X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSecondaryStructure.java;fp=src%2Fjalview%2Fschemabinding%2Fversion2%2FSecondaryStructure.java;h=eb88fc40d70460c1e0bf12ba53a14320cc7c6fe4;hb=bf01811b6e0c8eb15630a73700a602f14908f6a0;hp=d2f97fb0ce57f3173ad6e7dfb16954c8579d99dc;hpb=be2b1727035f39e94c4e5e320ac6011af984bcc6;p=jalview.git diff --git a/src/jalview/schemabinding/version2/SecondaryStructure.java b/src/jalview/schemabinding/version2/SecondaryStructure.java index d2f97fb..eb88fc4 100644 --- a/src/jalview/schemabinding/version2/SecondaryStructure.java +++ b/src/jalview/schemabinding/version2/SecondaryStructure.java @@ -7,8 +7,8 @@ package jalview.schemabinding.version2; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -19,272 +19,272 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); + } }