src/uk/ac/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:Alignment.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 Alignment.
  28  *
  29  * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  30  */
  31 public class Alignment extends uk.ac.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      * Primary Key for vamsas object referencing
  57      *
  58      */
  59     private java.lang.String _id;
  60
  61     /**
  62      * Field _modifiable
  63      */
  64     private java.lang.String _modifiable;
  65
  66     /**
  67      * This is annotation over the coordinate frame
  68      *  defined by all the columns in the alignment.
  69      *
  70      */
  71     private java.util.Vector _alignmentAnnotationList;
  72
  73     /**
  74      * Field _treeList
  75      */
  76     private java.util.Vector _treeList;
  77
  78     /**
  79      * Field _alignmentSequenceList
  80      */
  81     private java.util.Vector _alignmentSequenceList;
  82
  83     /**
  84      * typical properties may be additional
  85      *  alignment score objects
  86      */
  87     private java.util.Vector _propertyList;
  88
  89     /**
  90      * Field _provenance
  91      */
  92     private uk.ac.vamsas.objects.core.Provenance _provenance;
  93
  94
  95       //----------------/
  96      //- Constructors -/
  97     //----------------/
  98
  99     public Alignment()
 100      {
 101         super();
 102         _alignmentAnnotationList = new Vector();
 103         _treeList = new Vector();
 104         _alignmentSequenceList = new Vector();
 105         _propertyList = new Vector();
 106     } //-- uk.ac.vamsas.objects.core.Alignment()
 107
 108
 109       //-----------/
 110      //- Methods -/
 111     //-----------/
 112
 113     /**
 114      * Method addAlignmentAnnotation
 115      *
 116      *
 117      *
 118      * @param vAlignmentAnnotation
 119      */
 120     public void addAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
 121         throws java.lang.IndexOutOfBoundsException
 122     {
 123         _alignmentAnnotationList.addElement(vAlignmentAnnotation);
 124     } //-- void addAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation)
 125
 126     /**
 127      * Method addAlignmentAnnotation
 128      *
 129      *
 130      *
 131      * @param index
 132      * @param vAlignmentAnnotation
 133      */
 134     public void addAlignmentAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
 135         throws java.lang.IndexOutOfBoundsException
 136     {
 137         _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index);
 138     } //-- void addAlignmentAnnotation(int, uk.ac.vamsas.objects.core.AlignmentAnnotation)
 139
 140     /**
 141      * Method addAlignmentSequence
 142      *
 143      *
 144      *
 145      * @param vAlignmentSequence
 146      */
 147     public void addAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 148         throws java.lang.IndexOutOfBoundsException
 149     {
 150         _alignmentSequenceList.addElement(vAlignmentSequence);
 151     } //-- void addAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence)
 152
 153     /**
 154      * Method addAlignmentSequence
 155      *
 156      *
 157      *
 158      * @param index
 159      * @param vAlignmentSequence
 160      */
 161     public void addAlignmentSequence(int index, uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 162         throws java.lang.IndexOutOfBoundsException
 163     {
 164         _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
 165     } //-- void addAlignmentSequence(int, uk.ac.vamsas.objects.core.AlignmentSequence)
 166
 167     /**
 168      * Method addProperty
 169      *
 170      *
 171      *
 172      * @param vProperty
 173      */
 174     public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
 175         throws java.lang.IndexOutOfBoundsException
 176     {
 177         _propertyList.addElement(vProperty);
 178     } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
 179
 180     /**
 181      * Method addProperty
 182      *
 183      *
 184      *
 185      * @param index
 186      * @param vProperty
 187      */
 188     public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
 189         throws java.lang.IndexOutOfBoundsException
 190     {
 191         _propertyList.insertElementAt(vProperty, index);
 192     } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property)
 193
 194     /**
 195      * Method addTree
 196      *
 197      *
 198      *
 199      * @param vTree
 200      */
 201     public void addTree(uk.ac.vamsas.objects.core.Tree vTree)
 202         throws java.lang.IndexOutOfBoundsException
 203     {
 204         _treeList.addElement(vTree);
 205     } //-- void addTree(uk.ac.vamsas.objects.core.Tree)
 206
 207     /**
 208      * Method addTree
 209      *
 210      *
 211      *
 212      * @param index
 213      * @param vTree
 214      */
 215     public void addTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
 216         throws java.lang.IndexOutOfBoundsException
 217     {
 218         _treeList.insertElementAt(vTree, index);
 219     } //-- void addTree(int, uk.ac.vamsas.objects.core.Tree)
 220
 221     /**
 222      * Method deleteAligned
 223      *
 224      */
 225     public void deleteAligned()
 226     {
 227         this._has_aligned= false;
 228     } //-- void deleteAligned()
 229
 230     /**
 231      * Method enumerateAlignmentAnnotation
 232      *
 233      *
 234      *
 235      * @return Enumeration
 236      */
 237     public java.util.Enumeration enumerateAlignmentAnnotation()
 238     {
 239         return _alignmentAnnotationList.elements();
 240     } //-- java.util.Enumeration enumerateAlignmentAnnotation()
 241
 242     /**
 243      * Method enumerateAlignmentSequence
 244      *
 245      *
 246      *
 247      * @return Enumeration
 248      */
 249     public java.util.Enumeration enumerateAlignmentSequence()
 250     {
 251         return _alignmentSequenceList.elements();
 252     } //-- java.util.Enumeration enumerateAlignmentSequence()
 253
 254     /**
 255      * Method enumerateProperty
 256      *
 257      *
 258      *
 259      * @return Enumeration
 260      */
 261     public java.util.Enumeration enumerateProperty()
 262     {
 263         return _propertyList.elements();
 264     } //-- java.util.Enumeration enumerateProperty()
 265
 266     /**
 267      * Method enumerateTree
 268      *
 269      *
 270      *
 271      * @return Enumeration
 272      */
 273     public java.util.Enumeration enumerateTree()
 274     {
 275         return _treeList.elements();
 276     } //-- java.util.Enumeration enumerateTree()
 277
 278     /**
 279      * Note: hashCode() has not been overriden
 280      *
 281      * @param obj
 282      * @return boolean
 283      */
 284     public boolean equals(java.lang.Object obj)
 285     {
 286         if ( this == obj )
 287             return true;
 288
 289         if (super.equals(obj)==false)
 290             return false;
 291
 292         if (obj instanceof Alignment) {
 293
 294             Alignment temp = (Alignment)obj;
 295             if (this._gapChar != null) {
 296                 if (temp._gapChar == null) return false;
 297                 else if (!(this._gapChar.equals(temp._gapChar)))
 298                     return false;
 299             }
 300             else if (temp._gapChar != null)
 301                 return false;
 302             if (this._aligned != temp._aligned)
 303                 return false;
 304             if (this._has_aligned != temp._has_aligned)
 305                 return false;
 306             if (this._id != null) {
 307                 if (temp._id == null) return false;
 308                 else if (!(this._id.equals(temp._id)))
 309                     return false;
 310             }
 311             else if (temp._id != null)
 312                 return false;
 313             if (this._modifiable != null) {
 314                 if (temp._modifiable == null) return false;
 315                 else if (!(this._modifiable.equals(temp._modifiable)))
 316                     return false;
 317             }
 318             else if (temp._modifiable != null)
 319                 return false;
 320             if (this._alignmentAnnotationList != null) {
 321                 if (temp._alignmentAnnotationList == null) return false;
 322                 else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList)))
 323                     return false;
 324             }
 325             else if (temp._alignmentAnnotationList != null)
 326                 return false;
 327             if (this._treeList != null) {
 328                 if (temp._treeList == null) return false;
 329                 else if (!(this._treeList.equals(temp._treeList)))
 330                     return false;
 331             }
 332             else if (temp._treeList != null)
 333                 return false;
 334             if (this._alignmentSequenceList != null) {
 335                 if (temp._alignmentSequenceList == null) return false;
 336                 else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList)))
 337                     return false;
 338             }
 339             else if (temp._alignmentSequenceList != null)
 340                 return false;
 341             if (this._propertyList != null) {
 342                 if (temp._propertyList == null) return false;
 343                 else if (!(this._propertyList.equals(temp._propertyList)))
 344                     return false;
 345             }
 346             else if (temp._propertyList != null)
 347                 return false;
 348             if (this._provenance != null) {
 349                 if (temp._provenance == null) return false;
 350                 else if (!(this._provenance.equals(temp._provenance)))
 351                     return false;
 352             }
 353             else if (temp._provenance != null)
 354                 return false;
 355             return true;
 356         }
 357         return false;
 358     } //-- boolean equals(java.lang.Object)
 359
 360     /**
 361      * Returns the value of field 'aligned'.
 362      *
 363      * @return boolean
 364      * @return the value of field 'aligned'.
 365      */
 366     public boolean getAligned()
 367     {
 368         return this._aligned;
 369     } //-- boolean getAligned()
 370
 371     /**
 372      * Method getAlignmentAnnotation
 373      *
 374      *
 375      *
 376      * @param index
 377      * @return AlignmentAnnotation
 378      */
 379     public uk.ac.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index)
 380         throws java.lang.IndexOutOfBoundsException
 381     {
 382         //-- check bounds for index
 383         if ((index < 0) || (index > _alignmentAnnotationList.size())) {
 384             throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
 385         }
 386
 387         return (uk.ac.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
 388     } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int)
 389
 390     /**
 391      * Method getAlignmentAnnotation
 392      *
 393      *
 394      *
 395      * @return AlignmentAnnotation
 396      */
 397     public uk.ac.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
 398     {
 399         int size = _alignmentAnnotationList.size();
 400         uk.ac.vamsas.objects.core.AlignmentAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentAnnotation[size];
 401         for (int index = 0; index < size; index++) {
 402             mArray[index] = (uk.ac.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
 403         }
 404         return mArray;
 405     } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
 406
 407     /**
 408      * Method getAlignmentAnnotationCount
 409      *
 410      *
 411      *
 412      * @return int
 413      */
 414     public int getAlignmentAnnotationCount()
 415     {
 416         return _alignmentAnnotationList.size();
 417     } //-- int getAlignmentAnnotationCount()
 418
 419     /**
 420      * Method getAlignmentSequence
 421      *
 422      *
 423      *
 424      * @param index
 425      * @return AlignmentSequence
 426      */
 427     public uk.ac.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index)
 428         throws java.lang.IndexOutOfBoundsException
 429     {
 430         //-- check bounds for index
 431         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 432             throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 433         }
 434
 435         return (uk.ac.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 436     } //-- uk.ac.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
 437
 438     /**
 439      * Method getAlignmentSequence
 440      *
 441      *
 442      *
 443      * @return AlignmentSequence
 444      */
 445     public uk.ac.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 446     {
 447         int size = _alignmentSequenceList.size();
 448         uk.ac.vamsas.objects.core.AlignmentSequence[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequence[size];
 449         for (int index = 0; index < size; index++) {
 450             mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 451         }
 452         return mArray;
 453     } //-- uk.ac.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 454
 455     /**
 456      * Method getAlignmentSequenceCount
 457      *
 458      *
 459      *
 460      * @return int
 461      */
 462     public int getAlignmentSequenceCount()
 463     {
 464         return _alignmentSequenceList.size();
 465     } //-- int getAlignmentSequenceCount()
 466
 467     /**
 468      * Returns the value of field 'gapChar'.
 469      *
 470      * @return String
 471      * @return the value of field 'gapChar'.
 472      */
 473     public java.lang.String getGapChar()
 474     {
 475         return this._gapChar;
 476     } //-- java.lang.String getGapChar()
 477
 478     /**
 479      * Returns the value of field 'id'. The field 'id' has the
 480      * following description: Primary Key for vamsas object
 481      * referencing
 482      *
 483      *
 484      * @return String
 485      * @return the value of field 'id'.
 486      */
 487     public java.lang.String getId()
 488     {
 489         return this._id;
 490     } //-- java.lang.String getId()
 491
 492     /**
 493      * Returns the value of field 'modifiable'.
 494      *
 495      * @return String
 496      * @return the value of field 'modifiable'.
 497      */
 498     public java.lang.String getModifiable()
 499     {
 500         return this._modifiable;
 501     } //-- java.lang.String getModifiable()
 502
 503     /**
 504      * Method getProperty
 505      *
 506      *
 507      *
 508      * @param index
 509      * @return Property
 510      */
 511     public uk.ac.vamsas.objects.core.Property getProperty(int index)
 512         throws java.lang.IndexOutOfBoundsException
 513     {
 514         //-- check bounds for index
 515         if ((index < 0) || (index > _propertyList.size())) {
 516             throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
 517         }
 518
 519         return (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
 520     } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
 521
 522     /**
 523      * Method getProperty
 524      *
 525      *
 526      *
 527      * @return Property
 528      */
 529     public uk.ac.vamsas.objects.core.Property[] getProperty()
 530     {
 531         int size = _propertyList.size();
 532         uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
 533         for (int index = 0; index < size; index++) {
 534             mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
 535         }
 536         return mArray;
 537     } //-- uk.ac.vamsas.objects.core.Property[] getProperty()
 538
 539     /**
 540      * Method getPropertyCount
 541      *
 542      *
 543      *
 544      * @return int
 545      */
 546     public int getPropertyCount()
 547     {
 548         return _propertyList.size();
 549     } //-- int getPropertyCount()
 550
 551     /**
 552      * Returns the value of field 'provenance'.
 553      *
 554      * @return Provenance
 555      * @return the value of field 'provenance'.
 556      */
 557     public uk.ac.vamsas.objects.core.Provenance getProvenance()
 558     {
 559         return this._provenance;
 560     } //-- uk.ac.vamsas.objects.core.Provenance getProvenance()
 561
 562     /**
 563      * Method getTree
 564      *
 565      *
 566      *
 567      * @param index
 568      * @return Tree
 569      */
 570     public uk.ac.vamsas.objects.core.Tree getTree(int index)
 571         throws java.lang.IndexOutOfBoundsException
 572     {
 573         //-- check bounds for index
 574         if ((index < 0) || (index > _treeList.size())) {
 575             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 576         }
 577
 578         return (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
 579     } //-- uk.ac.vamsas.objects.core.Tree getTree(int)
 580
 581     /**
 582      * Method getTree
 583      *
 584      *
 585      *
 586      * @return Tree
 587      */
 588     public uk.ac.vamsas.objects.core.Tree[] getTree()
 589     {
 590         int size = _treeList.size();
 591         uk.ac.vamsas.objects.core.Tree[] mArray = new uk.ac.vamsas.objects.core.Tree[size];
 592         for (int index = 0; index < size; index++) {
 593             mArray[index] = (uk.ac.vamsas.objects.core.Tree) _treeList.elementAt(index);
 594         }
 595         return mArray;
 596     } //-- uk.ac.vamsas.objects.core.Tree[] getTree()
 597
 598     /**
 599      * Method getTreeCount
 600      *
 601      *
 602      *
 603      * @return int
 604      */
 605     public int getTreeCount()
 606     {
 607         return _treeList.size();
 608     } //-- int getTreeCount()
 609
 610     /**
 611      * Method hasAligned
 612      *
 613      *
 614      *
 615      * @return boolean
 616      */
 617     public boolean hasAligned()
 618     {
 619         return this._has_aligned;
 620     } //-- boolean hasAligned()
 621
 622     /**
 623      * Method isValid
 624      *
 625      *
 626      *
 627      * @return boolean
 628      */
 629     public boolean isValid()
 630     {
 631         try {
 632             validate();
 633         }
 634         catch (org.exolab.castor.xml.ValidationException vex) {
 635             return false;
 636         }
 637         return true;
 638     } //-- boolean isValid()
 639
 640     /**
 641      * Method marshal
 642      *
 643      *
 644      *
 645      * @param out
 646      */
 647     public void marshal(java.io.Writer out)
 648         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 649     {
 650
 651         Marshaller.marshal(this, out);
 652     } //-- void marshal(java.io.Writer)
 653
 654     /**
 655      * Method marshal
 656      *
 657      *
 658      *
 659      * @param handler
 660      */
 661     public void marshal(org.xml.sax.ContentHandler handler)
 662         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 663     {
 664
 665         Marshaller.marshal(this, handler);
 666     } //-- void marshal(org.xml.sax.ContentHandler)
 667
 668     /**
 669      * Method removeAlignmentAnnotation
 670      *
 671      *
 672      *
 673      * @param index
 674      * @return AlignmentAnnotation
 675      */
 676     public uk.ac.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index)
 677     {
 678         java.lang.Object obj = _alignmentAnnotationList.elementAt(index);
 679         _alignmentAnnotationList.removeElementAt(index);
 680         return (uk.ac.vamsas.objects.core.AlignmentAnnotation) obj;
 681     } //-- uk.ac.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int)
 682
 683     /**
 684      * Method removeAlignmentSequence
 685      *
 686      *
 687      *
 688      * @param index
 689      * @return AlignmentSequence
 690      */
 691     public uk.ac.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
 692     {
 693         java.lang.Object obj = _alignmentSequenceList.elementAt(index);
 694         _alignmentSequenceList.removeElementAt(index);
 695         return (uk.ac.vamsas.objects.core.AlignmentSequence) obj;
 696     } //-- uk.ac.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
 697
 698     /**
 699      * Method removeAllAlignmentAnnotation
 700      *
 701      */
 702     public void removeAllAlignmentAnnotation()
 703     {
 704         _alignmentAnnotationList.removeAllElements();
 705     } //-- void removeAllAlignmentAnnotation()
 706
 707     /**
 708      * Method removeAllAlignmentSequence
 709      *
 710      */
 711     public void removeAllAlignmentSequence()
 712     {
 713         _alignmentSequenceList.removeAllElements();
 714     } //-- void removeAllAlignmentSequence()
 715
 716     /**
 717      * Method removeAllProperty
 718      *
 719      */
 720     public void removeAllProperty()
 721     {
 722         _propertyList.removeAllElements();
 723     } //-- void removeAllProperty()
 724
 725     /**
 726      * Method removeAllTree
 727      *
 728      */
 729     public void removeAllTree()
 730     {
 731         _treeList.removeAllElements();
 732     } //-- void removeAllTree()
 733
 734     /**
 735      * Method removeProperty
 736      *
 737      *
 738      *
 739      * @param index
 740      * @return Property
 741      */
 742     public uk.ac.vamsas.objects.core.Property removeProperty(int index)
 743     {
 744         java.lang.Object obj = _propertyList.elementAt(index);
 745         _propertyList.removeElementAt(index);
 746         return (uk.ac.vamsas.objects.core.Property) obj;
 747     } //-- uk.ac.vamsas.objects.core.Property removeProperty(int)
 748
 749     /**
 750      * Method removeTree
 751      *
 752      *
 753      *
 754      * @param index
 755      * @return Tree
 756      */
 757     public uk.ac.vamsas.objects.core.Tree removeTree(int index)
 758     {
 759         java.lang.Object obj = _treeList.elementAt(index);
 760         _treeList.removeElementAt(index);
 761         return (uk.ac.vamsas.objects.core.Tree) obj;
 762     } //-- uk.ac.vamsas.objects.core.Tree removeTree(int)
 763
 764     /**
 765      * Sets the value of field 'aligned'.
 766      *
 767      * @param aligned the value of field 'aligned'.
 768      */
 769     public void setAligned(boolean aligned)
 770     {
 771         this._aligned = aligned;
 772         this._has_aligned = true;
 773     } //-- void setAligned(boolean)
 774
 775     /**
 776      * Method setAlignmentAnnotation
 777      *
 778      *
 779      *
 780      * @param index
 781      * @param vAlignmentAnnotation
 782      */
 783     public void setAlignmentAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
 784         throws java.lang.IndexOutOfBoundsException
 785     {
 786         //-- check bounds for index
 787         if ((index < 0) || (index > _alignmentAnnotationList.size())) {
 788             throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
 789         }
 790         _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index);
 791     } //-- void setAlignmentAnnotation(int, uk.ac.vamsas.objects.core.AlignmentAnnotation)
 792
 793     /**
 794      * Method setAlignmentAnnotation
 795      *
 796      *
 797      *
 798      * @param alignmentAnnotationArray
 799      */
 800     public void setAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray)
 801     {
 802         //-- copy array
 803         _alignmentAnnotationList.removeAllElements();
 804         for (int i = 0; i < alignmentAnnotationArray.length; i++) {
 805             _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]);
 806         }
 807     } //-- void setAlignmentAnnotation(uk.ac.vamsas.objects.core.AlignmentAnnotation)
 808
 809     /**
 810      * Method setAlignmentSequence
 811      *
 812      *
 813      *
 814      * @param index
 815      * @param vAlignmentSequence
 816      */
 817     public void setAlignmentSequence(int index, uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 818         throws java.lang.IndexOutOfBoundsException
 819     {
 820         //-- check bounds for index
 821         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 822             throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 823         }
 824         _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
 825     } //-- void setAlignmentSequence(int, uk.ac.vamsas.objects.core.AlignmentSequence)
 826
 827     /**
 828      * Method setAlignmentSequence
 829      *
 830      *
 831      *
 832      * @param alignmentSequenceArray
 833      */
 834     public void setAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
 835     {
 836         //-- copy array
 837         _alignmentSequenceList.removeAllElements();
 838         for (int i = 0; i < alignmentSequenceArray.length; i++) {
 839             _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
 840         }
 841     } //-- void setAlignmentSequence(uk.ac.vamsas.objects.core.AlignmentSequence)
 842
 843     /**
 844      * Sets the value of field 'gapChar'.
 845      *
 846      * @param gapChar the value of field 'gapChar'.
 847      */
 848     public void setGapChar(java.lang.String gapChar)
 849     {
 850         this._gapChar = gapChar;
 851     } //-- void setGapChar(java.lang.String)
 852
 853     /**
 854      * Sets the value of field 'id'. The field 'id' has the
 855      * following description: Primary Key for vamsas object
 856      * referencing
 857      *
 858      *
 859      * @param id the value of field 'id'.
 860      */
 861     public void setId(java.lang.String id)
 862     {
 863         this._id = id;
 864     } //-- void setId(java.lang.String)
 865
 866     /**
 867      * Sets the value of field 'modifiable'.
 868      *
 869      * @param modifiable the value of field 'modifiable'.
 870      */
 871     public void setModifiable(java.lang.String modifiable)
 872     {
 873         this._modifiable = modifiable;
 874     } //-- void setModifiable(java.lang.String)
 875
 876     /**
 877      * Method setProperty
 878      *
 879      *
 880      *
 881      * @param index
 882      * @param vProperty
 883      */
 884     public void setProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
 885         throws java.lang.IndexOutOfBoundsException
 886     {
 887         //-- check bounds for index
 888         if ((index < 0) || (index > _propertyList.size())) {
 889             throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
 890         }
 891         _propertyList.setElementAt(vProperty, index);
 892     } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property)
 893
 894     /**
 895      * Method setProperty
 896      *
 897      *
 898      *
 899      * @param propertyArray
 900      */
 901     public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
 902     {
 903         //-- copy array
 904         _propertyList.removeAllElements();
 905         for (int i = 0; i < propertyArray.length; i++) {
 906             _propertyList.addElement(propertyArray[i]);
 907         }
 908     } //-- void setProperty(uk.ac.vamsas.objects.core.Property)
 909
 910     /**
 911      * Sets the value of field 'provenance'.
 912      *
 913      * @param provenance the value of field 'provenance'.
 914      */
 915     public void setProvenance(uk.ac.vamsas.objects.core.Provenance provenance)
 916     {
 917         this._provenance = provenance;
 918     } //-- void setProvenance(uk.ac.vamsas.objects.core.Provenance)
 919
 920     /**
 921      * Method setTree
 922      *
 923      *
 924      *
 925      * @param index
 926      * @param vTree
 927      */
 928     public void setTree(int index, uk.ac.vamsas.objects.core.Tree vTree)
 929         throws java.lang.IndexOutOfBoundsException
 930     {
 931         //-- check bounds for index
 932         if ((index < 0) || (index > _treeList.size())) {
 933             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 934         }
 935         _treeList.setElementAt(vTree, index);
 936     } //-- void setTree(int, uk.ac.vamsas.objects.core.Tree)
 937
 938     /**
 939      * Method setTree
 940      *
 941      *
 942      *
 943      * @param treeArray
 944      */
 945     public void setTree(uk.ac.vamsas.objects.core.Tree[] treeArray)
 946     {
 947         //-- copy array
 948         _treeList.removeAllElements();
 949         for (int i = 0; i < treeArray.length; i++) {
 950             _treeList.addElement(treeArray[i]);
 951         }
 952     } //-- void setTree(uk.ac.vamsas.objects.core.Tree)
 953
 954     /**
 955      * Method unmarshal
 956      *
 957      *
 958      *
 959      * @param reader
 960      * @return Alignment
 961      */
 962     public static uk.ac.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
 963         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 964     {
 965         return (uk.ac.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Alignment.class, reader);
 966     } //-- uk.ac.vamsas.objects.core.Alignment unmarshal(java.io.Reader)
 967
 968     /**
 969      * Method validate
 970      *
 971      */
 972     public void validate()
 973         throws org.exolab.castor.xml.ValidationException
 974     {
 975         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 976         validator.validate(this);
 977     } //-- void validate()
 978
 979 }