src/uk/ac/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:AlignmentSequence.java 264 2006-12-14 17:42:54Z JimP $
   6  */
   7
   8 package uk.ac.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:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
  30  */
  31 public class AlignmentSequence extends uk.ac.vamsas.objects.core.SequenceType
  32 implements java.io.Serializable
  33 {
  34
  35
  36       //--------------------------/
  37      //- Class/Member Variables -/
  38     //--------------------------/
  39
  40     /**
  41      * Primary Key for vamsas object
  42      *  referencing
  43      */
  44     private java.lang.String _id;
  45
  46     /**
  47      * Dataset Sequence from which
  48      *  this alignment sequence is taken from
  49      *
  50      */
  51     private java.lang.Object _refid;
  52
  53     /**
  54      * Field _alignmentSequenceAnnotationList
  55      */
  56     private java.util.Vector _alignmentSequenceAnnotationList;
  57
  58
  59       //----------------/
  60      //- Constructors -/
  61     //----------------/
  62
  63     public AlignmentSequence()
  64      {
  65         super();
  66         _alignmentSequenceAnnotationList = new Vector();
  67     } //-- uk.ac.vamsas.objects.core.AlignmentSequence()
  68
  69
  70       //-----------/
  71      //- Methods -/
  72     //-----------/
  73
  74     /**
  75      * Method addAlignmentSequenceAnnotation
  76      *
  77      *
  78      *
  79      * @param vAlignmentSequenceAnnotation
  80      */
  81     public void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
  82         throws java.lang.IndexOutOfBoundsException
  83     {
  84         _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
  85     } //-- void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
  86
  87     /**
  88      * Method addAlignmentSequenceAnnotation
  89      *
  90      *
  91      *
  92      * @param index
  93      * @param vAlignmentSequenceAnnotation
  94      */
  95     public void addAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
  96         throws java.lang.IndexOutOfBoundsException
  97     {
  98         _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
  99     } //-- void addAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
 100
 101     /**
 102      * Method enumerateAlignmentSequenceAnnotation
 103      *
 104      *
 105      *
 106      * @return Enumeration
 107      */
 108     public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
 109     {
 110         return _alignmentSequenceAnnotationList.elements();
 111     } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation()
 112
 113     /**
 114      * Note: hashCode() has not been overriden
 115      *
 116      * @param obj
 117      * @return boolean
 118      */
 119     public boolean equals(java.lang.Object obj)
 120     {
 121         if ( this == obj )
 122             return true;
 123
 124         if (super.equals(obj)==false)
 125             return false;
 126
 127         if (obj instanceof AlignmentSequence) {
 128
 129             AlignmentSequence temp = (AlignmentSequence)obj;
 130             if (this._id != null) {
 131                 if (temp._id == null) return false;
 132                 else if (!(this._id.equals(temp._id)))
 133                     return false;
 134             }
 135             else if (temp._id != null)
 136                 return false;
 137             if (this._refid != null) {
 138                 if (temp._refid == null) return false;
 139                 else if (!(this._refid.equals(temp._refid)))
 140                     return false;
 141             }
 142             else if (temp._refid != null)
 143                 return false;
 144             if (this._alignmentSequenceAnnotationList != null) {
 145                 if (temp._alignmentSequenceAnnotationList == null) return false;
 146                 else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)))
 147                     return false;
 148             }
 149             else if (temp._alignmentSequenceAnnotationList != null)
 150                 return false;
 151             return true;
 152         }
 153         return false;
 154     } //-- boolean equals(java.lang.Object)
 155
 156     /**
 157      * Method getAlignmentSequenceAnnotation
 158      *
 159      *
 160      *
 161      * @param index
 162      * @return AlignmentSequenceAnnotation
 163      */
 164     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
 165         throws java.lang.IndexOutOfBoundsException
 166     {
 167         //-- check bounds for index
 168         if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
 169             throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
 170         }
 171
 172         return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
 173     } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int)
 174
 175     /**
 176      * Method getAlignmentSequenceAnnotation
 177      *
 178      *
 179      *
 180      * @return AlignmentSequenceAnnotation
 181      */
 182     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
 183     {
 184         int size = _alignmentSequenceAnnotationList.size();
 185         uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[size];
 186         for (int index = 0; index < size; index++) {
 187             mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
 188         }
 189         return mArray;
 190     } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
 191
 192     /**
 193      * Method getAlignmentSequenceAnnotationCount
 194      *
 195      *
 196      *
 197      * @return int
 198      */
 199     public int getAlignmentSequenceAnnotationCount()
 200     {
 201         return _alignmentSequenceAnnotationList.size();
 202     } //-- int getAlignmentSequenceAnnotationCount()
 203
 204     /**
 205      * Returns the value of field 'id'. The field 'id' has the
 206      * following description: Primary Key for vamsas object
 207      *  referencing
 208      *
 209      * @return String
 210      * @return the value of field 'id'.
 211      */
 212     public java.lang.String getId()
 213     {
 214         return this._id;
 215     } //-- java.lang.String getId()
 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 Object
 224      * @return the value of field 'refid'.
 225      */
 226     public java.lang.Object getRefid()
 227     {
 228         return this._refid;
 229     } //-- java.lang.Object getRefid()
 230
 231     /**
 232      * Method isValid
 233      *
 234      *
 235      *
 236      * @return boolean
 237      */
 238     public boolean isValid()
 239     {
 240         try {
 241             validate();
 242         }
 243         catch (org.exolab.castor.xml.ValidationException vex) {
 244             return false;
 245         }
 246         return true;
 247     } //-- boolean isValid()
 248
 249     /**
 250      * Method marshal
 251      *
 252      *
 253      *
 254      * @param out
 255      */
 256     public void marshal(java.io.Writer out)
 257         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 258     {
 259
 260         Marshaller.marshal(this, out);
 261     } //-- void marshal(java.io.Writer)
 262
 263     /**
 264      * Method marshal
 265      *
 266      *
 267      *
 268      * @param handler
 269      */
 270     public void marshal(org.xml.sax.ContentHandler handler)
 271         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 272     {
 273
 274         Marshaller.marshal(this, handler);
 275     } //-- void marshal(org.xml.sax.ContentHandler)
 276
 277     /**
 278      * Method removeAlignmentSequenceAnnotation
 279      *
 280      *
 281      *
 282      * @param index
 283      * @return AlignmentSequenceAnnotation
 284      */
 285     public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
 286     {
 287         java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
 288         _alignmentSequenceAnnotationList.removeElementAt(index);
 289         return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
 290     } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int)
 291
 292     /**
 293      * Method removeAllAlignmentSequenceAnnotation
 294      *
 295      */
 296     public void removeAllAlignmentSequenceAnnotation()
 297     {
 298         _alignmentSequenceAnnotationList.removeAllElements();
 299     } //-- void removeAllAlignmentSequenceAnnotation()
 300
 301     /**
 302      * Method setAlignmentSequenceAnnotation
 303      *
 304      *
 305      *
 306      * @param index
 307      * @param vAlignmentSequenceAnnotation
 308      */
 309     public void setAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
 310         throws java.lang.IndexOutOfBoundsException
 311     {
 312         //-- check bounds for index
 313         if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
 314             throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
 315         }
 316         _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index);
 317     } //-- void setAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
 318
 319     /**
 320      * Method setAlignmentSequenceAnnotation
 321      *
 322      *
 323      *
 324      * @param alignmentSequenceAnnotationArray
 325      */
 326     public void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
 327     {
 328         //-- copy array
 329         _alignmentSequenceAnnotationList.removeAllElements();
 330         for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
 331             _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
 332         }
 333     } //-- void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
 334
 335     /**
 336      * Sets the value of field 'id'. The field 'id' has the
 337      * following description: Primary Key for vamsas object
 338      *  referencing
 339      *
 340      * @param id the value of field 'id'.
 341      */
 342     public void setId(java.lang.String id)
 343     {
 344         this._id = id;
 345     } //-- void setId(java.lang.String)
 346
 347     /**
 348      * Sets the value of field 'refid'. The field 'refid' has the
 349      * following description: Dataset Sequence from which
 350      *  this alignment sequence is taken from
 351      *
 352      *
 353      * @param refid the value of field 'refid'.
 354      */
 355     public void setRefid(java.lang.Object refid)
 356     {
 357         this._refid = refid;
 358     } //-- void setRefid(java.lang.Object)
 359
 360     /**
 361      * Method unmarshal
 362      *
 363      *
 364      *
 365      * @param reader
 366      * @return SequenceType
 367      */
 368     public static uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
 369         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 370     {
 371         return (uk.ac.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
 372     } //-- uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
 373
 374     /**
 375      * Method validate
 376      *
 377      */
 378     public void validate()
 379         throws org.exolab.castor.xml.ValidationException
 380     {
 381         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 382         validator.validate(this);
 383     } //-- void validate()
 384
 385 }