src/uk/ac/vamsas/objects/core/DataSet.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:DataSet.java 264 2006-12-14 17:42:54Z JimP $
   6  */
   7
   8 package uk.ac.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 DataSet.
  28  *
  29  * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  30  */
  31 public class DataSet extends uk.ac.vamsas.client.Vobject
  32 implements java.io.Serializable
  33 {
  34
  35
  36       //--------------------------/
  37      //- Class/Member Variables -/
  38     //--------------------------/
  39
  40     /**
  41      * Primary Key for vamsas object referencing
  42      */
  43     private java.lang.String _id;
  44
  45     /**
  46      * Field _sequenceList
  47      */
  48     private java.util.Vector _sequenceList;
  49
  50     /**
  51      * Field _dataSetAnnotationsList
  52      */
  53     private java.util.Vector _dataSetAnnotationsList;
  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 uk.ac.vamsas.objects.core.Provenance _provenance;
  69
  70
  71       //----------------/
  72      //- Constructors -/
  73     //----------------/
  74
  75     public DataSet()
  76      {
  77         super();
  78         _sequenceList = new Vector();
  79         _dataSetAnnotationsList = new Vector();
  80         _alignmentList = new Vector();
  81         _treeList = new Vector();
  82     } //-- uk.ac.vamsas.objects.core.DataSet()
  83
  84
  85       //-----------/
  86      //- Methods -/
  87     //-----------/
  88
  89     /**
  90      * Method addAlignment
  91      *
  92      *
  93      *
  94      * @param vAlignment
  95      */
  96     public void addAlignment(uk.ac.vamsas.objects.core.Alignment vAlignment)
  97         throws java.lang.IndexOutOfBoundsException
  98     {
  99         _alignmentList.addElement(vAlignment);
 100     } //-- void addAlignment(uk.ac.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, uk.ac.vamsas.objects.core.Alignment vAlignment)
 111         throws java.lang.IndexOutOfBoundsException
 112     {
 113         _alignmentList.insertElementAt(vAlignment, index);
 114     } //-- void addAlignment(int, uk.ac.vamsas.objects.core.Alignment)
 115
 116     /**
 117      * Method addDataSetAnnotations
 118      *
 119      *
 120      *
 121      * @param vDataSetAnnotations
 122      */
 123     public void addDataSetAnnotations(uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
 124         throws java.lang.IndexOutOfBoundsException
 125     {
 126         _dataSetAnnotationsList.addElement(vDataSetAnnotations);
 127     } //-- void addDataSetAnnotations(uk.ac.vamsas.objects.core.DataSetAnnotations)
 128
 129     /**
 130      * Method addDataSetAnnotations
 131      *
 132      *
 133      *
 134      * @param index
 135      * @param vDataSetAnnotations
 136      */
 137     public void addDataSetAnnotations(int index, uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
 138         throws java.lang.IndexOutOfBoundsException
 139     {
 140         _dataSetAnnotationsList.insertElementAt(vDataSetAnnotations, index);
 141     } //-- void addDataSetAnnotations(int, uk.ac.vamsas.objects.core.DataSetAnnotations)
 142
 143     /**
 144      * Method addSequence
 145      *
 146      *
 147      *
 148      * @param vSequence
 149      */
 150     public void addSequence(uk.ac.vamsas.objects.core.Sequence vSequence)
 151         throws java.lang.IndexOutOfBoundsException
 152     {
 153         _sequenceList.addElement(vSequence);
 154     } //-- void addSequence(uk.ac.vamsas.objects.core.Sequence)
 155
 156     /**
 157      * Method addSequence
 158      *
 159      *
 160      *
 161      * @param index
 162      * @param vSequence
 163      */
 164     public void addSequence(int index, uk.ac.vamsas.objects.core.Sequence vSequence)
 165         throws java.lang.IndexOutOfBoundsException
 166     {
 167         _sequenceList.insertElementAt(vSequence, index);
 168     } //-- void addSequence(int, uk.ac.vamsas.objects.core.Sequence)
 169
 170     /**
 171      * Method addTree
 172      *
 173      *
 174      *
 175      * @param vTree
 176      */
 177     public void addTree(uk.ac.vamsas.objects.core.Tree vTree)
 178         throws java.lang.IndexOutOfBoundsException
 179     {
 180         _treeList.addElement(vTree);
 181     } //-- void addTree(uk.ac.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, uk.ac.vamsas.objects.core.Tree vTree)
 192         throws java.lang.IndexOutOfBoundsException
 193     {
 194         _treeList.insertElementAt(vTree, index);
 195     } //-- void addTree(int, uk.ac.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 enumerateDataSetAnnotations
 211      *
 212      *
 213      *
 214      * @return Enumeration
 215      */
 216     public java.util.Enumeration enumerateDataSetAnnotations()
 217     {
 218         return _dataSetAnnotationsList.elements();
 219     } //-- java.util.Enumeration enumerateDataSetAnnotations()
 220
 221     /**
 222      * Method enumerateSequence
 223      *
 224      *
 225      *
 226      * @return Enumeration
 227      */
 228     public java.util.Enumeration enumerateSequence()
 229     {
 230         return _sequenceList.elements();
 231     } //-- java.util.Enumeration enumerateSequence()
 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 DataSet) {
 260
 261             DataSet temp = (DataSet)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._dataSetAnnotationsList != null) {
 277                 if (temp._dataSetAnnotationsList == null) return false;
 278                 else if (!(this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList)))
 279                     return false;
 280             }
 281             else if (temp._dataSetAnnotationsList != 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 uk.ac.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 (uk.ac.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 326     } //-- uk.ac.vamsas.objects.core.Alignment getAlignment(int)
 327
 328     /**
 329      * Method getAlignment
 330      *
 331      *
 332      *
 333      * @return Alignment
 334      */
 335     public uk.ac.vamsas.objects.core.Alignment[] getAlignment()
 336     {
 337         int size = _alignmentList.size();
 338         uk.ac.vamsas.objects.core.Alignment[] mArray = new uk.ac.vamsas.objects.core.Alignment[size];
 339         for (int index = 0; index < size; index++) {
 340             mArray[index] = (uk.ac.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
 341         }
 342         return mArray;
 343     } //-- uk.ac.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      * Method getDataSetAnnotations
 359      *
 360      *
 361      *
 362      * @param index
 363      * @return DataSetAnnotations
 364      */
 365     public uk.ac.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int index)
 366         throws java.lang.IndexOutOfBoundsException
 367     {
 368         //-- check bounds for index
 369         if ((index < 0) || (index > _dataSetAnnotationsList.size())) {
 370             throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");
 371         }
 372
 373         return (uk.ac.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
 374     } //-- uk.ac.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int)
 375
 376     /**
 377      * Method getDataSetAnnotations
 378      *
 379      *
 380      *
 381      * @return DataSetAnnotations
 382      */
 383     public uk.ac.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
 384     {
 385         int size = _dataSetAnnotationsList.size();
 386         uk.ac.vamsas.objects.core.DataSetAnnotations[] mArray = new uk.ac.vamsas.objects.core.DataSetAnnotations[size];
 387         for (int index = 0; index < size; index++) {
 388             mArray[index] = (uk.ac.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
 389         }
 390         return mArray;
 391     } //-- uk.ac.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
 392
 393     /**
 394      * Method getDataSetAnnotationsCount
 395      *
 396      *
 397      *
 398      * @return int
 399      */
 400     public int getDataSetAnnotationsCount()
 401     {
 402         return _dataSetAnnotationsList.size();
 403     } //-- int getDataSetAnnotationsCount()
 404
 405     /**
 406      * Returns the value of field 'id'. The field 'id' has the
 407      * following description: Primary Key for vamsas object
 408      * referencing
 409      *
 410      * @return String
 411      * @return the value of field 'id'.
 412      */
 413     public java.lang.String getId()
 414     {
 415         return this._id;
 416     } //-- java.lang.String getId()
 417
 418     /**
 419      * Returns the value of field 'provenance'.
 420      *
 421      * @return Provenance
 422      * @return the value of field 'provenance'.
 423      */
 424     public uk.ac.vamsas.objects.core.Provenance getProvenance()
 425     {
 426         return this._provenance;
 427     } //-- uk.ac.vamsas.objects.core.Provenance getProvenance()
 428
 429     /**
 430      * Method getSequence
 431      *
 432      *
 433      *
 434      * @param index
 435      * @return Sequence
 436      */
 437     public uk.ac.vamsas.objects.core.Sequence getSequence(int index)
 438         throws java.lang.IndexOutOfBoundsException
 439     {
 440         //-- check bounds for index
 441         if ((index < 0) || (index > _sequenceList.size())) {
 442             throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 443         }
 444
 445         return (uk.ac.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 446     } //-- uk.ac.vamsas.objects.core.Sequence getSequence(int)
 447
 448     /**
 449      * Method getSequence
 450      *
 451      *
 452      *
 453      * @return Sequence
 454      */
 455     public uk.ac.vamsas.objects.core.Sequence[] getSequence()
 456     {
 457         int size = _sequenceList.size();
 458         uk.ac.vamsas.objects.core.Sequence[] mArray = new uk.ac.vamsas.objects.core.Sequence[size];
 459         for (int index = 0; index < size; index++) {
 460             mArray[index] = (uk.ac.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
 461         }
 462         return mArray;
 463     } //-- uk.ac.vamsas.objects.core.Sequence[] getSequence()
 464
 465     /**
 466      * Method getSequenceCount
 467      *
 468      *
 469      *
 470      * @return int
 471      */
 472     public int getSequenceCount()
 473     {
 474         return _sequenceList.size();
 475     } //-- int getSequenceCount()
 476
 477     /**
 478      * Method getTree
 479      *
 480      *
 481      *
 482      * @param index
 483      * @return Tree
 484      */
 485     public uk.ac.vamsas.objects.core.Tree getTree(int index)
 486         throws java.lang.IndexOutOfBoundsException
 487     {
 488         //-- check bounds for index
 489         if ((index < 0) || (index > _treeList.size())) {
 490             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 491         }
 492
 493         return (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
 494     } //-- uk.ac.vamsas.objects.core.Tree getTree(int)
 495
 496     /**
 497      * Method getTree
 498      *
 499      *
 500      *
 501      * @return Tree
 502      */
 503     public uk.ac.vamsas.objects.core.Tree[] getTree()
 504     {
 505         int size = _treeList.size();
 506         uk.ac.vamsas.objects.core.Tree[] mArray = new uk.ac.vamsas.objects.core.Tree[size];
 507         for (int index = 0; index < size; index++) {
 508             mArray[index] = (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
 509         }
 510         return mArray;
 511     } //-- uk.ac.vamsas.objects.core.Tree[] getTree()
 512
 513     /**
 514      * Method getTreeCount
 515      *
 516      *
 517      *
 518      * @return int
 519      */
 520     public int getTreeCount()
 521     {
 522         return _treeList.size();
 523     } //-- int getTreeCount()
 524
 525     /**
 526      * Method isValid
 527      *
 528      *
 529      *
 530      * @return boolean
 531      */
 532     public boolean isValid()
 533     {
 534         try {
 535             validate();
 536         }
 537         catch (org.exolab.castor.xml.ValidationException vex) {
 538             return false;
 539         }
 540         return true;
 541     } //-- boolean isValid()
 542
 543     /**
 544      * Method marshal
 545      *
 546      *
 547      *
 548      * @param out
 549      */
 550     public void marshal(java.io.Writer out)
 551         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 552     {
 553
 554         Marshaller.marshal(this, out);
 555     } //-- void marshal(java.io.Writer)
 556
 557     /**
 558      * Method marshal
 559      *
 560      *
 561      *
 562      * @param handler
 563      */
 564     public void marshal(org.xml.sax.ContentHandler handler)
 565         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 566     {
 567
 568         Marshaller.marshal(this, handler);
 569     } //-- void marshal(org.xml.sax.ContentHandler)
 570
 571     /**
 572      * Method removeAlignment
 573      *
 574      *
 575      *
 576      * @param index
 577      * @return Alignment
 578      */
 579     public uk.ac.vamsas.objects.core.Alignment removeAlignment(int index)
 580     {
 581         java.lang.Object obj = _alignmentList.elementAt(index);
 582         _alignmentList.removeElementAt(index);
 583         return (uk.ac.vamsas.objects.core.Alignment) obj;
 584     } //-- uk.ac.vamsas.objects.core.Alignment removeAlignment(int)
 585
 586     /**
 587      * Method removeAllAlignment
 588      *
 589      */
 590     public void removeAllAlignment()
 591     {
 592         _alignmentList.removeAllElements();
 593     } //-- void removeAllAlignment()
 594
 595     /**
 596      * Method removeAllDataSetAnnotations
 597      *
 598      */
 599     public void removeAllDataSetAnnotations()
 600     {
 601         _dataSetAnnotationsList.removeAllElements();
 602     } //-- void removeAllDataSetAnnotations()
 603
 604     /**
 605      * Method removeAllSequence
 606      *
 607      */
 608     public void removeAllSequence()
 609     {
 610         _sequenceList.removeAllElements();
 611     } //-- void removeAllSequence()
 612
 613     /**
 614      * Method removeAllTree
 615      *
 616      */
 617     public void removeAllTree()
 618     {
 619         _treeList.removeAllElements();
 620     } //-- void removeAllTree()
 621
 622     /**
 623      * Method removeDataSetAnnotations
 624      *
 625      *
 626      *
 627      * @param index
 628      * @return DataSetAnnotations
 629      */
 630     public uk.ac.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int index)
 631     {
 632         java.lang.Object obj = _dataSetAnnotationsList.elementAt(index);
 633         _dataSetAnnotationsList.removeElementAt(index);
 634         return (uk.ac.vamsas.objects.core.DataSetAnnotations) obj;
 635     } //-- uk.ac.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int)
 636
 637     /**
 638      * Method removeSequence
 639      *
 640      *
 641      *
 642      * @param index
 643      * @return Sequence
 644      */
 645     public uk.ac.vamsas.objects.core.Sequence removeSequence(int index)
 646     {
 647         java.lang.Object obj = _sequenceList.elementAt(index);
 648         _sequenceList.removeElementAt(index);
 649         return (uk.ac.vamsas.objects.core.Sequence) obj;
 650     } //-- uk.ac.vamsas.objects.core.Sequence removeSequence(int)
 651
 652     /**
 653      * Method removeTree
 654      *
 655      *
 656      *
 657      * @param index
 658      * @return Tree
 659      */
 660     public uk.ac.vamsas.objects.core.Tree removeTree(int index)
 661     {
 662         java.lang.Object obj = _treeList.elementAt(index);
 663         _treeList.removeElementAt(index);
 664         return (uk.ac.vamsas.objects.core.Tree) obj;
 665     } //-- uk.ac.vamsas.objects.core.Tree removeTree(int)
 666
 667     /**
 668      * Method setAlignment
 669      *
 670      *
 671      *
 672      * @param index
 673      * @param vAlignment
 674      */
 675     public void setAlignment(int index, uk.ac.vamsas.objects.core.Alignment vAlignment)
 676         throws java.lang.IndexOutOfBoundsException
 677     {
 678         //-- check bounds for index
 679         if ((index < 0) || (index > _alignmentList.size())) {
 680             throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 681         }
 682         _alignmentList.setElementAt(vAlignment, index);
 683     } //-- void setAlignment(int, uk.ac.vamsas.objects.core.Alignment)
 684
 685     /**
 686      * Method setAlignment
 687      *
 688      *
 689      *
 690      * @param alignmentArray
 691      */
 692     public void setAlignment(uk.ac.vamsas.objects.core.Alignment[] alignmentArray)
 693     {
 694         //-- copy array
 695         _alignmentList.removeAllElements();
 696         for (int i = 0; i < alignmentArray.length; i++) {
 697             _alignmentList.addElement(alignmentArray[i]);
 698         }
 699     } //-- void setAlignment(uk.ac.vamsas.objects.core.Alignment)
 700
 701     /**
 702      * Method setDataSetAnnotations
 703      *
 704      *
 705      *
 706      * @param index
 707      * @param vDataSetAnnotations
 708      */
 709     public void setDataSetAnnotations(int index, uk.ac.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
 710         throws java.lang.IndexOutOfBoundsException
 711     {
 712         //-- check bounds for index
 713         if ((index < 0) || (index > _dataSetAnnotationsList.size())) {
 714             throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");
 715         }
 716         _dataSetAnnotationsList.setElementAt(vDataSetAnnotations, index);
 717     } //-- void setDataSetAnnotations(int, uk.ac.vamsas.objects.core.DataSetAnnotations)
 718
 719     /**
 720      * Method setDataSetAnnotations
 721      *
 722      *
 723      *
 724      * @param dataSetAnnotationsArray
 725      */
 726     public void setDataSetAnnotations(uk.ac.vamsas.objects.core.DataSetAnnotations[] dataSetAnnotationsArray)
 727     {
 728         //-- copy array
 729         _dataSetAnnotationsList.removeAllElements();
 730         for (int i = 0; i < dataSetAnnotationsArray.length; i++) {
 731             _dataSetAnnotationsList.addElement(dataSetAnnotationsArray[i]);
 732         }
 733     } //-- void setDataSetAnnotations(uk.ac.vamsas.objects.core.DataSetAnnotations)
 734
 735     /**
 736      * Sets the value of field 'id'. The field 'id' has the
 737      * following description: Primary Key for vamsas object
 738      * referencing
 739      *
 740      * @param id the value of field 'id'.
 741      */
 742     public void setId(java.lang.String id)
 743     {
 744         this._id = id;
 745     } //-- void setId(java.lang.String)
 746
 747     /**
 748      * Sets the value of field 'provenance'.
 749      *
 750      * @param provenance the value of field 'provenance'.
 751      */
 752     public void setProvenance(uk.ac.vamsas.objects.core.Provenance provenance)
 753     {
 754         this._provenance = provenance;
 755     } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance)
 756
 757     /**
 758      * Method setSequence
 759      *
 760      *
 761      *
 762      * @param index
 763      * @param vSequence
 764      */
 765     public void setSequence(int index, uk.ac.vamsas.objects.core.Sequence vSequence)
 766         throws java.lang.IndexOutOfBoundsException
 767     {
 768         //-- check bounds for index
 769         if ((index < 0) || (index > _sequenceList.size())) {
 770             throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 771         }
 772         _sequenceList.setElementAt(vSequence, index);
 773     } //-- void setSequence(int, uk.ac.vamsas.objects.core.Sequence)
 774
 775     /**
 776      * Method setSequence
 777      *
 778      *
 779      *
 780      * @param sequenceArray
 781      */
 782     public void setSequence(uk.ac.vamsas.objects.core.Sequence[] sequenceArray)
 783     {
 784         //-- copy array
 785         _sequenceList.removeAllElements();
 786         for (int i = 0; i < sequenceArray.length; i++) {
 787             _sequenceList.addElement(sequenceArray[i]);
 788         }
 789     } //-- void setSequence(uk.ac.vamsas.objects.core.Sequence)
 790
 791     /**
 792      * Method setTree
 793      *
 794      *
 795      *
 796      * @param index
 797      * @param vTree
 798      */
 799     public void setTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
 800         throws java.lang.IndexOutOfBoundsException
 801     {
 802         //-- check bounds for index
 803         if ((index < 0) || (index > _treeList.size())) {
 804             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 805         }
 806         _treeList.setElementAt(vTree, index);
 807     } //-- void setTree(int, uk.ac.vamsas.objects.core.Tree)
 808
 809     /**
 810      * Method setTree
 811      *
 812      *
 813      *
 814      * @param treeArray
 815      */
 816     public void setTree(uk.ac.vamsas.objects.core.Tree[] treeArray)
 817     {
 818         //-- copy array
 819         _treeList.removeAllElements();
 820         for (int i = 0; i < treeArray.length; i++) {
 821             _treeList.addElement(treeArray[i]);
 822         }
 823     } //-- void setTree(uk.ac.vamsas.objects.core.Tree)
 824
 825     /**
 826      * Method unmarshal
 827      *
 828      *
 829      *
 830      * @param reader
 831      * @return DataSet
 832      */
 833     public static uk.ac.vamsas.objects.core.DataSet unmarshal(java.io.Reader reader)
 834         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 835     {
 836         return (uk.ac.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.DataSet.class, reader);
 837     } //-- uk.ac.vamsas.objects.core.DataSet unmarshal(java.io.Reader)
 838
 839     /**
 840      * Method validate
 841      *
 842      */
 843     public void validate()
 844         throws org.exolab.castor.xml.ValidationException
 845     {
 846         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 847         validator.validate(this);
 848     } //-- void validate()
 849
 850 }