--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SecondaryStructure.
+ *
+ * @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 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