src/org/vamsas/objects/core/Alignment.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 Alignment.
  28  *
  29  * @version $Revision$ $Date$
  30  */
  31 public class Alignment extends org.vamsas.client.Vobject
  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 _alignmentAnnotationsList
  62      */
  63     private java.util.Vector _alignmentAnnotationsList;
  64
  65     /**
  66      * Field _treeList
  67      */
  68     private java.util.Vector _treeList;
  69
  70     /**
  71      * Field _alignmentSequenceList
  72      */
  73     private java.util.Vector _alignmentSequenceList;
  74
  75     /**
  76      * Field _provenance
  77      */
  78     private org.vamsas.objects.core.Provenance _provenance;
  79
  80
  81       //----------------/
  82      //- Constructors -/
  83     //----------------/
  84
  85     public Alignment()
  86      {
  87         super();
  88         _alignmentAnnotationsList = new Vector();
  89         _treeList = new Vector();
  90         _alignmentSequenceList = new Vector();
  91     } //-- org.vamsas.objects.core.Alignment()
  92
  93
  94       //-----------/
  95      //- Methods -/
  96     //-----------/
  97
  98     /**
  99      * Method addAlignmentAnnotations
 100      *
 101      *
 102      *
 103      * @param vAlignmentAnnotations
 104      */
 105     public void addAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
 106         throws java.lang.IndexOutOfBoundsException
 107     {
 108         _alignmentAnnotationsList.addElement(vAlignmentAnnotations);
 109     } //-- void addAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
 110
 111     /**
 112      * Method addAlignmentAnnotations
 113      *
 114      *
 115      *
 116      * @param index
 117      * @param vAlignmentAnnotations
 118      */
 119     public void addAlignmentAnnotations(int index, org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
 120         throws java.lang.IndexOutOfBoundsException
 121     {
 122         _alignmentAnnotationsList.insertElementAt(vAlignmentAnnotations, index);
 123     } //-- void addAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations)
 124
 125     /**
 126      * Method addAlignmentSequence
 127      *
 128      *
 129      *
 130      * @param vAlignmentSequence
 131      */
 132     public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 133         throws java.lang.IndexOutOfBoundsException
 134     {
 135         _alignmentSequenceList.addElement(vAlignmentSequence);
 136     } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
 137
 138     /**
 139      * Method addAlignmentSequence
 140      *
 141      *
 142      *
 143      * @param index
 144      * @param vAlignmentSequence
 145      */
 146     public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 147         throws java.lang.IndexOutOfBoundsException
 148     {
 149         _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
 150     } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 151
 152     /**
 153      * Method addTree
 154      *
 155      *
 156      *
 157      * @param vTree
 158      */
 159     public void addTree(org.vamsas.objects.core.Tree vTree)
 160         throws java.lang.IndexOutOfBoundsException
 161     {
 162         _treeList.addElement(vTree);
 163     } //-- void addTree(org.vamsas.objects.core.Tree)
 164
 165     /**
 166      * Method addTree
 167      *
 168      *
 169      *
 170      * @param index
 171      * @param vTree
 172      */
 173     public void addTree(int index, org.vamsas.objects.core.Tree vTree)
 174         throws java.lang.IndexOutOfBoundsException
 175     {
 176         _treeList.insertElementAt(vTree, index);
 177     } //-- void addTree(int, org.vamsas.objects.core.Tree)
 178
 179     /**
 180      * Method deleteAligned
 181      *
 182      */
 183     public void deleteAligned()
 184     {
 185         this._has_aligned= false;
 186     } //-- void deleteAligned()
 187
 188     /**
 189      * Method enumerateAlignmentAnnotations
 190      *
 191      *
 192      *
 193      * @return Enumeration
 194      */
 195     public java.util.Enumeration enumerateAlignmentAnnotations()
 196     {
 197         return _alignmentAnnotationsList.elements();
 198     } //-- java.util.Enumeration enumerateAlignmentAnnotations()
 199
 200     /**
 201      * Method enumerateAlignmentSequence
 202      *
 203      *
 204      *
 205      * @return Enumeration
 206      */
 207     public java.util.Enumeration enumerateAlignmentSequence()
 208     {
 209         return _alignmentSequenceList.elements();
 210     } //-- java.util.Enumeration enumerateAlignmentSequence()
 211
 212     /**
 213      * Method enumerateTree
 214      *
 215      *
 216      *
 217      * @return Enumeration
 218      */
 219     public java.util.Enumeration enumerateTree()
 220     {
 221         return _treeList.elements();
 222     } //-- java.util.Enumeration enumerateTree()
 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 Alignment) {
 239
 240             Alignment temp = (Alignment)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._id != null) {
 253                 if (temp._id == null) return false;
 254                 else if (!(this._id.equals(temp._id)))
 255                     return false;
 256             }
 257             else if (temp._id != null)
 258                 return false;
 259             if (this._alignmentAnnotationsList != null) {
 260                 if (temp._alignmentAnnotationsList == null) return false;
 261                 else if (!(this._alignmentAnnotationsList.equals(temp._alignmentAnnotationsList)))
 262                     return false;
 263             }
 264             else if (temp._alignmentAnnotationsList != null)
 265                 return false;
 266             if (this._treeList != null) {
 267                 if (temp._treeList == null) return false;
 268                 else if (!(this._treeList.equals(temp._treeList)))
 269                     return false;
 270             }
 271             else if (temp._treeList != null)
 272                 return false;
 273             if (this._alignmentSequenceList != null) {
 274                 if (temp._alignmentSequenceList == null) return false;
 275                 else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList)))
 276                     return false;
 277             }
 278             else if (temp._alignmentSequenceList != 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 getAlignmentAnnotations
 305      *
 306      *
 307      *
 308      * @param index
 309      * @return AlignmentAnnotations
 310      */
 311     public org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations(int index)
 312         throws java.lang.IndexOutOfBoundsException
 313     {
 314         //-- check bounds for index
 315         if ((index < 0) || (index > _alignmentAnnotationsList.size())) {
 316             throw new IndexOutOfBoundsException("getAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");
 317         }
 318
 319         return (org.vamsas.objects.core.AlignmentAnnotations) _alignmentAnnotationsList.elementAt(index);
 320     } //-- org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations(int)
 321
 322     /**
 323      * Method getAlignmentAnnotations
 324      *
 325      *
 326      *
 327      * @return AlignmentAnnotations
 328      */
 329     public org.vamsas.objects.core.AlignmentAnnotations[] getAlignmentAnnotations()
 330     {
 331         int size = _alignmentAnnotationsList.size();
 332         org.vamsas.objects.core.AlignmentAnnotations[] mArray = new org.vamsas.objects.core.AlignmentAnnotations[size];
 333         for (int index = 0; index < size; index++) {
 334             mArray[index] = (org.vamsas.objects.core.AlignmentAnnotations) _alignmentAnnotationsList.elementAt(index);
 335         }
 336         return mArray;
 337     } //-- org.vamsas.objects.core.AlignmentAnnotations[] getAlignmentAnnotations()
 338
 339     /**
 340      * Method getAlignmentAnnotationsCount
 341      *
 342      *
 343      *
 344      * @return int
 345      */
 346     public int getAlignmentAnnotationsCount()
 347     {
 348         return _alignmentAnnotationsList.size();
 349     } //-- int getAlignmentAnnotationsCount()
 350
 351     /**
 352      * Method getAlignmentSequence
 353      *
 354      *
 355      *
 356      * @param index
 357      * @return AlignmentSequence
 358      */
 359     public org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index)
 360         throws java.lang.IndexOutOfBoundsException
 361     {
 362         //-- check bounds for index
 363         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 364             throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 365         }
 366
 367         return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 368     } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
 369
 370     /**
 371      * Method getAlignmentSequence
 372      *
 373      *
 374      *
 375      * @return AlignmentSequence
 376      */
 377     public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 378     {
 379         int size = _alignmentSequenceList.size();
 380         org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size];
 381         for (int index = 0; index < size; index++) {
 382             mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 383         }
 384         return mArray;
 385     } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 386
 387     /**
 388      * Method getAlignmentSequenceCount
 389      *
 390      *
 391      *
 392      * @return int
 393      */
 394     public int getAlignmentSequenceCount()
 395     {
 396         return _alignmentSequenceList.size();
 397     } //-- int getAlignmentSequenceCount()
 398
 399     /**
 400      * Returns the value of field 'gapChar'.
 401      *
 402      * @return String
 403      * @return the value of field 'gapChar'.
 404      */
 405     public java.lang.String getGapChar()
 406     {
 407         return this._gapChar;
 408     } //-- java.lang.String getGapChar()
 409
 410     /**
 411      * Returns the value of field 'id'.
 412      *
 413      * @return String
 414      * @return the value of field 'id'.
 415      */
 416     public java.lang.String getId()
 417     {
 418         return this._id;
 419     } //-- java.lang.String getId()
 420
 421     /**
 422      * Returns the value of field 'provenance'.
 423      *
 424      * @return Provenance
 425      * @return the value of field 'provenance'.
 426      */
 427     public org.vamsas.objects.core.Provenance getProvenance()
 428     {
 429         return this._provenance;
 430     } //-- org.vamsas.objects.core.Provenance getProvenance()
 431
 432     /**
 433      * Method getTree
 434      *
 435      *
 436      *
 437      * @param index
 438      * @return Tree
 439      */
 440     public org.vamsas.objects.core.Tree getTree(int index)
 441         throws java.lang.IndexOutOfBoundsException
 442     {
 443         //-- check bounds for index
 444         if ((index < 0) || (index > _treeList.size())) {
 445             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 446         }
 447
 448         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 449     } //-- org.vamsas.objects.core.Tree getTree(int)
 450
 451     /**
 452      * Method getTree
 453      *
 454      *
 455      *
 456      * @return Tree
 457      */
 458     public org.vamsas.objects.core.Tree[] getTree()
 459     {
 460         int size = _treeList.size();
 461         org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
 462         for (int index = 0; index < size; index++) {
 463             mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 464         }
 465         return mArray;
 466     } //-- org.vamsas.objects.core.Tree[] getTree()
 467
 468     /**
 469      * Method getTreeCount
 470      *
 471      *
 472      *
 473      * @return int
 474      */
 475     public int getTreeCount()
 476     {
 477         return _treeList.size();
 478     } //-- int getTreeCount()
 479
 480     /**
 481      * Method hasAligned
 482      *
 483      *
 484      *
 485      * @return boolean
 486      */
 487     public boolean hasAligned()
 488     {
 489         return this._has_aligned;
 490     } //-- boolean hasAligned()
 491
 492     /**
 493      * Method isValid
 494      *
 495      *
 496      *
 497      * @return boolean
 498      */
 499     public boolean isValid()
 500     {
 501         try {
 502             validate();
 503         }
 504         catch (org.exolab.castor.xml.ValidationException vex) {
 505             return false;
 506         }
 507         return true;
 508     } //-- boolean isValid()
 509
 510     /**
 511      * Method marshal
 512      *
 513      *
 514      *
 515      * @param out
 516      */
 517     public void marshal(java.io.Writer out)
 518         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 519     {
 520
 521         Marshaller.marshal(this, out);
 522     } //-- void marshal(java.io.Writer)
 523
 524     /**
 525      * Method marshal
 526      *
 527      *
 528      *
 529      * @param handler
 530      */
 531     public void marshal(org.xml.sax.ContentHandler handler)
 532         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 533     {
 534
 535         Marshaller.marshal(this, handler);
 536     } //-- void marshal(org.xml.sax.ContentHandler)
 537
 538     /**
 539      * Method removeAlignmentAnnotations
 540      *
 541      *
 542      *
 543      * @param index
 544      * @return AlignmentAnnotations
 545      */
 546     public org.vamsas.objects.core.AlignmentAnnotations removeAlignmentAnnotations(int index)
 547     {
 548         java.lang.Object obj = _alignmentAnnotationsList.elementAt(index);
 549         _alignmentAnnotationsList.removeElementAt(index);
 550         return (org.vamsas.objects.core.AlignmentAnnotations) obj;
 551     } //-- org.vamsas.objects.core.AlignmentAnnotations removeAlignmentAnnotations(int)
 552
 553     /**
 554      * Method removeAlignmentSequence
 555      *
 556      *
 557      *
 558      * @param index
 559      * @return AlignmentSequence
 560      */
 561     public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
 562     {
 563         java.lang.Object obj = _alignmentSequenceList.elementAt(index);
 564         _alignmentSequenceList.removeElementAt(index);
 565         return (org.vamsas.objects.core.AlignmentSequence) obj;
 566     } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
 567
 568     /**
 569      * Method removeAllAlignmentAnnotations
 570      *
 571      */
 572     public void removeAllAlignmentAnnotations()
 573     {
 574         _alignmentAnnotationsList.removeAllElements();
 575     } //-- void removeAllAlignmentAnnotations()
 576
 577     /**
 578      * Method removeAllAlignmentSequence
 579      *
 580      */
 581     public void removeAllAlignmentSequence()
 582     {
 583         _alignmentSequenceList.removeAllElements();
 584     } //-- void removeAllAlignmentSequence()
 585
 586     /**
 587      * Method removeAllTree
 588      *
 589      */
 590     public void removeAllTree()
 591     {
 592         _treeList.removeAllElements();
 593     } //-- void removeAllTree()
 594
 595     /**
 596      * Method removeTree
 597      *
 598      *
 599      *
 600      * @param index
 601      * @return Tree
 602      */
 603     public org.vamsas.objects.core.Tree removeTree(int index)
 604     {
 605         java.lang.Object obj = _treeList.elementAt(index);
 606         _treeList.removeElementAt(index);
 607         return (org.vamsas.objects.core.Tree) obj;
 608     } //-- org.vamsas.objects.core.Tree removeTree(int)
 609
 610     /**
 611      * Sets the value of field 'aligned'.
 612      *
 613      * @param aligned the value of field 'aligned'.
 614      */
 615     public void setAligned(boolean aligned)
 616     {
 617         this._aligned = aligned;
 618         this._has_aligned = true;
 619     } //-- void setAligned(boolean)
 620
 621     /**
 622      * Method setAlignmentAnnotations
 623      *
 624      *
 625      *
 626      * @param index
 627      * @param vAlignmentAnnotations
 628      */
 629     public void setAlignmentAnnotations(int index, org.vamsas.objects.core.AlignmentAnnotations vAlignmentAnnotations)
 630         throws java.lang.IndexOutOfBoundsException
 631     {
 632         //-- check bounds for index
 633         if ((index < 0) || (index > _alignmentAnnotationsList.size())) {
 634             throw new IndexOutOfBoundsException("setAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");
 635         }
 636         _alignmentAnnotationsList.setElementAt(vAlignmentAnnotations, index);
 637     } //-- void setAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations)
 638
 639     /**
 640      * Method setAlignmentAnnotations
 641      *
 642      *
 643      *
 644      * @param alignmentAnnotationsArray
 645      */
 646     public void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations[] alignmentAnnotationsArray)
 647     {
 648         //-- copy array
 649         _alignmentAnnotationsList.removeAllElements();
 650         for (int i = 0; i < alignmentAnnotationsArray.length; i++) {
 651             _alignmentAnnotationsList.addElement(alignmentAnnotationsArray[i]);
 652         }
 653     } //-- void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
 654
 655     /**
 656      * Method setAlignmentSequence
 657      *
 658      *
 659      *
 660      * @param index
 661      * @param vAlignmentSequence
 662      */
 663     public void setAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 664         throws java.lang.IndexOutOfBoundsException
 665     {
 666         //-- check bounds for index
 667         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 668             throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 669         }
 670         _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
 671     } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 672
 673     /**
 674      * Method setAlignmentSequence
 675      *
 676      *
 677      *
 678      * @param alignmentSequenceArray
 679      */
 680     public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
 681     {
 682         //-- copy array
 683         _alignmentSequenceList.removeAllElements();
 684         for (int i = 0; i < alignmentSequenceArray.length; i++) {
 685             _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
 686         }
 687     } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
 688
 689     /**
 690      * Sets the value of field 'gapChar'.
 691      *
 692      * @param gapChar the value of field 'gapChar'.
 693      */
 694     public void setGapChar(java.lang.String gapChar)
 695     {
 696         this._gapChar = gapChar;
 697     } //-- void setGapChar(java.lang.String)
 698
 699     /**
 700      * Sets the value of field 'id'.
 701      *
 702      * @param id the value of field 'id'.
 703      */
 704     public void setId(java.lang.String id)
 705     {
 706         this._id = id;
 707     } //-- void setId(java.lang.String)
 708
 709     /**
 710      * Sets the value of field 'provenance'.
 711      *
 712      * @param provenance the value of field 'provenance'.
 713      */
 714     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 715     {
 716         this._provenance = provenance;
 717     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 718
 719     /**
 720      * Method setTree
 721      *
 722      *
 723      *
 724      * @param index
 725      * @param vTree
 726      */
 727     public void setTree(int index, org.vamsas.objects.core.Tree vTree)
 728         throws java.lang.IndexOutOfBoundsException
 729     {
 730         //-- check bounds for index
 731         if ((index < 0) || (index > _treeList.size())) {
 732             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 733         }
 734         _treeList.setElementAt(vTree, index);
 735     } //-- void setTree(int, org.vamsas.objects.core.Tree)
 736
 737     /**
 738      * Method setTree
 739      *
 740      *
 741      *
 742      * @param treeArray
 743      */
 744     public void setTree(org.vamsas.objects.core.Tree[] treeArray)
 745     {
 746         //-- copy array
 747         _treeList.removeAllElements();
 748         for (int i = 0; i < treeArray.length; i++) {
 749             _treeList.addElement(treeArray[i]);
 750         }
 751     } //-- void setTree(org.vamsas.objects.core.Tree)
 752
 753     /**
 754      * Method unmarshal
 755      *
 756      *
 757      *
 758      * @param reader
 759      * @return Alignment
 760      */
 761     public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
 762         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 763     {
 764         return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);
 765     } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader)
 766
 767     /**
 768      * Method validate
 769      *
 770      */
 771     public void validate()
 772         throws org.exolab.castor.xml.ValidationException
 773     {
 774         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 775         validator.validate(this);
 776     } //-- void validate()
 777
 778 }