package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
*
* @version $Revision$ $Date$
*/
-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
+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 validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
+ 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
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
git://source.jalview.org / jalview.git / blobdiff