2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
\r
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
5 * This file is part of Jalview.
\r
7 * Jalview is free software: you can redistribute it and/or
\r
8 * modify it under the terms of the GNU General Public License
\r
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
\r
11 * Jalview is distributed in the hope that it will be useful, but
\r
12 * WITHOUT ANY WARRANTY; without even the implied warranty
\r
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
\r
14 * PURPOSE. See the GNU General Public License for more details.
\r
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
\r
18 package jalview.schemabinding.version2.descriptors;
\r
20 //---------------------------------/
\r
21 //- Imported classes and packages -/
\r
22 //---------------------------------/
\r
24 import jalview.schemabinding.version2.Sequence;
\r
27 * Class SequenceDescriptor.
\r
29 * @version $Revision$ $Date$
\r
31 public class SequenceDescriptor extends
\r
32 jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor
\r
35 // --------------------------/
\r
36 // - Class/Member Variables -/
\r
37 // --------------------------/
\r
40 * Field _elementDefinition.
\r
42 private boolean _elementDefinition;
\r
47 private java.lang.String _nsPrefix;
\r
52 private java.lang.String _nsURI;
\r
57 private java.lang.String _xmlName;
\r
59 // ----------------/
\r
60 // - Constructors -/
\r
61 // ----------------/
\r
63 public SequenceDescriptor()
\r
66 setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor());
\r
67 _nsURI = "www.vamsas.ac.uk/jalview/version2";
\r
68 _xmlName = "Sequence";
\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, "_dsseqid", "dsseqid",
\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 Sequence target = (Sequence) object;
\r
89 return target.getDsseqid();
\r
92 public void setValue(java.lang.Object object, java.lang.Object value)
\r
93 throws IllegalStateException, IllegalArgumentException
\r
97 Sequence target = (Sequence) object;
\r
98 target.setDsseqid((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.setMultivalued(false);
\r
112 addFieldDescriptor(desc);
\r
114 // -- validation code for: _dsseqid
\r
115 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
116 { // -- local scope
\r
117 org.exolab.castor.xml.validators.StringValidator typeValidator;
\r
118 typeValidator = new org.exolab.castor.xml.validators.StringValidator();
\r
119 fieldValidator.setValidator(typeValidator);
\r
120 typeValidator.setWhiteSpace("preserve");
\r
122 desc.setValidator(fieldValidator);
\r
123 // -- initialize element descriptors
\r
126 desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
\r
127 jalview.schemabinding.version2.DBRef.class, "_DBRefList",
\r
128 "DBRef", org.exolab.castor.xml.NodeType.Element);
\r
129 handler = new org.exolab.castor.xml.XMLFieldHandler()
\r
131 public java.lang.Object getValue(java.lang.Object object)
\r
132 throws IllegalStateException
\r
134 Sequence target = (Sequence) object;
\r
135 return target.getDBRef();
\r
138 public void setValue(java.lang.Object object, java.lang.Object value)
\r
139 throws IllegalStateException, IllegalArgumentException
\r
143 Sequence target = (Sequence) object;
\r
144 target.addDBRef((jalview.schemabinding.version2.DBRef) value);
\r
145 } catch (java.lang.Exception ex)
\r
147 throw new IllegalStateException(ex.toString());
\r
151 public void resetValue(Object object) throws IllegalStateException,
\r
152 IllegalArgumentException
\r
156 Sequence target = (Sequence) object;
\r
157 target.removeAllDBRef();
\r
158 } catch (java.lang.Exception ex)
\r
160 throw new IllegalStateException(ex.toString());
\r
164 public java.lang.Object newInstance(java.lang.Object parent)
\r
166 return new jalview.schemabinding.version2.DBRef();
\r
169 desc.setHandler(handler);
\r
170 desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
\r
171 desc.setMultivalued(true);
\r
172 addFieldDescriptor(desc);
\r
174 // -- validation code for: _DBRefList
\r
175 fieldValidator = new org.exolab.castor.xml.FieldValidator();
\r
176 fieldValidator.setMinOccurs(0);
\r
177 { // -- local scope
\r
179 desc.setValidator(fieldValidator);
\r
187 * Method getAccessMode.
\r
189 * @return the access mode specified for this class.
\r
191 public org.exolab.castor.mapping.AccessMode getAccessMode()
\r
197 * Method getIdentity.
\r
199 * @return the identity field, null if this class has no identity.
\r
201 public org.exolab.castor.mapping.FieldDescriptor getIdentity()
\r
203 return super.getIdentity();
\r
207 * Method getJavaClass.
\r
209 * @return the Java class represented by this descriptor.
\r
211 public java.lang.Class getJavaClass()
\r
213 return jalview.schemabinding.version2.Sequence.class;
\r
217 * Method getNameSpacePrefix.
\r
219 * @return the namespace prefix to use when marshaling as XML.
\r
221 public java.lang.String getNameSpacePrefix()
\r
227 * Method getNameSpaceURI.
\r
229 * @return the namespace URI used when marshaling and unmarshaling as XML.
\r
231 public java.lang.String getNameSpaceURI()
\r
237 * Method getValidator.
\r
239 * @return a specific validator for the class described by this
\r
242 public org.exolab.castor.xml.TypeValidator getValidator()
\r
248 * Method getXMLName.
\r
250 * @return the XML Name for the Class being described.
\r
252 public java.lang.String getXMLName()
\r
258 * Method isElementDefinition.
\r
260 * @return true if XML schema definition of this Class is that of a global
\r
261 * element or element with anonymous type definition.
\r
263 public boolean isElementDefinition()
\r
265 return _elementDefinition;
\r