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      * Primary Key for vamsas object
  57      *  referencing
  58      *
  59      */
  60     private java.lang.String _id;
  61
  62     /**
  63      * objects with modifiable=false will
  64      *  not be modified by a vamsas client
  65      *  update
  66      *
  67      */
  68     private boolean _modifiable = true;
  69
  70     /**
  71      * keeps track of state for field: _modifiable
  72      */
  73     private boolean _has_modifiable;
  74
  75     /**
  76      * This is annotation over the
  77      *  coordinate frame defined by all
  78      *  the columns in the alignment.
  79      *
  80      */
  81     private java.util.Vector _alignmentAnnotationList;
  82
  83     /**
  84      * Field _treeList
  85      */
  86     private java.util.Vector _treeList;
  87
  88     /**
  89      * Field _alignmentSequenceList
  90      */
  91     private java.util.Vector _alignmentSequenceList;
  92
  93     /**
  94      * typical properties may be
  95      *  additional alignment score
  96      *  objects
  97      *
  98      */
  99     private java.util.Vector _propertyList;
 100
 101     /**
 102      * Field _provenance
 103      */
 104     private org.vamsas.objects.core.Provenance _provenance;
 105
 106
 107       //----------------/
 108      //- Constructors -/
 109     //----------------/
 110
 111     public Alignment()
 112      {
 113         super();
 114         _alignmentAnnotationList = new Vector();
 115         _treeList = new Vector();
 116         _alignmentSequenceList = new Vector();
 117         _propertyList = new Vector();
 118     } //-- org.vamsas.objects.core.Alignment()
 119
 120
 121       //-----------/
 122      //- Methods -/
 123     //-----------/
 124
 125     /**
 126      * Method addAlignmentAnnotation
 127      *
 128      *
 129      *
 130      * @param vAlignmentAnnotation
 131      */
 132     public void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
 133         throws java.lang.IndexOutOfBoundsException
 134     {
 135         _alignmentAnnotationList.addElement(vAlignmentAnnotation);
 136     } //-- void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
 137
 138     /**
 139      * Method addAlignmentAnnotation
 140      *
 141      *
 142      *
 143      * @param index
 144      * @param vAlignmentAnnotation
 145      */
 146     public void addAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
 147         throws java.lang.IndexOutOfBoundsException
 148     {
 149         _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index);
 150     } //-- void addAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
 151
 152     /**
 153      * Method addAlignmentSequence
 154      *
 155      *
 156      *
 157      * @param vAlignmentSequence
 158      */
 159     public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 160         throws java.lang.IndexOutOfBoundsException
 161     {
 162         _alignmentSequenceList.addElement(vAlignmentSequence);
 163     } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
 164
 165     /**
 166      * Method addAlignmentSequence
 167      *
 168      *
 169      *
 170      * @param index
 171      * @param vAlignmentSequence
 172      */
 173     public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 174         throws java.lang.IndexOutOfBoundsException
 175     {
 176         _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
 177     } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 178
 179     /**
 180      * Method addProperty
 181      *
 182      *
 183      *
 184      * @param vProperty
 185      */
 186     public void addProperty(org.vamsas.objects.core.Property vProperty)
 187         throws java.lang.IndexOutOfBoundsException
 188     {
 189         _propertyList.addElement(vProperty);
 190     } //-- void addProperty(org.vamsas.objects.core.Property)
 191
 192     /**
 193      * Method addProperty
 194      *
 195      *
 196      *
 197      * @param index
 198      * @param vProperty
 199      */
 200     public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
 201         throws java.lang.IndexOutOfBoundsException
 202     {
 203         _propertyList.insertElementAt(vProperty, index);
 204     } //-- void addProperty(int, org.vamsas.objects.core.Property)
 205
 206     /**
 207      * Method addTree
 208      *
 209      *
 210      *
 211      * @param vTree
 212      */
 213     public void addTree(org.vamsas.objects.core.Tree vTree)
 214         throws java.lang.IndexOutOfBoundsException
 215     {
 216         _treeList.addElement(vTree);
 217     } //-- void addTree(org.vamsas.objects.core.Tree)
 218
 219     /**
 220      * Method addTree
 221      *
 222      *
 223      *
 224      * @param index
 225      * @param vTree
 226      */
 227     public void addTree(int index, org.vamsas.objects.core.Tree vTree)
 228         throws java.lang.IndexOutOfBoundsException
 229     {
 230         _treeList.insertElementAt(vTree, index);
 231     } //-- void addTree(int, org.vamsas.objects.core.Tree)
 232
 233     /**
 234      * Method deleteAligned
 235      *
 236      */
 237     public void deleteAligned()
 238     {
 239         this._has_aligned= false;
 240     } //-- void deleteAligned()
 241
 242     /**
 243      * Method deleteModifiable
 244      *
 245      */
 246     public void deleteModifiable()
 247     {
 248         this._has_modifiable= false;
 249     } //-- void deleteModifiable()
 250
 251     /**
 252      * Method enumerateAlignmentAnnotation
 253      *
 254      *
 255      *
 256      * @return Enumeration
 257      */
 258     public java.util.Enumeration enumerateAlignmentAnnotation()
 259     {
 260         return _alignmentAnnotationList.elements();
 261     } //-- java.util.Enumeration enumerateAlignmentAnnotation()
 262
 263     /**
 264      * Method enumerateAlignmentSequence
 265      *
 266      *
 267      *
 268      * @return Enumeration
 269      */
 270     public java.util.Enumeration enumerateAlignmentSequence()
 271     {
 272         return _alignmentSequenceList.elements();
 273     } //-- java.util.Enumeration enumerateAlignmentSequence()
 274
 275     /**
 276      * Method enumerateProperty
 277      *
 278      *
 279      *
 280      * @return Enumeration
 281      */
 282     public java.util.Enumeration enumerateProperty()
 283     {
 284         return _propertyList.elements();
 285     } //-- java.util.Enumeration enumerateProperty()
 286
 287     /**
 288      * Method enumerateTree
 289      *
 290      *
 291      *
 292      * @return Enumeration
 293      */
 294     public java.util.Enumeration enumerateTree()
 295     {
 296         return _treeList.elements();
 297     } //-- java.util.Enumeration enumerateTree()
 298
 299     /**
 300      * Note: hashCode() has not been overriden
 301      *
 302      * @param obj
 303      * @return boolean
 304      */
 305     public boolean equals(java.lang.Object obj)
 306     {
 307         if ( this == obj )
 308             return true;
 309
 310         if (super.equals(obj)==false)
 311             return false;
 312
 313         if (obj instanceof Alignment) {
 314
 315             Alignment temp = (Alignment)obj;
 316             if (this._gapChar != null) {
 317                 if (temp._gapChar == null) return false;
 318                 else if (!(this._gapChar.equals(temp._gapChar)))
 319                     return false;
 320             }
 321             else if (temp._gapChar != null)
 322                 return false;
 323             if (this._aligned != temp._aligned)
 324                 return false;
 325             if (this._has_aligned != temp._has_aligned)
 326                 return false;
 327             if (this._id != null) {
 328                 if (temp._id == null) return false;
 329                 else if (!(this._id.equals(temp._id)))
 330                     return false;
 331             }
 332             else if (temp._id != null)
 333                 return false;
 334             if (this._modifiable != temp._modifiable)
 335                 return false;
 336             if (this._has_modifiable != temp._has_modifiable)
 337                 return false;
 338             if (this._alignmentAnnotationList != null) {
 339                 if (temp._alignmentAnnotationList == null) return false;
 340                 else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList)))
 341                     return false;
 342             }
 343             else if (temp._alignmentAnnotationList != null)
 344                 return false;
 345             if (this._treeList != null) {
 346                 if (temp._treeList == null) return false;
 347                 else if (!(this._treeList.equals(temp._treeList)))
 348                     return false;
 349             }
 350             else if (temp._treeList != null)
 351                 return false;
 352             if (this._alignmentSequenceList != null) {
 353                 if (temp._alignmentSequenceList == null) return false;
 354                 else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList)))
 355                     return false;
 356             }
 357             else if (temp._alignmentSequenceList != null)
 358                 return false;
 359             if (this._propertyList != null) {
 360                 if (temp._propertyList == null) return false;
 361                 else if (!(this._propertyList.equals(temp._propertyList)))
 362                     return false;
 363             }
 364             else if (temp._propertyList != null)
 365                 return false;
 366             if (this._provenance != null) {
 367                 if (temp._provenance == null) return false;
 368                 else if (!(this._provenance.equals(temp._provenance)))
 369                     return false;
 370             }
 371             else if (temp._provenance != null)
 372                 return false;
 373             return true;
 374         }
 375         return false;
 376     } //-- boolean equals(java.lang.Object)
 377
 378     /**
 379      * Returns the value of field 'aligned'.
 380      *
 381      * @return boolean
 382      * @return the value of field 'aligned'.
 383      */
 384     public boolean getAligned()
 385     {
 386         return this._aligned;
 387     } //-- boolean getAligned()
 388
 389     /**
 390      * Method getAlignmentAnnotation
 391      *
 392      *
 393      *
 394      * @param index
 395      * @return AlignmentAnnotation
 396      */
 397     public org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index)
 398         throws java.lang.IndexOutOfBoundsException
 399     {
 400         //-- check bounds for index
 401         if ((index < 0) || (index > _alignmentAnnotationList.size())) {
 402             throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
 403         }
 404
 405         return (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
 406     } //-- org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int)
 407
 408     /**
 409      * Method getAlignmentAnnotation
 410      *
 411      *
 412      *
 413      * @return AlignmentAnnotation
 414      */
 415     public org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
 416     {
 417         int size = _alignmentAnnotationList.size();
 418         org.vamsas.objects.core.AlignmentAnnotation[] mArray = new org.vamsas.objects.core.AlignmentAnnotation[size];
 419         for (int index = 0; index < size; index++) {
 420             mArray[index] = (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
 421         }
 422         return mArray;
 423     } //-- org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
 424
 425     /**
 426      * Method getAlignmentAnnotationCount
 427      *
 428      *
 429      *
 430      * @return int
 431      */
 432     public int getAlignmentAnnotationCount()
 433     {
 434         return _alignmentAnnotationList.size();
 435     } //-- int getAlignmentAnnotationCount()
 436
 437     /**
 438      * Method getAlignmentSequence
 439      *
 440      *
 441      *
 442      * @param index
 443      * @return AlignmentSequence
 444      */
 445     public org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index)
 446         throws java.lang.IndexOutOfBoundsException
 447     {
 448         //-- check bounds for index
 449         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 450             throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 451         }
 452
 453         return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 454     } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
 455
 456     /**
 457      * Method getAlignmentSequence
 458      *
 459      *
 460      *
 461      * @return AlignmentSequence
 462      */
 463     public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 464     {
 465         int size = _alignmentSequenceList.size();
 466         org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size];
 467         for (int index = 0; index < size; index++) {
 468             mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
 469         }
 470         return mArray;
 471     } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
 472
 473     /**
 474      * Method getAlignmentSequenceCount
 475      *
 476      *
 477      *
 478      * @return int
 479      */
 480     public int getAlignmentSequenceCount()
 481     {
 482         return _alignmentSequenceList.size();
 483     } //-- int getAlignmentSequenceCount()
 484
 485     /**
 486      * Returns the value of field 'gapChar'.
 487      *
 488      * @return String
 489      * @return the value of field 'gapChar'.
 490      */
 491     public java.lang.String getGapChar()
 492     {
 493         return this._gapChar;
 494     } //-- java.lang.String getGapChar()
 495
 496     /**
 497      * Returns the value of field 'id'. The field 'id' has the
 498      * following description: Primary Key for vamsas object
 499      *  referencing
 500      *
 501      *
 502      * @return String
 503      * @return the value of field 'id'.
 504      */
 505     public java.lang.String getId()
 506     {
 507         return this._id;
 508     } //-- java.lang.String getId()
 509
 510     /**
 511      * Returns the value of field 'modifiable'. The field
 512      * 'modifiable' has the following description: objects with
 513      * modifiable=false will
 514      *  not be modified by a vamsas client
 515      *  update
 516      *
 517      *
 518      * @return boolean
 519      * @return the value of field 'modifiable'.
 520      */
 521     public boolean getModifiable()
 522     {
 523         return this._modifiable;
 524     } //-- boolean getModifiable()
 525
 526     /**
 527      * Method getProperty
 528      *
 529      *
 530      *
 531      * @param index
 532      * @return Property
 533      */
 534     public org.vamsas.objects.core.Property getProperty(int index)
 535         throws java.lang.IndexOutOfBoundsException
 536     {
 537         //-- check bounds for index
 538         if ((index < 0) || (index > _propertyList.size())) {
 539             throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
 540         }
 541
 542         return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
 543     } //-- org.vamsas.objects.core.Property getProperty(int)
 544
 545     /**
 546      * Method getProperty
 547      *
 548      *
 549      *
 550      * @return Property
 551      */
 552     public org.vamsas.objects.core.Property[] getProperty()
 553     {
 554         int size = _propertyList.size();
 555         org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
 556         for (int index = 0; index < size; index++) {
 557             mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
 558         }
 559         return mArray;
 560     } //-- org.vamsas.objects.core.Property[] getProperty()
 561
 562     /**
 563      * Method getPropertyCount
 564      *
 565      *
 566      *
 567      * @return int
 568      */
 569     public int getPropertyCount()
 570     {
 571         return _propertyList.size();
 572     } //-- int getPropertyCount()
 573
 574     /**
 575      * Returns the value of field 'provenance'.
 576      *
 577      * @return Provenance
 578      * @return the value of field 'provenance'.
 579      */
 580     public org.vamsas.objects.core.Provenance getProvenance()
 581     {
 582         return this._provenance;
 583     } //-- org.vamsas.objects.core.Provenance getProvenance()
 584
 585     /**
 586      * Method getTree
 587      *
 588      *
 589      *
 590      * @param index
 591      * @return Tree
 592      */
 593     public org.vamsas.objects.core.Tree getTree(int index)
 594         throws java.lang.IndexOutOfBoundsException
 595     {
 596         //-- check bounds for index
 597         if ((index < 0) || (index > _treeList.size())) {
 598             throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 599         }
 600
 601         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 602     } //-- org.vamsas.objects.core.Tree getTree(int)
 603
 604     /**
 605      * Method getTree
 606      *
 607      *
 608      *
 609      * @return Tree
 610      */
 611     public org.vamsas.objects.core.Tree[] getTree()
 612     {
 613         int size = _treeList.size();
 614         org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
 615         for (int index = 0; index < size; index++) {
 616             mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
 617         }
 618         return mArray;
 619     } //-- org.vamsas.objects.core.Tree[] getTree()
 620
 621     /**
 622      * Method getTreeCount
 623      *
 624      *
 625      *
 626      * @return int
 627      */
 628     public int getTreeCount()
 629     {
 630         return _treeList.size();
 631     } //-- int getTreeCount()
 632
 633     /**
 634      * Method hasAligned
 635      *
 636      *
 637      *
 638      * @return boolean
 639      */
 640     public boolean hasAligned()
 641     {
 642         return this._has_aligned;
 643     } //-- boolean hasAligned()
 644
 645     /**
 646      * Method hasModifiable
 647      *
 648      *
 649      *
 650      * @return boolean
 651      */
 652     public boolean hasModifiable()
 653     {
 654         return this._has_modifiable;
 655     } //-- boolean hasModifiable()
 656
 657     /**
 658      * Method isValid
 659      *
 660      *
 661      *
 662      * @return boolean
 663      */
 664     public boolean isValid()
 665     {
 666         try {
 667             validate();
 668         }
 669         catch (org.exolab.castor.xml.ValidationException vex) {
 670             return false;
 671         }
 672         return true;
 673     } //-- boolean isValid()
 674
 675     /**
 676      * Method marshal
 677      *
 678      *
 679      *
 680      * @param out
 681      */
 682     public void marshal(java.io.Writer out)
 683         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 684     {
 685
 686         Marshaller.marshal(this, out);
 687     } //-- void marshal(java.io.Writer)
 688
 689     /**
 690      * Method marshal
 691      *
 692      *
 693      *
 694      * @param handler
 695      */
 696     public void marshal(org.xml.sax.ContentHandler handler)
 697         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 698     {
 699
 700         Marshaller.marshal(this, handler);
 701     } //-- void marshal(org.xml.sax.ContentHandler)
 702
 703     /**
 704      * Method removeAlignmentAnnotation
 705      *
 706      *
 707      *
 708      * @param index
 709      * @return AlignmentAnnotation
 710      */
 711     public org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index)
 712     {
 713         java.lang.Object obj = _alignmentAnnotationList.elementAt(index);
 714         _alignmentAnnotationList.removeElementAt(index);
 715         return (org.vamsas.objects.core.AlignmentAnnotation) obj;
 716     } //-- org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int)
 717
 718     /**
 719      * Method removeAlignmentSequence
 720      *
 721      *
 722      *
 723      * @param index
 724      * @return AlignmentSequence
 725      */
 726     public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
 727     {
 728         java.lang.Object obj = _alignmentSequenceList.elementAt(index);
 729         _alignmentSequenceList.removeElementAt(index);
 730         return (org.vamsas.objects.core.AlignmentSequence) obj;
 731     } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
 732
 733     /**
 734      * Method removeAllAlignmentAnnotation
 735      *
 736      */
 737     public void removeAllAlignmentAnnotation()
 738     {
 739         _alignmentAnnotationList.removeAllElements();
 740     } //-- void removeAllAlignmentAnnotation()
 741
 742     /**
 743      * Method removeAllAlignmentSequence
 744      *
 745      */
 746     public void removeAllAlignmentSequence()
 747     {
 748         _alignmentSequenceList.removeAllElements();
 749     } //-- void removeAllAlignmentSequence()
 750
 751     /**
 752      * Method removeAllProperty
 753      *
 754      */
 755     public void removeAllProperty()
 756     {
 757         _propertyList.removeAllElements();
 758     } //-- void removeAllProperty()
 759
 760     /**
 761      * Method removeAllTree
 762      *
 763      */
 764     public void removeAllTree()
 765     {
 766         _treeList.removeAllElements();
 767     } //-- void removeAllTree()
 768
 769     /**
 770      * Method removeProperty
 771      *
 772      *
 773      *
 774      * @param index
 775      * @return Property
 776      */
 777     public org.vamsas.objects.core.Property removeProperty(int index)
 778     {
 779         java.lang.Object obj = _propertyList.elementAt(index);
 780         _propertyList.removeElementAt(index);
 781         return (org.vamsas.objects.core.Property) obj;
 782     } //-- org.vamsas.objects.core.Property removeProperty(int)
 783
 784     /**
 785      * Method removeTree
 786      *
 787      *
 788      *
 789      * @param index
 790      * @return Tree
 791      */
 792     public org.vamsas.objects.core.Tree removeTree(int index)
 793     {
 794         java.lang.Object obj = _treeList.elementAt(index);
 795         _treeList.removeElementAt(index);
 796         return (org.vamsas.objects.core.Tree) obj;
 797     } //-- org.vamsas.objects.core.Tree removeTree(int)
 798
 799     /**
 800      * Sets the value of field 'aligned'.
 801      *
 802      * @param aligned the value of field 'aligned'.
 803      */
 804     public void setAligned(boolean aligned)
 805     {
 806         this._aligned = aligned;
 807         this._has_aligned = true;
 808     } //-- void setAligned(boolean)
 809
 810     /**
 811      * Method setAlignmentAnnotation
 812      *
 813      *
 814      *
 815      * @param index
 816      * @param vAlignmentAnnotation
 817      */
 818     public void setAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
 819         throws java.lang.IndexOutOfBoundsException
 820     {
 821         //-- check bounds for index
 822         if ((index < 0) || (index > _alignmentAnnotationList.size())) {
 823             throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
 824         }
 825         _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index);
 826     } //-- void setAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
 827
 828     /**
 829      * Method setAlignmentAnnotation
 830      *
 831      *
 832      *
 833      * @param alignmentAnnotationArray
 834      */
 835     public void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray)
 836     {
 837         //-- copy array
 838         _alignmentAnnotationList.removeAllElements();
 839         for (int i = 0; i < alignmentAnnotationArray.length; i++) {
 840             _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]);
 841         }
 842     } //-- void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
 843
 844     /**
 845      * Method setAlignmentSequence
 846      *
 847      *
 848      *
 849      * @param index
 850      * @param vAlignmentSequence
 851      */
 852     public void setAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
 853         throws java.lang.IndexOutOfBoundsException
 854     {
 855         //-- check bounds for index
 856         if ((index < 0) || (index > _alignmentSequenceList.size())) {
 857             throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
 858         }
 859         _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
 860     } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
 861
 862     /**
 863      * Method setAlignmentSequence
 864      *
 865      *
 866      *
 867      * @param alignmentSequenceArray
 868      */
 869     public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
 870     {
 871         //-- copy array
 872         _alignmentSequenceList.removeAllElements();
 873         for (int i = 0; i < alignmentSequenceArray.length; i++) {
 874             _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
 875         }
 876     } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
 877
 878     /**
 879      * Sets the value of field 'gapChar'.
 880      *
 881      * @param gapChar the value of field 'gapChar'.
 882      */
 883     public void setGapChar(java.lang.String gapChar)
 884     {
 885         this._gapChar = gapChar;
 886     } //-- void setGapChar(java.lang.String)
 887
 888     /**
 889      * Sets the value of field 'id'. The field 'id' has the
 890      * following description: Primary Key for vamsas object
 891      *  referencing
 892      *
 893      *
 894      * @param id the value of field 'id'.
 895      */
 896     public void setId(java.lang.String id)
 897     {
 898         this._id = id;
 899     } //-- void setId(java.lang.String)
 900
 901     /**
 902      * Sets the value of field 'modifiable'. The field 'modifiable'
 903      * has the following description: objects with modifiable=false
 904      * will
 905      *  not be modified by a vamsas client
 906      *  update
 907      *
 908      *
 909      * @param modifiable the value of field 'modifiable'.
 910      */
 911     public void setModifiable(boolean modifiable)
 912     {
 913         this._modifiable = modifiable;
 914         this._has_modifiable = true;
 915     } //-- void setModifiable(boolean)
 916
 917     /**
 918      * Method setProperty
 919      *
 920      *
 921      *
 922      * @param index
 923      * @param vProperty
 924      */
 925     public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
 926         throws java.lang.IndexOutOfBoundsException
 927     {
 928         //-- check bounds for index
 929         if ((index < 0) || (index > _propertyList.size())) {
 930             throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
 931         }
 932         _propertyList.setElementAt(vProperty, index);
 933     } //-- void setProperty(int, org.vamsas.objects.core.Property)
 934
 935     /**
 936      * Method setProperty
 937      *
 938      *
 939      *
 940      * @param propertyArray
 941      */
 942     public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
 943     {
 944         //-- copy array
 945         _propertyList.removeAllElements();
 946         for (int i = 0; i < propertyArray.length; i++) {
 947             _propertyList.addElement(propertyArray[i]);
 948         }
 949     } //-- void setProperty(org.vamsas.objects.core.Property)
 950
 951     /**
 952      * Sets the value of field 'provenance'.
 953      *
 954      * @param provenance the value of field 'provenance'.
 955      */
 956     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 957     {
 958         this._provenance = provenance;
 959     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 960
 961     /**
 962      * Method setTree
 963      *
 964      *
 965      *
 966      * @param index
 967      * @param vTree
 968      */
 969     public void setTree(int index, org.vamsas.objects.core.Tree vTree)
 970         throws java.lang.IndexOutOfBoundsException
 971     {
 972         //-- check bounds for index
 973         if ((index < 0) || (index > _treeList.size())) {
 974             throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
 975         }
 976         _treeList.setElementAt(vTree, index);
 977     } //-- void setTree(int, org.vamsas.objects.core.Tree)
 978
 979     /**
 980      * Method setTree
 981      *
 982      *
 983      *
 984      * @param treeArray
 985      */
 986     public void setTree(org.vamsas.objects.core.Tree[] treeArray)
 987     {
 988         //-- copy array
 989         _treeList.removeAllElements();
 990         for (int i = 0; i < treeArray.length; i++) {
 991             _treeList.addElement(treeArray[i]);
 992         }
 993     } //-- void setTree(org.vamsas.objects.core.Tree)
 994
 995     /**
 996      * Method unmarshal
 997      *
 998      *
 999      *
1000      * @param reader
1001      * @return Alignment
1002      */
1003     public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
1004         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
1005     {
1006         return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);
1007     } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader)
1008
1009     /**
1010      * Method validate
1011      *
1012      */
1013     public void validate()
1014         throws org.exolab.castor.xml.ValidationException
1015     {
1016         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
1017         validator.validate(this);
1018     } //-- void validate()
1019
1020 }