2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.schemabinding.version2.descriptors;
20 //---------------------------------/
21 //- Imported classes and packages -/
22 //---------------------------------/
24 import jalview.schemabinding.version2.Feature;
27 * Class FeatureDescriptor.
29 * @version $Revision$ $Date$
31 public class FeatureDescriptor extends
32 org.exolab.castor.xml.util.XMLClassDescriptorImpl
35 // --------------------------/
36 // - Class/Member Variables -/
37 // --------------------------/
40 * Field _elementDefinition.
42 private boolean _elementDefinition;
47 private java.lang.String _nsPrefix;
52 private java.lang.String _nsURI;
57 private java.lang.String _xmlName;
63 public FeatureDescriptor()
66 _nsURI = "www.jalview.org";
68 _elementDefinition = false;
70 // -- set grouping compositor
71 setCompositorAsSequence();
72 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
73 org.exolab.castor.mapping.FieldHandler handler = null;
74 org.exolab.castor.xml.FieldValidator fieldValidator = null;
75 // -- initialize attribute descriptors
78 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
79 java.lang.Integer.TYPE, "_begin", "begin",
80 org.exolab.castor.xml.NodeType.Attribute);
81 handler = new org.exolab.castor.xml.XMLFieldHandler()
83 public java.lang.Object getValue(java.lang.Object object)
84 throws IllegalStateException
86 Feature target = (Feature) object;
87 if (!target.hasBegin())
91 return new java.lang.Integer(target.getBegin());
94 public void setValue(java.lang.Object object, java.lang.Object value)
95 throws IllegalStateException, IllegalArgumentException
99 Feature target = (Feature) object;
100 // ignore null values for non optional primitives
106 target.setBegin(((java.lang.Integer) value).intValue());
107 } catch (java.lang.Exception ex)
109 throw new IllegalStateException(ex.toString());
113 public java.lang.Object newInstance(java.lang.Object parent)
118 desc.setHandler(handler);
119 desc.setRequired(true);
120 desc.setMultivalued(false);
121 addFieldDescriptor(desc);
123 // -- validation code for: _begin
124 fieldValidator = new org.exolab.castor.xml.FieldValidator();
125 fieldValidator.setMinOccurs(1);
127 org.exolab.castor.xml.validators.IntValidator typeValidator;
128 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
129 fieldValidator.setValidator(typeValidator);
130 typeValidator.setMinInclusive(-2147483648);
131 typeValidator.setMaxInclusive(2147483647);
133 desc.setValidator(fieldValidator);
135 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
136 java.lang.Integer.TYPE, "_end", "end",
137 org.exolab.castor.xml.NodeType.Attribute);
138 handler = new org.exolab.castor.xml.XMLFieldHandler()
140 public java.lang.Object getValue(java.lang.Object object)
141 throws IllegalStateException
143 Feature target = (Feature) object;
144 if (!target.hasEnd())
148 return new java.lang.Integer(target.getEnd());
151 public void setValue(java.lang.Object object, java.lang.Object value)
152 throws IllegalStateException, IllegalArgumentException
156 Feature target = (Feature) object;
157 // ignore null values for non optional primitives
163 target.setEnd(((java.lang.Integer) value).intValue());
164 } catch (java.lang.Exception ex)
166 throw new IllegalStateException(ex.toString());
170 public java.lang.Object newInstance(java.lang.Object parent)
175 desc.setHandler(handler);
176 desc.setRequired(true);
177 desc.setMultivalued(false);
178 addFieldDescriptor(desc);
180 // -- validation code for: _end
181 fieldValidator = new org.exolab.castor.xml.FieldValidator();
182 fieldValidator.setMinOccurs(1);
184 org.exolab.castor.xml.validators.IntValidator typeValidator;
185 typeValidator = new org.exolab.castor.xml.validators.IntValidator();
186 fieldValidator.setValidator(typeValidator);
187 typeValidator.setMinInclusive(-2147483648);
188 typeValidator.setMaxInclusive(2147483647);
190 desc.setValidator(fieldValidator);
192 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
193 java.lang.String.class, "_type", "type",
194 org.exolab.castor.xml.NodeType.Attribute);
195 desc.setImmutable(true);
196 handler = new org.exolab.castor.xml.XMLFieldHandler()
198 public java.lang.Object getValue(java.lang.Object object)
199 throws IllegalStateException
201 Feature target = (Feature) object;
202 return target.getType();
205 public void setValue(java.lang.Object object, java.lang.Object value)
206 throws IllegalStateException, IllegalArgumentException
210 Feature target = (Feature) object;
211 target.setType((java.lang.String) value);
212 } catch (java.lang.Exception ex)
214 throw new IllegalStateException(ex.toString());
218 public java.lang.Object newInstance(java.lang.Object parent)
223 desc.setHandler(handler);
224 desc.setRequired(true);
225 desc.setMultivalued(false);
226 addFieldDescriptor(desc);
228 // -- validation code for: _type
229 fieldValidator = new org.exolab.castor.xml.FieldValidator();
230 fieldValidator.setMinOccurs(1);
232 org.exolab.castor.xml.validators.StringValidator typeValidator;
233 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
234 fieldValidator.setValidator(typeValidator);
235 typeValidator.setWhiteSpace("preserve");
237 desc.setValidator(fieldValidator);
239 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
240 java.lang.String.class, "_description", "description",
241 org.exolab.castor.xml.NodeType.Attribute);
242 desc.setImmutable(true);
243 handler = new org.exolab.castor.xml.XMLFieldHandler()
245 public java.lang.Object getValue(java.lang.Object object)
246 throws IllegalStateException
248 Feature target = (Feature) object;
249 return target.getDescription();
252 public void setValue(java.lang.Object object, java.lang.Object value)
253 throws IllegalStateException, IllegalArgumentException
257 Feature target = (Feature) object;
258 target.setDescription((java.lang.String) value);
259 } catch (java.lang.Exception ex)
261 throw new IllegalStateException(ex.toString());
265 public java.lang.Object newInstance(java.lang.Object parent)
270 desc.setHandler(handler);
271 desc.setMultivalued(false);
272 addFieldDescriptor(desc);
274 // -- validation code for: _description
275 fieldValidator = new org.exolab.castor.xml.FieldValidator();
277 org.exolab.castor.xml.validators.StringValidator typeValidator;
278 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
279 fieldValidator.setValidator(typeValidator);
280 typeValidator.setWhiteSpace("preserve");
282 desc.setValidator(fieldValidator);
284 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
285 java.lang.String.class, "_status", "status",
286 org.exolab.castor.xml.NodeType.Attribute);
287 desc.setImmutable(true);
288 handler = new org.exolab.castor.xml.XMLFieldHandler()
290 public java.lang.Object getValue(java.lang.Object object)
291 throws IllegalStateException
293 Feature target = (Feature) object;
294 return target.getStatus();
297 public void setValue(java.lang.Object object, java.lang.Object value)
298 throws IllegalStateException, IllegalArgumentException
302 Feature target = (Feature) object;
303 target.setStatus((java.lang.String) value);
304 } catch (java.lang.Exception ex)
306 throw new IllegalStateException(ex.toString());
310 public java.lang.Object newInstance(java.lang.Object parent)
315 desc.setHandler(handler);
316 desc.setMultivalued(false);
317 addFieldDescriptor(desc);
319 // -- validation code for: _status
320 fieldValidator = new org.exolab.castor.xml.FieldValidator();
322 org.exolab.castor.xml.validators.StringValidator typeValidator;
323 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
324 fieldValidator.setValidator(typeValidator);
325 typeValidator.setWhiteSpace("preserve");
327 desc.setValidator(fieldValidator);
329 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
330 java.lang.String.class, "_featureGroup", "featureGroup",
331 org.exolab.castor.xml.NodeType.Attribute);
332 desc.setImmutable(true);
333 handler = new org.exolab.castor.xml.XMLFieldHandler()
335 public java.lang.Object getValue(java.lang.Object object)
336 throws IllegalStateException
338 Feature target = (Feature) object;
339 return target.getFeatureGroup();
342 public void setValue(java.lang.Object object, java.lang.Object value)
343 throws IllegalStateException, IllegalArgumentException
347 Feature target = (Feature) object;
348 target.setFeatureGroup((java.lang.String) value);
349 } catch (java.lang.Exception ex)
351 throw new IllegalStateException(ex.toString());
355 public java.lang.Object newInstance(java.lang.Object parent)
360 desc.setHandler(handler);
361 desc.setMultivalued(false);
362 addFieldDescriptor(desc);
364 // -- validation code for: _featureGroup
365 fieldValidator = new org.exolab.castor.xml.FieldValidator();
367 org.exolab.castor.xml.validators.StringValidator typeValidator;
368 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
369 fieldValidator.setValidator(typeValidator);
370 typeValidator.setWhiteSpace("preserve");
372 desc.setValidator(fieldValidator);
374 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
375 java.lang.Float.TYPE, "_score", "score",
376 org.exolab.castor.xml.NodeType.Attribute);
377 handler = new org.exolab.castor.xml.XMLFieldHandler()
379 public java.lang.Object getValue(java.lang.Object object)
380 throws IllegalStateException
382 Feature target = (Feature) object;
383 if (!target.hasScore())
387 return new java.lang.Float(target.getScore());
390 public void setValue(java.lang.Object object, java.lang.Object value)
391 throws IllegalStateException, IllegalArgumentException
395 Feature target = (Feature) object;
396 // if null, use delete method for optional primitives
399 target.deleteScore();
402 target.setScore(((java.lang.Float) value).floatValue());
403 } catch (java.lang.Exception ex)
405 throw new IllegalStateException(ex.toString());
409 public java.lang.Object newInstance(java.lang.Object parent)
414 desc.setHandler(handler);
415 desc.setMultivalued(false);
416 addFieldDescriptor(desc);
418 // -- validation code for: _score
419 fieldValidator = new org.exolab.castor.xml.FieldValidator();
421 org.exolab.castor.xml.validators.FloatValidator typeValidator;
422 typeValidator = new org.exolab.castor.xml.validators.FloatValidator();
423 fieldValidator.setValidator(typeValidator);
424 typeValidator.setMinInclusive((float) -3.4028235E38);
425 typeValidator.setMaxInclusive((float) 3.4028235E38);
427 desc.setValidator(fieldValidator);
428 // -- initialize element descriptors
431 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
432 jalview.schemabinding.version2.OtherData.class,
433 "_otherDataList", "otherData",
434 org.exolab.castor.xml.NodeType.Element);
435 handler = new org.exolab.castor.xml.XMLFieldHandler()
437 public java.lang.Object getValue(java.lang.Object object)
438 throws IllegalStateException
440 Feature target = (Feature) object;
441 return target.getOtherData();
444 public void setValue(java.lang.Object object, java.lang.Object value)
445 throws IllegalStateException, IllegalArgumentException
449 Feature target = (Feature) object;
450 target.addOtherData((jalview.schemabinding.version2.OtherData) value);
451 } catch (java.lang.Exception ex)
453 throw new IllegalStateException(ex.toString());
457 public void resetValue(Object object) throws IllegalStateException,
458 IllegalArgumentException
462 Feature target = (Feature) object;
463 target.removeAllOtherData();
464 } catch (java.lang.Exception ex)
466 throw new IllegalStateException(ex.toString());
470 public java.lang.Object newInstance(java.lang.Object parent)
472 return new jalview.schemabinding.version2.OtherData();
475 desc.setHandler(handler);
476 desc.setNameSpaceURI("www.jalview.org");
477 desc.setMultivalued(true);
478 addFieldDescriptor(desc);
480 // -- validation code for: _otherDataList
481 fieldValidator = new org.exolab.castor.xml.FieldValidator();
482 fieldValidator.setMinOccurs(0);
485 desc.setValidator(fieldValidator);
493 * Method getAccessMode.
495 * @return the access mode specified for this class.
497 public org.exolab.castor.mapping.AccessMode getAccessMode()
503 * Method getIdentity.
505 * @return the identity field, null if this class has no identity.
507 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
509 return super.getIdentity();
513 * Method getJavaClass.
515 * @return the Java class represented by this descriptor.
517 public java.lang.Class getJavaClass()
519 return jalview.schemabinding.version2.Feature.class;
523 * Method getNameSpacePrefix.
525 * @return the namespace prefix to use when marshaling as XML.
527 public java.lang.String getNameSpacePrefix()
533 * Method getNameSpaceURI.
535 * @return the namespace URI used when marshaling and unmarshaling as XML.
537 public java.lang.String getNameSpaceURI()
543 * Method getValidator.
545 * @return a specific validator for the class described by this
548 public org.exolab.castor.xml.TypeValidator getValidator()
556 * @return the XML Name for the Class being described.
558 public java.lang.String getXMLName()
564 * Method isElementDefinition.
566 * @return true if XML schema definition of this Class is that of a global
567 * element or element with anonymous type definition.
569 public boolean isElementDefinition()
571 return _elementDefinition;