/* * 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 _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; /** * 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 _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 deleteGraph( ) { this._has_graph= false; } /** */ public void deleteGraphColour( ) { this._has_graphColour= false; } /** */ public void deleteGraphGroup( ) { this._has_graphGroup= false; } /** */ public void deleteGraphType( ) { this._has_graphType= false; } /** */ public void deleteScore( ) { this._has_score= false; } /** */ public void deleteScoreOnly( ) { this._has_scoreOnly= 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 '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 '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 '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 '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 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 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 hasVisible. * * @return true if at least one Visible has been added */ public boolean hasVisible( ) { return this._has_visible; } /** * Returns the value of field 'graph'. * * @return the value of field 'Graph'. */ public boolean isGraph( ) { return this._graph; } /** * Returns the value of field 'scoreOnly'. * * @return the value of field 'ScoreOnly'. */ public boolean isScoreOnly( ) { return this._scoreOnly; } /** * 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 '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 '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 '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 '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); } }