Note: Just in case the - * collection contents are changing in another thread, we pass - * a 0-length Array of the correct type into the API call. - * This way we know that the Array returned is of - * exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.AnnotationElement[] getAnnotationElement( - ) { - jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0]; - return (jalview.binding.AnnotationElement[]) this._annotationElementList.toArray(array); - } - - /** - * Method getAnnotationElementCount. - * - * @return the size of this collection - */ - public int getAnnotationElementCount( - ) { - return this._annotationElementList.size(); - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription( - ) { - return this._description; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean getGraph( - ) { - return this._graph; +public class Annotation implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _graph. + */ + private boolean _graph; + + /** + * keeps track of state for field: _graph + */ + private boolean _has_graph; + + /** + * Field _graphType. + */ + private int _graphType; + + /** + * keeps track of state for field: _graphType + */ + private boolean _has_graphType; + + /** + * Field _annotationElementList. + */ + private java.util.Vector _annotationElementList; + + /** + * Field _label. + */ + private java.lang.String _label; + + /** + * Field _description. + */ + private java.lang.String _description; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public Annotation() + { + super(); + this._annotationElementList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAnnotationElement( + final jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + this._annotationElementList.addElement(vAnnotationElement); + } + + /** + * + * + * @param index + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAnnotationElement(final int index, + final jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + this._annotationElementList.add(index, vAnnotationElement); + } + + /** + */ + public void deleteGraph() + { + this._has_graph = false; + } + + /** + */ + public void deleteGraphType() + { + this._has_graphType = false; + } + + /** + * Method enumerateAnnotationElement. + * + * @return an Enumeration over all jalview.binding.AnnotationElement elements + */ + public java.util.Enumeration enumerateAnnotationElement() + { + return this._annotationElementList.elements(); + } + + /** + * Method getAnnotationElement. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + * @return the value of the jalview.binding.AnnotationElement at the given + * index + */ + public jalview.binding.AnnotationElement getAnnotationElement( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._annotationElementList.size()) + { + throw new IndexOutOfBoundsException( + "getAnnotationElement: Index value '" + index + + "' not in range [0.." + + (this._annotationElementList.size() - 1) + "]"); } - /** - * Returns the value of field 'graphType'. - * - * @return the value of field 'GraphType'. - */ - public int getGraphType( - ) { - return this._graphType; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel( - ) { - return this._label; - } - - /** - * Method hasGraph. - * - * @return true if at least one Graph has been added - */ - public boolean hasGraph( - ) { - return this._has_graph; - } - - /** - * Method hasGraphType. - * - * @return true if at least one GraphType has been added - */ - public boolean hasGraphType( - ) { - return this._has_graphType; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean isGraph( - ) { - return this._graph; - } - - /** - * 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); - } - - /** - */ - public void removeAllAnnotationElement( - ) { - this._annotationElementList.clear(); - } - - /** - * Method removeAnnotationElement. - * - * @param vAnnotationElement - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotationElement( - final jalview.binding.AnnotationElement vAnnotationElement) { - boolean removed = _annotationElementList.remove(vAnnotationElement); - return removed; - } - - /** - * Method removeAnnotationElementAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.AnnotationElement removeAnnotationElementAt( - final int index) { - java.lang.Object obj = this._annotationElementList.remove(index); - return (jalview.binding.AnnotationElement) obj; - } - - /** - * - * - * @param index - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAnnotationElement( - final int index, - final jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._annotationElementList.size()) { - throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]"); - } - - this._annotationElementList.set(index, vAnnotationElement); - } - - /** - * - * - * @param vAnnotationElementArray - */ - public void setAnnotationElement( - final jalview.binding.AnnotationElement[] vAnnotationElementArray) { - //-- copy array - _annotationElementList.clear(); - - for (int i = 0; i < vAnnotationElementArray.length; i++) { - this._annotationElementList.add(vAnnotationElementArray[i]); - } - } - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription( - final java.lang.String description) { - this._description = description; + return (jalview.binding.AnnotationElement) _annotationElementList + .get(index); + } + + /** + * Method getAnnotationElement.Returns the contents of the collection in an + * Array. + *
+ * Note: Just in case the collection contents are changing in another thread, + * we pass a 0-length Array of the correct type into the API call. This way we + * know that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.AnnotationElement[] getAnnotationElement() + { + jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0]; + return (jalview.binding.AnnotationElement[]) this._annotationElementList + .toArray(array); + } + + /** + * Method getAnnotationElementCount. + * + * @return the size of this collection + */ + public int getAnnotationElementCount() + { + return this._annotationElementList.size(); + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription() + { + return this._description; + } + + /** + * Returns the value of field 'graph'. + * + * @return the value of field 'Graph'. + */ + public boolean getGraph() + { + return this._graph; + } + + /** + * Returns the value of field 'graphType'. + * + * @return the value of field 'GraphType'. + */ + public int getGraphType() + { + return this._graphType; + } + + /** + * Returns the value of field 'label'. + * + * @return the value of field 'Label'. + */ + public java.lang.String getLabel() + { + return this._label; + } + + /** + * Method hasGraph. + * + * @return true if at least one Graph has been added + */ + public boolean hasGraph() + { + return this._has_graph; + } + + /** + * Method hasGraphType. + * + * @return true if at least one GraphType has been added + */ + public boolean hasGraphType() + { + return this._has_graphType; + } + + /** + * Returns the value of field 'graph'. + * + * @return the value of field 'Graph'. + */ + public boolean isGraph() + { + return this._graph; + } + + /** + * 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; } - - /** - * Sets the value of field 'graph'. - * - * @param graph the value of field 'graph'. - */ - public void setGraph( - final boolean graph) { - this._graph = graph; - this._has_graph = true; + 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); + } + + /** + */ + public void removeAllAnnotationElement() + { + this._annotationElementList.clear(); + } + + /** + * Method removeAnnotationElement. + * + * @param vAnnotationElement + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotationElement( + final jalview.binding.AnnotationElement vAnnotationElement) + { + boolean removed = _annotationElementList.remove(vAnnotationElement); + return removed; + } + + /** + * Method removeAnnotationElementAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.AnnotationElement removeAnnotationElementAt( + final int index) + { + java.lang.Object obj = this._annotationElementList.remove(index); + return (jalview.binding.AnnotationElement) obj; + } + + /** + * + * + * @param index + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setAnnotationElement(final int index, + final jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._annotationElementList.size()) + { + throw new IndexOutOfBoundsException( + "setAnnotationElement: Index value '" + index + + "' not in range [0.." + + (this._annotationElementList.size() - 1) + "]"); } - /** - * Sets the value of field 'graphType'. - * - * @param graphType the value of field 'graphType'. - */ - public void setGraphType( - final int graphType) { - this._graphType = graphType; - this._has_graphType = true; - } - - /** - * Sets the value of field 'label'. - * - * @param label the value of field 'label'. - */ - public void setLabel( - final java.lang.String label) { - this._label = label; - } - - /** - * 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.binding.Annotation - */ - public static jalview.binding.Annotation unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.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); + this._annotationElementList.set(index, vAnnotationElement); + } + + /** + * + * + * @param vAnnotationElementArray + */ + public void setAnnotationElement( + final jalview.binding.AnnotationElement[] vAnnotationElementArray) + { + // -- copy array + _annotationElementList.clear(); + + for (int i = 0; i < vAnnotationElementArray.length; i++) + { + this._annotationElementList.add(vAnnotationElementArray[i]); } + } + + /** + * Sets the value of field 'description'. + * + * @param description + * the value of field 'description'. + */ + public void setDescription(final java.lang.String description) + { + this._description = description; + } + + /** + * Sets the value of field 'graph'. + * + * @param graph + * the value of field 'graph'. + */ + public void setGraph(final boolean graph) + { + this._graph = graph; + this._has_graph = true; + } + + /** + * Sets the value of field 'graphType'. + * + * @param graphType + * the value of field 'graphType'. + */ + public void setGraphType(final int graphType) + { + this._graphType = graphType; + this._has_graphType = true; + } + + /** + * Sets the value of field 'label'. + * + * @param label + * the value of field 'label'. + */ + public void setLabel(final java.lang.String label) + { + this._label = label; + } + + /** + * 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.binding.Annotation + */ + public static jalview.binding.Annotation unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.binding.Annotation) Unmarshaller.unmarshal( + jalview.binding.Annotation.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); + } }