src/org/vamsas/objects/core/AlignmentDescriptor.java

   1 /*\r
   2  * This class was automatically generated with \r
   3  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
   4  * Schema.\r
   5  * $Id$\r
   6  */\r
   7 \r
   8 package org.vamsas.objects.core;\r
   9 \r
  10   //---------------------------------/\r
  11  //- Imported classes and packages -/\r
  12 //---------------------------------/\r
  13 \r
  14 import org.exolab.castor.mapping.AccessMode;\r
  15 import org.exolab.castor.xml.TypeValidator;\r
  16 import org.exolab.castor.xml.XMLFieldDescriptor;\r
  17 import org.exolab.castor.xml.validators.*;\r
  18 \r
  19 /**\r
  20  * Class AlignmentDescriptor.\r
  21  * \r
  22  * @version $Revision$ $Date$\r
  23  */\r
  24 public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
  25 \r
  26 \r
  27       //--------------------------/\r
  28      //- Class/Member Variables -/\r
  29     //--------------------------/\r
  30 \r
  31     /**\r
  32      * Field nsPrefix\r
  33      */\r
  34     private java.lang.String nsPrefix;\r
  35 \r
  36     /**\r
  37      * Field nsURI\r
  38      */\r
  39     private java.lang.String nsURI;\r
  40 \r
  41     /**\r
  42      * Field xmlName\r
  43      */\r
  44     private java.lang.String xmlName;\r
  45 \r
  46     /**\r
  47      * Field identity\r
  48      */\r
  49     private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
  50 \r
  51 \r
  52       //----------------/\r
  53      //- Constructors -/\r
  54     //----------------/\r
  55 \r
  56     public AlignmentDescriptor() {\r
  57         super();\r
  58         nsURI = "http://www.vamsas.org";\r
  59         xmlName = "Alignment";\r
  60         \r
  61         //-- set grouping compositor\r
  62         setCompositorAsSequence();\r
  63         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
  64         org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
  65         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
  66         //-- initialize attribute descriptors\r
  67         \r
  68         //-- _gapChar\r
  69         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);\r
  70         desc.setImmutable(true);\r
  71         handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
  72             public java.lang.Object getValue( java.lang.Object object ) \r
  73                 throws IllegalStateException\r
  74             {\r
  75                 Alignment target = (Alignment) object;\r
  76                 return target.getGapChar();\r
  77             }\r
  78             public void setValue( java.lang.Object object, java.lang.Object value) \r
  79                 throws IllegalStateException, IllegalArgumentException\r
  80             {\r
  81                 try {\r
  82                     Alignment target = (Alignment) object;\r
  83                     target.setGapChar( (java.lang.String) value);\r
  84                 }\r
  85                 catch (java.lang.Exception ex) {\r
  86                     throw new IllegalStateException(ex.toString());\r
  87                 }\r
  88             }\r
  89             public java.lang.Object newInstance( java.lang.Object parent ) {\r
  90                 return null;\r
  91             }\r
  92         } );\r
  93         desc.setHandler(handler);\r
  94         desc.setRequired(true);\r
  95         addFieldDescriptor(desc);\r
  96         \r
  97         //-- validation code for: _gapChar\r
  98         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
  99         fieldValidator.setMinOccurs(1);\r
 100         { //-- local scope\r
 101             StringValidator typeValidator = new StringValidator();\r
 102             typeValidator.setWhiteSpace("preserve");\r
 103             fieldValidator.setValidator(typeValidator);\r
 104         }\r
 105         desc.setValidator(fieldValidator);\r
 106         //-- _aligned\r
 107         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);\r
 108         handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
 109             public java.lang.Object getValue( java.lang.Object object ) \r
 110                 throws IllegalStateException\r
 111             {\r
 112                 Alignment target = (Alignment) object;\r
 113                 if(!target.hasAligned())\r
 114                     return null;\r
 115                 return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
 116             }\r
 117             public void setValue( java.lang.Object object, java.lang.Object value) \r
 118                 throws IllegalStateException, IllegalArgumentException\r
 119             {\r
 120                 try {\r
 121                     Alignment target = (Alignment) object;\r
 122                     // if null, use delete method for optional primitives \r
 123                     if (value == null) {\r
 124                         target.deleteAligned();\r
 125                         return;\r
 126                     }\r
 127                     target.setAligned( ((java.lang.Boolean)value).booleanValue());\r
 128                 }\r
 129                 catch (java.lang.Exception ex) {\r
 130                     throw new IllegalStateException(ex.toString());\r
 131                 }\r
 132             }\r
 133             public java.lang.Object newInstance( java.lang.Object parent ) {\r
 134                 return null;\r
 135             }\r
 136         } );\r
 137         desc.setHandler(handler);\r
 138         addFieldDescriptor(desc);\r
 139         \r
 140         //-- validation code for: _aligned\r
 141         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 142         { //-- local scope\r
 143             BooleanValidator typeValidator = new BooleanValidator();\r
 144             fieldValidator.setValidator(typeValidator);\r
 145         }\r
 146         desc.setValidator(fieldValidator);\r
 147         //-- _id\r
 148         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
 149         this.identity = desc;\r
 150         handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
 151             public java.lang.Object getValue( java.lang.Object object ) \r
 152                 throws IllegalStateException\r
 153             {\r
 154                 Alignment target = (Alignment) object;\r
 155                 return target.getId();\r
 156             }\r
 157             public void setValue( java.lang.Object object, java.lang.Object value) \r
 158                 throws IllegalStateException, IllegalArgumentException\r
 159             {\r
 160                 try {\r
 161                     Alignment target = (Alignment) object;\r
 162                     target.setId( (java.lang.String) value);\r
 163                 }\r
 164                 catch (java.lang.Exception ex) {\r
 165                     throw new IllegalStateException(ex.toString());\r
 166                 }\r
 167             }\r
 168             public java.lang.Object newInstance( java.lang.Object parent ) {\r
 169                 return new java.lang.String();\r
 170             }\r
 171         } );\r
 172         desc.setHandler(handler);\r
 173         addFieldDescriptor(desc);\r
 174         \r
 175         //-- validation code for: _id\r
 176         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 177         { //-- local scope\r
 178         }\r
 179         desc.setValidator(fieldValidator);\r
 180         //-- initialize element descriptors\r
 181         \r
 182         //-- _alignmentAnnotationsList\r
 183         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotations.class, "_alignmentAnnotationsList", "AlignmentAnnotations", org.exolab.castor.xml.NodeType.Element);\r
 184         handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
 185             public java.lang.Object getValue( java.lang.Object object ) \r
 186                 throws IllegalStateException\r
 187             {\r
 188                 Alignment target = (Alignment) object;\r
 189                 return target.getAlignmentAnnotations();\r
 190             }\r
 191             public void setValue( java.lang.Object object, java.lang.Object value) \r
 192                 throws IllegalStateException, IllegalArgumentException\r
 193             {\r
 194                 try {\r
 195                     Alignment target = (Alignment) object;\r
 196                     target.addAlignmentAnnotations( (org.vamsas.objects.core.AlignmentAnnotations) value);\r
 197                 }\r
 198                 catch (java.lang.Exception ex) {\r
 199                     throw new IllegalStateException(ex.toString());\r
 200                 }\r
 201             }\r
 202             public java.lang.Object newInstance( java.lang.Object parent ) {\r
 203                 return new org.vamsas.objects.core.AlignmentAnnotations();\r
 204             }\r
 205         } );\r
 206         desc.setHandler(handler);\r
 207         desc.setNameSpaceURI("http://www.vamsas.org");\r
 208         desc.setMultivalued(true);\r
 209         addFieldDescriptor(desc);\r
 210         \r
 211         //-- validation code for: _alignmentAnnotationsList\r
 212         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 213         fieldValidator.setMinOccurs(0);\r
 214         { //-- local scope\r
 215         }\r
 216         desc.setValidator(fieldValidator);\r
 217         //-- _treeList\r
 218         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);\r
 219         handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
 220             public java.lang.Object getValue( java.lang.Object object ) \r
 221                 throws IllegalStateException\r
 222             {\r
 223                 Alignment target = (Alignment) object;\r
 224                 return target.getTree();\r
 225             }\r
 226             public void setValue( java.lang.Object object, java.lang.Object value) \r
 227                 throws IllegalStateException, IllegalArgumentException\r
 228             {\r
 229                 try {\r
 230                     Alignment target = (Alignment) object;\r
 231                     target.addTree( (org.vamsas.objects.core.Tree) value);\r
 232                 }\r
 233                 catch (java.lang.Exception ex) {\r
 234                     throw new IllegalStateException(ex.toString());\r
 235                 }\r
 236             }\r
 237             public java.lang.Object newInstance( java.lang.Object parent ) {\r
 238                 return new org.vamsas.objects.core.Tree();\r
 239             }\r
 240         } );\r
 241         desc.setHandler(handler);\r
 242         desc.setNameSpaceURI("http://www.vamsas.org");\r
 243         desc.setMultivalued(true);\r
 244         addFieldDescriptor(desc);\r
 245         \r
 246         //-- validation code for: _treeList\r
 247         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 248         fieldValidator.setMinOccurs(0);\r
 249         { //-- local scope\r
 250         }\r
 251         desc.setValidator(fieldValidator);\r
 252         //-- _alignmentSequenceList\r
 253         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", org.exolab.castor.xml.NodeType.Element);\r
 254         handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
 255             public java.lang.Object getValue( java.lang.Object object ) \r
 256                 throws IllegalStateException\r
 257             {\r
 258                 Alignment target = (Alignment) object;\r
 259                 return target.getAlignmentSequence();\r
 260             }\r
 261             public void setValue( java.lang.Object object, java.lang.Object value) \r
 262                 throws IllegalStateException, IllegalArgumentException\r
 263             {\r
 264                 try {\r
 265                     Alignment target = (Alignment) object;\r
 266                     target.addAlignmentSequence( (org.vamsas.objects.core.AlignmentSequence) value);\r
 267                 }\r
 268                 catch (java.lang.Exception ex) {\r
 269                     throw new IllegalStateException(ex.toString());\r
 270                 }\r
 271             }\r
 272             public java.lang.Object newInstance( java.lang.Object parent ) {\r
 273                 return new org.vamsas.objects.core.AlignmentSequence();\r
 274             }\r
 275         } );\r
 276         desc.setHandler(handler);\r
 277         desc.setNameSpaceURI("http://www.vamsas.org");\r
 278         desc.setRequired(true);\r
 279         desc.setMultivalued(true);\r
 280         addFieldDescriptor(desc);\r
 281         \r
 282         //-- validation code for: _alignmentSequenceList\r
 283         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 284         fieldValidator.setMinOccurs(1);\r
 285         { //-- local scope\r
 286         }\r
 287         desc.setValidator(fieldValidator);\r
 288         //-- _provenance\r
 289         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
 290         handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
 291             public java.lang.Object getValue( java.lang.Object object ) \r
 292                 throws IllegalStateException\r
 293             {\r
 294                 Alignment target = (Alignment) object;\r
 295                 return target.getProvenance();\r
 296             }\r
 297             public void setValue( java.lang.Object object, java.lang.Object value) \r
 298                 throws IllegalStateException, IllegalArgumentException\r
 299             {\r
 300                 try {\r
 301                     Alignment target = (Alignment) object;\r
 302                     target.setProvenance( (org.vamsas.objects.core.Provenance) value);\r
 303                 }\r
 304                 catch (java.lang.Exception ex) {\r
 305                     throw new IllegalStateException(ex.toString());\r
 306                 }\r
 307             }\r
 308             public java.lang.Object newInstance( java.lang.Object parent ) {\r
 309                 return new org.vamsas.objects.core.Provenance();\r
 310             }\r
 311         } );\r
 312         desc.setHandler(handler);\r
 313         desc.setNameSpaceURI("http://www.vamsas.org");\r
 314         desc.setRequired(true);\r
 315         desc.setMultivalued(false);\r
 316         addFieldDescriptor(desc);\r
 317         \r
 318         //-- validation code for: _provenance\r
 319         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 320         fieldValidator.setMinOccurs(1);\r
 321         { //-- local scope\r
 322         }\r
 323         desc.setValidator(fieldValidator);\r
 324     } //-- org.vamsas.objects.core.AlignmentDescriptor()\r
 325 \r
 326 \r
 327       //-----------/\r
 328      //- Methods -/\r
 329     //-----------/\r
 330 \r
 331     /**\r
 332      * Method getAccessMode\r
 333      * \r
 334      * \r
 335      * \r
 336      * @return AccessMode\r
 337      */\r
 338     public org.exolab.castor.mapping.AccessMode getAccessMode()\r
 339     {\r
 340         return null;\r
 341     } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
 342 \r
 343     /**\r
 344      * Method getExtends\r
 345      * \r
 346      * \r
 347      * \r
 348      * @return ClassDescriptor\r
 349      */\r
 350     public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
 351     {\r
 352         return null;\r
 353     } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
 354 \r
 355     /**\r
 356      * Method getIdentity\r
 357      * \r
 358      * \r
 359      * \r
 360      * @return FieldDescriptor\r
 361      */\r
 362     public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
 363     {\r
 364         return identity;\r
 365     } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
 366 \r
 367     /**\r
 368      * Method getJavaClass\r
 369      * \r
 370      * \r
 371      * \r
 372      * @return Class\r
 373      */\r
 374     public java.lang.Class getJavaClass()\r
 375     {\r
 376         return org.vamsas.objects.core.Alignment.class;\r
 377     } //-- java.lang.Class getJavaClass() \r
 378 \r
 379     /**\r
 380      * Method getNameSpacePrefix\r
 381      * \r
 382      * \r
 383      * \r
 384      * @return String\r
 385      */\r
 386     public java.lang.String getNameSpacePrefix()\r
 387     {\r
 388         return nsPrefix;\r
 389     } //-- java.lang.String getNameSpacePrefix() \r
 390 \r
 391     /**\r
 392      * Method getNameSpaceURI\r
 393      * \r
 394      * \r
 395      * \r
 396      * @return String\r
 397      */\r
 398     public java.lang.String getNameSpaceURI()\r
 399     {\r
 400         return nsURI;\r
 401     } //-- java.lang.String getNameSpaceURI() \r
 402 \r
 403     /**\r
 404      * Method getValidator\r
 405      * \r
 406      * \r
 407      * \r
 408      * @return TypeValidator\r
 409      */\r
 410     public org.exolab.castor.xml.TypeValidator getValidator()\r
 411     {\r
 412         return this;\r
 413     } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
 414 \r
 415     /**\r
 416      * Method getXMLName\r
 417      * \r
 418      * \r
 419      * \r
 420      * @return String\r
 421      */\r
 422     public java.lang.String getXMLName()\r
 423     {\r
 424         return xmlName;\r
 425     } //-- java.lang.String getXMLName() \r
 426 \r
 427 }\r