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

   1 /*
   2  * This class was automatically generated with
   3  * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
   4  * Schema.
   5  * $Id$
   6  */
   7
   8 package org.vamsas.client.objects;
   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 _sequenceList
  57      */
  58     private java.util.Vector _sequenceList;
  59
  60     /**
  61      * Field _sequenceSetAnnotationsList
  62      */
  63     private java.util.Vector _sequenceSetAnnotationsList;
  64
  65     /**
  66      * Field _alignmentList
  67      */
  68     private java.util.Vector _alignmentList;
  69
  70     /**
  71      * Field _tree
  72      */
  73     private org.vamsas.client.objects.Tree _tree;
  74
  75     /**
  76      * Field _provenance
  77      */
  78     private org.vamsas.client.objects.Provenance _provenance;
  79
  80
  81       //----------------/
  82      //- Constructors -/
  83     //----------------/
  84
  85     public SequenceSet()
  86      {
  87         super();
  88         _sequenceList = new Vector();
  89         _sequenceSetAnnotationsList = new Vector();
  90         _alignmentList = new Vector();
  91     } //-- org.vamsas.client.objects.SequenceSet()
  92
  93
  94       //-----------/
  95      //- Methods -/
  96     //-----------/
  97
  98     /**
  99      * Method addAlignment
 100      *
 101      *
 102      *
 103      * @param vAlignment
 104      */
 105     public void addAlignment(org.vamsas.client.objects.Alignment vAlignment)
 106         throws java.lang.IndexOutOfBoundsException
 107     {
 108         _alignmentList.addElement(vAlignment);
 109     } //-- void addAlignment(org.vamsas.client.objects.Alignment)
 110
 111     /**
 112      * Method addAlignment
 113      *
 114      *
 115      *
 116      * @param index
 117      * @param vAlignment
 118      */
 119     public void addAlignment(int index, org.vamsas.client.objects.Alignment vAlignment)
 120         throws java.lang.IndexOutOfBoundsException
 121     {
 122         _alignmentList.insertElementAt(vAlignment, index);
 123     } //-- void addAlignment(int, org.vamsas.client.objects.Alignment)
 124
 125     /**
 126      * Method addSequence
 127      *
 128      *
 129      *
 130      * @param vSequence
 131      */
 132     public void addSequence(org.vamsas.client.objects.Sequence vSequence)
 133         throws java.lang.IndexOutOfBoundsException
 134     {
 135         _sequenceList.addElement(vSequence);
 136     } //-- void addSequence(org.vamsas.client.objects.Sequence)
 137
 138     /**
 139      * Method addSequence
 140      *
 141      *
 142      *
 143      * @param index
 144      * @param vSequence
 145      */
 146     public void addSequence(int index, org.vamsas.client.objects.Sequence vSequence)
 147         throws java.lang.IndexOutOfBoundsException
 148     {
 149         _sequenceList.insertElementAt(vSequence, index);
 150     } //-- void addSequence(int, org.vamsas.client.objects.Sequence)
 151
 152     /**
 153      * Method addSequenceSetAnnotations
 154      *
 155      *
 156      *
 157      * @param vSequenceSetAnnotations
 158      */
 159     public void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
 160         throws java.lang.IndexOutOfBoundsException
 161     {
 162         _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
 163     } //-- void addSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations)
 164
 165     /**
 166      * Method addSequenceSetAnnotations
 167      *
 168      *
 169      *
 170      * @param index
 171      * @param vSequenceSetAnnotations
 172      */
 173     public void addSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
 174         throws java.lang.IndexOutOfBoundsException
 175     {
 176         _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
 177     } //-- void addSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations)
 178
 179     /**
 180      * Method deleteAligned
 181      *
 182      */
 183     public void deleteAligned()
 184     {
 185         this._has_aligned= false;
 186     } //-- void deleteAligned()
 187
 188     /**
 189      * Method enumerateAlignment
 190      *
 191      *
 192      *
 193      * @return Enumeration
 194      */
 195     public java.util.Enumeration enumerateAlignment()
 196     {
 197         return _alignmentList.elements();
 198     } //-- java.util.Enumeration enumerateAlignment()
 199
 200     /**
 201      * Method enumerateSequence
 202      *
 203      *
 204      *
 205      * @return Enumeration
 206      */
 207     public java.util.Enumeration enumerateSequence()
 208     {
 209         return _sequenceList.elements();
 210     } //-- java.util.Enumeration enumerateSequence()
 211
 212     /**
 213      * Method enumerateSequenceSetAnnotations
 214      *
 215      *
 216      *
 217      * @return Enumeration
 218      */
 219     public java.util.Enumeration enumerateSequenceSetAnnotations()
 220     {
 221         return _sequenceSetAnnotationsList.elements();
 222     } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
 223
 224     /**
 225      * Note: hashCode() has not been overriden
 226      *
 227      * @param obj
 228      * @return boolean
 229      */
 230     public boolean equals(java.lang.Object obj)
 231     {
 232         if ( this == obj )
 233             return true;
 234
 235         if (super.equals(obj)==false)
 236             return false;
 237
 238         if (obj instanceof SequenceSet) {
 239
 240             SequenceSet temp = (SequenceSet)obj;
 241             if (this._gapChar != null) {
 242                 if (temp._gapChar == null) return false;
 243                 else if (!(this._gapChar.equals(temp._gapChar)))
 244                     return false;
 245             }
 246             else if (temp._gapChar != null)
 247                 return false;
 248             if (this._aligned != temp._aligned)
 249                 return false;
 250             if (this._has_aligned != temp._has_aligned)
 251                 return false;
 252             if (this._sequenceList != null) {
 253                 if (temp._sequenceList == null) return false;
 254                 else if (!(this._sequenceList.equals(temp._sequenceList)))
 255                     return false;
 256             }
 257             else if (temp._sequenceList != null)
 258                 return false;
 259             if (this._sequenceSetAnnotationsList != null) {
 260                 if (temp._sequenceSetAnnotationsList == null) return false;
 261                 else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
 262                     return false;
 263             }
 264             else if (temp._sequenceSetAnnotationsList != null)
 265                 return false;
 266             if (this._alignmentList != null) {
 267                 if (temp._alignmentList == null) return false;
 268                 else if (!(this._alignmentList.equals(temp._alignmentList)))
 269                     return false;
 270             }
 271             else if (temp._alignmentList != null)
 272                 return false;
 273             if (this._tree != null) {
 274                 if (temp._tree == null) return false;
 275                 else if (!(this._tree.equals(temp._tree)))
 276                     return false;
 277             }
 278             else if (temp._tree != null)
 279                 return false;
 280             if (this._provenance != null) {
 281                 if (temp._provenance == null) return false;
 282                 else if (!(this._provenance.equals(temp._provenance)))
 283                     return false;
 284             }
 285             else if (temp._provenance != null)
 286                 return false;
 287             return true;
 288         }
 289         return false;
 290     } //-- boolean equals(java.lang.Object)
 291
 292     /**
 293      * Returns the value of field 'aligned'.
 294      *
 295      * @return boolean
 296      * @return the value of field 'aligned'.
 297      */
 298     public boolean getAligned()
 299     {
 300         return this._aligned;
 301     } //-- boolean getAligned()
 302
 303     /**
 304      * Method getAlignment
 305      *
 306      *
 307      *
 308      * @param index
 309      * @return Alignment
 310      */
 311     public org.vamsas.client.objects.Alignment getAlignment(int index)
 312         throws java.lang.IndexOutOfBoundsException
 313     {
 314         //-- check bounds for index
 315         if ((index < 0) || (index > _alignmentList.size())) {
 316             throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 317         }
 318
 319         return (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index);
 320     } //-- org.vamsas.client.objects.Alignment getAlignment(int)
 321
 322     /**
 323      * Method getAlignment
 324      *
 325      *
 326      *
 327      * @return Alignment
 328      */
 329     public org.vamsas.client.objects.Alignment[] getAlignment()
 330     {
 331         int size = _alignmentList.size();
 332         org.vamsas.client.objects.Alignment[] mArray = new org.vamsas.client.objects.Alignment[size];
 333         for (int index = 0; index < size; index++) {
 334             mArray[index] = (org.vamsas.client.objects.Alignment) _alignmentList.elementAt(index);
 335         }
 336         return mArray;
 337     } //-- org.vamsas.client.objects.Alignment[] getAlignment()
 338
 339     /**
 340      * Method getAlignmentAsReference
 341      *
 342      * Returns a reference to 'alignment'. No type checking is
 343      * performed on any modications to the Vector.
 344      *
 345      * @return Vector
 346      * @return returns a reference to the Vector.
 347      */
 348     public java.util.Vector getAlignmentAsReference()
 349     {
 350         return _alignmentList;
 351     } //-- java.util.Vector getAlignmentAsReference()
 352
 353     /**
 354      * Method getAlignmentCount
 355      *
 356      *
 357      *
 358      * @return int
 359      */
 360     public int getAlignmentCount()
 361     {
 362         return _alignmentList.size();
 363     } //-- int getAlignmentCount()
 364
 365     /**
 366      * Returns the value of field 'gapChar'.
 367      *
 368      * @return String
 369      * @return the value of field 'gapChar'.
 370      */
 371     public java.lang.String getGapChar()
 372     {
 373         return this._gapChar;
 374     } //-- java.lang.String getGapChar()
 375
 376     /**
 377      * Returns the value of field 'provenance'.
 378      *
 379      * @return Provenance
 380      * @return the value of field 'provenance'.
 381      */
 382     public org.vamsas.client.objects.Provenance getProvenance()
 383     {
 384         return this._provenance;
 385     } //-- org.vamsas.client.objects.Provenance getProvenance()
 386
 387     /**
 388      * Method getSequence
 389      *
 390      *
 391      *
 392      * @param index
 393      * @return Sequence
 394      */
 395     public org.vamsas.client.objects.Sequence getSequence(int index)
 396         throws java.lang.IndexOutOfBoundsException
 397     {
 398         //-- check bounds for index
 399         if ((index < 0) || (index > _sequenceList.size())) {
 400             throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 401         }
 402
 403         return (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index);
 404     } //-- org.vamsas.client.objects.Sequence getSequence(int)
 405
 406     /**
 407      * Method getSequence
 408      *
 409      *
 410      *
 411      * @return Sequence
 412      */
 413     public org.vamsas.client.objects.Sequence[] getSequence()
 414     {
 415         int size = _sequenceList.size();
 416         org.vamsas.client.objects.Sequence[] mArray = new org.vamsas.client.objects.Sequence[size];
 417         for (int index = 0; index < size; index++) {
 418             mArray[index] = (org.vamsas.client.objects.Sequence) _sequenceList.elementAt(index);
 419         }
 420         return mArray;
 421     } //-- org.vamsas.client.objects.Sequence[] getSequence()
 422
 423     /**
 424      * Method getSequenceAsReference
 425      *
 426      * Returns a reference to 'sequence'. No type checking is
 427      * performed on any modications to the Vector.
 428      *
 429      * @return Vector
 430      * @return returns a reference to the Vector.
 431      */
 432     public java.util.Vector getSequenceAsReference()
 433     {
 434         return _sequenceList;
 435     } //-- java.util.Vector getSequenceAsReference()
 436
 437     /**
 438      * Method getSequenceCount
 439      *
 440      *
 441      *
 442      * @return int
 443      */
 444     public int getSequenceCount()
 445     {
 446         return _sequenceList.size();
 447     } //-- int getSequenceCount()
 448
 449     /**
 450      * Method getSequenceSetAnnotations
 451      *
 452      *
 453      *
 454      * @param index
 455      * @return SequenceSetAnnotations
 456      */
 457     public org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int index)
 458         throws java.lang.IndexOutOfBoundsException
 459     {
 460         //-- check bounds for index
 461         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 462             throw new IndexOutOfBoundsException("getSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 463         }
 464
 465         return (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 466     } //-- org.vamsas.client.objects.SequenceSetAnnotations getSequenceSetAnnotations(int)
 467
 468     /**
 469      * Method getSequenceSetAnnotations
 470      *
 471      *
 472      *
 473      * @return SequenceSetAnnotations
 474      */
 475     public org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations()
 476     {
 477         int size = _sequenceSetAnnotationsList.size();
 478         org.vamsas.client.objects.SequenceSetAnnotations[] mArray = new org.vamsas.client.objects.SequenceSetAnnotations[size];
 479         for (int index = 0; index < size; index++) {
 480             mArray[index] = (org.vamsas.client.objects.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
 481         }
 482         return mArray;
 483     } //-- org.vamsas.client.objects.SequenceSetAnnotations[] getSequenceSetAnnotations()
 484
 485     /**
 486      * Method getSequenceSetAnnotationsAsReference
 487      *
 488      * Returns a reference to 'sequenceSetAnnotations'. No type
 489      * checking is performed on any modications to the Vector.
 490      *
 491      * @return Vector
 492      * @return returns a reference to the Vector.
 493      */
 494     public java.util.Vector getSequenceSetAnnotationsAsReference()
 495     {
 496         return _sequenceSetAnnotationsList;
 497     } //-- java.util.Vector getSequenceSetAnnotationsAsReference()
 498
 499     /**
 500      * Method getSequenceSetAnnotationsCount
 501      *
 502      *
 503      *
 504      * @return int
 505      */
 506     public int getSequenceSetAnnotationsCount()
 507     {
 508         return _sequenceSetAnnotationsList.size();
 509     } //-- int getSequenceSetAnnotationsCount()
 510
 511     /**
 512      * Returns the value of field 'tree'.
 513      *
 514      * @return Tree
 515      * @return the value of field 'tree'.
 516      */
 517     public org.vamsas.client.objects.Tree getTree()
 518     {
 519         return this._tree;
 520     } //-- org.vamsas.client.objects.Tree getTree()
 521
 522     /**
 523      * Method hasAligned
 524      *
 525      *
 526      *
 527      * @return boolean
 528      */
 529     public boolean hasAligned()
 530     {
 531         return this._has_aligned;
 532     } //-- boolean hasAligned()
 533
 534     /**
 535      * Method isValid
 536      *
 537      *
 538      *
 539      * @return boolean
 540      */
 541     public boolean isValid()
 542     {
 543         try {
 544             validate();
 545         }
 546         catch (org.exolab.castor.xml.ValidationException vex) {
 547             return false;
 548         }
 549         return true;
 550     } //-- boolean isValid()
 551
 552     /**
 553      * Method marshal
 554      *
 555      *
 556      *
 557      * @param out
 558      */
 559     public void marshal(java.io.Writer out)
 560         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 561     {
 562
 563         Marshaller.marshal(this, out);
 564     } //-- void marshal(java.io.Writer)
 565
 566     /**
 567      * Method marshal
 568      *
 569      *
 570      *
 571      * @param handler
 572      */
 573     public void marshal(org.xml.sax.ContentHandler handler)
 574         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 575     {
 576
 577         Marshaller.marshal(this, handler);
 578     } //-- void marshal(org.xml.sax.ContentHandler)
 579
 580     /**
 581      * Method removeAlignment
 582      *
 583      *
 584      *
 585      * @param index
 586      * @return Alignment
 587      */
 588     public org.vamsas.client.objects.Alignment removeAlignment(int index)
 589     {
 590         java.lang.Object obj = _alignmentList.elementAt(index);
 591         _alignmentList.removeElementAt(index);
 592         return (org.vamsas.client.objects.Alignment) obj;
 593     } //-- org.vamsas.client.objects.Alignment removeAlignment(int)
 594
 595     /**
 596      * Method removeAllAlignment
 597      *
 598      */
 599     public void removeAllAlignment()
 600     {
 601         _alignmentList.removeAllElements();
 602     } //-- void removeAllAlignment()
 603
 604     /**
 605      * Method removeAllSequence
 606      *
 607      */
 608     public void removeAllSequence()
 609     {
 610         _sequenceList.removeAllElements();
 611     } //-- void removeAllSequence()
 612
 613     /**
 614      * Method removeAllSequenceSetAnnotations
 615      *
 616      */
 617     public void removeAllSequenceSetAnnotations()
 618     {
 619         _sequenceSetAnnotationsList.removeAllElements();
 620     } //-- void removeAllSequenceSetAnnotations()
 621
 622     /**
 623      * Method removeSequence
 624      *
 625      *
 626      *
 627      * @param index
 628      * @return Sequence
 629      */
 630     public org.vamsas.client.objects.Sequence removeSequence(int index)
 631     {
 632         java.lang.Object obj = _sequenceList.elementAt(index);
 633         _sequenceList.removeElementAt(index);
 634         return (org.vamsas.client.objects.Sequence) obj;
 635     } //-- org.vamsas.client.objects.Sequence removeSequence(int)
 636
 637     /**
 638      * Method removeSequenceSetAnnotations
 639      *
 640      *
 641      *
 642      * @param index
 643      * @return SequenceSetAnnotations
 644      */
 645     public org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
 646     {
 647         java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
 648         _sequenceSetAnnotationsList.removeElementAt(index);
 649         return (org.vamsas.client.objects.SequenceSetAnnotations) obj;
 650     } //-- org.vamsas.client.objects.SequenceSetAnnotations removeSequenceSetAnnotations(int)
 651
 652     /**
 653      * Sets the value of field 'aligned'.
 654      *
 655      * @param aligned the value of field 'aligned'.
 656      */
 657     public void setAligned(boolean aligned)
 658     {
 659         this._aligned = aligned;
 660         this._has_aligned = true;
 661     } //-- void setAligned(boolean)
 662
 663     /**
 664      * Method setAlignment
 665      *
 666      *
 667      *
 668      * @param index
 669      * @param vAlignment
 670      */
 671     public void setAlignment(int index, org.vamsas.client.objects.Alignment vAlignment)
 672         throws java.lang.IndexOutOfBoundsException
 673     {
 674         //-- check bounds for index
 675         if ((index < 0) || (index > _alignmentList.size())) {
 676             throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
 677         }
 678         _alignmentList.setElementAt(vAlignment, index);
 679     } //-- void setAlignment(int, org.vamsas.client.objects.Alignment)
 680
 681     /**
 682      * Method setAlignment
 683      *
 684      *
 685      *
 686      * @param alignmentArray
 687      */
 688     public void setAlignment(org.vamsas.client.objects.Alignment[] alignmentArray)
 689     {
 690         //-- copy array
 691         _alignmentList.removeAllElements();
 692         for (int i = 0; i < alignmentArray.length; i++) {
 693             _alignmentList.addElement(alignmentArray[i]);
 694         }
 695     } //-- void setAlignment(org.vamsas.client.objects.Alignment)
 696
 697     /**
 698      * Method setAlignment
 699      *
 700      * Sets the value of 'alignment' by copying the given Vector.
 701      *
 702      * @param alignmentVector the Vector to copy.
 703      */
 704     public void setAlignment(java.util.Vector alignmentVector)
 705     {
 706         //-- copy vector
 707         _alignmentList.removeAllElements();
 708         for (int i = 0; i < alignmentVector.size(); i++) {
 709             _alignmentList.addElement((org.vamsas.client.objects.Alignment)alignmentVector.elementAt(i));
 710         }
 711     } //-- void setAlignment(java.util.Vector)
 712
 713     /**
 714      * Method setAlignmentAsReference
 715      *
 716      * Sets the value of 'alignment' by setting it to the given
 717      * Vector. No type checking is performed.
 718      *
 719      * @param alignmentVector the Vector to copy.
 720      */
 721     public void setAlignmentAsReference(java.util.Vector alignmentVector)
 722     {
 723         _alignmentList = alignmentVector;
 724     } //-- void setAlignmentAsReference(java.util.Vector)
 725
 726     /**
 727      * Sets the value of field 'gapChar'.
 728      *
 729      * @param gapChar the value of field 'gapChar'.
 730      */
 731     public void setGapChar(java.lang.String gapChar)
 732     {
 733         this._gapChar = gapChar;
 734     } //-- void setGapChar(java.lang.String)
 735
 736     /**
 737      * Sets the value of field 'provenance'.
 738      *
 739      * @param provenance the value of field 'provenance'.
 740      */
 741     public void setProvenance(org.vamsas.client.objects.Provenance provenance)
 742     {
 743         this._provenance = provenance;
 744     } //-- void setProvenance(org.vamsas.client.objects.Provenance)
 745
 746     /**
 747      * Method setSequence
 748      *
 749      *
 750      *
 751      * @param index
 752      * @param vSequence
 753      */
 754     public void setSequence(int index, org.vamsas.client.objects.Sequence vSequence)
 755         throws java.lang.IndexOutOfBoundsException
 756     {
 757         //-- check bounds for index
 758         if ((index < 0) || (index > _sequenceList.size())) {
 759             throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
 760         }
 761         _sequenceList.setElementAt(vSequence, index);
 762     } //-- void setSequence(int, org.vamsas.client.objects.Sequence)
 763
 764     /**
 765      * Method setSequence
 766      *
 767      *
 768      *
 769      * @param sequenceArray
 770      */
 771     public void setSequence(org.vamsas.client.objects.Sequence[] sequenceArray)
 772     {
 773         //-- copy array
 774         _sequenceList.removeAllElements();
 775         for (int i = 0; i < sequenceArray.length; i++) {
 776             _sequenceList.addElement(sequenceArray[i]);
 777         }
 778     } //-- void setSequence(org.vamsas.client.objects.Sequence)
 779
 780     /**
 781      * Method setSequence
 782      *
 783      * Sets the value of 'sequence' by copying the given Vector.
 784      *
 785      * @param sequenceVector the Vector to copy.
 786      */
 787     public void setSequence(java.util.Vector sequenceVector)
 788     {
 789         //-- copy vector
 790         _sequenceList.removeAllElements();
 791         for (int i = 0; i < sequenceVector.size(); i++) {
 792             _sequenceList.addElement((org.vamsas.client.objects.Sequence)sequenceVector.elementAt(i));
 793         }
 794     } //-- void setSequence(java.util.Vector)
 795
 796     /**
 797      * Method setSequenceAsReference
 798      *
 799      * Sets the value of 'sequence' by setting it to the given
 800      * Vector. No type checking is performed.
 801      *
 802      * @param sequenceVector the Vector to copy.
 803      */
 804     public void setSequenceAsReference(java.util.Vector sequenceVector)
 805     {
 806         _sequenceList = sequenceVector;
 807     } //-- void setSequenceAsReference(java.util.Vector)
 808
 809     /**
 810      * Method setSequenceSetAnnotations
 811      *
 812      *
 813      *
 814      * @param index
 815      * @param vSequenceSetAnnotations
 816      */
 817     public void setSequenceSetAnnotations(int index, org.vamsas.client.objects.SequenceSetAnnotations vSequenceSetAnnotations)
 818         throws java.lang.IndexOutOfBoundsException
 819     {
 820         //-- check bounds for index
 821         if ((index < 0) || (index > _sequenceSetAnnotationsList.size())) {
 822             throw new IndexOutOfBoundsException("setSequenceSetAnnotations: Index value '"+index+"' not in range [0.."+_sequenceSetAnnotationsList.size()+ "]");
 823         }
 824         _sequenceSetAnnotationsList.setElementAt(vSequenceSetAnnotations, index);
 825     } //-- void setSequenceSetAnnotations(int, org.vamsas.client.objects.SequenceSetAnnotations)
 826
 827     /**
 828      * Method setSequenceSetAnnotations
 829      *
 830      *
 831      *
 832      * @param sequenceSetAnnotationsArray
 833      */
 834     public void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
 835     {
 836         //-- copy array
 837         _sequenceSetAnnotationsList.removeAllElements();
 838         for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
 839             _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
 840         }
 841     } //-- void setSequenceSetAnnotations(org.vamsas.client.objects.SequenceSetAnnotations)
 842
 843     /**
 844      * Method setSequenceSetAnnotations
 845      *
 846      * Sets the value of 'sequenceSetAnnotations' by copying the
 847      * given Vector.
 848      *
 849      * @param sequenceSetAnnotationsVector the Vector to copy.
 850      */
 851     public void setSequenceSetAnnotations(java.util.Vector sequenceSetAnnotationsVector)
 852     {
 853         //-- copy vector
 854         _sequenceSetAnnotationsList.removeAllElements();
 855         for (int i = 0; i < sequenceSetAnnotationsVector.size(); i++) {
 856             _sequenceSetAnnotationsList.addElement((org.vamsas.client.objects.SequenceSetAnnotations)sequenceSetAnnotationsVector.elementAt(i));
 857         }
 858     } //-- void setSequenceSetAnnotations(java.util.Vector)
 859
 860     /**
 861      * Method setSequenceSetAnnotationsAsReference
 862      *
 863      * Sets the value of 'sequenceSetAnnotations' by setting it to
 864      * the given Vector. No type checking is performed.
 865      *
 866      * @param sequenceSetAnnotationsVector the Vector to copy.
 867      */
 868     public void setSequenceSetAnnotationsAsReference(java.util.Vector sequenceSetAnnotationsVector)
 869     {
 870         _sequenceSetAnnotationsList = sequenceSetAnnotationsVector;
 871     } //-- void setSequenceSetAnnotationsAsReference(java.util.Vector)
 872
 873     /**
 874      * Sets the value of field 'tree'.
 875      *
 876      * @param tree the value of field 'tree'.
 877      */
 878     public void setTree(org.vamsas.client.objects.Tree tree)
 879     {
 880         this._tree = tree;
 881     } //-- void setTree(org.vamsas.client.objects.Tree)
 882
 883     /**
 884      * Method unmarshal
 885      *
 886      *
 887      *
 888      * @param reader
 889      * @return SequenceSet
 890      */
 891     public static org.vamsas.client.objects.SequenceSet unmarshal(java.io.Reader reader)
 892         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 893     {
 894         return (org.vamsas.client.objects.SequenceSet) Unmarshaller.unmarshal(org.vamsas.client.objects.SequenceSet.class, reader);
 895     } //-- org.vamsas.client.objects.SequenceSet unmarshal(java.io.Reader)
 896
 897     /**
 898      * Method validate
 899      *
 900      */
 901     public void validate()
 902         throws org.exolab.castor.xml.ValidationException
 903     {
 904         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 905         validator.validate(this);
 906     } //-- void validate()
 907
 908 }