2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
\r
3 * Copyright (C) 2008 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.Sequence;
\r
28 * Class SequenceDescriptor.
\r
30 * @version $Revision$ $Date$
\r
32 public class SequenceDescriptor extends
\r
33 jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor
\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 SequenceDescriptor()
\r
67 setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());
\r
68 _nsURI = "www.vamsas.ac.uk/jalview/version2";
\r
69 _xmlName = "Sequence";
\r
70 _elementDefinition = true;
\r
72 // -- set grouping compositor
\r
73 setCompositorAsSequence();
\r
74 org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;
\r
75 org.exolab.castor.mapping.FieldHandler handler = null;
\r
76 org.exolab.castor.xml.FieldValidator fieldValidator = null;
\r
77 // -- initialize attribute descriptors
\r
80 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
81 java.lang.String.class, "_dsseqid", "dsseqid",
\r
82 org.exolab.castor.xml.NodeType.Attribute);
\r
83 desc.setImmutable(true);
\r
84 handler = new org.exolab.castor.xml.XMLFieldHandler()
\r
86 public java.lang.Object getValue(java.lang.Object object)
\r
87 throws IllegalStateException
\r
89 Sequence target = (Sequence) object;
\r
90 return target.getDsseqid();
\r
93 public void setValue(java.lang.Object object, java.lang.Object value)
\r
94 throws IllegalStateException, IllegalArgumentException
\r
98 Sequence target = (Sequence) object;
\r
99 target.setDsseqid((java.lang.String) value);
\r
100 } catch (java.lang.Exception ex)
\r
102 throw new IllegalStateException(ex.toString());
\r
106 public java.lang.Object newInstance(java.lang.Object parent)
\r
111 desc.setHandler(handler);
\r
112 desc.setMultivalued(false);
\r
113 addFieldDescriptor(desc);
\r
115 // -- validation code for: _dsseqid
\r
116 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
117 { // -- local scope
\r
118 org.exolab.castor.xml.validators.StringValidator typeValidator;
\r
119 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
\r
120 fieldValidator.setValidator(typeValidator);
\r
121 typeValidator.setWhiteSpace("preserve");
\r
123 desc.setValidator(fieldValidator);
\r
124 // -- initialize element descriptors
\r
127 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
128 jalview.schemabinding.version2.DBRef.class, "_DBRefList",
\r
129 "DBRef", org.exolab.castor.xml.NodeType.Element);
\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 Sequence target = (Sequence) object;
\r
136 return target.getDBRef();
\r
139 public void setValue(java.lang.Object object, java.lang.Object value)
\r
140 throws IllegalStateException, IllegalArgumentException
\r
144 Sequence target = (Sequence) object;
\r
145 target.addDBRef((jalview.schemabinding.version2.DBRef) value);
\r
146 } catch (java.lang.Exception ex)
\r
148 throw new IllegalStateException(ex.toString());
\r
152 public void resetValue(Object object) throws IllegalStateException,
\r
153 IllegalArgumentException
\r
157 Sequence target = (Sequence) object;
\r
158 target.removeAllDBRef();
\r
159 } catch (java.lang.Exception ex)
\r
161 throw new IllegalStateException(ex.toString());
\r
165 public java.lang.Object newInstance(java.lang.Object parent)
\r
167 return new jalview.schemabinding.version2.DBRef();
\r
170 desc.setHandler(handler);
\r
171 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
\r
172 desc.setMultivalued(true);
\r
173 addFieldDescriptor(desc);
\r
175 // -- validation code for: _DBRefList
\r
176 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
177 fieldValidator.setMinOccurs(0);
\r
178 { // -- local scope
\r
180 desc.setValidator(fieldValidator);
\r
188 * Method getAccessMode.
\r
190 * @return the access mode specified for this class.
\r
192 public org.exolab.castor.mapping.AccessMode getAccessMode()
\r
198 * Method getIdentity.
\r
200 * @return the identity field, null if this class has no identity.
\r
202 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
\r
204 return super.getIdentity();
\r
208 * Method getJavaClass.
\r
210 * @return the Java class represented by this descriptor.
\r
212 public java.lang.Class getJavaClass()
\r
214 return jalview.schemabinding.version2.Sequence.class;
\r
218 * Method getNameSpacePrefix.
\r
220 * @return the namespace prefix to use when marshaling as XML.
\r
222 public java.lang.String getNameSpacePrefix()
\r
228 * Method getNameSpaceURI.
\r
230 * @return the namespace URI used when marshaling and unmarshaling as XML.
\r
232 public java.lang.String getNameSpaceURI()
\r
238 * Method getValidator.
\r
240 * @return a specific validator for the class described by this
\r
243 public org.exolab.castor.xml.TypeValidator getValidator()
\r
249 * Method getXMLName.
\r
251 * @return the XML Name for the Class being described.
\r
253 public java.lang.String getXMLName()
\r
259 * Method isElementDefinition.
\r
261 * @return true if XML schema definition of this Class is that of a global
\r
262 * element or element with anonymous type definition.
\r
264 public boolean isElementDefinition()
\r
266 return _elementDefinition;
\r