-public class SecondaryStructure implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _title.
- */
- private java.lang.String _title;
-
- /**
- * id attribute of Annotation in
- * vamsasModel for
- * the secondary structure annotation shown
- * in the viewer
- *
- */
- private java.lang.String _annotationId;
-
- /**
- * if true the RNA structure is shown with gaps, if false
- * without
- *
- */
- private boolean _gapped;
-
- /**
- * keeps track of state for field: _gapped
- */
- private boolean _has_gapped;
-
- /**
- * name of the project jar entry that holds
- * the VARNA viewer state for the structure
- *
- */
- private java.lang.String _viewerState;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SecondaryStructure() {
- super();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- */
- public void deleteGapped(
- ) {
- this._has_gapped= false;
- }
-
- /**
- * Returns the value of field 'annotationId'. The field
- * 'annotationId' has the following description: id attribute
- * of Annotation in
- * vamsasModel for
- * the secondary structure annotation shown
- * in the viewer
- *
- *
- * @return the value of field 'AnnotationId'.
- */
- public java.lang.String getAnnotationId(
- ) {
- return this._annotationId;
- }
-
- /**
- * Returns the value of field 'gapped'. The field 'gapped' has
- * the following description: if true the RNA structure is
- * shown with gaps, if false without
- *
- *
- * @return the value of field 'Gapped'.
- */
- public boolean getGapped(
- ) {
- return this._gapped;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle(
- ) {
- return this._title;
- }
-
- /**
- * Returns the value of field 'viewerState'. The field
- * 'viewerState' has the following description: name of the
- * project jar entry that holds
- * the VARNA viewer state for the structure
- *
- *
- * @return the value of field 'ViewerState'.
- */
- public java.lang.String getViewerState(
- ) {
- return this._viewerState;
- }
-
- /**
- * Method hasGapped.
- *
- * @return true if at least one Gapped has been added
- */
- public boolean hasGapped(
- ) {
- return this._has_gapped;
- }
-
- /**
- * Returns the value of field 'gapped'. The field 'gapped' has
- * the following description: if true the RNA structure is
- * shown with gaps, if false without
- *
- *
- * @return the value of field 'Gapped'.
- */
- public boolean isGapped(
- ) {
- return this._gapped;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'annotationId'. The field
- * 'annotationId' has the following description: id attribute
- * of Annotation in
- * vamsasModel for
- * the secondary structure annotation shown
- * in the viewer
- *
- *
- * @param annotationId the value of field 'annotationId'.
- */
- public void setAnnotationId(
- final java.lang.String annotationId) {
- this._annotationId = annotationId;
- }
-
- /**
- * Sets the value of field 'gapped'. The field 'gapped' has the
- * following description: if true the RNA structure is shown
- * with gaps, if false without
- *
- *
- * @param gapped the value of field 'gapped'.
- */
- public void setGapped(
- final boolean gapped) {
- this._gapped = gapped;
- this._has_gapped = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title the value of field 'title'.
- */
- public void setTitle(
- final java.lang.String title) {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'viewerState'. The field
- * 'viewerState' has the following description: name of the
- * project jar entry that holds
- * the VARNA viewer state for the structure
- *
- *
- * @param viewerState the value of field 'viewerState'.
- */
- public void setViewerState(
- final java.lang.String viewerState) {
- this._viewerState = viewerState;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled
- * jalview.schemabinding.version2.SecondaryStructure
- */
- public static jalview.schemabinding.version2.SecondaryStructure unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SecondaryStructure) Unmarshaller.unmarshal(jalview.schemabinding.version2.SecondaryStructure.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema