src/org/vamsas/objects/core/AlignmentSequenceAnnotation.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 org.exolab.castor.xml.MarshalException;
  19 import org.exolab.castor.xml.Marshaller;
  20 import org.exolab.castor.xml.Unmarshaller;
  21 import org.exolab.castor.xml.ValidationException;
  22 import org.xml.sax.ContentHandler;
  23
  24 /**
  25  * Class AlignmentSequenceAnnotation.
  26  *
  27  * @version $Revision$ $Date$
  28  */
  29 public class AlignmentSequenceAnnotation extends org.vamsas.objects.core.RangeAnnotation
  30 implements java.io.Serializable
  31 {
  32
  33
  34       //--------------------------/
  35      //- Class/Member Variables -/
  36     //--------------------------/
  37
  38     /**
  39      * TODO:
  40      *  decide
  41      *  if
  42      *  this
  43      *  flag
  44      *  is
  45      *  redundant
  46      *  -
  47      *  when
  48      *  true
  49      *  it
  50      *  would
  51      *  suggest
  52      *  that
  53      *  the
  54      *  annotationElement
  55      *  values
  56      *  together
  57      *  form
  58      *  a
  59      *  graph
  60      *
  61      */
  62     private boolean _graph;
  63
  64     /**
  65      * keeps track of state for field: _graph
  66      */
  67     private boolean _has_graph;
  68
  69     /**
  70      * Field _provenance
  71      */
  72     private org.vamsas.objects.core.Provenance _provenance;
  73
  74
  75       //----------------/
  76      //- Constructors -/
  77     //----------------/
  78
  79     public AlignmentSequenceAnnotation()
  80      {
  81         super();
  82     } //-- org.vamsas.objects.core.AlignmentSequenceAnnotation()
  83
  84
  85       //-----------/
  86      //- Methods -/
  87     //-----------/
  88
  89     /**
  90      * Method deleteGraph
  91      *
  92      */
  93     public void deleteGraph()
  94     {
  95         this._has_graph= false;
  96     } //-- void deleteGraph()
  97
  98     /**
  99      * Note: hashCode() has not been overriden
 100      *
 101      * @param obj
 102      * @return boolean
 103      */
 104     public boolean equals(java.lang.Object obj)
 105     {
 106         if ( this == obj )
 107             return true;
 108
 109         if (super.equals(obj)==false)
 110             return false;
 111
 112         if (obj instanceof AlignmentSequenceAnnotation) {
 113
 114             AlignmentSequenceAnnotation temp = (AlignmentSequenceAnnotation)obj;
 115             if (this._graph != temp._graph)
 116                 return false;
 117             if (this._has_graph != temp._has_graph)
 118                 return false;
 119             if (this._provenance != null) {
 120                 if (temp._provenance == null) return false;
 121                 else if (!(this._provenance.equals(temp._provenance)))
 122                     return false;
 123             }
 124             else if (temp._provenance != null)
 125                 return false;
 126             return true;
 127         }
 128         return false;
 129     } //-- boolean equals(java.lang.Object)
 130
 131     /**
 132      * Returns the value of field 'graph'. The field 'graph' has
 133      * the following description: TODO:
 134      *  decide
 135      *  if
 136      *  this
 137      *  flag
 138      *  is
 139      *  redundant
 140      *  -
 141      *  when
 142      *  true
 143      *  it
 144      *  would
 145      *  suggest
 146      *  that
 147      *  the
 148      *  annotationElement
 149      *  values
 150      *  together
 151      *  form
 152      *  a
 153      *  graph
 154      *
 155      *
 156      * @return boolean
 157      * @return the value of field 'graph'.
 158      */
 159     public boolean getGraph()
 160     {
 161         return this._graph;
 162     } //-- boolean getGraph()
 163
 164     /**
 165      * Returns the value of field 'provenance'.
 166      *
 167      * @return Provenance
 168      * @return the value of field 'provenance'.
 169      */
 170     public org.vamsas.objects.core.Provenance getProvenance()
 171     {
 172         return this._provenance;
 173     } //-- org.vamsas.objects.core.Provenance getProvenance()
 174
 175     /**
 176      * Method hasGraph
 177      *
 178      *
 179      *
 180      * @return boolean
 181      */
 182     public boolean hasGraph()
 183     {
 184         return this._has_graph;
 185     } //-- boolean hasGraph()
 186
 187     /**
 188      * Method isValid
 189      *
 190      *
 191      *
 192      * @return boolean
 193      */
 194     public boolean isValid()
 195     {
 196         try {
 197             validate();
 198         }
 199         catch (org.exolab.castor.xml.ValidationException vex) {
 200             return false;
 201         }
 202         return true;
 203     } //-- boolean isValid()
 204
 205     /**
 206      * Method marshal
 207      *
 208      *
 209      *
 210      * @param out
 211      */
 212     public void marshal(java.io.Writer out)
 213         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 214     {
 215
 216         Marshaller.marshal(this, out);
 217     } //-- void marshal(java.io.Writer)
 218
 219     /**
 220      * Method marshal
 221      *
 222      *
 223      *
 224      * @param handler
 225      */
 226     public void marshal(org.xml.sax.ContentHandler handler)
 227         throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 228     {
 229
 230         Marshaller.marshal(this, handler);
 231     } //-- void marshal(org.xml.sax.ContentHandler)
 232
 233     /**
 234      * Sets the value of field 'graph'. The field 'graph' has the
 235      * following description: TODO:
 236      *  decide
 237      *  if
 238      *  this
 239      *  flag
 240      *  is
 241      *  redundant
 242      *  -
 243      *  when
 244      *  true
 245      *  it
 246      *  would
 247      *  suggest
 248      *  that
 249      *  the
 250      *  annotationElement
 251      *  values
 252      *  together
 253      *  form
 254      *  a
 255      *  graph
 256      *
 257      *
 258      * @param graph the value of field 'graph'.
 259      */
 260     public void setGraph(boolean graph)
 261     {
 262         this._graph = graph;
 263         this._has_graph = true;
 264     } //-- void setGraph(boolean)
 265
 266     /**
 267      * Sets the value of field 'provenance'.
 268      *
 269      * @param provenance the value of field 'provenance'.
 270      */
 271     public void setProvenance(org.vamsas.objects.core.Provenance provenance)
 272     {
 273         this._provenance = provenance;
 274     } //-- void setProvenance(org.vamsas.objects.core.Provenance)
 275
 276     /**
 277      * Method unmarshal
 278      *
 279      *
 280      *
 281      * @param reader
 282      * @return RangeType
 283      */
 284     public static org.vamsas.objects.core.RangeType unmarshal(java.io.Reader reader)
 285         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
 286     {
 287         return (org.vamsas.objects.core.AlignmentSequenceAnnotation) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequenceAnnotation.class, reader);
 288     } //-- org.vamsas.objects.core.RangeType unmarshal(java.io.Reader)
 289
 290     /**
 291      * Method validate
 292      *
 293      */
 294     public void validate()
 295         throws org.exolab.castor.xml.ValidationException
 296     {
 297         org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
 298         validator.validate(this);
 299     } //-- void validate()
 300
 301 }