src/org/vamsas/objects/core/AlignmentSequence.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 AlignmentSequence.
  28  *
  29  * @version $Revision$ $Date$
  30  */
  31 public class AlignmentSequence extends org.vamsas.objects.core.SequenceType
  32 implements java.io.Serializable
  33 {
  34
  35
  36       //--------------------------/
  37      //- Class/Member Variables -/
  38     //--------------------------/
  39
  40     /**
  41      * Primary Key for
  42      *  vamsas object
  43      *  referencing
  44      *
  45      */
  46     private java.lang.String _id;
  47
  48     /**
  49      * Dataset Sequence
  50      *  from which this
  51      *  alignment
  52      *  sequence is
  53      *  taken from
  54      *
  55      */
  56     private java.lang.Object _refid;
  57
  58     /**
  59      * Field _alignmentSequenceAnnotationList
  60      */
  61     private java.util.Vector _alignmentSequenceAnnotationList;
  62
  63
  64       //----------------/
  65      //- Constructors -/
  66     //----------------/
  67
  68     public AlignmentSequence()
  69      {
  70         super();
  71         _alignmentSequenceAnnotationList = new Vector();
  72     } //-- org.vamsas.objects.core.AlignmentSequence()
  73
  74
  75       //-----------/
  76      //- Methods -/
  77     //-----------/
  78
  79     /**
  80      * Method addAlignmentSequenceAnnotation
  81      *
  82      *
  83      *
  84      * @param vAlignmentSequenceAnnotation
  85      */
  86     public void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
  87         throws java.lang.IndexOutOfBoundsException
  88     {
  89         _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
  90     } //-- void addAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation)
  91
  92     /**
  93      * Method addAlignmentSequenceAnnotation
  94      *
  95      *
  96      *
  97      * @param index
  98      * @param vAlignmentSequenceAnnotation
  99      */
 100     public void addAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
 101         throws java.lang.IndexOutOfBoundsException
 102     {
 103         _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
 104     } //-- void addAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation)
 105
 106     /**
 107      * Method enumerateAlignmentSequenceAnnotation
 108      *
 109      *
 110      *
 111      * @return Enumeration
 112      */
 113     public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
 114     {
 115         return _alignmentSequenceAnnotationList.elements();
 116     } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation()
 117
 118     /**
 119      * Note: hashCode() has not been overriden
 120      *
 121      * @param obj
 122      * @return boolean
 123      */
 124     public boolean equals(java.lang.Object obj)
 125     {
 126         if ( this == obj )
 127             return true;
 128
 129         if (super.equals(obj)==false)
 130             return false;
 131
 132         if (obj instanceof AlignmentSequence) {
 133
 134             AlignmentSequence temp = (AlignmentSequence)obj;
 135             if (this._id != null) {
 136                 if (temp._id == null) return false;
 137                 else if (!(this._id.equals(temp._id)))
 138                     return false;
 139             }
 140             else if (temp._id != null)
 141                 return false;
 142             if (this._refid != null) {
 143                 if (temp._refid == null) return false;
 144                 else if (!(this._refid.equals(temp._refid)))
 145                     return false;
 146             }
 147             else if (temp._refid != null)
 148                 return false;
 149             if (this._alignmentSequenceAnnotationList != null) {
 150                 if (temp._alignmentSequenceAnnotationList == null) return false;
 151                 else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)))
 152                     return false;
 153             }
 154             else if (temp._alignmentSequenceAnnotationList != null)
 155                 return false;
 156             return true;
 157         }
 158         return false;
 159     } //-- boolean equals(java.lang.Object)
 160
 161     /**
 162      * Method getAlignmentSequenceAnnotation
 163      *
 164      *
 165      *
 166      * @param index
 167      * @return AlignmentSequenceAnnotation
 168      */
 169     public org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
 170         throws java.lang.IndexOutOfBoundsException
 171     {
 172         //-- check bounds for index
 173         if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
 174             throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
 175         }
 176
 177         return (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
 178     } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int)
 179
 180     /**
 181      * Method getAlignmentSequenceAnnotation
 182      *
 183      *
 184      *
 185      * @return AlignmentSequenceAnnotation
 186      */
 187     public org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
 188     {
 189         int size = _alignmentSequenceAnnotationList.size();
 190         org.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new org.vamsas.objects.core.AlignmentSequenceAnnotation[size];
 191         for (int index = 0; index < size; index++) {
 192             mArray[index] = (org.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
 193         }
 194         return mArray;
 195     } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
 196
 197     /**
 198      * Method getAlignmentSequenceAnnotationCount
 199      *
 200      *
 201      *
 202      * @return int
 203      */
 204     public int getAlignmentSequenceAnnotationCount()
 205     {
 206         return _alignmentSequenceAnnotationList.size();
 207     } //-- int getAlignmentSequenceAnnotationCount()
 208
 209     /**
 210      * Returns the value of field 'id'. The field 'id' has the
 211      * following description: Primary Key for
 212      *  vamsas object
 213      *  referencing
 214      *
 215      *
 216      * @return String
 217      * @return the value of field 'id'.
 218      */
 219     public java.lang.String getId()
 220     {
 221         return this._id;
 222     } //-- java.lang.String getId()
 223
 224     /**
 225      * Returns the value of field 'refid'. The field 'refid' has
 226      * the following description: Dataset Sequence
 227      *  from which this
 228      *  alignment
 229      *  sequence is
 230      *  taken from
 231      *
 232      *
 233      * @return Object
 234      * @return the value of field 'refid'.
 235      */
 236     public java.lang.Object getRefid()
 237     {
 238         return this._refid;
 239     } //-- java.lang.Object getRefid()
 240
 241     /**
 242      * Method isValid
 243      *
 244      *
 245      *
 246      * @return boolean
 247      */
 248     public boolean isValid()
 249     {
 250         try {
 251             validate();
 252         }
 253         catch (org.exolab.castor.xml.ValidationException vex) {
 254             return false;
 255         }
 256         return true;
 257     } //-- boolean isValid()
 258
 259     /**
 260      * Method marshal
 261      *
 262      *
 263      *
 264      * @param out
 265      */
 266     public void marshal(java.io.Writer out)
 267         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 268     {
 269
 270         Marshaller.marshal(this, out);
 271     } //-- void marshal(java.io.Writer)
 272
 273     /**
 274      * Method marshal
 275      *
 276      *
 277      *
 278      * @param handler
 279      */
 280     public void marshal(org.xml.sax.ContentHandler handler)
 281         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 282     {
 283
 284         Marshaller.marshal(this, handler);
 285     } //-- void marshal(org.xml.sax.ContentHandler)
 286
 287     /**
 288      * Method removeAlignmentSequenceAnnotation
 289      *
 290      *
 291      *
 292      * @param index
 293      * @return AlignmentSequenceAnnotation
 294      */
 295     public org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
 296     {
 297         java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
 298         _alignmentSequenceAnnotationList.removeElementAt(index);
 299         return (org.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
 300     } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int)
 301
 302     /**
 303      * Method removeAllAlignmentSequenceAnnotation
 304      *
 305      */
 306     public void removeAllAlignmentSequenceAnnotation()
 307     {
 308         _alignmentSequenceAnnotationList.removeAllElements();
 309     } //-- void removeAllAlignmentSequenceAnnotation()
 310
 311     /**
 312      * Method setAlignmentSequenceAnnotation
 313      *
 314      *
 315      *
 316      * @param index
 317      * @param vAlignmentSequenceAnnotation
 318      */
 319     public void setAlignmentSequenceAnnotation(int index, org.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
 320         throws java.lang.IndexOutOfBoundsException
 321     {
 322         //-- check bounds for index
 323         if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
 324             throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
 325         }
 326         _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index);
 327     } //-- void setAlignmentSequenceAnnotation(int, org.vamsas.objects.core.AlignmentSequenceAnnotation)
 328
 329     /**
 330      * Method setAlignmentSequenceAnnotation
 331      *
 332      *
 333      *
 334      * @param alignmentSequenceAnnotationArray
 335      */
 336     public void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
 337     {
 338         //-- copy array
 339         _alignmentSequenceAnnotationList.removeAllElements();
 340         for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
 341             _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
 342         }
 343     } //-- void setAlignmentSequenceAnnotation(org.vamsas.objects.core.AlignmentSequenceAnnotation)
 344
 345     /**
 346      * Sets the value of field 'id'. The field 'id' has the
 347      * following description: Primary Key for
 348      *  vamsas object
 349      *  referencing
 350      *
 351      *
 352      * @param id the value of field 'id'.
 353      */
 354     public void setId(java.lang.String id)
 355     {
 356         this._id = id;
 357     } //-- void setId(java.lang.String)
 358
 359     /**
 360      * Sets the value of field 'refid'. The field 'refid' has the
 361      * following description: Dataset Sequence
 362      *  from which this
 363      *  alignment
 364      *  sequence is
 365      *  taken from
 366      *
 367      *
 368      * @param refid the value of field 'refid'.
 369      */
 370     public void setRefid(java.lang.Object refid)
 371     {
 372         this._refid = refid;
 373     } //-- void setRefid(java.lang.Object)
 374
 375     /**
 376      * Method unmarshal
 377      *
 378      *
 379      *
 380      * @param reader
 381      * @return SequenceType
 382      */
 383     public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
 384         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 385     {
 386         return (org.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequence.class, reader);
 387     } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
 388
 389     /**
 390      * Method validate
 391      *
 392      */
 393     public void validate()
 394         throws org.exolab.castor.xml.ValidationException
 395     {
 396         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 397         validator.validate(this);
 398     } //-- void validate()
 399
 400 }