2 * This file is part of the Vamsas Client version 0.2.
\r
3 * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite,
\r
4 * Andrew Waterhouse and Dominik Lindner.
\r
6 * Earlier versions have also been incorporated into Jalview version 2.4
\r
7 * since 2008, and TOPALi version 2 since 2007.
\r
9 * The Vamsas Client is free software: you can redistribute it and/or modify
\r
10 * it under the terms of the GNU Lesser General Public License as published by
\r
11 * the Free Software Foundation, either version 3 of the License, or
\r
12 * (at your option) any later version.
\r
14 * The Vamsas Client is distributed in the hope that it will be useful,
\r
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
17 * GNU Lesser General Public License for more details.
\r
19 * You should have received a copy of the GNU Lesser General Public License
\r
20 * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
\r
22 package uk.ac.vamsas.objects.core.descriptors;
\r
24 //---------------------------------/
\r
25 //- Imported classes and packages -/
\r
26 //---------------------------------/
\r
28 import uk.ac.vamsas.objects.core.Sequence;
\r
31 * Class SequenceDescriptor.
\r
33 * @version $Revision$ $Date$
\r
35 public class SequenceDescriptor extends
\r
36 uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor {
\r
38 // --------------------------/
\r
39 // - Class/Member Variables -/
\r
40 // --------------------------/
\r
43 * Field _elementDefinition.
\r
45 private boolean _elementDefinition;
\r
50 private java.lang.String _nsPrefix;
\r
55 private java.lang.String _nsURI;
\r
60 private java.lang.String _xmlName;
\r
62 // ----------------/
\r
63 // - Constructors -/
\r
64 // ----------------/
\r
66 public SequenceDescriptor() {
\r
68 setExtendsWithoutFlatten(new uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor());
\r
69 _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
\r
70 _xmlName = "Sequence";
\r
71 _elementDefinition = true;
\r
73 // -- set grouping compositor
\r
74 setCompositorAsSequence();
\r
75 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
\r
76 org.exolab.castor.mapping.FieldHandler handler = null;
\r
77 org.exolab.castor.xml.FieldValidator fieldValidator = null;
\r
78 // -- initialize attribute descriptors
\r
81 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
82 java.lang.String.class, "_id", "id",
\r
83 org.exolab.castor.xml.NodeType.Attribute);
\r
84 super.setIdentity(desc);
\r
85 handler = new org.exolab.castor.xml.XMLFieldHandler() {
\r
86 public java.lang.Object getValue(java.lang.Object object)
\r
87 throws IllegalStateException {
\r
88 Sequence target = (Sequence) object;
\r
89 return target.getId();
\r
92 public void setValue(java.lang.Object object, java.lang.Object value)
\r
93 throws IllegalStateException, IllegalArgumentException {
\r
95 Sequence target = (Sequence) object;
\r
96 target.setId((java.lang.String) value);
\r
97 } catch (java.lang.Exception ex) {
\r
98 throw new IllegalStateException(ex.toString());
\r
102 public java.lang.Object newInstance(java.lang.Object parent) {
\r
103 return new java.lang.String();
\r
106 desc.setHandler(handler);
\r
107 desc.setMultivalued(false);
\r
108 addFieldDescriptor(desc);
\r
110 // -- validation code for: _id
\r
111 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
112 { // -- local scope
\r
113 org.exolab.castor.xml.validators.IdValidator typeValidator;
\r
114 typeValidator = new org.exolab.castor.xml.validators.IdValidator();
\r
115 fieldValidator.setValidator(typeValidator);
\r
117 desc.setValidator(fieldValidator);
\r
119 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
120 java.lang.String.class, "_dictionary", "dictionary",
\r
121 org.exolab.castor.xml.NodeType.Attribute);
\r
122 desc.setImmutable(true);
\r
123 handler = new org.exolab.castor.xml.XMLFieldHandler() {
\r
124 public java.lang.Object getValue(java.lang.Object object)
\r
125 throws IllegalStateException {
\r
126 Sequence target = (Sequence) object;
\r
127 return target.getDictionary();
\r
130 public void setValue(java.lang.Object object, java.lang.Object value)
\r
131 throws IllegalStateException, IllegalArgumentException {
\r
133 Sequence target = (Sequence) object;
\r
134 target.setDictionary((java.lang.String) value);
\r
135 } catch (java.lang.Exception ex) {
\r
136 throw new IllegalStateException(ex.toString());
\r
140 public java.lang.Object newInstance(java.lang.Object parent) {
\r
144 desc.setHandler(handler);
\r
145 desc.setRequired(true);
\r
146 desc.setMultivalued(false);
\r
147 addFieldDescriptor(desc);
\r
149 // -- validation code for: _dictionary
\r
150 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
151 fieldValidator.setMinOccurs(1);
\r
152 { // -- local scope
\r
153 org.exolab.castor.xml.validators.StringValidator typeValidator;
\r
154 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
\r
155 fieldValidator.setValidator(typeValidator);
\r
156 typeValidator.setWhiteSpace("preserve");
\r
158 desc.setValidator(fieldValidator);
\r
159 // -- initialize element descriptors
\r
162 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
163 uk.ac.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef",
\r
164 org.exolab.castor.xml.NodeType.Element);
\r
165 handler = new org.exolab.castor.xml.XMLFieldHandler() {
\r
166 public java.lang.Object getValue(java.lang.Object object)
\r
167 throws IllegalStateException {
\r
168 Sequence target = (Sequence) object;
\r
169 return target.getDbRef();
\r
172 public void setValue(java.lang.Object object, java.lang.Object value)
\r
173 throws IllegalStateException, IllegalArgumentException {
\r
175 Sequence target = (Sequence) object;
\r
176 target.addDbRef((uk.ac.vamsas.objects.core.DbRef) value);
\r
177 } catch (java.lang.Exception ex) {
\r
178 throw new IllegalStateException(ex.toString());
\r
182 public void resetValue(Object object) throws IllegalStateException,
\r
183 IllegalArgumentException {
\r
185 Sequence target = (Sequence) object;
\r
186 target.removeAllDbRef();
\r
187 } catch (java.lang.Exception ex) {
\r
188 throw new IllegalStateException(ex.toString());
\r
192 public java.lang.Object newInstance(java.lang.Object parent) {
\r
193 return new uk.ac.vamsas.objects.core.DbRef();
\r
196 desc.setHandler(handler);
\r
197 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
\r
198 desc.setMultivalued(true);
\r
199 addFieldDescriptor(desc);
\r
201 // -- validation code for: _dbRefList
\r
202 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
203 fieldValidator.setMinOccurs(0);
\r
204 { // -- local scope
\r
206 desc.setValidator(fieldValidator);
\r
208 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
209 uk.ac.vamsas.objects.core.Vxref.class, "_vxrefList", "vxref",
\r
210 org.exolab.castor.xml.NodeType.Element);
\r
211 handler = new org.exolab.castor.xml.XMLFieldHandler() {
\r
212 public java.lang.Object getValue(java.lang.Object object)
\r
213 throws IllegalStateException {
\r
214 Sequence target = (Sequence) object;
\r
215 return target.getVxref();
\r
218 public void setValue(java.lang.Object object, java.lang.Object value)
\r
219 throws IllegalStateException, IllegalArgumentException {
\r
221 Sequence target = (Sequence) object;
\r
222 target.addVxref((uk.ac.vamsas.objects.core.Vxref) value);
\r
223 } catch (java.lang.Exception ex) {
\r
224 throw new IllegalStateException(ex.toString());
\r
228 public void resetValue(Object object) throws IllegalStateException,
\r
229 IllegalArgumentException {
\r
231 Sequence target = (Sequence) object;
\r
232 target.removeAllVxref();
\r
233 } catch (java.lang.Exception ex) {
\r
234 throw new IllegalStateException(ex.toString());
\r
238 public java.lang.Object newInstance(java.lang.Object parent) {
\r
239 return new uk.ac.vamsas.objects.core.Vxref();
\r
242 desc.setHandler(handler);
\r
243 desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
\r
244 desc.setMultivalued(true);
\r
245 addFieldDescriptor(desc);
\r
247 // -- validation code for: _vxrefList
\r
248 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
249 fieldValidator.setMinOccurs(0);
\r
250 { // -- local scope
\r
252 desc.setValidator(fieldValidator);
\r
260 * Method getAccessMode.
\r
262 * @return the access mode specified for this class.
\r
264 public org.exolab.castor.mapping.AccessMode getAccessMode() {
\r
269 * Method getIdentity.
\r
271 * @return the identity field, null if this class has no identity.
\r
273 public org.exolab.castor.mapping.FieldDescriptor getIdentity() {
\r
274 return super.getIdentity();
\r
278 * Method getJavaClass.
\r
280 * @return the Java class represented by this descriptor.
\r
282 public java.lang.Class getJavaClass() {
\r
283 return uk.ac.vamsas.objects.core.Sequence.class;
\r
287 * Method getNameSpacePrefix.
\r
289 * @return the namespace prefix to use when marshaling as XML.
\r
291 public java.lang.String getNameSpacePrefix() {
\r
296 * Method getNameSpaceURI.
\r
298 * @return the namespace URI used when marshaling and unmarshaling as XML.
\r
300 public java.lang.String getNameSpaceURI() {
\r
305 * Method getValidator.
\r
307 * @return a specific validator for the class described by this
\r
310 public org.exolab.castor.xml.TypeValidator getValidator() {
\r
315 * Method getXMLName.
\r
317 * @return the XML Name for the Class being described.
\r
319 public java.lang.String getXMLName() {
\r
324 * Method isElementDefinition.
\r
326 * @return true if XML schema definition of this Class is that of a global
\r
327 * element or element with anonymous type definition.
\r
329 public boolean isElementDefinition() {
\r
330 return _elementDefinition;
\r