File: VAMSAS.java

package info (click to toggle)
libvamsas-client-java 0.2~git2011.10.17+1b42648-1
  • links: PTS, VCS
  • area: main
  • in suites: buster, jessie, jessie-kfreebsd, stretch, wheezy
  • size: 4,108 kB
  • ctags: 5,456
  • sloc: java: 32,555; xml: 417; sh: 47; makefile: 6
file content (735 lines) | stat: -rw-r--r-- 22,222 bytes parent folder | download | duplicates (3)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
/*
 * This file is part of the Vamsas Client version 0.2. 
 * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite, 
 *  Andrew Waterhouse and Dominik Lindner.
 * 
 * Earlier versions have also been incorporated into Jalview version 2.4 
 * since 2008, and TOPALi version 2 since 2007.
 * 
 * The Vamsas Client is free software: you can redistribute it and/or modify
 * it under the terms of the GNU Lesser General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *  
 * The Vamsas Client is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 * 
 * You should have received a copy of the GNU Lesser General Public License
 * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
 */
package uk.ac.vamsas.objects.core;

//---------------------------------/
//- Imported classes and packages -/
//---------------------------------/

import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;

/**
 * contains unassociated trees and a number of analysis sets
 * 
 * 
 * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
 *          $
 */
public class VAMSAS extends uk.ac.vamsas.client.Vobject implements
    java.io.Serializable {

  // --------------------------/
  // - Class/Member Variables -/
  // --------------------------/

  /**
   * Primary Key for vamsas object referencing
   */
  private java.lang.String _id;

  /**
   * Field _modifiable.
   */
  private java.lang.String _modifiable;

  /**
   * Field _treeList.
   */
  private java.util.Vector _treeList;

  /**
   * Field _dataSetList.
   */
  private java.util.Vector _dataSetList;

  // ----------------/
  // - Constructors -/
  // ----------------/

  public VAMSAS() {
    super();
    this._treeList = new java.util.Vector();
    this._dataSetList = new java.util.Vector();
  }

  // -----------/
  // - Methods -/
  // -----------/

  /**
   * 
   * 
   * @param vDataSet
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void addDataSet(final uk.ac.vamsas.objects.core.DataSet vDataSet)
      throws java.lang.IndexOutOfBoundsException {
    this._dataSetList.addElement(vDataSet);
  }

  /**
   * 
   * 
   * @param index
   * @param vDataSet
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void addDataSet(final int index,
      final uk.ac.vamsas.objects.core.DataSet vDataSet)
      throws java.lang.IndexOutOfBoundsException {
    this._dataSetList.add(index, vDataSet);
  }

  /**
   * 
   * 
   * @param vTree
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void addTree(final uk.ac.vamsas.objects.core.Tree vTree)
      throws java.lang.IndexOutOfBoundsException {
    this._treeList.addElement(vTree);
  }

  /**
   * 
   * 
   * @param index
   * @param vTree
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void addTree(final int index,
      final uk.ac.vamsas.objects.core.Tree vTree)
      throws java.lang.IndexOutOfBoundsException {
    this._treeList.add(index, vTree);
  }

  /**
   * Method enumerateDataSet.
   * 
   * @return an Enumeration over all uk.ac.vamsas.objects.core.DataSet elements
   */
  public java.util.Enumeration enumerateDataSet() {
    return this._dataSetList.elements();
  }

  /**
   * Method enumerateTree.
   * 
   * @return an Enumeration over all uk.ac.vamsas.objects.core.Tree elements
   */
  public java.util.Enumeration enumerateTree() {
    return this._treeList.elements();
  }

  /**
   * Overrides the java.lang.Object.equals method.
   * 
   * @param obj
   * @return true if the objects are equal.
   */
  public boolean equals(final java.lang.Object obj) {
    if (this == obj)
      return true;

    if (super.equals(obj) == false)
      return false;

    if (obj instanceof VAMSAS) {

      VAMSAS temp = (VAMSAS) obj;
      boolean thcycle;
      boolean tmcycle;
      if (this._id != null) {
        if (temp._id == null)
          return false;
        if (this._id != temp._id) {
          thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._id);
          tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._id);
          if (thcycle != tmcycle) {
            if (!thcycle) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
            }
            ;
            if (!tmcycle) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
            }
            ;
            return false;
          }
          if (!thcycle) {
            if (!this._id.equals(temp._id)) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
              org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
              return false;
            }
            org.castor.core.util.CycleBreaker.releaseCycleHandle(this._id);
            org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._id);
          }
        }
      } else if (temp._id != null)
        return false;
      if (this._modifiable != null) {
        if (temp._modifiable == null)
          return false;
        if (this._modifiable != temp._modifiable) {
          thcycle = org.castor.core.util.CycleBreaker
              .startingToCycle(this._modifiable);
          tmcycle = org.castor.core.util.CycleBreaker
              .startingToCycle(temp._modifiable);
          if (thcycle != tmcycle) {
            if (!thcycle) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
            }
            ;
            if (!tmcycle) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
            }
            ;
            return false;
          }
          if (!thcycle) {
            if (!this._modifiable.equals(temp._modifiable)) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
              org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
              return false;
            }
            org.castor.core.util.CycleBreaker.releaseCycleHandle(this._modifiable);
            org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
          }
        }
      } else if (temp._modifiable != null)
        return false;
      if (this._treeList != null) {
        if (temp._treeList == null)
          return false;
        if (this._treeList != temp._treeList) {
          thcycle = org.castor.core.util.CycleBreaker
              .startingToCycle(this._treeList);
          tmcycle = org.castor.core.util.CycleBreaker
              .startingToCycle(temp._treeList);
          if (thcycle != tmcycle) {
            if (!thcycle) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
            }
            ;
            if (!tmcycle) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
            }
            ;
            return false;
          }
          if (!thcycle) {
            if (!this._treeList.equals(temp._treeList)) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
              org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
              return false;
            }
            org.castor.core.util.CycleBreaker.releaseCycleHandle(this._treeList);
            org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._treeList);
          }
        }
      } else if (temp._treeList != null)
        return false;
      if (this._dataSetList != null) {
        if (temp._dataSetList == null)
          return false;
        if (this._dataSetList != temp._dataSetList) {
          thcycle = org.castor.core.util.CycleBreaker
              .startingToCycle(this._dataSetList);
          tmcycle = org.castor.core.util.CycleBreaker
              .startingToCycle(temp._dataSetList);
          if (thcycle != tmcycle) {
            if (!thcycle) {
              org.castor.core.util.CycleBreaker
                  .releaseCycleHandle(this._dataSetList);
            }
            ;
            if (!tmcycle) {
              org.castor.core.util.CycleBreaker
                  .releaseCycleHandle(temp._dataSetList);
            }
            ;
            return false;
          }
          if (!thcycle) {
            if (!this._dataSetList.equals(temp._dataSetList)) {
              org.castor.core.util.CycleBreaker
                  .releaseCycleHandle(this._dataSetList);
              org.castor.core.util.CycleBreaker
                  .releaseCycleHandle(temp._dataSetList);
              return false;
            }
            org.castor.core.util.CycleBreaker.releaseCycleHandle(this._dataSetList);
            org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._dataSetList);
          }
        }
      } else if (temp._dataSetList != null)
        return false;
      return true;
    }
    return false;
  }

  /**
   * Method getDataSet.
   * 
   * @param index
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   * @return the value of the uk.ac.vamsas.objects.core.DataSet at the given
   *         index
   */
  public uk.ac.vamsas.objects.core.DataSet getDataSet(final int index)
      throws java.lang.IndexOutOfBoundsException {
    // check bounds for index
    if (index < 0 || index >= this._dataSetList.size()) {
      throw new IndexOutOfBoundsException("getDataSet: Index value '" + index
          + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
    }

    return (uk.ac.vamsas.objects.core.DataSet) _dataSetList.get(index);
  }

  /**
   * Method getDataSet.Returns the contents of the collection in an Array.
   * <p>
   * Note: Just in case the collection contents are changing in another thread,
   * we pass a 0-length Array of the correct type into the API call. This way we
   * <i>know</i> that the Array returned is of exactly the correct length.
   * 
   * @return this collection as an Array
   */
  public uk.ac.vamsas.objects.core.DataSet[] getDataSet() {
    uk.ac.vamsas.objects.core.DataSet[] array = new uk.ac.vamsas.objects.core.DataSet[0];
    return (uk.ac.vamsas.objects.core.DataSet[]) this._dataSetList
        .toArray(array);
  }

  /**
   * Method getDataSetAsReference.Returns a reference to '_dataSetList'. No type
   * checking is performed on any modifications to the Vector.
   * 
   * @return a reference to the Vector backing this class
   */
  public java.util.Vector getDataSetAsReference() {
    return this._dataSetList;
  }

  /**
   * Method getDataSetCount.
   * 
   * @return the size of this collection
   */
  public int getDataSetCount() {
    return this._dataSetList.size();
  }

  /**
   * Returns the value of field 'id'. The field 'id' has the following
   * description: Primary Key for vamsas object referencing
   * 
   * @return the value of field 'Id'.
   */
  public java.lang.String getId() {
    return this._id;
  }

  /**
   * Returns the value of field 'modifiable'.
   * 
   * @return the value of field 'Modifiable'.
   */
  public java.lang.String getModifiable() {
    return this._modifiable;
  }

  /**
   * Method getTree.
   * 
   * @param index
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   * @return the value of the uk.ac.vamsas.objects.core.Tree at the given index
   */
  public uk.ac.vamsas.objects.core.Tree getTree(final int index)
      throws java.lang.IndexOutOfBoundsException {
    // check bounds for index
    if (index < 0 || index >= this._treeList.size()) {
      throw new IndexOutOfBoundsException("getTree: Index value '" + index
          + "' not in range [0.." + (this._treeList.size() - 1) + "]");
    }

    return (uk.ac.vamsas.objects.core.Tree) _treeList.get(index);
  }

  /**
   * Method getTree.Returns the contents of the collection in an Array.
   * <p>
   * Note: Just in case the collection contents are changing in another thread,
   * we pass a 0-length Array of the correct type into the API call. This way we
   * <i>know</i> that the Array returned is of exactly the correct length.
   * 
   * @return this collection as an Array
   */
  public uk.ac.vamsas.objects.core.Tree[] getTree() {
    uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0];
    return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array);
  }

  /**
   * Method getTreeAsReference.Returns a reference to '_treeList'. No type
   * checking is performed on any modifications to the Vector.
   * 
   * @return a reference to the Vector backing this class
   */
  public java.util.Vector getTreeAsReference() {
    return this._treeList;
  }

  /**
   * Method getTreeCount.
   * 
   * @return the size of this collection
   */
  public int getTreeCount() {
    return this._treeList.size();
  }

  /**
   * Overrides the java.lang.Object.hashCode method.
   * <p>
   * The following steps came from <b>Effective Java Programming Language
   * Guide</b> by Joshua Bloch, Chapter 3
   * 
   * @return a hash code value for the object.
   */
  public int hashCode() {
    int result = super.hashCode();

    long tmp;
    if (_id != null && !org.castor.core.util.CycleBreaker.startingToCycle(_id)) {
      result = 37 * result + _id.hashCode();
      org.castor.core.util.CycleBreaker.releaseCycleHandle(_id);
    }
    if (_modifiable != null
        && !org.castor.core.util.CycleBreaker.startingToCycle(_modifiable)) {
      result = 37 * result + _modifiable.hashCode();
      org.castor.core.util.CycleBreaker.releaseCycleHandle(_modifiable);
    }
    if (_treeList != null
        && !org.castor.core.util.CycleBreaker.startingToCycle(_treeList)) {
      result = 37 * result + _treeList.hashCode();
      org.castor.core.util.CycleBreaker.releaseCycleHandle(_treeList);
    }
    if (_dataSetList != null
        && !org.castor.core.util.CycleBreaker.startingToCycle(_dataSetList)) {
      result = 37 * result + _dataSetList.hashCode();
      org.castor.core.util.CycleBreaker.releaseCycleHandle(_dataSetList);
    }

    return result;
  }

  /**
   * Method isValid.
   * 
   * @return true if this object is valid according to the schema
   */
  public boolean isValid() {
    try {
      validate();
    } catch (org.exolab.castor.xml.ValidationException vex) {
      return false;
    }
    return true;
  }

  /**
   * 
   * 
   * @param out
   * @throws org.exolab.castor.xml.MarshalException
   *           if object is null or if any SAXException is thrown during
   *           marshaling
   * @throws org.exolab.castor.xml.ValidationException
   *           if this object is an invalid instance according to the schema
   */
  public void marshal(final java.io.Writer out)
      throws org.exolab.castor.xml.MarshalException,
      org.exolab.castor.xml.ValidationException {
    Marshaller.marshal(this, out);
  }

  /**
   * 
   * 
   * @param handler
   * @throws java.io.IOException
   *           if an IOException occurs during marshaling
   * @throws org.exolab.castor.xml.ValidationException
   *           if this object is an invalid instance according to the schema
   * @throws org.exolab.castor.xml.MarshalException
   *           if object is null or if any SAXException is thrown during
   *           marshaling
   */
  public void marshal(final org.xml.sax.ContentHandler handler)
      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
      org.exolab.castor.xml.ValidationException {
    Marshaller.marshal(this, handler);
  }

  /**
     */
  public void removeAllDataSet() {
    this._dataSetList.clear();
  }

  /**
     */
  public void removeAllTree() {
    this._treeList.clear();
  }

  /**
   * Method removeDataSet.
   * 
   * @param vDataSet
   * @return true if the object was removed from the collection.
   */
  public boolean removeDataSet(final uk.ac.vamsas.objects.core.DataSet vDataSet) {
    boolean removed = _dataSetList.remove(vDataSet);
    return removed;
  }

  /**
   * Method removeDataSetAt.
   * 
   * @param index
   * @return the element removed from the collection
   */
  public uk.ac.vamsas.objects.core.DataSet removeDataSetAt(final int index) {
    java.lang.Object obj = this._dataSetList.remove(index);
    return (uk.ac.vamsas.objects.core.DataSet) obj;
  }

  /**
   * Method removeTree.
   * 
   * @param vTree
   * @return true if the object was removed from the collection.
   */
  public boolean removeTree(final uk.ac.vamsas.objects.core.Tree vTree) {
    boolean removed = _treeList.remove(vTree);
    return removed;
  }

  /**
   * Method removeTreeAt.
   * 
   * @param index
   * @return the element removed from the collection
   */
  public uk.ac.vamsas.objects.core.Tree removeTreeAt(final int index) {
    java.lang.Object obj = this._treeList.remove(index);
    return (uk.ac.vamsas.objects.core.Tree) obj;
  }

  /**
   * 
   * 
   * @param index
   * @param vDataSet
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void setDataSet(final int index,
      final uk.ac.vamsas.objects.core.DataSet vDataSet)
      throws java.lang.IndexOutOfBoundsException {
    // check bounds for index
    if (index < 0 || index >= this._dataSetList.size()) {
      throw new IndexOutOfBoundsException("setDataSet: Index value '" + index
          + "' not in range [0.." + (this._dataSetList.size() - 1) + "]");
    }

    this._dataSetList.set(index, vDataSet);
  }

  /**
   * 
   * 
   * @param vDataSetArray
   */
  public void setDataSet(final uk.ac.vamsas.objects.core.DataSet[] vDataSetArray) {
    // -- copy array
    _dataSetList.clear();

    for (int i = 0; i < vDataSetArray.length; i++) {
      this._dataSetList.add(vDataSetArray[i]);
    }
  }

  /**
   * Sets the value of '_dataSetList' by copying the given Vector. All elements
   * will be checked for type safety.
   * 
   * @param vDataSetList
   *          the Vector to copy.
   */
  public void setDataSet(final java.util.Vector vDataSetList) {
    // copy vector
    this._dataSetList.clear();

    this._dataSetList.addAll(vDataSetList);
  }

  /**
   * Sets the value of '_dataSetList' by setting it to the given Vector. No type
   * checking is performed.
   * 
   * @deprecated
   * 
   * @param dataSetVector
   *          the Vector to set.
   */
  public void setDataSetAsReference(final java.util.Vector dataSetVector) {
    this._dataSetList = dataSetVector;
  }

  /**
   * Sets the value of field 'id'. The field 'id' has the following description:
   * Primary Key for vamsas object referencing
   * 
   * @param id
   *          the value of field 'id'.
   */
  public void setId(final java.lang.String id) {
    this._id = id;
  }

  /**
   * Sets the value of field 'modifiable'.
   * 
   * @param modifiable
   *          the value of field 'modifiable'.
   */
  public void setModifiable(final java.lang.String modifiable) {
    this._modifiable = modifiable;
  }

  /**
   * 
   * 
   * @param index
   * @param vTree
   * @throws java.lang.IndexOutOfBoundsException
   *           if the index given is outside the bounds of the collection
   */
  public void setTree(final int index,
      final uk.ac.vamsas.objects.core.Tree vTree)
      throws java.lang.IndexOutOfBoundsException {
    // check bounds for index
    if (index < 0 || index >= this._treeList.size()) {
      throw new IndexOutOfBoundsException("setTree: Index value '" + index
          + "' not in range [0.." + (this._treeList.size() - 1) + "]");
    }

    this._treeList.set(index, vTree);
  }

  /**
   * 
   * 
   * @param vTreeArray
   */
  public void setTree(final uk.ac.vamsas.objects.core.Tree[] vTreeArray) {
    // -- copy array
    _treeList.clear();

    for (int i = 0; i < vTreeArray.length; i++) {
      this._treeList.add(vTreeArray[i]);
    }
  }

  /**
   * Sets the value of '_treeList' by copying the given Vector. All elements
   * will be checked for type safety.
   * 
   * @param vTreeList
   *          the Vector to copy.
   */
  public void setTree(final java.util.Vector vTreeList) {
    // copy vector
    this._treeList.clear();

    this._treeList.addAll(vTreeList);
  }

  /**
   * Sets the value of '_treeList' by setting it to the given Vector. No type
   * checking is performed.
   * 
   * @deprecated
   * 
   * @param treeVector
   *          the Vector to set.
   */
  public void setTreeAsReference(final java.util.Vector treeVector) {
    this._treeList = treeVector;
  }

  /**
   * Method unmarshal.
   * 
   * @param reader
   * @throws org.exolab.castor.xml.MarshalException
   *           if object is null or if any SAXException is thrown during
   *           marshaling
   * @throws org.exolab.castor.xml.ValidationException
   *           if this object is an invalid instance according to the schema
   * @return the unmarshaled uk.ac.vamsas.objects.core.VAMSAS
   */
  public static uk.ac.vamsas.objects.core.VAMSAS unmarshal(
      final java.io.Reader reader)
      throws org.exolab.castor.xml.MarshalException,
      org.exolab.castor.xml.ValidationException {
    return (uk.ac.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(
        uk.ac.vamsas.objects.core.VAMSAS.class, reader);
  }

  /**
   * 
   * 
   * @throws org.exolab.castor.xml.ValidationException
   *           if this object is an invalid instance according to the schema
   */
  public void validate() throws org.exolab.castor.xml.ValidationException {
    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
    validator.validate(this);
  }

}