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.SequenceSet;
27 * Class SequenceSetDescriptor.
29 * @version $Revision$ $Date$
31 public class SequenceSetDescriptor 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 SequenceSetDescriptor()
66 _nsURI = "www.vamsas.ac.uk/jalview/version2";
67 _xmlName = "SequenceSet";
68 _elementDefinition = true;
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.String.class, "_gapChar", "gapChar",
80 org.exolab.castor.xml.NodeType.Attribute);
81 desc.setImmutable(true);
82 handler = new org.exolab.castor.xml.XMLFieldHandler()
84 public java.lang.Object getValue(java.lang.Object object)
85 throws IllegalStateException
87 SequenceSet target = (SequenceSet) object;
88 return target.getGapChar();
91 public void setValue(java.lang.Object object, java.lang.Object value)
92 throws IllegalStateException, IllegalArgumentException
96 SequenceSet target = (SequenceSet) object;
97 target.setGapChar((java.lang.String) value);
98 } catch (java.lang.Exception ex)
100 throw new IllegalStateException(ex.toString());
104 public java.lang.Object newInstance(java.lang.Object parent)
109 desc.setHandler(handler);
110 desc.setRequired(true);
111 desc.setMultivalued(false);
112 addFieldDescriptor(desc);
114 // -- validation code for: _gapChar
115 fieldValidator = new org.exolab.castor.xml.FieldValidator();
116 fieldValidator.setMinOccurs(1);
118 org.exolab.castor.xml.validators.StringValidator typeValidator;
119 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
120 fieldValidator.setValidator(typeValidator);
121 typeValidator.setWhiteSpace("preserve");
123 desc.setValidator(fieldValidator);
125 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
126 java.lang.String.class, "_datasetId", "datasetId",
127 org.exolab.castor.xml.NodeType.Attribute);
128 desc.setImmutable(true);
129 handler = new org.exolab.castor.xml.XMLFieldHandler()
131 public java.lang.Object getValue(java.lang.Object object)
132 throws IllegalStateException
134 SequenceSet target = (SequenceSet) object;
135 return target.getDatasetId();
138 public void setValue(java.lang.Object object, java.lang.Object value)
139 throws IllegalStateException, IllegalArgumentException
143 SequenceSet target = (SequenceSet) object;
144 target.setDatasetId((java.lang.String) value);
145 } catch (java.lang.Exception ex)
147 throw new IllegalStateException(ex.toString());
151 public java.lang.Object newInstance(java.lang.Object parent)
156 desc.setHandler(handler);
157 desc.setMultivalued(false);
158 addFieldDescriptor(desc);
160 // -- validation code for: _datasetId
161 fieldValidator = new org.exolab.castor.xml.FieldValidator();
163 org.exolab.castor.xml.validators.StringValidator typeValidator;
164 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
165 fieldValidator.setValidator(typeValidator);
166 typeValidator.setWhiteSpace("preserve");
168 desc.setValidator(fieldValidator);
169 // -- initialize element descriptors
172 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
173 jalview.schemabinding.version2.Sequence.class, "_sequenceList",
174 "Sequence", org.exolab.castor.xml.NodeType.Element);
175 handler = new org.exolab.castor.xml.XMLFieldHandler()
177 public java.lang.Object getValue(java.lang.Object object)
178 throws IllegalStateException
180 SequenceSet target = (SequenceSet) object;
181 return target.getSequence();
184 public void setValue(java.lang.Object object, java.lang.Object value)
185 throws IllegalStateException, IllegalArgumentException
189 SequenceSet target = (SequenceSet) object;
190 target.addSequence((jalview.schemabinding.version2.Sequence) value);
191 } catch (java.lang.Exception ex)
193 throw new IllegalStateException(ex.toString());
197 public void resetValue(Object object) throws IllegalStateException,
198 IllegalArgumentException
202 SequenceSet target = (SequenceSet) object;
203 target.removeAllSequence();
204 } catch (java.lang.Exception ex)
206 throw new IllegalStateException(ex.toString());
210 public java.lang.Object newInstance(java.lang.Object parent)
212 return new jalview.schemabinding.version2.Sequence();
215 desc.setHandler(handler);
216 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
217 desc.setMultivalued(true);
218 addFieldDescriptor(desc);
220 // -- validation code for: _sequenceList
221 fieldValidator = new org.exolab.castor.xml.FieldValidator();
222 fieldValidator.setMinOccurs(0);
225 desc.setValidator(fieldValidator);
226 // -- _annotationList
227 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
228 jalview.schemabinding.version2.Annotation.class,
229 "_annotationList", "Annotation",
230 org.exolab.castor.xml.NodeType.Element);
231 handler = new org.exolab.castor.xml.XMLFieldHandler()
233 public java.lang.Object getValue(java.lang.Object object)
234 throws IllegalStateException
236 SequenceSet target = (SequenceSet) object;
237 return target.getAnnotation();
240 public void setValue(java.lang.Object object, java.lang.Object value)
241 throws IllegalStateException, IllegalArgumentException
245 SequenceSet target = (SequenceSet) object;
246 target.addAnnotation((jalview.schemabinding.version2.Annotation) value);
247 } catch (java.lang.Exception ex)
249 throw new IllegalStateException(ex.toString());
253 public void resetValue(Object object) throws IllegalStateException,
254 IllegalArgumentException
258 SequenceSet target = (SequenceSet) object;
259 target.removeAllAnnotation();
260 } catch (java.lang.Exception ex)
262 throw new IllegalStateException(ex.toString());
266 public java.lang.Object newInstance(java.lang.Object parent)
268 return new jalview.schemabinding.version2.Annotation();
271 desc.setHandler(handler);
272 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
273 desc.setMultivalued(true);
274 addFieldDescriptor(desc);
276 // -- validation code for: _annotationList
277 fieldValidator = new org.exolab.castor.xml.FieldValidator();
278 fieldValidator.setMinOccurs(0);
281 desc.setValidator(fieldValidator);
282 // -- _sequenceSetPropertiesList
283 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
284 jalview.schemabinding.version2.SequenceSetProperties.class,
285 "_sequenceSetPropertiesList", "sequenceSetProperties",
286 org.exolab.castor.xml.NodeType.Element);
287 handler = new org.exolab.castor.xml.XMLFieldHandler()
289 public java.lang.Object getValue(java.lang.Object object)
290 throws IllegalStateException
292 SequenceSet target = (SequenceSet) object;
293 return target.getSequenceSetProperties();
296 public void setValue(java.lang.Object object, java.lang.Object value)
297 throws IllegalStateException, IllegalArgumentException
301 SequenceSet target = (SequenceSet) object;
302 target.addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value);
303 } catch (java.lang.Exception ex)
305 throw new IllegalStateException(ex.toString());
309 public void resetValue(Object object) throws IllegalStateException,
310 IllegalArgumentException
314 SequenceSet target = (SequenceSet) object;
315 target.removeAllSequenceSetProperties();
316 } catch (java.lang.Exception ex)
318 throw new IllegalStateException(ex.toString());
322 public java.lang.Object newInstance(java.lang.Object parent)
324 return new jalview.schemabinding.version2.SequenceSetProperties();
327 desc.setHandler(handler);
328 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
329 desc.setMultivalued(true);
330 addFieldDescriptor(desc);
332 // -- validation code for: _sequenceSetPropertiesList
333 fieldValidator = new org.exolab.castor.xml.FieldValidator();
334 fieldValidator.setMinOccurs(0);
337 desc.setValidator(fieldValidator);
338 // -- _alcodonFrameList
339 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
340 jalview.schemabinding.version2.AlcodonFrame.class,
341 "_alcodonFrameList", "AlcodonFrame",
342 org.exolab.castor.xml.NodeType.Element);
343 handler = new org.exolab.castor.xml.XMLFieldHandler()
345 public java.lang.Object getValue(java.lang.Object object)
346 throws IllegalStateException
348 SequenceSet target = (SequenceSet) object;
349 return target.getAlcodonFrame();
352 public void setValue(java.lang.Object object, java.lang.Object value)
353 throws IllegalStateException, IllegalArgumentException
357 SequenceSet target = (SequenceSet) object;
358 target.addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value);
359 } catch (java.lang.Exception ex)
361 throw new IllegalStateException(ex.toString());
365 public void resetValue(Object object) throws IllegalStateException,
366 IllegalArgumentException
370 SequenceSet target = (SequenceSet) object;
371 target.removeAllAlcodonFrame();
372 } catch (java.lang.Exception ex)
374 throw new IllegalStateException(ex.toString());
378 public java.lang.Object newInstance(java.lang.Object parent)
380 return new jalview.schemabinding.version2.AlcodonFrame();
383 desc.setHandler(handler);
384 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
385 desc.setMultivalued(true);
386 addFieldDescriptor(desc);
388 // -- validation code for: _alcodonFrameList
389 fieldValidator = new org.exolab.castor.xml.FieldValidator();
390 fieldValidator.setMinOccurs(0);
393 desc.setValidator(fieldValidator);
401 * Method getAccessMode.
403 * @return the access mode specified for this class.
405 public org.exolab.castor.mapping.AccessMode getAccessMode()
411 * Method getIdentity.
413 * @return the identity field, null if this class has no identity.
415 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
417 return super.getIdentity();
421 * Method getJavaClass.
423 * @return the Java class represented by this descriptor.
425 public java.lang.Class getJavaClass()
427 return jalview.schemabinding.version2.SequenceSet.class;
431 * Method getNameSpacePrefix.
433 * @return the namespace prefix to use when marshaling as XML.
435 public java.lang.String getNameSpacePrefix()
441 * Method getNameSpaceURI.
443 * @return the namespace URI used when marshaling and unmarshaling as XML.
445 public java.lang.String getNameSpaceURI()
451 * Method getValidator.
453 * @return a specific validator for the class described by this
456 public org.exolab.castor.xml.TypeValidator getValidator()
464 * @return the XML Name for the Class being described.
466 public java.lang.String getXMLName()
472 * Method isElementDefinition.
474 * @return true if XML schema definition of this Class is that of a global
475 * element or element with anonymous type definition.
477 public boolean isElementDefinition()
479 return _elementDefinition;