src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java

   1 /*\r
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)\r
   3  * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
   4  * \r
   5  * This program is free software; you can redistribute it and/or\r
   6  * modify it under the terms of the GNU General Public License\r
   7  * as published by the Free Software Foundation; either version 2\r
   8  * of the License, or (at your option) any later version.\r
   9  * \r
  10  * This program is distributed in the hope that it will be useful,\r
  11  * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
  12  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
  13  * GNU General Public License for more details.\r
  14  * \r
  15  * You should have received a copy of the GNU General Public License\r
  16  * along with this program; if not, write to the Free Software\r
  17  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
  18  */\r
  19 package jalview.schemabinding.version2.descriptors;\r
  20 \r
  21   //---------------------------------/\r
  22  //- Imported classes and packages -/\r
  23 //---------------------------------/\r
  24 \r
  25 import jalview.schemabinding.version2.SequenceSet;\r
  26 \r
  27 /**\r
  28  * Class SequenceSetDescriptor.\r
  29  * \r
  30  * @version $Revision$ $Date$\r
  31  */\r
  32 public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
  33 \r
  34 \r
  35       //--------------------------/\r
  36      //- Class/Member Variables -/\r
  37     //--------------------------/\r
  38 \r
  39     /**\r
  40      * Field _elementDefinition.\r
  41      */\r
  42     private boolean _elementDefinition;\r
  43 \r
  44     /**\r
  45      * Field _nsPrefix.\r
  46      */\r
  47     private java.lang.String _nsPrefix;\r
  48 \r
  49     /**\r
  50      * Field _nsURI.\r
  51      */\r
  52     private java.lang.String _nsURI;\r
  53 \r
  54     /**\r
  55      * Field _xmlName.\r
  56      */\r
  57     private java.lang.String _xmlName;\r
  58 \r
  59 \r
  60       //----------------/\r
  61      //- Constructors -/\r
  62     //----------------/\r
  63 \r
  64     public SequenceSetDescriptor() {\r
  65         super();\r
  66         _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
  67         _xmlName = "SequenceSet";\r
  68         _elementDefinition = true;\r
  69         \r
  70         //-- set grouping compositor\r
  71         setCompositorAsSequence();\r
  72         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
  73         org.exolab.castor.mapping.FieldHandler             handler        = null;\r
  74         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
  75         //-- initialize attribute descriptors\r
  76         \r
  77         //-- _gapChar\r
  78         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);\r
  79         desc.setImmutable(true);\r
  80         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
  81             public java.lang.Object getValue( java.lang.Object object ) \r
  82                 throws IllegalStateException\r
  83             {\r
  84                 SequenceSet target = (SequenceSet) object;\r
  85                 return target.getGapChar();\r
  86             }\r
  87             public void setValue( java.lang.Object object, java.lang.Object value) \r
  88                 throws IllegalStateException, IllegalArgumentException\r
  89             {\r
  90                 try {\r
  91                     SequenceSet target = (SequenceSet) object;\r
  92                     target.setGapChar( (java.lang.String) value);\r
  93                 } catch (java.lang.Exception ex) {\r
  94                     throw new IllegalStateException(ex.toString());\r
  95                 }\r
  96             }\r
  97             public java.lang.Object newInstance(java.lang.Object parent) {\r
  98                 return null;\r
  99             }\r
 100         };\r
 101         desc.setHandler(handler);\r
 102         desc.setRequired(true);\r
 103         desc.setMultivalued(false);\r
 104         addFieldDescriptor(desc);\r
 105         \r
 106         //-- validation code for: _gapChar\r
 107         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 108         fieldValidator.setMinOccurs(1);\r
 109         { //-- local scope\r
 110             org.exolab.castor.xml.validators.StringValidator typeValidator;\r
 111             typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
 112             fieldValidator.setValidator(typeValidator);\r
 113             typeValidator.setWhiteSpace("preserve");\r
 114         }\r
 115         desc.setValidator(fieldValidator);\r
 116         //-- _datasetId\r
 117         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute);\r
 118         desc.setImmutable(true);\r
 119         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
 120             public java.lang.Object getValue( java.lang.Object object ) \r
 121                 throws IllegalStateException\r
 122             {\r
 123                 SequenceSet target = (SequenceSet) object;\r
 124                 return target.getDatasetId();\r
 125             }\r
 126             public void setValue( java.lang.Object object, java.lang.Object value) \r
 127                 throws IllegalStateException, IllegalArgumentException\r
 128             {\r
 129                 try {\r
 130                     SequenceSet target = (SequenceSet) object;\r
 131                     target.setDatasetId( (java.lang.String) value);\r
 132                 } catch (java.lang.Exception ex) {\r
 133                     throw new IllegalStateException(ex.toString());\r
 134                 }\r
 135             }\r
 136             public java.lang.Object newInstance(java.lang.Object parent) {\r
 137                 return null;\r
 138             }\r
 139         };\r
 140         desc.setHandler(handler);\r
 141         desc.setMultivalued(false);\r
 142         addFieldDescriptor(desc);\r
 143         \r
 144         //-- validation code for: _datasetId\r
 145         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 146         { //-- local scope\r
 147             org.exolab.castor.xml.validators.StringValidator typeValidator;\r
 148             typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
 149             fieldValidator.setValidator(typeValidator);\r
 150             typeValidator.setWhiteSpace("preserve");\r
 151         }\r
 152         desc.setValidator(fieldValidator);\r
 153         //-- initialize element descriptors\r
 154         \r
 155         //-- _sequenceList\r
 156         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);\r
 157         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
 158             public java.lang.Object getValue( java.lang.Object object ) \r
 159                 throws IllegalStateException\r
 160             {\r
 161                 SequenceSet target = (SequenceSet) object;\r
 162                 return target.getSequence();\r
 163             }\r
 164             public void setValue( java.lang.Object object, java.lang.Object value) \r
 165                 throws IllegalStateException, IllegalArgumentException\r
 166             {\r
 167                 try {\r
 168                     SequenceSet target = (SequenceSet) object;\r
 169                     target.addSequence( (jalview.schemabinding.version2.Sequence) value);\r
 170                 } catch (java.lang.Exception ex) {\r
 171                     throw new IllegalStateException(ex.toString());\r
 172                 }\r
 173             }\r
 174             public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
 175                 try {\r
 176                     SequenceSet target = (SequenceSet) object;\r
 177                     target.removeAllSequence();\r
 178                 } catch (java.lang.Exception ex) {\r
 179                     throw new IllegalStateException(ex.toString());\r
 180                 }\r
 181             }\r
 182             public java.lang.Object newInstance(java.lang.Object parent) {\r
 183                 return new jalview.schemabinding.version2.Sequence();\r
 184             }\r
 185         };\r
 186         desc.setHandler(handler);\r
 187         desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
 188         desc.setMultivalued(true);\r
 189         addFieldDescriptor(desc);\r
 190         \r
 191         //-- validation code for: _sequenceList\r
 192         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 193         fieldValidator.setMinOccurs(0);\r
 194         { //-- local scope\r
 195         }\r
 196         desc.setValidator(fieldValidator);\r
 197         //-- _annotationList\r
 198         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);\r
 199         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
 200             public java.lang.Object getValue( java.lang.Object object ) \r
 201                 throws IllegalStateException\r
 202             {\r
 203                 SequenceSet target = (SequenceSet) object;\r
 204                 return target.getAnnotation();\r
 205             }\r
 206             public void setValue( java.lang.Object object, java.lang.Object value) \r
 207                 throws IllegalStateException, IllegalArgumentException\r
 208             {\r
 209                 try {\r
 210                     SequenceSet target = (SequenceSet) object;\r
 211                     target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);\r
 212                 } catch (java.lang.Exception ex) {\r
 213                     throw new IllegalStateException(ex.toString());\r
 214                 }\r
 215             }\r
 216             public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
 217                 try {\r
 218                     SequenceSet target = (SequenceSet) object;\r
 219                     target.removeAllAnnotation();\r
 220                 } catch (java.lang.Exception ex) {\r
 221                     throw new IllegalStateException(ex.toString());\r
 222                 }\r
 223             }\r
 224             public java.lang.Object newInstance(java.lang.Object parent) {\r
 225                 return new jalview.schemabinding.version2.Annotation();\r
 226             }\r
 227         };\r
 228         desc.setHandler(handler);\r
 229         desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
 230         desc.setMultivalued(true);\r
 231         addFieldDescriptor(desc);\r
 232         \r
 233         //-- validation code for: _annotationList\r
 234         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 235         fieldValidator.setMinOccurs(0);\r
 236         { //-- local scope\r
 237         }\r
 238         desc.setValidator(fieldValidator);\r
 239         //-- _sequenceSetPropertiesList\r
 240         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element);\r
 241         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
 242             public java.lang.Object getValue( java.lang.Object object ) \r
 243                 throws IllegalStateException\r
 244             {\r
 245                 SequenceSet target = (SequenceSet) object;\r
 246                 return target.getSequenceSetProperties();\r
 247             }\r
 248             public void setValue( java.lang.Object object, java.lang.Object value) \r
 249                 throws IllegalStateException, IllegalArgumentException\r
 250             {\r
 251                 try {\r
 252                     SequenceSet target = (SequenceSet) object;\r
 253                     target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value);\r
 254                 } catch (java.lang.Exception ex) {\r
 255                     throw new IllegalStateException(ex.toString());\r
 256                 }\r
 257             }\r
 258             public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
 259                 try {\r
 260                     SequenceSet target = (SequenceSet) object;\r
 261                     target.removeAllSequenceSetProperties();\r
 262                 } catch (java.lang.Exception ex) {\r
 263                     throw new IllegalStateException(ex.toString());\r
 264                 }\r
 265             }\r
 266             public java.lang.Object newInstance(java.lang.Object parent) {\r
 267                 return new jalview.schemabinding.version2.SequenceSetProperties();\r
 268             }\r
 269         };\r
 270         desc.setHandler(handler);\r
 271         desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
 272         desc.setMultivalued(true);\r
 273         addFieldDescriptor(desc);\r
 274         \r
 275         //-- validation code for: _sequenceSetPropertiesList\r
 276         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 277         fieldValidator.setMinOccurs(0);\r
 278         { //-- local scope\r
 279         }\r
 280         desc.setValidator(fieldValidator);\r
 281         //-- _alcodonFrameList\r
 282         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element);\r
 283         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
 284             public java.lang.Object getValue( java.lang.Object object ) \r
 285                 throws IllegalStateException\r
 286             {\r
 287                 SequenceSet target = (SequenceSet) object;\r
 288                 return target.getAlcodonFrame();\r
 289             }\r
 290             public void setValue( java.lang.Object object, java.lang.Object value) \r
 291                 throws IllegalStateException, IllegalArgumentException\r
 292             {\r
 293                 try {\r
 294                     SequenceSet target = (SequenceSet) object;\r
 295                     target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value);\r
 296                 } catch (java.lang.Exception ex) {\r
 297                     throw new IllegalStateException(ex.toString());\r
 298                 }\r
 299             }\r
 300             public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
 301                 try {\r
 302                     SequenceSet target = (SequenceSet) object;\r
 303                     target.removeAllAlcodonFrame();\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 jalview.schemabinding.version2.AlcodonFrame();\r
 310             }\r
 311         };\r
 312         desc.setHandler(handler);\r
 313         desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
 314         desc.setMultivalued(true);\r
 315         addFieldDescriptor(desc);\r
 316         \r
 317         //-- validation code for: _alcodonFrameList\r
 318         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
 319         fieldValidator.setMinOccurs(0);\r
 320         { //-- local scope\r
 321         }\r
 322         desc.setValidator(fieldValidator);\r
 323     }\r
 324 \r
 325 \r
 326       //-----------/\r
 327      //- Methods -/\r
 328     //-----------/\r
 329 \r
 330     /**\r
 331      * Method getAccessMode.\r
 332      * \r
 333      * @return the access mode specified for this class.\r
 334      */\r
 335     public org.exolab.castor.mapping.AccessMode getAccessMode(\r
 336     ) {\r
 337         return null;\r
 338     }\r
 339 \r
 340     /**\r
 341      * Method getIdentity.\r
 342      * \r
 343      * @return the identity field, null if this class has no\r
 344      * identity.\r
 345      */\r
 346     public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
 347     ) {\r
 348         return super.getIdentity();\r
 349     }\r
 350 \r
 351     /**\r
 352      * Method getJavaClass.\r
 353      * \r
 354      * @return the Java class represented by this descriptor.\r
 355      */\r
 356     public java.lang.Class getJavaClass(\r
 357     ) {\r
 358         return jalview.schemabinding.version2.SequenceSet.class;\r
 359     }\r
 360 \r
 361     /**\r
 362      * Method getNameSpacePrefix.\r
 363      * \r
 364      * @return the namespace prefix to use when marshaling as XML.\r
 365      */\r
 366     public java.lang.String getNameSpacePrefix(\r
 367     ) {\r
 368         return _nsPrefix;\r
 369     }\r
 370 \r
 371     /**\r
 372      * Method getNameSpaceURI.\r
 373      * \r
 374      * @return the namespace URI used when marshaling and\r
 375      * unmarshaling as XML.\r
 376      */\r
 377     public java.lang.String getNameSpaceURI(\r
 378     ) {\r
 379         return _nsURI;\r
 380     }\r
 381 \r
 382     /**\r
 383      * Method getValidator.\r
 384      * \r
 385      * @return a specific validator for the class described by this\r
 386      * ClassDescriptor.\r
 387      */\r
 388     public org.exolab.castor.xml.TypeValidator getValidator(\r
 389     ) {\r
 390         return this;\r
 391     }\r
 392 \r
 393     /**\r
 394      * Method getXMLName.\r
 395      * \r
 396      * @return the XML Name for the Class being described.\r
 397      */\r
 398     public java.lang.String getXMLName(\r
 399     ) {\r
 400         return _xmlName;\r
 401     }\r
 402 \r
 403     /**\r
 404      * Method isElementDefinition.\r
 405      * \r
 406      * @return true if XML schema definition of this Class is that\r
 407      * of a global\r
 408      * element or element with anonymous type definition.\r
 409      */\r
 410     public boolean isElementDefinition(\r
 411     ) {\r
 412         return _elementDefinition;\r
 413     }\r
 414 \r
 415 }\r