File: AlignmentSequence.java

package info (click to toggle)
libvamsas-client-java 0.2%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: experimental
  • size: 4,112 kB
  • sloc: java: 32,555; xml: 415; makefile: 3
file content (548 lines) | stat: -rw-r--r-- 18,389 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
/*
 * 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;

/**
 * Class AlignmentSequence.
 * 
 * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
 *          $
 */
public class AlignmentSequence extends uk.ac.vamsas.objects.core.SequenceType
    implements java.io.Serializable {

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

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

  /**
   * Dataset Sequence from which this alignment sequence is taken from
   * 
   */
  private java.lang.Object _refid;

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

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

  public AlignmentSequence() {
    super();
    this._alignmentSequenceAnnotationList = new java.util.Vector();
  }

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

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

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

  /**
   * Method enumerateAlignmentSequenceAnnotation.
   * 
   * @return an Enumeration over all
   *         uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation element
   */
  public java.util.Enumeration enumerateAlignmentSequenceAnnotation() {
    return this._alignmentSequenceAnnotationList.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 AlignmentSequence) {

      AlignmentSequence temp = (AlignmentSequence) 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._refid != null) {
        if (temp._refid == null)
          return false;
        if (this._refid != temp._refid) {
          thcycle = org.castor.core.util.CycleBreaker.startingToCycle(this._refid);
          tmcycle = org.castor.core.util.CycleBreaker.startingToCycle(temp._refid);
          if (thcycle != tmcycle) {
            if (!thcycle) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
            }
            ;
            if (!tmcycle) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
            }
            ;
            return false;
          }
          if (!thcycle) {
            if (!this._refid.equals(temp._refid)) {
              org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
              org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
              return false;
            }
            org.castor.core.util.CycleBreaker.releaseCycleHandle(this._refid);
            org.castor.core.util.CycleBreaker.releaseCycleHandle(temp._refid);
          }
        }
      } else if (temp._refid != null)
        return false;
      if (this._alignmentSequenceAnnotationList != null) {
        if (temp._alignmentSequenceAnnotationList == null)
          return false;
        if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) {
          thcycle = org.castor.core.util.CycleBreaker
              .startingToCycle(this._alignmentSequenceAnnotationList);
          tmcycle = org.castor.core.util.CycleBreaker
              .startingToCycle(temp._alignmentSequenceAnnotationList);
          if (thcycle != tmcycle) {
            if (!thcycle) {
              org.castor.core.util.CycleBreaker
                  .releaseCycleHandle(this._alignmentSequenceAnnotationList);
            }
            ;
            if (!tmcycle) {
              org.castor.core.util.CycleBreaker
                  .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
            }
            ;
            return false;
          }
          if (!thcycle) {
            if (!this._alignmentSequenceAnnotationList
                .equals(temp._alignmentSequenceAnnotationList)) {
              org.castor.core.util.CycleBreaker
                  .releaseCycleHandle(this._alignmentSequenceAnnotationList);
              org.castor.core.util.CycleBreaker
                  .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
              return false;
            }
            org.castor.core.util.CycleBreaker
                .releaseCycleHandle(this._alignmentSequenceAnnotationList);
            org.castor.core.util.CycleBreaker
                .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
          }
        }
      } else if (temp._alignmentSequenceAnnotationList != null)
        return false;
      return true;
    }
    return false;
  }

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

    return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList
        .get(index);
  }

  /**
   * Method getAlignmentSequenceAnnotation.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.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() {
    uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0];
    return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList
        .toArray(array);
  }

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

  /**
   * Method getAlignmentSequenceAnnotationCount.
   * 
   * @return the size of this collection
   */
  public int getAlignmentSequenceAnnotationCount() {
    return this._alignmentSequenceAnnotationList.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 'refid'. The field 'refid' has the following
   * description: Dataset Sequence from which this alignment sequence is taken
   * from
   * 
   * 
   * @return the value of field 'Refid'.
   */
  public java.lang.Object getRefid() {
    return this._refid;
  }

  /**
   * 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 (_refid != null && !org.castor.core.util.CycleBreaker.startingToCycle(_refid)) {
      result = 37 * result + _refid.hashCode();
      org.castor.core.util.CycleBreaker.releaseCycleHandle(_refid);
    }
    if (_alignmentSequenceAnnotationList != null
        && !org.castor.core.util.CycleBreaker
            .startingToCycle(_alignmentSequenceAnnotationList)) {
      result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
      org.castor.core.util.CycleBreaker
          .releaseCycleHandle(_alignmentSequenceAnnotationList);
    }

    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);
  }

  /**
   * Method removeAlignmentSequenceAnnotation.
   * 
   * @param vAlignmentSequenceAnnotation
   * @return true if the object was removed from the collection.
   */
  public boolean removeAlignmentSequenceAnnotation(
      final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) {
    boolean removed = _alignmentSequenceAnnotationList
        .remove(vAlignmentSequenceAnnotation);
    return removed;
  }

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

  /**
     */
  public void removeAllAlignmentSequenceAnnotation() {
    this._alignmentSequenceAnnotationList.clear();
  }

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

    this._alignmentSequenceAnnotationList.set(index,
        vAlignmentSequenceAnnotation);
  }

  /**
   * 
   * 
   * @param vAlignmentSequenceAnnotationArray
   */
  public void setAlignmentSequenceAnnotation(
      final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray) {
    // -- copy array
    _alignmentSequenceAnnotationList.clear();

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

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

    this._alignmentSequenceAnnotationList
        .addAll(vAlignmentSequenceAnnotationList);
  }

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

  /**
   * 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 'refid'. The field 'refid' has the following
   * description: Dataset Sequence from which this alignment sequence is taken
   * from
   * 
   * 
   * @param refid
   *          the value of field 'refid'.
   */
  public void setRefid(final java.lang.Object refid) {
    this._refid = refid;
  }

  /**
   * 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.SequenceTyp
   */
  public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
      final java.io.Reader reader)
      throws org.exolab.castor.xml.MarshalException,
      org.exolab.castor.xml.ValidationException {
    return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(
        uk.ac.vamsas.objects.core.AlignmentSequence.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);
  }

}