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.schemabinding.version2.AnnotationElement[] getAnnotationElement( - ) { - jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; - return (jalview.schemabinding.version2.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 'autoCalculated'. The field - * 'autoCalculated' has the following description: is an - * autocalculated annotation row - * - * @return the value of field 'AutoCalculated'. - */ - public boolean getAutoCalculated( - ) { - return this._autoCalculated; - } - - /** - * Returns the value of field 'centreColLabels'. - * - * @return the value of field 'CentreColLabels'. - */ - public boolean getCentreColLabels( - ) { - return this._centreColLabels; - } - - /** - * 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 'graphColour'. - * - * @return the value of field 'GraphColour'. - */ - public int getGraphColour( - ) { - return this._graphColour; - } - - /** - * Returns the value of field 'graphGroup'. - * - * @return the value of field 'GraphGroup'. - */ - public int getGraphGroup( - ) { - return this._graphGroup; - } - - /** - * Returns the value of field 'graphType'. - * - * @return the value of field 'GraphType'. - */ - public int getGraphType( - ) { - return this._graphType; - } - - /** - * Returns the value of field 'groupRef'. - * - * @return the value of field 'GroupRef'. - */ - public java.lang.String getGroupRef( - ) { - return this._groupRef; - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId( - ) { - return this._id; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel( - ) { - return this._label; - } - - /** - * Returns the value of field 'scaleColLabels'. - * - * @return the value of field 'ScaleColLabels'. - */ - public boolean getScaleColLabels( - ) { - return this._scaleColLabels; - } - - /** - * Returns the value of field 'score'. - * - * @return the value of field 'Score'. - */ - public double getScore( - ) { - return this._score; - } - - /** - * Returns the value of field 'scoreOnly'. - * - * @return the value of field 'ScoreOnly'. - */ - public boolean getScoreOnly( - ) { - return this._scoreOnly; - } - - /** - * Returns the value of field 'sequenceRef'. - * - * @return the value of field 'SequenceRef'. - */ - public java.lang.String getSequenceRef( - ) { - return this._sequenceRef; - } - - /** - * Returns the value of field 'showAllColLabels'. - * - * @return the value of field 'ShowAllColLabels'. - */ - public boolean getShowAllColLabels( - ) { - return this._showAllColLabels; - } - - /** - * Returns the value of field 'thresholdLine'. - * - * @return the value of field 'ThresholdLine'. - */ - public jalview.schemabinding.version2.ThresholdLine getThresholdLine( - ) { - return this._thresholdLine; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean getVisible( - ) { - return this._visible; - } - - /** - * Method hasAutoCalculated. - * - * @return true if at least one AutoCalculated has been added - */ - public boolean hasAutoCalculated( - ) { - return this._has_autoCalculated; - } - - /** - * Method hasCentreColLabels. - * - * @return true if at least one CentreColLabels has been added - */ - public boolean hasCentreColLabels( - ) { - return this._has_centreColLabels; - } - - /** - * Method hasGraph. - * - * @return true if at least one Graph has been added - */ - public boolean hasGraph( - ) { - return this._has_graph; - } - - /** - * Method hasGraphColour. - * - * @return true if at least one GraphColour has been added - */ - public boolean hasGraphColour( - ) { - return this._has_graphColour; - } - - /** - * Method hasGraphGroup. - * - * @return true if at least one GraphGroup has been added - */ - public boolean hasGraphGroup( - ) { - return this._has_graphGroup; - } - - /** - * Method hasGraphType. - * - * @return true if at least one GraphType has been added - */ - public boolean hasGraphType( - ) { - return this._has_graphType; - } - - /** - * Method hasScaleColLabels. - * - * @return true if at least one ScaleColLabels has been added - */ - public boolean hasScaleColLabels( - ) { - return this._has_scaleColLabels; - } - - /** - * Method hasScore. - * - * @return true if at least one Score has been added - */ - public boolean hasScore( - ) { - return this._has_score; - } - - /** - * Method hasScoreOnly. - * - * @return true if at least one ScoreOnly has been added - */ - public boolean hasScoreOnly( - ) { - return this._has_scoreOnly; - } - - /** - * Method hasShowAllColLabels. - * - * @return true if at least one ShowAllColLabels has been added - */ - public boolean hasShowAllColLabels( - ) { - return this._has_showAllColLabels; - } - - /** - * Method hasVisible. - * - * @return true if at least one Visible has been added - */ - public boolean hasVisible( - ) { - return this._has_visible; - } - - /** - * Returns the value of field 'autoCalculated'. The field - * 'autoCalculated' has the following description: is an - * autocalculated annotation row - * - * @return the value of field 'AutoCalculated'. - */ - public boolean isAutoCalculated( - ) { - return this._autoCalculated; - } - - /** - * Returns the value of field 'centreColLabels'. - * - * @return the value of field 'CentreColLabels'. - */ - public boolean isCentreColLabels( - ) { - return this._centreColLabels; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean isGraph( - ) { - return this._graph; - } - - /** - * Returns the value of field 'scaleColLabels'. - * - * @return the value of field 'ScaleColLabels'. - */ - public boolean isScaleColLabels( - ) { - return this._scaleColLabels; - } - - /** - * Returns the value of field 'scoreOnly'. - * - * @return the value of field 'ScoreOnly'. - */ - public boolean isScoreOnly( - ) { - return this._scoreOnly; - } - - /** - * Returns the value of field 'showAllColLabels'. - * - * @return the value of field 'ShowAllColLabels'. - */ - public boolean isShowAllColLabels( - ) { - return this._showAllColLabels; - } - - /** - * 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; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean isVisible( - ) { - return this._visible; - } - - /** - * - * - * @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.schemabinding.version2.AnnotationElement vAnnotationElement) { - boolean removed = _annotationElementList.remove(vAnnotationElement); - return removed; - } - - /** - * Method removeAnnotationElementAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt( - final int index) { - java.lang.Object obj = this._annotationElementList.remove(index); - return (jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) { - //-- copy array - _annotationElementList.clear(); - - for (int i = 0; i < vAnnotationElementArray.length; i++) { - this._annotationElementList.add(vAnnotationElementArray[i]); - } - } - - /** - * Sets the value of field 'autoCalculated'. The field - * 'autoCalculated' has the following description: is an - * autocalculated annotation row - * - * @param autoCalculated the value of field 'autoCalculated'. - */ - public void setAutoCalculated( - final boolean autoCalculated) { - this._autoCalculated = autoCalculated; - this._has_autoCalculated = true; - } - - /** - * Sets the value of field 'centreColLabels'. - * - * @param centreColLabels the value of field 'centreColLabels'. - */ - public void setCentreColLabels( - final boolean centreColLabels) { - this._centreColLabels = centreColLabels; - this._has_centreColLabels = true; - } - - /** - * 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 'graphColour'. - * - * @param graphColour the value of field 'graphColour'. - */ - public void setGraphColour( - final int graphColour) { - this._graphColour = graphColour; - this._has_graphColour = true; - } - - /** - * Sets the value of field 'graphGroup'. - * - * @param graphGroup the value of field 'graphGroup'. - */ - public void setGraphGroup( - final int graphGroup) { - this._graphGroup = graphGroup; - this._has_graphGroup = 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 'groupRef'. - * - * @param groupRef the value of field 'groupRef'. - */ - public void setGroupRef( - final java.lang.String groupRef) { - this._groupRef = groupRef; - } - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId( - final java.lang.String id) { - this._id = id; - } - - /** - * Sets the value of field 'label'. - * - * @param label the value of field 'label'. - */ - public void setLabel( - final java.lang.String label) { - this._label = label; - } - - /** - * Sets the value of field 'scaleColLabels'. - * - * @param scaleColLabels the value of field 'scaleColLabels'. - */ - public void setScaleColLabels( - final boolean scaleColLabels) { - this._scaleColLabels = scaleColLabels; - this._has_scaleColLabels = true; - } - - /** - * Sets the value of field 'score'. - * - * @param score the value of field 'score'. - */ - public void setScore( - final double score) { - this._score = score; - this._has_score = true; - } - - /** - * Sets the value of field 'scoreOnly'. - * - * @param scoreOnly the value of field 'scoreOnly'. - */ - public void setScoreOnly( - final boolean scoreOnly) { - this._scoreOnly = scoreOnly; - this._has_scoreOnly = true; - } - - /** - * Sets the value of field 'sequenceRef'. - * - * @param sequenceRef the value of field 'sequenceRef'. - */ - public void setSequenceRef( - final java.lang.String sequenceRef) { - this._sequenceRef = sequenceRef; - } - - /** - * Sets the value of field 'showAllColLabels'. - * - * @param showAllColLabels the value of field 'showAllColLabels' - */ - public void setShowAllColLabels( - final boolean showAllColLabels) { - this._showAllColLabels = showAllColLabels; - this._has_showAllColLabels = true; - } - - /** - * Sets the value of field 'thresholdLine'. - * - * @param thresholdLine the value of field 'thresholdLine'. - */ - public void setThresholdLine( - final jalview.schemabinding.version2.ThresholdLine thresholdLine) { - this._thresholdLine = thresholdLine; - } - - /** - * Sets the value of field 'visible'. - * - * @param visible the value of field 'visible'. - */ - public void setVisible( - final boolean visible) { - this._visible = visible; - this._has_visible = true; - } - - /** - * 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.Annotation - */ - public static jalview.schemabinding.version2.Annotation unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.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 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 Annotation. + * + * @version $Revision$ $Date$ + */ +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 _sequenceRef. + */ + private java.lang.String _sequenceRef; + + /** + * Field _groupRef. + */ + private java.lang.String _groupRef; + + /** + * Field _graphColour. + */ + private int _graphColour; + + /** + * keeps track of state for field: _graphColour + */ + private boolean _has_graphColour; + + /** + * Field _graphGroup. + */ + private int _graphGroup; + + /** + * keeps track of state for field: _graphGroup + */ + private boolean _has_graphGroup; + + /** + * height in pixels for the graph if this is a graph-type + * annotation. + */ + private int _graphHeight; + + /** + * keeps track of state for field: _graphHeight + */ + private boolean _has_graphHeight; + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _scoreOnly. + */ + private boolean _scoreOnly = false; + + /** + * keeps track of state for field: _scoreOnly + */ + private boolean _has_scoreOnly; + + /** + * Field _score. + */ + private double _score; + + /** + * keeps track of state for field: _score + */ + private boolean _has_score; + + /** + * Field _visible. + */ + private boolean _visible; + + /** + * keeps track of state for field: _visible + */ + private boolean _has_visible; + + /** + * Field _centreColLabels. + */ + private boolean _centreColLabels; + + /** + * keeps track of state for field: _centreColLabels + */ + private boolean _has_centreColLabels; + + /** + * Field _scaleColLabels. + */ + private boolean _scaleColLabels; + + /** + * keeps track of state for field: _scaleColLabels + */ + private boolean _has_scaleColLabels; + + /** + * Field _showAllColLabels. + */ + private boolean _showAllColLabels; + + /** + * keeps track of state for field: _showAllColLabels + */ + private boolean _has_showAllColLabels; + + /** + * is an autocalculated annotation row + */ + private boolean _autoCalculated = false; + + /** + * keeps track of state for field: _autoCalculated + */ + private boolean _has_autoCalculated; + + /** + * Field _annotationElementList. + */ + private java.util.Vector _annotationElementList; + + /** + * Field _label. + */ + private java.lang.String _label; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _thresholdLine. + */ + private jalview.schemabinding.version2.ThresholdLine _thresholdLine; + + + //----------------/ + //- 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.schemabinding.version2.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.schemabinding.version2.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + this._annotationElementList.add(index, vAnnotationElement); + } + + /** + */ + public void deleteAutoCalculated( + ) { + this._has_autoCalculated= false; + } + + /** + */ + public void deleteCentreColLabels( + ) { + this._has_centreColLabels= false; + } + + /** + */ + public void deleteGraph( + ) { + this._has_graph= false; + } + + /** + */ + public void deleteGraphColour( + ) { + this._has_graphColour= false; + } + + /** + */ + public void deleteGraphGroup( + ) { + this._has_graphGroup= false; + } + + /** + */ + public void deleteGraphHeight( + ) { + this._has_graphHeight= false; + } + + /** + */ + public void deleteGraphType( + ) { + this._has_graphType= false; + } + + /** + */ + public void deleteScaleColLabels( + ) { + this._has_scaleColLabels= false; + } + + /** + */ + public void deleteScore( + ) { + this._has_score= false; + } + + /** + */ + public void deleteScoreOnly( + ) { + this._has_scoreOnly= false; + } + + /** + */ + public void deleteShowAllColLabels( + ) { + this._has_showAllColLabels= false; + } + + /** + */ + public void deleteVisible( + ) { + this._has_visible= false; + } + + /** + * Method enumerateAnnotationElement. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.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.schemabinding.version2.AnnotationElement at the + * given index + */ + public jalview.schemabinding.version2.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) + "]"); + } + + return (jalview.schemabinding.version2.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.schemabinding.version2.AnnotationElement[] getAnnotationElement( + ) { + jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; + return (jalview.schemabinding.version2.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 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @return the value of field 'AutoCalculated'. + */ + public boolean getAutoCalculated( + ) { + return this._autoCalculated; + } + + /** + * Returns the value of field 'centreColLabels'. + * + * @return the value of field 'CentreColLabels'. + */ + public boolean getCentreColLabels( + ) { + return this._centreColLabels; + } + + /** + * 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 'graphColour'. + * + * @return the value of field 'GraphColour'. + */ + public int getGraphColour( + ) { + return this._graphColour; + } + + /** + * Returns the value of field 'graphGroup'. + * + * @return the value of field 'GraphGroup'. + */ + public int getGraphGroup( + ) { + return this._graphGroup; + } + + /** + * Returns the value of field 'graphHeight'. The field + * 'graphHeight' has the following description: height in + * pixels for the graph if this is a graph-type annotation. + * + * @return the value of field 'GraphHeight'. + */ + public int getGraphHeight( + ) { + return this._graphHeight; + } + + /** + * Returns the value of field 'graphType'. + * + * @return the value of field 'GraphType'. + */ + public int getGraphType( + ) { + return this._graphType; + } + + /** + * Returns the value of field 'groupRef'. + * + * @return the value of field 'GroupRef'. + */ + public java.lang.String getGroupRef( + ) { + return this._groupRef; + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'label'. + * + * @return the value of field 'Label'. + */ + public java.lang.String getLabel( + ) { + return this._label; + } + + /** + * Returns the value of field 'scaleColLabels'. + * + * @return the value of field 'ScaleColLabels'. + */ + public boolean getScaleColLabels( + ) { + return this._scaleColLabels; + } + + /** + * Returns the value of field 'score'. + * + * @return the value of field 'Score'. + */ + public double getScore( + ) { + return this._score; + } + + /** + * Returns the value of field 'scoreOnly'. + * + * @return the value of field 'ScoreOnly'. + */ + public boolean getScoreOnly( + ) { + return this._scoreOnly; + } + + /** + * Returns the value of field 'sequenceRef'. + * + * @return the value of field 'SequenceRef'. + */ + public java.lang.String getSequenceRef( + ) { + return this._sequenceRef; + } + + /** + * Returns the value of field 'showAllColLabels'. + * + * @return the value of field 'ShowAllColLabels'. + */ + public boolean getShowAllColLabels( + ) { + return this._showAllColLabels; + } + + /** + * Returns the value of field 'thresholdLine'. + * + * @return the value of field 'ThresholdLine'. + */ + public jalview.schemabinding.version2.ThresholdLine getThresholdLine( + ) { + return this._thresholdLine; + } + + /** + * Returns the value of field 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean getVisible( + ) { + return this._visible; + } + + /** + * Method hasAutoCalculated. + * + * @return true if at least one AutoCalculated has been added + */ + public boolean hasAutoCalculated( + ) { + return this._has_autoCalculated; + } + + /** + * Method hasCentreColLabels. + * + * @return true if at least one CentreColLabels has been added + */ + public boolean hasCentreColLabels( + ) { + return this._has_centreColLabels; + } + + /** + * Method hasGraph. + * + * @return true if at least one Graph has been added + */ + public boolean hasGraph( + ) { + return this._has_graph; + } + + /** + * Method hasGraphColour. + * + * @return true if at least one GraphColour has been added + */ + public boolean hasGraphColour( + ) { + return this._has_graphColour; + } + + /** + * Method hasGraphGroup. + * + * @return true if at least one GraphGroup has been added + */ + public boolean hasGraphGroup( + ) { + return this._has_graphGroup; + } + + /** + * Method hasGraphHeight. + * + * @return true if at least one GraphHeight has been added + */ + public boolean hasGraphHeight( + ) { + return this._has_graphHeight; + } + + /** + * Method hasGraphType. + * + * @return true if at least one GraphType has been added + */ + public boolean hasGraphType( + ) { + return this._has_graphType; + } + + /** + * Method hasScaleColLabels. + * + * @return true if at least one ScaleColLabels has been added + */ + public boolean hasScaleColLabels( + ) { + return this._has_scaleColLabels; + } + + /** + * Method hasScore. + * + * @return true if at least one Score has been added + */ + public boolean hasScore( + ) { + return this._has_score; + } + + /** + * Method hasScoreOnly. + * + * @return true if at least one ScoreOnly has been added + */ + public boolean hasScoreOnly( + ) { + return this._has_scoreOnly; + } + + /** + * Method hasShowAllColLabels. + * + * @return true if at least one ShowAllColLabels has been added + */ + public boolean hasShowAllColLabels( + ) { + return this._has_showAllColLabels; + } + + /** + * Method hasVisible. + * + * @return true if at least one Visible has been added + */ + public boolean hasVisible( + ) { + return this._has_visible; + } + + /** + * Returns the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @return the value of field 'AutoCalculated'. + */ + public boolean isAutoCalculated( + ) { + return this._autoCalculated; + } + + /** + * Returns the value of field 'centreColLabels'. + * + * @return the value of field 'CentreColLabels'. + */ + public boolean isCentreColLabels( + ) { + return this._centreColLabels; + } + + /** + * Returns the value of field 'graph'. + * + * @return the value of field 'Graph'. + */ + public boolean isGraph( + ) { + return this._graph; + } + + /** + * Returns the value of field 'scaleColLabels'. + * + * @return the value of field 'ScaleColLabels'. + */ + public boolean isScaleColLabels( + ) { + return this._scaleColLabels; + } + + /** + * Returns the value of field 'scoreOnly'. + * + * @return the value of field 'ScoreOnly'. + */ + public boolean isScoreOnly( + ) { + return this._scoreOnly; + } + + /** + * Returns the value of field 'showAllColLabels'. + * + * @return the value of field 'ShowAllColLabels'. + */ + public boolean isShowAllColLabels( + ) { + return this._showAllColLabels; + } + + /** + * 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; + } + + /** + * Returns the value of field 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean isVisible( + ) { + return this._visible; + } + + /** + * + * + * @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.schemabinding.version2.AnnotationElement vAnnotationElement) { + boolean removed = _annotationElementList.remove(vAnnotationElement); + return removed; + } + + /** + * Method removeAnnotationElementAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt( + final int index) { + java.lang.Object obj = this._annotationElementList.remove(index); + return (jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) { + //-- copy array + _annotationElementList.clear(); + + for (int i = 0; i < vAnnotationElementArray.length; i++) { + this._annotationElementList.add(vAnnotationElementArray[i]); + } + } + + /** + * Sets the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @param autoCalculated the value of field 'autoCalculated'. + */ + public void setAutoCalculated( + final boolean autoCalculated) { + this._autoCalculated = autoCalculated; + this._has_autoCalculated = true; + } + + /** + * Sets the value of field 'centreColLabels'. + * + * @param centreColLabels the value of field 'centreColLabels'. + */ + public void setCentreColLabels( + final boolean centreColLabels) { + this._centreColLabels = centreColLabels; + this._has_centreColLabels = true; + } + + /** + * 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 'graphColour'. + * + * @param graphColour the value of field 'graphColour'. + */ + public void setGraphColour( + final int graphColour) { + this._graphColour = graphColour; + this._has_graphColour = true; + } + + /** + * Sets the value of field 'graphGroup'. + * + * @param graphGroup the value of field 'graphGroup'. + */ + public void setGraphGroup( + final int graphGroup) { + this._graphGroup = graphGroup; + this._has_graphGroup = true; + } + + /** + * Sets the value of field 'graphHeight'. The field + * 'graphHeight' has the following description: height in + * pixels for the graph if this is a graph-type annotation. + * + * @param graphHeight the value of field 'graphHeight'. + */ + public void setGraphHeight( + final int graphHeight) { + this._graphHeight = graphHeight; + this._has_graphHeight = 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 'groupRef'. + * + * @param groupRef the value of field 'groupRef'. + */ + public void setGroupRef( + final java.lang.String groupRef) { + this._groupRef = groupRef; + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'label'. + * + * @param label the value of field 'label'. + */ + public void setLabel( + final java.lang.String label) { + this._label = label; + } + + /** + * Sets the value of field 'scaleColLabels'. + * + * @param scaleColLabels the value of field 'scaleColLabels'. + */ + public void setScaleColLabels( + final boolean scaleColLabels) { + this._scaleColLabels = scaleColLabels; + this._has_scaleColLabels = true; + } + + /** + * Sets the value of field 'score'. + * + * @param score the value of field 'score'. + */ + public void setScore( + final double score) { + this._score = score; + this._has_score = true; + } + + /** + * Sets the value of field 'scoreOnly'. + * + * @param scoreOnly the value of field 'scoreOnly'. + */ + public void setScoreOnly( + final boolean scoreOnly) { + this._scoreOnly = scoreOnly; + this._has_scoreOnly = true; + } + + /** + * Sets the value of field 'sequenceRef'. + * + * @param sequenceRef the value of field 'sequenceRef'. + */ + public void setSequenceRef( + final java.lang.String sequenceRef) { + this._sequenceRef = sequenceRef; + } + + /** + * Sets the value of field 'showAllColLabels'. + * + * @param showAllColLabels the value of field 'showAllColLabels' + */ + public void setShowAllColLabels( + final boolean showAllColLabels) { + this._showAllColLabels = showAllColLabels; + this._has_showAllColLabels = true; + } + + /** + * Sets the value of field 'thresholdLine'. + * + * @param thresholdLine the value of field 'thresholdLine'. + */ + public void setThresholdLine( + final jalview.schemabinding.version2.ThresholdLine thresholdLine) { + this._thresholdLine = thresholdLine; + } + + /** + * Sets the value of field 'visible'. + * + * @param visible the value of field 'visible'. + */ + public void setVisible( + final boolean visible) { + this._visible = visible; + this._has_visible = true; + } + + /** + * 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.Annotation + */ + public static jalview.schemabinding.version2.Annotation unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); + } + +}