         }
 370
 371         return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 372     } //-- org.vamsas.objects.core.Alignment getAlignment(int)
 373
 374     /**
 375      * Method getAlignment
 376      *
 377      *
 378      *
 379      * @return Alignment
 380      */
 381     public org.vamsas.objects.core.Alignment[] getAlignment()
 382     {
 383         int size = _alignmentList.size();
 384         org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size];
 385         for (int index = 0; index < size; index++) {
 386             mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 387         }
 388         return mArray;
 389     } //-- org.vamsas.objects.core.Alignment[] getAlignment()
 390
 391     /**
 392      * Method getAlignmentCount
 393      *
 394      *
 395      *
 396      * @return int
 397      */
 398     public int getAlignmentCount()
 399     {
 400         return _alignmentList.size();
 401     } //-- int getAlignmentCount()
 402
 403     /**
 404      * Returns the value of field 'gapChar'.
 405      *
 406      * @return String
 407      * @return the value of field 'gapChar'.
 408      */
 409     public java.lang.String getGapChar()
 410     {
 411         return this._gapChar;
 412     } //-- java.lang.String getGapChar()
 413
 414     /**
 415      * Returns the value of field 'id'.
 416      *
 417      * @return String
 418      * @return the value of field 'id'.
 419      */
 420     public java.lang.String getId()
 421     {
 422         return this._id;
 423     } //-- java.lang.String getId()
 424
 425     /**
 426      * Returns the value of field 'provenance'.
 427      *
 428      * @return Provenance
 429      * @return the value of field 'provenance'.
 430      */
 431     public org.vamsas.objects.core.Provenance getProvenance()
 432     {
 433         return this._provenance;
 434     } //-- org.vamsas.objects.core.Provenance getProvenance()
 435
 436     /**
 437      * Method getSequence
 438      *
 439      *
 440      *
 441      * @param index
 442      * @return Sequence
 443      */
 444     public org.vamsas.objects.core.Sequence getSequence(int index)
 445         throws java.lang.IndexOutOfBoundsException
 446     {
 447         //-- check bounds for index
 448         if ((index < 0) || (index > _sequenceList.size())) {
 449             throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 450         }
 451
 452         return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 453     } //-- org.vamsas.objects.core.Sequence getSequence(int)
 454
 455     /**
 456      * Method getSequence
 457      *
 458      *
 459      *
 460      * @return Sequence
 461      */
 462     public org.vamsas.objects.core.Sequence[] getSequence()
 463     {
 464         int size = _sequenceList.size();
 465         org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size];
 466         for (int index = 0; index < size; index++) {
 467             mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 468         }
 469         return mArray;
 470     } //-- org.vamsas.objects.core.Sequence[] getSequence()
 471
 472     /**
 473      * Method getSequenceCount
 474      *
 475      *
 476      *
 477      * @return int
 478      */
 479     public int getSequenceCount()
 480     {
 481         return _sequenceList.size();
 482     } //-- int getSequenceCount()
 483
 484     /**
 485      * Method getSequenceSetAnnotations
 486      *
 487      *
 488      *
 489      * @param index
 490      * @return SequenceSetAnnotations
 491      */
 492     public org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int index)
 493         throws java.lang.IndexOutOfBoundsException
 494     {
 495         //-- check bounds for index
 496         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 497             throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 498         }
 499
 500         return (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 501     } //-- org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int)
 502
 503     /**
 504      * Method getSequenceSetAnnotations
 505      *
 506      *
 507      *
 508      * @return SequenceSetAnnotations
 509      */
 510     public org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
 511     {
 512         int size = _sequenceSetAnnotationsList.size();
 513         org.vamsas.objects.core.SequenceSetAnnotations[] mArray = new org.vamsas.objects.core.SequenceSetAnnotations[size];
 514         for (int index = 0; index < size; index++) {
 515             mArray[index] = (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 516         }
 517         return mArray;
 518     } //-- org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
 519
 520     /**
 521      * Method getSequenceSetAnnotationsCount
 522      *
 523      *
 524      *
 525      * @return int
 526      */
 527     public int getSequenceSetAnnotationsCount()
 528     {
 529         return _sequenceSetAnnotationsList.size();
 530     } //-- int getSequenceSetAnnotationsCount()
 531
 532     /**
 533      * Method getTree
 534      *
 535      *
 536      *
 537      * @param index
 538      * @return Tree
 539      */
 540     public org.vamsas.objects.core.Tree getTree(int index)
 541         throws java.lang.IndexOutOfBoundsException
 542     {
 543         //-- check bounds for index
 544         if ((index < 0) || (index > _treeList.size())) {
 545             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 546         }
 547
 548         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 549     } //-- org.vamsas.objects.core.Tree getTree(int)
 550
 551     /**
 552      * Method getTree
 553      *
 554      *
 555      *
 556      * @return Tree
 557      */
 558     public org.vamsas.objects.core.Tree[] getTree()
 559     {
 560         int size = _treeList.size();
 561         org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
 562         for (int index = 0; index < size; index++) {
 563             mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 564         }
 565         return mArray;
 566     } //-- org.vamsas.objects.core.Tree[] getTree()
 567
 568     /**
 569      * Method getTreeCount
 570      *
 571      *
 572      *
 573      * @return int
 574      */
 575     public int getTreeCount()
 576     {
 577         return _treeList.size();
 578     } //-- int getTreeCount()
 579
 580     /**
 581      * Method hasAligned
 582      *
 583      *
 584      *
 585      * @return boolean
 586      */
 587     public boolean hasAligned()
 588     {
 589         return this._has_aligned;
 590     } //-- boolean hasAligned()
 591
 592     /**
 593      * Method isValid
 594      *
 595      *
 596      *
 597      * @return boolean
 598      */
 599     public boolean isValid()
 600     {
 601         try {
 602             validate();
 603         }
 604         catch (org.exolab.castor.xml.ValidationException vex) {
 605             return false;
 606         }
 607         return true;
 608     } //-- boolean isValid()
 609
 610     /**
 611      * Method marshal
 612      *
 613      *
 614      *
 615      * @param out
 616      */
 617     public void marshal(java.io.Writer out)
 618         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 619     {
 620
 621         Marshaller.marshal(this, out);
 622     } //-- void marshal(java.io.Writer)
 623
 624     /**
 625      * Method marshal
 626      *
 627      *
 628      *
 629      * @param handler
 630      */
 631     public void marshal(org.xml.sax.ContentHandler handler)
 632         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 633     {
 634
 635         Marshaller.marshal(this, handler);
 636     } //-- void marshal(org.xml.sax.ContentHandler)
 637
 638     /**
 639      * Method removeAlignment
 640      *
 641      *
 642      *
 643      * @param index
 644      * @return Alignment
 645      */
 646     public org.vamsas.objects.core.Alignment removeAlignment(int index)
 647     {
 648         java.lang.Object obj = _alignmentList.elementAt(index);
 649         _alignmentList.removeElementAt(index);
 650         return (org.vamsas.objects.core.Alignment) obj;
 651     } //-- org.vamsas.objects.core.Alignment removeAlignment(int)
 652
 653     /**
 654      * Method removeAllAlignment
 655      *
 656      */
 657     public void removeAllAlignment()
 658     {
 659         _alignmentList.removeAllElements();
 660     } //-- void removeAllAlignment()
 661
 662     /**
 663      * Method removeAllSequence
 664      *
 665      */
 666     public void removeAllSequence()
 667     {
 668         _sequenceList.removeAllElements();
 669     } //-- void removeAllSequence()
 670
 671     /**
 672      * Method removeAllSequenceSetAnnotations
 673      *
 674      */
 675     public void removeAllSequenceSetAnnotations()
 676     {
 677         _sequenceSetAnnotationsList.removeAllElements();
 678     } //-- void removeAllSequenceSetAnnotations()
 679
 680     /**
 681      * Method removeAllTree
 682      *
 683      */
 684     public void removeAllTree()
 685     {
 686         _treeList.removeAllElements();
 687     } //-- void removeAllTree()
 688
 689     /**
 690      * Method removeSequence
 691      *
 692      *
 693      *
 694      * @param index
 695      * @return Sequence
 696      */
 697     public org.vamsas.objects.core.Sequence removeSequence(int index)
 698     {
 699         java.lang.Object obj = _sequenceList.elementAt(index);
 700         _sequenceList.removeElementAt(index);
 701         return (org.vamsas.objects.core.Sequence) obj;
 702     } //-- org.vamsas.objects.core.Sequence removeSequence(int)
 703
 704     /**
 705      * Method removeSequenceSetAnnotations
 706      *
 707      *
 708      *
 709      * @param index
 710      * @return SequenceSetAnnotations
 711      */
 712     public org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
 713     {
 714         java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
 715         _sequenceSetAnnotationsList.removeElementAt(index);
 716         return (org.vamsas.objects.core.SequenceSetAnnotations) obj;
 717     } //-- org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int)
 718
 719     /**
 720      * Method removeTree
 721      *
 722      *
 723      *
 724      * @param index
 725      * @return Tree
 726      */
 727     public org.vamsas.objects.core.Tree removeTree(int index)
 728     {
 729         java.lang.Object obj = _treeList.elementAt(index);
 730         _treeList.removeElementAt(index);
 731         return (org.vamsas.objects.core.Tree) obj;
 732     } //-- org.vamsas.objects.core.Tree removeTree(int)
 733
 734     /**
 735      * Sets the value of field 'aligned'.
 736      *
 737      * @param aligned the value of field 'aligned'.
 738      */
 739     public void setAligned(boolean aligned)
 740     {
 741         this._aligned = aligned;
 742         this._has_aligned = true;
 743     } //-- void setAligned(boolean)
 744
 745     /**
 746      * Method setAlignment
 747      *
 748      *
 749      *
 750      * @param index
 751      * @param vAlignment
 752      */
 753     public void setAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
 754         throws java.lang.IndexOutOfBoundsException
 755     {
 756         //-- check bounds for index
 757         if ((index < 0) || (index > _alignmentList.size())) {
 758             throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 759         }
 760         _alignmentList.setElementAt(vAlignment, index);
 761     } //-- void setAlignment(int, org.vamsas.objects.core.Alignment)
 762
 763     /**
 764      * Method setAlignment
 765      *
 766      *
 767      *
 768      * @param alignmentArray
 769      */
 770     public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray)
 771     {
 772         //-- copy array
 773         _alignmentList.removeAllElements();
 774         for (int i = 0; i < alignmentArray.length; i++) {
 775             _alignmentList.addElement(alignmentArray[i]);
 776         }
 777     } //-- void setAlignment(org.vamsas.objects.core.Alignment)
 778
 779     /**
 780      * Sets the value of field 'gapChar'.
 781      *
 782      * @param gapChar the value of field 'gapChar'.
 783      */
 784     public void setGapChar(java.lang.String gapChar)
 785     {
 786         this._gapChar = gapChar;
 787     } //-- void setGapChar(java.lang.String)
 788
 789     /**
 790      * Sets the value of field 'id'.
 791      *
 792      * @param id the value of field 'id'.
 793      */
 794     public void setId(java.lang.String id)
 795     {
 796         this._id = id;
 797     } //-- void setId(java.lang.String)
 798
 799     /**
 800      * Sets the value of field 'provenance'.
 801      *
 802      * @param provenance the value of field 'provenance'.
 803      */
 804     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 805     {
 806         this._provenance = provenance;
 807     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 808
 809     /**
 810      * Method setSequence
 811      *
 812      *
 813      *
 814      * @param index
 815      * @param vSequence
 816      */
 817     public void setSequence(int index, org.vamsas.objects.core.Sequence vSequence)
 818         throws java.lang.IndexOutOfBoundsException
 819     {
 820         //-- check bounds for index
 821         if ((index < 0) || (index > _sequenceList.size())) {
 822             throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 823         }
 824         _sequenceList.setElementAt(vSequence, index);
 825     } //-- void setSequence(int, org.vamsas.objects.core.Sequence)
 826
 827     /**
 828      * Method setSequence
 829      *
 830      *
 831      *
 832      * @param sequenceArray
 833      */
 834     public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray)
 835     {
 836         //-- copy array
 837         _sequenceList.removeAllElements();
 838         for (int i = 0; i < sequenceArray.length; i++) {
 839             _sequenceList.addElement(sequenceArray[i]);
 840         }
 841     } //-- void setSequence(org.vamsas.objects.core.Sequence)
 842
 843     /**
 844      * Method setSequenceSetAnnotations
 845      *
 846      *
 847      *
 848      * @param index
 849      * @param vSequenceSetAnnotations
 850      */
 851     public void setSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
 852         throws java.lang.IndexOutOfBoundsException
 853     {
 854         //-- check bounds for index
 855         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 856             throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 857         }
 858         _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index);
 859     } //-- void setSequenceSetAnnotations(int, org.vamsas.objects.core.SequenceSetAnnotations)
 860
 861     /**
 862      * Method setSequenceSetAnnotations
 863      *
 864      *
 865      *
 866      * @param sequenceSetAnnotationsArray
 867      */
 868     public void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
 869     {
 870         //-- copy array
 871         _sequenceSetAnnotationsList.removeAllElements();
 872         for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
 873             _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
 874         }
 875     } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
 876
 877     /**
 878      * Method setTree
 879      *
 880      *
 881      *
 882      * @param index
 883      * @param vTree
 884      */
 885     public void setTree(int index, org.vamsas.objects.core.Tree vTree)
 886         throws java.lang.IndexOutOfBoundsException
 887     {
 888         //-- check bounds for index
 889         if ((index < 0) || (index > _treeList.size())) {
 890             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 891         }
 892         _treeList.setElementAt(vTree, index);
 893     } //-- void setTree(int, org.vamsas.objects.core.Tree)
 894
 895     /**
 896      * Method setTree
 897      *
 898      *
 899      *
 900      * @param treeArray
 901      */
 902     public void setTree(org.vamsas.objects.core.Tree[] treeArray)
 903     {
 904         //-- copy array
 905         _treeList.removeAllElements();
 906         for (int i = 0; i < treeArray.length; i++) {
 907             _treeList.addElement(treeArray[i]);
 908         }
 909     } //-- void setTree(org.vamsas.objects.core.Tree)
 910
 911     /**
 912      * Method unmarshal
 913      *
 914      *
 915      *
 916      * @param reader
 917      * @return SequenceSet
 918      */
 919     public static org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader reader)
 920         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 921     {
 922         return (org.vamsas.objects.core.SequenceSet) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSet.class, reader);
 923     } //-- org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader)
 924
 925     /**
 926      * Method validate
 927      *
 928      */
 929     public void validate()
 930         throws org.exolab.castor.xml.ValidationException
 931     {
 932         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 933         validator.validate(this);
 934     } //-- void validate()
 935
 936 }