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=0000000000000000000000000000000000000000;hb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;hp=eb88fc40d70460c1e0bf12ba53a14320cc7c6fe4;hpb=382f5ff058a4c2fed1e9874bb712b40f16ec1a4e;p=jalview.git diff --git a/src/jalview/schemabinding/version2/SecondaryStructure.java b/src/jalview/schemabinding/version2/SecondaryStructure.java deleted file mode 100644 index eb88fc4..0000000 --- a/src/jalview/schemabinding/version2/SecondaryStructure.java +++ /dev/null @@ -1,290 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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); - } - -}