src/uk/ac/vamsas/objects/core/AlignmentSequence.java

   1 /*
   2  * This class was automatically generated with
   3  * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
   4  * Schema.
   5  * $Id$
   6  */
   7
   8 package uk.ac.vamsas.objects.core;
   9
  10   //---------------------------------/
  11  //- Imported classes and packages -/
  12 //---------------------------------/
  13
  14 import org.exolab.castor.xml.Marshaller;
  15 import org.exolab.castor.xml.Unmarshaller;
  16
  17 /**
  18  * Class AlignmentSequence.
  19  *
  20  * @version $Revision$ $Date$
  21  */
  22 public class AlignmentSequence extends uk.ac.vamsas.objects.core.SequenceType
  23 implements java.io.Serializable
  24 {
  25
  26
  27       //--------------------------/
  28      //- Class/Member Variables -/
  29     //--------------------------/
  30
  31     /**
  32      * Primary Key for vamsas object
  33      *  referencing
  34      */
  35     private java.lang.String _id;
  36
  37     /**
  38      * Dataset Sequence from which
  39      *  this alignment sequence is taken from
  40      *
  41      */
  42     private java.lang.Object _refid;
  43
  44     /**
  45      * Field _alignmentSequenceAnnotationList.
  46      */
  47     private java.util.Vector _alignmentSequenceAnnotationList;
  48
  49
  50       //----------------/
  51      //- Constructors -/
  52     //----------------/
  53
  54     public AlignmentSequence() {
  55         super();
  56         this._alignmentSequenceAnnotationList = new java.util.Vector();
  57     }
  58
  59
  60       //-----------/
  61      //- Methods -/
  62     //-----------/
  63
  64     /**
  65      *
  66      *
  67      * @param vAlignmentSequenceAnnotation
  68      * @throws java.lang.IndexOutOfBoundsException if the index
  69      * given is outside the bounds of the collection
  70      */
  71     public void addAlignmentSequenceAnnotation(
  72             final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
  73     throws java.lang.IndexOutOfBoundsException {
  74         this._alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
  75     }
  76
  77     /**
  78      *
  79      *
  80      * @param index
  81      * @param vAlignmentSequenceAnnotation
  82      * @throws java.lang.IndexOutOfBoundsException if the index
  83      * given is outside the bounds of the collection
  84      */
  85     public void addAlignmentSequenceAnnotation(
  86             final int index,
  87             final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
  88     throws java.lang.IndexOutOfBoundsException {
  89         this._alignmentSequenceAnnotationList.add(index, vAlignmentSequenceAnnotation);
  90     }
  91
  92     /**
  93      * Method enumerateAlignmentSequenceAnnotation.
  94      *
  95      * @return an Enumeration over all
  96      * uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation element
  97      */
  98     public java.util.Enumeration enumerateAlignmentSequenceAnnotation(
  99     ) {
 100         return this._alignmentSequenceAnnotationList.elements();
 101     }
 102
 103     /**
 104      * Overrides the java.lang.Object.equals method.
 105      *
 106      * @param obj
 107      * @return true if the objects are equal.
 108      */
 109     public boolean equals(
 110             final java.lang.Object obj) {
 111         if ( this == obj )
 112             return true;
 113
 114         if (super.equals(obj)==false)
 115             return false;
 116
 117         if (obj instanceof AlignmentSequence) {
 118
 119             AlignmentSequence temp = (AlignmentSequence)obj;
 120             boolean thcycle;
 121             boolean tmcycle;
 122             if (this._id != null) {
 123                 if (temp._id == null) return false;
 124                 if (this._id != temp._id) {
 125                     thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);
 126                     tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);
 127                     if (thcycle!=tmcycle) {
 128                         if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };
 129                         if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
 130                         return false;
 131                     }
 132                     if (!thcycle) {
 133                         if (!this._id.equals(temp._id)) {
 134                             org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
 135                             org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
 136                             return false;
 137                         }
 138                         org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
 139                         org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
 140                     }
 141                 }
 142             } else if (temp._id != null)
 143                 return false;
 144             if (this._refid != null) {
 145                 if (temp._refid == null) return false;
 146                 if (this._refid != temp._refid) {
 147                     thcycle=org.castor.util.CycleBreaker.startingToCycle(this._refid);
 148                     tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._refid);
 149                     if (thcycle!=tmcycle) {
 150                         if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._refid); };
 151                         if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid); };
 152                         return false;
 153                     }
 154                     if (!thcycle) {
 155                         if (!this._refid.equals(temp._refid)) {
 156                             org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
 157                             org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
 158                             return false;
 159                         }
 160                         org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
 161                         org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
 162                     }
 163                 }
 164             } else if (temp._refid != null)
 165                 return false;
 166             if (this._alignmentSequenceAnnotationList != null) {
 167                 if (temp._alignmentSequenceAnnotationList == null) return false;
 168                 if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) {
 169                     thcycle=org.castor.util.CycleBreaker.startingToCycle(this._alignmentSequenceAnnotationList);
 170                     tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._alignmentSequenceAnnotationList);
 171                     if (thcycle!=tmcycle) {
 172                         if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList); };
 173                         if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList); };
 174                         return false;
 175                     }
 176                     if (!thcycle) {
 177                         if (!this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)) {
 178                             org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList);
 179                             org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList);
 180                             return false;
 181                         }
 182                         org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceAnnotationList);
 183                         org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceAnnotationList);
 184                     }
 185                 }
 186             } else if (temp._alignmentSequenceAnnotationList != null)
 187                 return false;
 188             return true;
 189         }
 190         return false;
 191     }
 192
 193     /**
 194      * Method getAlignmentSequenceAnnotation.
 195      *
 196      * @param index
 197      * @throws java.lang.IndexOutOfBoundsException if the index
 198      * given is outside the bounds of the collection
 199      * @return the value of the
 200      * uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation at the
 201      * given index
 202      */
 203     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(
 204             final int index)
 205     throws java.lang.IndexOutOfBoundsException {
 206         // check bounds for index
 207         if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
 208             throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
 209         }
 210
 211         return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.get(index);
 212     }
 213
 214     /**
 215      * Method getAlignmentSequenceAnnotation.Returns the contents
 216      * of the collection in an Array.  <p>Note:  Just in case the
 217      * collection contents are changing in another thread, we pass
 218      * a 0-length Array of the correct type into the API call.
 219      * This way we <i>know</i> that the Array returned is of
 220      * exactly the correct length.
 221      *
 222      * @return this collection as an Array
 223      */
 224     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation(
 225     ) {
 226         uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0];
 227         return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList.toArray(array);
 228     }
 229
 230     /**
 231      * Method getAlignmentSequenceAnnotationAsReference.Returns a
 232      * reference to '_alignmentSequenceAnnotationList'. No type
 233      * checking is performed on any modifications to the Vector.
 234      *
 235      * @return a reference to the Vector backing this class
 236      */
 237     public java.util.Vector getAlignmentSequenceAnnotationAsReference(
 238     ) {
 239         return this._alignmentSequenceAnnotationList;
 240     }
 241
 242     /**
 243      * Method getAlignmentSequenceAnnotationCount.
 244      *
 245      * @return the size of this collection
 246      */
 247     public int getAlignmentSequenceAnnotationCount(
 248     ) {
 249         return this._alignmentSequenceAnnotationList.size();
 250     }
 251
 252     /**
 253      * Returns the value of field 'id'. The field 'id' has the
 254      * following description: Primary Key for vamsas object
 255      *  referencing
 256      *
 257      * @return the value of field 'Id'.
 258      */
 259     public java.lang.String getId(
 260     ) {
 261         return this._id;
 262     }
 263
 264     /**
 265      * Returns the value of field 'refid'. The field 'refid' has
 266      * the following description: Dataset Sequence from which
 267      *  this alignment sequence is taken from
 268      *
 269      *
 270      * @return the value of field 'Refid'.
 271      */
 272     public java.lang.Object getRefid(
 273     ) {
 274         return this._refid;
 275     }
 276
 277     /**
 278      * Overrides the java.lang.Object.hashCode method.
 279      * <p>
 280      * The following steps came from <b>Effective Java Programming
 281      * Language Guide</b> by Joshua Bloch, Chapter 3
 282      *
 283      * @return a hash code value for the object.
 284      */
 285     public int hashCode(
 286     ) {
 287         int result = super.hashCode();
 288
 289         long tmp;
 290         if (_id != null
 291             && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
 292            result = 37 * result + _id.hashCode();
 293            org.castor.util.CycleBreaker.releaseCycleHandle(_id);
 294         }
 295         if (_refid != null
 296             && !org.castor.util.CycleBreaker.startingToCycle(_refid)) {
 297            result = 37 * result + _refid.hashCode();
 298            org.castor.util.CycleBreaker.releaseCycleHandle(_refid);
 299         }
 300         if (_alignmentSequenceAnnotationList != null
 301             && !org.castor.util.CycleBreaker.startingToCycle(_alignmentSequenceAnnotationList)) {
 302            result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
 303            org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceAnnotationList);
 304         }
 305
 306         return result;
 307     }
 308
 309     /**
 310      * Method isValid.
 311      *
 312      * @return true if this object is valid according to the schema
 313      */
 314     public boolean isValid(
 315     ) {
 316         try {
 317             validate();
 318         } catch (org.exolab.castor.xml.ValidationException vex) {
 319             return false;
 320         }
 321         return true;
 322     }
 323
 324     /**
 325      *
 326      *
 327      * @param out
 328      * @throws org.exolab.castor.xml.MarshalException if object is
 329      * null or if any SAXException is thrown during marshaling
 330      * @throws org.exolab.castor.xml.ValidationException if this
 331      * object is an invalid instance according to the schema
 332      */
 333     public void marshal(
 334             final java.io.Writer out)
 335     throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
 336         Marshaller.marshal(this, out);
 337     }
 338
 339     /**
 340      *
 341      *
 342      * @param handler
 343      * @throws java.io.IOException if an IOException occurs during
 344      * marshaling
 345      * @throws org.exolab.castor.xml.ValidationException if this
 346      * object is an invalid instance according to the schema
 347      * @throws org.exolab.castor.xml.MarshalException if object is
 348      * null or if any SAXException is thrown during marshaling
 349      */
 350     public void marshal(
 351             final org.xml.sax.ContentHandler handler)
 352     throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
 353         Marshaller.marshal(this, handler);
 354     }
 355
 356     /**
 357      * Method removeAlignmentSequenceAnnotation.
 358      *
 359      * @param vAlignmentSequenceAnnotation
 360      * @return true if the object was removed from the collection.
 361      */
 362     public boolean removeAlignmentSequenceAnnotation(
 363             final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) {
 364         boolean removed = _alignmentSequenceAnnotationList.remove(vAlignmentSequenceAnnotation);
 365         return removed;
 366     }
 367
 368     /**
 369      * Method removeAlignmentSequenceAnnotationAt.
 370      *
 371      * @param index
 372      * @return the element removed from the collection
 373      */
 374     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt(
 375             final int index) {
 376         java.lang.Object obj = this._alignmentSequenceAnnotationList.remove(index);
 377         return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
 378     }
 379
 380     /**
 381      */
 382     public void removeAllAlignmentSequenceAnnotation(
 383     ) {
 384         this._alignmentSequenceAnnotationList.clear();
 385     }
 386
 387     /**
 388      *
 389      *
 390      * @param index
 391      * @param vAlignmentSequenceAnnotation
 392      * @throws java.lang.IndexOutOfBoundsException if the index
 393      * given is outside the bounds of the collection
 394      */
 395     public void setAlignmentSequenceAnnotation(
 396             final int index,
 397             final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
 398     throws java.lang.IndexOutOfBoundsException {
 399         // check bounds for index
 400         if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
 401             throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
 402         }
 403
 404         this._alignmentSequenceAnnotationList.set(index, vAlignmentSequenceAnnotation);
 405     }
 406
 407     /**
 408      *
 409      *
 410      * @param vAlignmentSequenceAnnotationArray
 411      */
 412     public void setAlignmentSequenceAnnotation(
 413             final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray) {
 414         //-- copy array
 415         _alignmentSequenceAnnotationList.clear();
 416
 417         for (int i = 0; i < vAlignmentSequenceAnnotationArray.length; i++) {
 418                 this._alignmentSequenceAnnotationList.add(vAlignmentSequenceAnnotationArray[i]);
 419         }
 420     }
 421
 422     /**
 423      * Sets the value of '_alignmentSequenceAnnotationList' by
 424      * copying the given Vector. All elements will be checked for
 425      * type safety.
 426      *
 427      * @param vAlignmentSequenceAnnotationList the Vector to copy.
 428      */
 429     public void setAlignmentSequenceAnnotation(
 430             final java.util.Vector vAlignmentSequenceAnnotationList) {
 431         // copy vector
 432         this._alignmentSequenceAnnotationList.clear();
 433
 434         this._alignmentSequenceAnnotationList.addAll(vAlignmentSequenceAnnotationList);
 435     }
 436
 437     /**
 438      * Sets the value of '_alignmentSequenceAnnotationList' by
 439      * setting it to the given Vector. No type checking is
 440      * performed.
 441      * @deprecated
 442      *
 443      * @param alignmentSequenceAnnotationVector the Vector to set.
 444      */
 445     public void setAlignmentSequenceAnnotationAsReference(
 446             final java.util.Vector alignmentSequenceAnnotationVector) {
 447         this._alignmentSequenceAnnotationList = alignmentSequenceAnnotationVector;
 448     }
 449
 450     /**
 451      * Sets the value of field 'id'. The field 'id' has the
 452      * following description: Primary Key for vamsas object
 453      *  referencing
 454      *
 455      * @param id the value of field 'id'.
 456      */
 457     public void setId(
 458             final java.lang.String id) {
 459         this._id = id;
 460     }
 461
 462     /**
 463      * Sets the value of field 'refid'. The field 'refid' has the
 464      * following description: Dataset Sequence from which
 465      *  this alignment sequence is taken from
 466      *
 467      *
 468      * @param refid the value of field 'refid'.
 469      */
 470     public void setRefid(
 471             final java.lang.Object refid) {
 472         this._refid = refid;
 473     }
 474
 475     /**
 476      * Method unmarshal.
 477      *
 478      * @param reader
 479      * @throws org.exolab.castor.xml.MarshalException if object is
 480      * null or if any SAXException is thrown during marshaling
 481      * @throws org.exolab.castor.xml.ValidationException if this
 482      * object is an invalid instance according to the schema
 483      * @return the unmarshaled uk.ac.vamsas.objects.core.SequenceTyp
 484      */
 485     public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
 486             final java.io.Reader reader)
 487     throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
 488         return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
 489     }
 490
 491     /**
 492      *
 493      *
 494      * @throws org.exolab.castor.xml.ValidationException if this
 495      * object is an invalid instance according to the schema
 496      */
 497     public void validate(
 498     )
 499     throws org.exolab.castor.xml.ValidationException {
 500         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 501         validator.validate(this);
 502     }
 503
 504 }