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             if (this._id != null) {
 121                 if (temp._id == null) return false;
 122                 else if (!(this._id.equals(temp._id)))
 123                     return false;
 124             }
 125             else if (temp._id != null)
 126                 return false;
 127             if (this._refid != null) {
 128                 if (temp._refid == null) return false;
 129                 else if (!(this._refid.equals(temp._refid)))
 130                     return false;
 131             }
 132             else if (temp._refid != null)
 133                 return false;
 134             if (this._alignmentSequenceAnnotationList != null) {
 135                 if (temp._alignmentSequenceAnnotationList == null) return false;
 136                 else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)))
 137                     return false;
 138             }
 139             else if (temp._alignmentSequenceAnnotationList != null)
 140                 return false;
 141             return true;
 142         }
 143         return false;
 144     }
 145
 146     /**
 147      * Method getAlignmentSequenceAnnotation.
 148      *
 149      * @param index
 150      * @throws java.lang.IndexOutOfBoundsException if the index
 151      * given is outside the bounds of the collection
 152      * @return the value of the
 153      * uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation at the
 154      * given index
 155      */
 156     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(
 157             final int index)
 158     throws java.lang.IndexOutOfBoundsException {
 159         // check bounds for index
 160         if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
 161             throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
 162         }
 163
 164         return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.get(index);
 165     }
 166
 167     /**
 168      * Method getAlignmentSequenceAnnotation.Returns the contents
 169      * of the collection in an Array.  <p>Note:  Just in case the
 170      * collection contents are changing in another thread, we pass
 171      * a 0-length Array of the correct type into the API call.
 172      * This way we <i>know</i> that the Array returned is of
 173      * exactly the correct length.
 174      *
 175      * @return this collection as an Array
 176      */
 177     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation(
 178     ) {
 179         uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0];
 180         return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList.toArray(array);
 181     }
 182
 183     /**
 184      * Method getAlignmentSequenceAnnotationAsReference.Returns a
 185      * reference to '_alignmentSequenceAnnotationList'. No type
 186      * checking is performed on any modifications to the Vector.
 187      *
 188      * @return a reference to the Vector backing this class
 189      */
 190     public java.util.Vector getAlignmentSequenceAnnotationAsReference(
 191     ) {
 192         return this._alignmentSequenceAnnotationList;
 193     }
 194
 195     /**
 196      * Method getAlignmentSequenceAnnotationCount.
 197      *
 198      * @return the size of this collection
 199      */
 200     public int getAlignmentSequenceAnnotationCount(
 201     ) {
 202         return this._alignmentSequenceAnnotationList.size();
 203     }
 204
 205     /**
 206      * Returns the value of field 'id'. The field 'id' has the
 207      * following description: Primary Key for vamsas object
 208      *  referencing
 209      *
 210      * @return the value of field 'Id'.
 211      */
 212     public java.lang.String getId(
 213     ) {
 214         return this._id;
 215     }
 216
 217     /**
 218      * Returns the value of field 'refid'. The field 'refid' has
 219      * the following description: Dataset Sequence from which
 220      *  this alignment sequence is taken from
 221      *
 222      *
 223      * @return the value of field 'Refid'.
 224      */
 225     public java.lang.Object getRefid(
 226     ) {
 227         return this._refid;
 228     }
 229
 230     /**
 231      * Overrides the java.lang.Object.hashCode method.
 232      * <p>
 233      * The following steps came from <b>Effective Java Programming
 234      * Language Guide</b> by Joshua Bloch, Chapter 3
 235      *
 236      * @return a hash code value for the object.
 237      */
 238     public int hashCode(
 239     ) {
 240         int result = super.hashCode();
 241
 242         long tmp;
 243         if (_id != null) {
 244            result = 37 * result + _id.hashCode();
 245         }
 246         if (_refid != null) {
 247            result = 37 * result + _refid.hashCode();
 248         }
 249         if (_alignmentSequenceAnnotationList != null) {
 250            result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
 251         }
 252
 253         return result;
 254     }
 255
 256     /**
 257      * Method isValid.
 258      *
 259      * @return true if this object is valid according to the schema
 260      */
 261     public boolean isValid(
 262     ) {
 263         try {
 264             validate();
 265         } catch (org.exolab.castor.xml.ValidationException vex) {
 266             return false;
 267         }
 268         return true;
 269     }
 270
 271     /**
 272      *
 273      *
 274      * @param out
 275      * @throws org.exolab.castor.xml.MarshalException if object is
 276      * null or if any SAXException is thrown during marshaling
 277      * @throws org.exolab.castor.xml.ValidationException if this
 278      * object is an invalid instance according to the schema
 279      */
 280     public void marshal(
 281             final java.io.Writer out)
 282     throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
 283         Marshaller.marshal(this, out);
 284     }
 285
 286     /**
 287      *
 288      *
 289      * @param handler
 290      * @throws java.io.IOException if an IOException occurs during
 291      * marshaling
 292      * @throws org.exolab.castor.xml.ValidationException if this
 293      * object is an invalid instance according to the schema
 294      * @throws org.exolab.castor.xml.MarshalException if object is
 295      * null or if any SAXException is thrown during marshaling
 296      */
 297     public void marshal(
 298             final org.xml.sax.ContentHandler handler)
 299     throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
 300         Marshaller.marshal(this, handler);
 301     }
 302
 303     /**
 304      * Method removeAlignmentSequenceAnnotation.
 305      *
 306      * @param vAlignmentSequenceAnnotation
 307      * @return true if the object was removed from the collection.
 308      */
 309     public boolean removeAlignmentSequenceAnnotation(
 310             final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) {
 311         boolean removed = _alignmentSequenceAnnotationList.remove(vAlignmentSequenceAnnotation);
 312         return removed;
 313     }
 314
 315     /**
 316      * Method removeAlignmentSequenceAnnotationAt.
 317      *
 318      * @param index
 319      * @return the element removed from the collection
 320      */
 321     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt(
 322             final int index) {
 323         java.lang.Object obj = this._alignmentSequenceAnnotationList.remove(index);
 324         return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
 325     }
 326
 327     /**
 328      */
 329     public void removeAllAlignmentSequenceAnnotation(
 330     ) {
 331         this._alignmentSequenceAnnotationList.clear();
 332     }
 333
 334     /**
 335      *
 336      *
 337      * @param index
 338      * @param vAlignmentSequenceAnnotation
 339      * @throws java.lang.IndexOutOfBoundsException if the index
 340      * given is outside the bounds of the collection
 341      */
 342     public void setAlignmentSequenceAnnotation(
 343             final int index,
 344             final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
 345     throws java.lang.IndexOutOfBoundsException {
 346         // check bounds for index
 347         if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
 348             throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
 349         }
 350
 351         this._alignmentSequenceAnnotationList.set(index, vAlignmentSequenceAnnotation);
 352     }
 353
 354     /**
 355      *
 356      *
 357      * @param vAlignmentSequenceAnnotationArray
 358      */
 359     public void setAlignmentSequenceAnnotation(
 360             final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray) {
 361         //-- copy array
 362         _alignmentSequenceAnnotationList.clear();
 363
 364         for (int i = 0; i < vAlignmentSequenceAnnotationArray.length; i++) {
 365                 this._alignmentSequenceAnnotationList.add(vAlignmentSequenceAnnotationArray[i]);
 366         }
 367     }
 368
 369     /**
 370      * Sets the value of '_alignmentSequenceAnnotationList' by
 371      * copying the given Vector. All elements will be checked for
 372      * type safety.
 373      *
 374      * @param vAlignmentSequenceAnnotationList the Vector to copy.
 375      */
 376     public void setAlignmentSequenceAnnotation(
 377             final java.util.Vector vAlignmentSequenceAnnotationList) {
 378         // copy vector
 379         this._alignmentSequenceAnnotationList.clear();
 380
 381         this._alignmentSequenceAnnotationList.addAll(vAlignmentSequenceAnnotationList);
 382     }
 383
 384     /**
 385      * Sets the value of '_alignmentSequenceAnnotationList' by
 386      * setting it to the given Vector. No type checking is
 387      * performed.
 388      * @deprecated
 389      *
 390      * @param alignmentSequenceAnnotationVector the Vector to set.
 391      */
 392     public void setAlignmentSequenceAnnotationAsReference(
 393             final java.util.Vector alignmentSequenceAnnotationVector) {
 394         this._alignmentSequenceAnnotationList = alignmentSequenceAnnotationVector;
 395     }
 396
 397     /**
 398      * Sets the value of field 'id'. The field 'id' has the
 399      * following description: Primary Key for vamsas object
 400      *  referencing
 401      *
 402      * @param id the value of field 'id'.
 403      */
 404     public void setId(
 405             final java.lang.String id) {
 406         this._id = id;
 407     }
 408
 409     /**
 410      * Sets the value of field 'refid'. The field 'refid' has the
 411      * following description: Dataset Sequence from which
 412      *  this alignment sequence is taken from
 413      *
 414      *
 415      * @param refid the value of field 'refid'.
 416      */
 417     public void setRefid(
 418             final java.lang.Object refid) {
 419         this._refid = refid;
 420     }
 421
 422     /**
 423      * Method unmarshal.
 424      *
 425      * @param reader
 426      * @throws org.exolab.castor.xml.MarshalException if object is
 427      * null or if any SAXException is thrown during marshaling
 428      * @throws org.exolab.castor.xml.ValidationException if this
 429      * object is an invalid instance according to the schema
 430      * @return the unmarshaled uk.ac.vamsas.objects.core.SequenceTyp
 431      */
 432     public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
 433             final java.io.Reader reader)
 434     throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
 435         return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
 436     }
 437
 438     /**
 439      *
 440      *
 441      * @throws org.exolab.castor.xml.ValidationException if this
 442      * object is an invalid instance according to the schema
 443      */
 444     public void validate(
 445     )
 446     throws org.exolab.castor.xml.ValidationException {
 447         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 448         validator.validate(this);
 449     }
 450
 451 }