2 * This class was automatically generated with
3 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
8 package jalview.schemabinding.version2;
10 //---------------------------------/
11 //- Imported classes and packages -/
12 //---------------------------------/
14 import org.exolab.castor.xml.Marshaller;
15 import org.exolab.castor.xml.Unmarshaller;
18 * Class SecondaryStructure.
20 * @version $Revision$ $Date$
22 public class SecondaryStructure implements java.io.Serializable {
25 //--------------------------/
26 //- Class/Member Variables -/
27 //--------------------------/
32 private java.lang.String _title;
35 * id attribute of Annotation in
37 * the secondary structure annotation shown
41 private java.lang.String _annotationId;
44 * if true the RNA structure is shown with gaps, if false
48 private boolean _gapped;
51 * keeps track of state for field: _gapped
53 private boolean _has_gapped;
56 * name of the project jar entry that holds
57 * the VARNA viewer state for the structure
60 private java.lang.String _viewerState;
67 public SecondaryStructure() {
78 public void deleteGapped(
80 this._has_gapped= false;
84 * Returns the value of field 'annotationId'. The field
85 * 'annotationId' has the following description: id attribute
88 * the secondary structure annotation shown
92 * @return the value of field 'AnnotationId'.
94 public java.lang.String getAnnotationId(
96 return this._annotationId;
100 * Returns the value of field 'gapped'. The field 'gapped' has
101 * the following description: if true the RNA structure is
102 * shown with gaps, if false without
105 * @return the value of field 'Gapped'.
107 public boolean getGapped(
113 * Returns the value of field 'title'.
115 * @return the value of field 'Title'.
117 public java.lang.String getTitle(
123 * Returns the value of field 'viewerState'. The field
124 * 'viewerState' has the following description: name of the
125 * project jar entry that holds
126 * the VARNA viewer state for the structure
129 * @return the value of field 'ViewerState'.
131 public java.lang.String getViewerState(
133 return this._viewerState;
139 * @return true if at least one Gapped has been added
141 public boolean hasGapped(
143 return this._has_gapped;
147 * Returns the value of field 'gapped'. The field 'gapped' has
148 * the following description: if true the RNA structure is
149 * shown with gaps, if false without
152 * @return the value of field 'Gapped'.
154 public boolean isGapped(
162 * @return true if this object is valid according to the schema
164 public boolean isValid(
168 } catch (org.exolab.castor.xml.ValidationException vex) {
178 * @throws org.exolab.castor.xml.MarshalException if object is
179 * null or if any SAXException is thrown during marshaling
180 * @throws org.exolab.castor.xml.ValidationException if this
181 * object is an invalid instance according to the schema
184 final java.io.Writer out)
185 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
186 Marshaller.marshal(this, out);
193 * @throws java.io.IOException if an IOException occurs during
195 * @throws org.exolab.castor.xml.ValidationException if this
196 * object is an invalid instance according to the schema
197 * @throws org.exolab.castor.xml.MarshalException if object is
198 * null or if any SAXException is thrown during marshaling
201 final org.xml.sax.ContentHandler handler)
202 throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
203 Marshaller.marshal(this, handler);
207 * Sets the value of field 'annotationId'. The field
208 * 'annotationId' has the following description: id attribute
211 * the secondary structure annotation shown
215 * @param annotationId the value of field 'annotationId'.
217 public void setAnnotationId(
218 final java.lang.String annotationId) {
219 this._annotationId = annotationId;
223 * Sets the value of field 'gapped'. The field 'gapped' has the
224 * following description: if true the RNA structure is shown
225 * with gaps, if false without
228 * @param gapped the value of field 'gapped'.
230 public void setGapped(
231 final boolean gapped) {
232 this._gapped = gapped;
233 this._has_gapped = true;
237 * Sets the value of field 'title'.
239 * @param title the value of field 'title'.
241 public void setTitle(
242 final java.lang.String title) {
247 * Sets the value of field 'viewerState'. The field
248 * 'viewerState' has the following description: name of the
249 * project jar entry that holds
250 * the VARNA viewer state for the structure
253 * @param viewerState the value of field 'viewerState'.
255 public void setViewerState(
256 final java.lang.String viewerState) {
257 this._viewerState = viewerState;
264 * @throws org.exolab.castor.xml.MarshalException if object is
265 * null or if any SAXException is thrown during marshaling
266 * @throws org.exolab.castor.xml.ValidationException if this
267 * object is an invalid instance according to the schema
268 * @return the unmarshaled
269 * jalview.schemabinding.version2.SecondaryStructure
271 public static jalview.schemabinding.version2.SecondaryStructure unmarshal(
272 final java.io.Reader reader)
273 throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
274 return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller.unmarshal(jalview.schemabinding.version2.SecondaryStructure.class, reader);
280 * @throws org.exolab.castor.xml.ValidationException if this
281 * object is an invalid instance according to the schema
283 public void validate(
285 throws org.exolab.castor.xml.ValidationException {
286 org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
287 validator.validate(this);