2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.0.b2)
\r
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\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
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
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
19 package jalview.schemabinding.version2.descriptors;
\r
21 // ---------------------------------/
\r
22 // - Imported classes and packages -/
\r
23 // ---------------------------------/
\r
25 import jalview.schemabinding.version2.SequenceSet;
\r
28 * Class SequenceSetDescriptor.
\r
30 * @version $Revision$ $Date$
\r
32 public class SequenceSetDescriptor extends
\r
33 org.exolab.castor.xml.util.XMLClassDescriptorImpl
\r
36 // --------------------------/
\r
37 // - Class/Member Variables -/
\r
38 // --------------------------/
\r
41 * Field _elementDefinition.
\r
43 private boolean _elementDefinition;
\r
48 private java.lang.String _nsPrefix;
\r
53 private java.lang.String _nsURI;
\r
58 private java.lang.String _xmlName;
\r
60 // ----------------/
\r
61 // - Constructors -/
\r
62 // ----------------/
\r
64 public SequenceSetDescriptor()
\r
67 _nsURI = "www.vamsas.ac.uk/jalview/version2";
\r
68 _xmlName = "SequenceSet";
\r
69 _elementDefinition = true;
\r
71 // -- set grouping compositor
\r
72 setCompositorAsSequence();
\r
73 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
\r
74 org.exolab.castor.mapping.FieldHandler handler = null;
\r
75 org.exolab.castor.xml.FieldValidator fieldValidator = null;
\r
76 // -- initialize attribute descriptors
\r
79 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
80 java.lang.String.class, "_gapChar", "gapChar",
\r
81 org.exolab.castor.xml.NodeType.Attribute);
\r
82 desc.setImmutable(true);
\r
83 handler = new org.exolab.castor.xml.XMLFieldHandler()
\r
85 public java.lang.Object getValue(java.lang.Object object)
\r
86 throws IllegalStateException
\r
88 SequenceSet target = (SequenceSet) object;
\r
89 return target.getGapChar();
\r
92 public void setValue(java.lang.Object object, java.lang.Object value)
\r
93 throws IllegalStateException, IllegalArgumentException
\r
97 SequenceSet target = (SequenceSet) object;
\r
98 target.setGapChar((java.lang.String) value);
\r
99 } catch (java.lang.Exception ex)
\r
101 throw new IllegalStateException(ex.toString());
\r
105 public java.lang.Object newInstance(java.lang.Object parent)
\r
110 desc.setHandler(handler);
\r
111 desc.setRequired(true);
\r
112 desc.setMultivalued(false);
\r
113 addFieldDescriptor(desc);
\r
115 // -- validation code for: _gapChar
\r
116 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
117 fieldValidator.setMinOccurs(1);
\r
118 { // -- local scope
\r
119 org.exolab.castor.xml.validators.StringValidator typeValidator;
\r
120 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
\r
121 fieldValidator.setValidator(typeValidator);
\r
122 typeValidator.setWhiteSpace("preserve");
\r
124 desc.setValidator(fieldValidator);
\r
126 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
127 java.lang.String.class, "_datasetId", "datasetId",
\r
128 org.exolab.castor.xml.NodeType.Attribute);
\r
129 desc.setImmutable(true);
\r
130 handler = new org.exolab.castor.xml.XMLFieldHandler()
\r
132 public java.lang.Object getValue(java.lang.Object object)
\r
133 throws IllegalStateException
\r
135 SequenceSet target = (SequenceSet) object;
\r
136 return target.getDatasetId();
\r
139 public void setValue(java.lang.Object object, java.lang.Object value)
\r
140 throws IllegalStateException, IllegalArgumentException
\r
144 SequenceSet target = (SequenceSet) object;
\r
145 target.setDatasetId((java.lang.String) value);
\r
146 } catch (java.lang.Exception ex)
\r
148 throw new IllegalStateException(ex.toString());
\r
152 public java.lang.Object newInstance(java.lang.Object parent)
\r
157 desc.setHandler(handler);
\r
158 desc.setMultivalued(false);
\r
159 addFieldDescriptor(desc);
\r
161 // -- validation code for: _datasetId
\r
162 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
163 { // -- local scope
\r
164 org.exolab.castor.xml.validators.StringValidator typeValidator;
\r
165 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
\r
166 fieldValidator.setValidator(typeValidator);
\r
167 typeValidator.setWhiteSpace("preserve");
\r
169 desc.setValidator(fieldValidator);
\r
170 // -- initialize element descriptors
\r
172 // -- _sequenceList
\r
173 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
174 jalview.schemabinding.version2.Sequence.class, "_sequenceList",
\r
175 "Sequence", org.exolab.castor.xml.NodeType.Element);
\r
176 handler = new org.exolab.castor.xml.XMLFieldHandler()
\r
178 public java.lang.Object getValue(java.lang.Object object)
\r
179 throws IllegalStateException
\r
181 SequenceSet target = (SequenceSet) object;
\r
182 return target.getSequence();
\r
185 public void setValue(java.lang.Object object, java.lang.Object value)
\r
186 throws IllegalStateException, IllegalArgumentException
\r
190 SequenceSet target = (SequenceSet) object;
\r
192 .addSequence((jalview.schemabinding.version2.Sequence) value);
\r
193 } catch (java.lang.Exception ex)
\r
195 throw new IllegalStateException(ex.toString());
\r
199 public void resetValue(Object object) throws IllegalStateException,
\r
200 IllegalArgumentException
\r
204 SequenceSet target = (SequenceSet) object;
\r
205 target.removeAllSequence();
\r
206 } catch (java.lang.Exception ex)
\r
208 throw new IllegalStateException(ex.toString());
\r
212 public java.lang.Object newInstance(java.lang.Object parent)
\r
214 return new jalview.schemabinding.version2.Sequence();
\r
217 desc.setHandler(handler);
\r
218 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
\r
219 desc.setMultivalued(true);
\r
220 addFieldDescriptor(desc);
\r
222 // -- validation code for: _sequenceList
\r
223 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
224 fieldValidator.setMinOccurs(0);
\r
225 { // -- local scope
\r
227 desc.setValidator(fieldValidator);
\r
228 // -- _annotationList
\r
229 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
230 jalview.schemabinding.version2.Annotation.class,
\r
231 "_annotationList", "Annotation",
\r
232 org.exolab.castor.xml.NodeType.Element);
\r
233 handler = new org.exolab.castor.xml.XMLFieldHandler()
\r
235 public java.lang.Object getValue(java.lang.Object object)
\r
236 throws IllegalStateException
\r
238 SequenceSet target = (SequenceSet) object;
\r
239 return target.getAnnotation();
\r
242 public void setValue(java.lang.Object object, java.lang.Object value)
\r
243 throws IllegalStateException, IllegalArgumentException
\r
247 SequenceSet target = (SequenceSet) object;
\r
249 .addAnnotation((jalview.schemabinding.version2.Annotation) value);
\r
250 } catch (java.lang.Exception ex)
\r
252 throw new IllegalStateException(ex.toString());
\r
256 public void resetValue(Object object) throws IllegalStateException,
\r
257 IllegalArgumentException
\r
261 SequenceSet target = (SequenceSet) object;
\r
262 target.removeAllAnnotation();
\r
263 } catch (java.lang.Exception ex)
\r
265 throw new IllegalStateException(ex.toString());
\r
269 public java.lang.Object newInstance(java.lang.Object parent)
\r
271 return new jalview.schemabinding.version2.Annotation();
\r
274 desc.setHandler(handler);
\r
275 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
\r
276 desc.setMultivalued(true);
\r
277 addFieldDescriptor(desc);
\r
279 // -- validation code for: _annotationList
\r
280 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
281 fieldValidator.setMinOccurs(0);
\r
282 { // -- local scope
\r
284 desc.setValidator(fieldValidator);
\r
285 // -- _sequenceSetPropertiesList
\r
286 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
287 jalview.schemabinding.version2.SequenceSetProperties.class,
\r
288 "_sequenceSetPropertiesList", "sequenceSetProperties",
\r
289 org.exolab.castor.xml.NodeType.Element);
\r
290 handler = new org.exolab.castor.xml.XMLFieldHandler()
\r
292 public java.lang.Object getValue(java.lang.Object object)
\r
293 throws IllegalStateException
\r
295 SequenceSet target = (SequenceSet) object;
\r
296 return target.getSequenceSetProperties();
\r
299 public void setValue(java.lang.Object object, java.lang.Object value)
\r
300 throws IllegalStateException, IllegalArgumentException
\r
304 SequenceSet target = (SequenceSet) object;
\r
306 .addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value);
\r
307 } catch (java.lang.Exception ex)
\r
309 throw new IllegalStateException(ex.toString());
\r
313 public void resetValue(Object object) throws IllegalStateException,
\r
314 IllegalArgumentException
\r
318 SequenceSet target = (SequenceSet) object;
\r
319 target.removeAllSequenceSetProperties();
\r
320 } catch (java.lang.Exception ex)
\r
322 throw new IllegalStateException(ex.toString());
\r
326 public java.lang.Object newInstance(java.lang.Object parent)
\r
328 return new jalview.schemabinding.version2.SequenceSetProperties();
\r
331 desc.setHandler(handler);
\r
332 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
\r
333 desc.setMultivalued(true);
\r
334 addFieldDescriptor(desc);
\r
336 // -- validation code for: _sequenceSetPropertiesList
\r
337 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
338 fieldValidator.setMinOccurs(0);
\r
339 { // -- local scope
\r
341 desc.setValidator(fieldValidator);
\r
342 // -- _alcodonFrameList
\r
343 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
344 jalview.schemabinding.version2.AlcodonFrame.class,
\r
345 "_alcodonFrameList", "AlcodonFrame",
\r
346 org.exolab.castor.xml.NodeType.Element);
\r
347 handler = new org.exolab.castor.xml.XMLFieldHandler()
\r
349 public java.lang.Object getValue(java.lang.Object object)
\r
350 throws IllegalStateException
\r
352 SequenceSet target = (SequenceSet) object;
\r
353 return target.getAlcodonFrame();
\r
356 public void setValue(java.lang.Object object, java.lang.Object value)
\r
357 throws IllegalStateException, IllegalArgumentException
\r
361 SequenceSet target = (SequenceSet) object;
\r
363 .addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value);
\r
364 } catch (java.lang.Exception ex)
\r
366 throw new IllegalStateException(ex.toString());
\r
370 public void resetValue(Object object) throws IllegalStateException,
\r
371 IllegalArgumentException
\r
375 SequenceSet target = (SequenceSet) object;
\r
376 target.removeAllAlcodonFrame();
\r
377 } catch (java.lang.Exception ex)
\r
379 throw new IllegalStateException(ex.toString());
\r
383 public java.lang.Object newInstance(java.lang.Object parent)
\r
385 return new jalview.schemabinding.version2.AlcodonFrame();
\r
388 desc.setHandler(handler);
\r
389 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
\r
390 desc.setMultivalued(true);
\r
391 addFieldDescriptor(desc);
\r
393 // -- validation code for: _alcodonFrameList
\r
394 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
395 fieldValidator.setMinOccurs(0);
\r
396 { // -- local scope
\r
398 desc.setValidator(fieldValidator);
\r
406 * Method getAccessMode.
\r
408 * @return the access mode specified for this class.
\r
410 public org.exolab.castor.mapping.AccessMode getAccessMode()
\r
416 * Method getIdentity.
\r
418 * @return the identity field, null if this class has no identity.
\r
420 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
\r
422 return super.getIdentity();
\r
426 * Method getJavaClass.
\r
428 * @return the Java class represented by this descriptor.
\r
430 public java.lang.Class getJavaClass()
\r
432 return jalview.schemabinding.version2.SequenceSet.class;
\r
436 * Method getNameSpacePrefix.
\r
438 * @return the namespace prefix to use when marshaling as XML.
\r
440 public java.lang.String getNameSpacePrefix()
\r
446 * Method getNameSpaceURI.
\r
448 * @return the namespace URI used when marshaling and unmarshaling as XML.
\r
450 public java.lang.String getNameSpaceURI()
\r
456 * Method getValidator.
\r
458 * @return a specific validator for the class described by this
\r
461 public org.exolab.castor.xml.TypeValidator getValidator()
\r
467 * Method getXMLName.
\r
469 * @return the XML Name for the Class being described.
\r
471 public java.lang.String getXMLName()
\r
477 * Method isElementDefinition.
\r
479 * @return true if XML schema definition of this Class is that of a global
\r
480 * element or element with anonymous type definition.
\r
482 public boolean isElementDefinition()
\r
484 return _elementDefinition;
\r