src/uk/ac/vamsas/objects/core/AlignmentDescriptor.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 uk.ac.vamsas.objects.core;
   9
  10   //---------------------------------/
  11  //- Imported classes and packages -/
  12 //---------------------------------/
  13
  14 import org.exolab.castor.mapping.AccessMode;
  15 import org.exolab.castor.xml.TypeValidator;
  16 import org.exolab.castor.xml.XMLFieldDescriptor;
  17 import org.exolab.castor.xml.validators.*;
  18
  19 /**
  20  * Class AlignmentDescriptor.
  21  *
  22  * @version $Revision$ $Date$
  23  */
  24 public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
  25
  26
  27       //--------------------------/
  28      //- Class/Member Variables -/
  29     //--------------------------/
  30
  31     /**
  32      * Field nsPrefix
  33      */
  34     private java.lang.String nsPrefix;
  35
  36     /**
  37      * Field nsURI
  38      */
  39     private java.lang.String nsURI;
  40
  41     /**
  42      * Field xmlName
  43      */
  44     private java.lang.String xmlName;
  45
  46     /**
  47      * Field identity
  48      */
  49     private org.exolab.castor.xml.XMLFieldDescriptor identity;
  50
  51
  52       //----------------/
  53      //- Constructors -/
  54     //----------------/
  55
  56     public AlignmentDescriptor()
  57      {
  58         super();
  59         nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
  60         xmlName = "Alignment";
  61
  62         //-- set grouping compositor
  63         setCompositorAsSequence();
  64         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
  65         org.exolab.castor.mapping.FieldHandler             handler        = null;
  66         org.exolab.castor.xml.FieldValidator               fieldValidator = null;
  67         //-- initialize attribute descriptors
  68
  69         //-- _gapChar
  70         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);
  71         desc.setImmutable(true);
  72         handler = new org.exolab.castor.xml.XMLFieldHandler() {
  73             public java.lang.Object getValue( java.lang.Object object )
  74                 throws IllegalStateException
  75             {
  76                 Alignment target = (Alignment) object;
  77                 return target.getGapChar();
  78             }
  79             public void setValue( java.lang.Object object, java.lang.Object value)
  80                 throws IllegalStateException, IllegalArgumentException
  81             {
  82                 try {
  83                     Alignment target = (Alignment) object;
  84                     target.setGapChar( (java.lang.String) value);
  85                 }
  86                 catch (java.lang.Exception ex) {
  87                     throw new IllegalStateException(ex.toString());
  88                 }
  89             }
  90             public java.lang.Object newInstance( java.lang.Object parent ) {
  91                 return null;
  92             }
  93         };
  94         desc.setHandler(handler);
  95         desc.setRequired(true);
  96         desc.setMultivalued(false);
  97         addFieldDescriptor(desc);
  98
  99         //-- validation code for: _gapChar
 100         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 101         fieldValidator.setMinOccurs(1);
 102         { //-- local scope
 103             StringValidator typeValidator = new StringValidator();
 104             typeValidator.setWhiteSpace("preserve");
 105             fieldValidator.setValidator(typeValidator);
 106         }
 107         desc.setValidator(fieldValidator);
 108         //-- _aligned
 109         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);
 110         handler = new org.exolab.castor.xml.XMLFieldHandler() {
 111             public java.lang.Object getValue( java.lang.Object object )
 112                 throws IllegalStateException
 113             {
 114                 Alignment target = (Alignment) object;
 115                 if(!target.hasAligned())
 116                     return null;
 117                 return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
 118             }
 119             public void setValue( java.lang.Object object, java.lang.Object value)
 120                 throws IllegalStateException, IllegalArgumentException
 121             {
 122                 try {
 123                     Alignment target = (Alignment) object;
 124                     // if null, use delete method for optional primitives
 125                     if (value == null) {
 126                         target.deleteAligned();
 127                         return;
 128                     }
 129                     target.setAligned( ((java.lang.Boolean)value).booleanValue());
 130                 }
 131                 catch (java.lang.Exception ex) {
 132                     throw new IllegalStateException(ex.toString());
 133                 }
 134             }
 135             public java.lang.Object newInstance( java.lang.Object parent ) {
 136                 return null;
 137             }
 138         };
 139         desc.setHandler(handler);
 140         desc.setMultivalued(false);
 141         addFieldDescriptor(desc);
 142
 143         //-- validation code for: _aligned
 144         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 145         { //-- local scope
 146             BooleanValidator typeValidator = new BooleanValidator();
 147             fieldValidator.setValidator(typeValidator);
 148         }
 149         desc.setValidator(fieldValidator);
 150         //-- _id
 151         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
 152         this.identity = desc;
 153         handler = new org.exolab.castor.xml.XMLFieldHandler() {
 154             public java.lang.Object getValue( java.lang.Object object )
 155                 throws IllegalStateException
 156             {
 157                 Alignment target = (Alignment) object;
 158                 return target.getId();
 159             }
 160             public void setValue( java.lang.Object object, java.lang.Object value)
 161                 throws IllegalStateException, IllegalArgumentException
 162             {
 163                 try {
 164                     Alignment target = (Alignment) object;
 165                     target.setId( (java.lang.String) value);
 166                 }
 167                 catch (java.lang.Exception ex) {
 168                     throw new IllegalStateException(ex.toString());
 169                 }
 170             }
 171             public java.lang.Object newInstance( java.lang.Object parent ) {
 172                 return new java.lang.String();
 173             }
 174         };
 175         desc.setHandler(handler);
 176         desc.setMultivalued(false);
 177         addFieldDescriptor(desc);
 178
 179         //-- validation code for: _id
 180         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 181         { //-- local scope
 182         }
 183         desc.setValidator(fieldValidator);
 184         //-- _modifiable
 185         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_modifiable", "modifiable", org.exolab.castor.xml.NodeType.Attribute);
 186         desc.setImmutable(true);
 187         handler = new org.exolab.castor.xml.XMLFieldHandler() {
 188             public java.lang.Object getValue( java.lang.Object object )
 189                 throws IllegalStateException
 190             {
 191                 Alignment target = (Alignment) object;
 192                 return target.getModifiable();
 193             }
 194             public void setValue( java.lang.Object object, java.lang.Object value)
 195                 throws IllegalStateException, IllegalArgumentException
 196             {
 197                 try {
 198                     Alignment target = (Alignment) object;
 199                     target.setModifiable( (java.lang.String) value);
 200                 }
 201                 catch (java.lang.Exception ex) {
 202                     throw new IllegalStateException(ex.toString());
 203                 }
 204             }
 205             public java.lang.Object newInstance( java.lang.Object parent ) {
 206                 return null;
 207             }
 208         };
 209         desc.setHandler(handler);
 210         desc.setMultivalued(false);
 211         addFieldDescriptor(desc);
 212
 213         //-- validation code for: _modifiable
 214         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 215         { //-- local scope
 216             StringValidator typeValidator = new StringValidator();
 217             typeValidator.setWhiteSpace("preserve");
 218             fieldValidator.setValidator(typeValidator);
 219         }
 220         desc.setValidator(fieldValidator);
 221         //-- initialize element descriptors
 222
 223         //-- _alignmentAnnotationList
 224         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.AlignmentAnnotation.class, "_alignmentAnnotationList", "AlignmentAnnotation", org.exolab.castor.xml.NodeType.Element);
 225         handler = new org.exolab.castor.xml.XMLFieldHandler() {
 226             public java.lang.Object getValue( java.lang.Object object )
 227                 throws IllegalStateException
 228             {
 229                 Alignment target = (Alignment) object;
 230                 return target.getAlignmentAnnotation();
 231             }
 232             public void setValue( java.lang.Object object, java.lang.Object value)
 233                 throws IllegalStateException, IllegalArgumentException
 234             {
 235                 try {
 236                     Alignment target = (Alignment) object;
 237                     target.addAlignmentAnnotation( (uk.ac.vamsas.objects.core.AlignmentAnnotation) value);
 238                 }
 239                 catch (java.lang.Exception ex) {
 240                     throw new IllegalStateException(ex.toString());
 241                 }
 242             }
 243             public java.lang.Object newInstance( java.lang.Object parent ) {
 244                 return new uk.ac.vamsas.objects.core.AlignmentAnnotation();
 245             }
 246         };
 247         desc.setHandler(handler);
 248         desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
 249         desc.setMultivalued(true);
 250         addFieldDescriptor(desc);
 251
 252         //-- validation code for: _alignmentAnnotationList
 253         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 254         fieldValidator.setMinOccurs(0);
 255         { //-- local scope
 256         }
 257         desc.setValidator(fieldValidator);
 258         //-- _treeList
 259         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
 260         handler = new org.exolab.castor.xml.XMLFieldHandler() {
 261             public java.lang.Object getValue( java.lang.Object object )
 262                 throws IllegalStateException
 263             {
 264                 Alignment target = (Alignment) object;
 265                 return target.getTree();
 266             }
 267             public void setValue( java.lang.Object object, java.lang.Object value)
 268                 throws IllegalStateException, IllegalArgumentException
 269             {
 270                 try {
 271                     Alignment target = (Alignment) object;
 272                     target.addTree( (uk.ac.vamsas.objects.core.Tree) value);
 273                 }
 274                 catch (java.lang.Exception ex) {
 275                     throw new IllegalStateException(ex.toString());
 276                 }
 277             }
 278             public java.lang.Object newInstance( java.lang.Object parent ) {
 279                 return new uk.ac.vamsas.objects.core.Tree();
 280             }
 281         };
 282         desc.setHandler(handler);
 283         desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
 284         desc.setMultivalued(true);
 285         addFieldDescriptor(desc);
 286
 287         //-- validation code for: _treeList
 288         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 289         fieldValidator.setMinOccurs(0);
 290         { //-- local scope
 291         }
 292         desc.setValidator(fieldValidator);
 293         //-- _alignmentSequenceList
 294         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", org.exolab.castor.xml.NodeType.Element);
 295         handler = new org.exolab.castor.xml.XMLFieldHandler() {
 296             public java.lang.Object getValue( java.lang.Object object )
 297                 throws IllegalStateException
 298             {
 299                 Alignment target = (Alignment) object;
 300                 return target.getAlignmentSequence();
 301             }
 302             public void setValue( java.lang.Object object, java.lang.Object value)
 303                 throws IllegalStateException, IllegalArgumentException
 304             {
 305                 try {
 306                     Alignment target = (Alignment) object;
 307                     target.addAlignmentSequence( (uk.ac.vamsas.objects.core.AlignmentSequence) value);
 308                 }
 309                 catch (java.lang.Exception ex) {
 310                     throw new IllegalStateException(ex.toString());
 311                 }
 312             }
 313             public java.lang.Object newInstance( java.lang.Object parent ) {
 314                 return new uk.ac.vamsas.objects.core.AlignmentSequence();
 315             }
 316         };
 317         desc.setHandler(handler);
 318         desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
 319         desc.setRequired(true);
 320         desc.setMultivalued(true);
 321         addFieldDescriptor(desc);
 322
 323         //-- validation code for: _alignmentSequenceList
 324         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 325         fieldValidator.setMinOccurs(1);
 326         { //-- local scope
 327         }
 328         desc.setValidator(fieldValidator);
 329         //-- _propertyList
 330         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element);
 331         handler = new org.exolab.castor.xml.XMLFieldHandler() {
 332             public java.lang.Object getValue( java.lang.Object object )
 333                 throws IllegalStateException
 334             {
 335                 Alignment target = (Alignment) object;
 336                 return target.getProperty();
 337             }
 338             public void setValue( java.lang.Object object, java.lang.Object value)
 339                 throws IllegalStateException, IllegalArgumentException
 340             {
 341                 try {
 342                     Alignment target = (Alignment) object;
 343                     target.addProperty( (uk.ac.vamsas.objects.core.Property) value);
 344                 }
 345                 catch (java.lang.Exception ex) {
 346                     throw new IllegalStateException(ex.toString());
 347                 }
 348             }
 349             public java.lang.Object newInstance( java.lang.Object parent ) {
 350                 return new uk.ac.vamsas.objects.core.Property();
 351             }
 352         };
 353         desc.setHandler(handler);
 354         desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
 355         desc.setMultivalued(true);
 356         addFieldDescriptor(desc);
 357
 358         //-- validation code for: _propertyList
 359         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 360         fieldValidator.setMinOccurs(0);
 361         { //-- local scope
 362         }
 363         desc.setValidator(fieldValidator);
 364         //-- _provenance
 365         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
 366         handler = new org.exolab.castor.xml.XMLFieldHandler() {
 367             public java.lang.Object getValue( java.lang.Object object )
 368                 throws IllegalStateException
 369             {
 370                 Alignment target = (Alignment) object;
 371                 return target.getProvenance();
 372             }
 373             public void setValue( java.lang.Object object, java.lang.Object value)
 374                 throws IllegalStateException, IllegalArgumentException
 375             {
 376                 try {
 377                     Alignment target = (Alignment) object;
 378                     target.setProvenance( (uk.ac.vamsas.objects.core.Provenance) value);
 379                 }
 380                 catch (java.lang.Exception ex) {
 381                     throw new IllegalStateException(ex.toString());
 382                 }
 383             }
 384             public java.lang.Object newInstance( java.lang.Object parent ) {
 385                 return new uk.ac.vamsas.objects.core.Provenance();
 386             }
 387         };
 388         desc.setHandler(handler);
 389         desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
 390         desc.setRequired(true);
 391         desc.setMultivalued(false);
 392         addFieldDescriptor(desc);
 393
 394         //-- validation code for: _provenance
 395         fieldValidator = new org.exolab.castor.xml.FieldValidator();
 396         fieldValidator.setMinOccurs(1);
 397         { //-- local scope
 398         }
 399         desc.setValidator(fieldValidator);
 400     } //-- uk.ac.vamsas.objects.core.AlignmentDescriptor()
 401
 402
 403       //-----------/
 404      //- Methods -/
 405     //-----------/
 406
 407     /**
 408      * Method getAccessMode
 409      *
 410      *
 411      *
 412      * @return AccessMode
 413      */
 414     public org.exolab.castor.mapping.AccessMode getAccessMode()
 415     {
 416         return null;
 417     } //-- org.exolab.castor.mapping.AccessMode getAccessMode()
 418
 419     /**
 420      * Method getExtends
 421      *
 422      *
 423      *
 424      * @return ClassDescriptor
 425      */
 426     public org.exolab.castor.mapping.ClassDescriptor getExtends()
 427     {
 428         return null;
 429     } //-- org.exolab.castor.mapping.ClassDescriptor getExtends()
 430
 431     /**
 432      * Method getIdentity
 433      *
 434      *
 435      *
 436      * @return FieldDescriptor
 437      */
 438     public org.exolab.castor.mapping.FieldDescriptor getIdentity()
 439     {
 440         return identity;
 441     } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity()
 442
 443     /**
 444      * Method getJavaClass
 445      *
 446      *
 447      *
 448      * @return Class
 449      */
 450     public java.lang.Class getJavaClass()
 451     {
 452         return uk.ac.vamsas.objects.core.Alignment.class;
 453     } //-- java.lang.Class getJavaClass()
 454
 455     /**
 456      * Method getNameSpacePrefix
 457      *
 458      *
 459      *
 460      * @return String
 461      */
 462     public java.lang.String getNameSpacePrefix()
 463     {
 464         return nsPrefix;
 465     } //-- java.lang.String getNameSpacePrefix()
 466
 467     /**
 468      * Method getNameSpaceURI
 469      *
 470      *
 471      *
 472      * @return String
 473      */
 474     public java.lang.String getNameSpaceURI()
 475     {
 476         return nsURI;
 477     } //-- java.lang.String getNameSpaceURI()
 478
 479     /**
 480      * Method getValidator
 481      *
 482      *
 483      *
 484      * @return TypeValidator
 485      */
 486     public org.exolab.castor.xml.TypeValidator getValidator()
 487     {
 488         return this;
 489     } //-- org.exolab.castor.xml.TypeValidator getValidator()
 490
 491     /**
 492      * Method getXMLName
 493      *
 494      *
 495      *
 496      * @return String
 497      */
 498     public java.lang.String getXMLName()
 499     {
 500         return xmlName;
 501     } //-- java.lang.String getXMLName()
 502
 503 }