/*
 * This class was automatically generated with 
 * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
 * Schema.
 * $Id$
 */

package uk.ac.vamsas.objects.core;

  //---------------------------------/
 //- Imported classes and packages -/
//---------------------------------/

import org.exolab.castor.xml.Marshaller;
import org.exolab.castor.xml.Unmarshaller;

/**
 * Annotation for a rangeSpec - values can be attached for the
 * whole
 *  specification, and to each position within the spec. following
 * the orientation
 *  specified by the ordered set of rangeSpec (pos, seg) elements. 
 * 
 * @version $Revision$ $Date$
 */
public class RangeAnnotation extends uk.ac.vamsas.objects.core.RangeType 
implements java.io.Serializable
{


      //--------------------------/
     //- Class/Member Variables -/
    //--------------------------/

    /**
     * Primary Key for vamsas object referencing
     *  
     */
    private java.lang.String _id;

    /**
     * Field _modifiable.
     */
    private java.lang.String _modifiable;

    /**
     * Annotation with the same non-empty group name are grouped
     *  together 
     */
    private java.lang.String _group = "";

    /**
     * A Das Feature has both a type and a Type ID. We go the
     *  route of requiring the type string to be taken from a
     * controlled
     *  vocabulary if an application expects others to make sense
     * of it. The
     *  type may qualified - so uniprot:CHAIN is a valid type name,
     * and
     *  considered distinct from someotherDB:CHAIN 
     */
    private java.lang.String _type;

    /**
     * Short, meaningful name for the annotation - if this
     *  is absent, then the type string should be used in its
     * place.
     *  
     */
    private java.lang.String _label;

    /**
     * Human readable description of the annotation
     *  
     */
    private java.lang.String _description;

    /**
     * TODO: specify this - we have considered taking the GO
     *  evidence codes as a model for assessing a measure of
     * quality to an
     *  annotation. 
     */
    private java.lang.String _status;

    /**
     * Annotation Element position maps to ordered positions
     *  defined by the sequence of rangeType pos positions or
     * concatenated
     *  seg start/end segments. 
     */
    private java.util.Vector _annotationElementList;

    /**
     * Ordered set of optionally named float values for the
     *  whole annotation 
     */
    private java.util.Vector _scoreList;

    /**
     * Field _linkList.
     */
    private java.util.Vector _linkList;

    /**
     * Note:These are mutable so an application should check
     *  them each time. 
     */
    private java.util.Vector _propertyList;


      //----------------/
     //- Constructors -/
    //----------------/

    public RangeAnnotation() {
        super();
        setGroup("");
        this._annotationElementList = new java.util.Vector();
        this._scoreList = new java.util.Vector();
        this._linkList = new java.util.Vector();
        this._propertyList = 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 uk.ac.vamsas.objects.core.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 uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement)
    throws java.lang.IndexOutOfBoundsException {
        this._annotationElementList.add(index, vAnnotationElement);
    }

    /**
     * 
     * 
     * @param vLink
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addLink(
            final uk.ac.vamsas.objects.core.Link vLink)
    throws java.lang.IndexOutOfBoundsException {
        this._linkList.addElement(vLink);
    }

    /**
     * 
     * 
     * @param index
     * @param vLink
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addLink(
            final int index,
            final uk.ac.vamsas.objects.core.Link vLink)
    throws java.lang.IndexOutOfBoundsException {
        this._linkList.add(index, vLink);
    }

    /**
     * 
     * 
     * @param vProperty
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addProperty(
            final uk.ac.vamsas.objects.core.Property vProperty)
    throws java.lang.IndexOutOfBoundsException {
        this._propertyList.addElement(vProperty);
    }

    /**
     * 
     * 
     * @param index
     * @param vProperty
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addProperty(
            final int index,
            final uk.ac.vamsas.objects.core.Property vProperty)
    throws java.lang.IndexOutOfBoundsException {
        this._propertyList.add(index, vProperty);
    }

    /**
     * 
     * 
     * @param vScore
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addScore(
            final uk.ac.vamsas.objects.core.Score vScore)
    throws java.lang.IndexOutOfBoundsException {
        this._scoreList.addElement(vScore);
    }

    /**
     * 
     * 
     * @param index
     * @param vScore
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addScore(
            final int index,
            final uk.ac.vamsas.objects.core.Score vScore)
    throws java.lang.IndexOutOfBoundsException {
        this._scoreList.add(index, vScore);
    }

    /**
     * Method enumerateAnnotationElement.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.AnnotationElement elements
     */
    public java.util.Enumeration enumerateAnnotationElement(
    ) {
        return this._annotationElementList.elements();
    }

    /**
     * Method enumerateLink.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.Link elements
     */
    public java.util.Enumeration enumerateLink(
    ) {
        return this._linkList.elements();
    }

    /**
     * Method enumerateProperty.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.Property elements
     */
    public java.util.Enumeration enumerateProperty(
    ) {
        return this._propertyList.elements();
    }

    /**
     * Method enumerateScore.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.Score elements
     */
    public java.util.Enumeration enumerateScore(
    ) {
        return this._scoreList.elements();
    }

    /**
     * Overrides the java.lang.Object.equals method.
     * 
     * @param obj
     * @return true if the objects are equal.
     */
    public boolean equals(
            final java.lang.Object obj) {
        if ( this == obj )
            return true;
        
        if (super.equals(obj)==false)
            return false;
        
        if (obj instanceof RangeAnnotation) {
        
            RangeAnnotation temp = (RangeAnnotation)obj;
            if (this._id != null) {
                if (temp._id == null) return false;
                else if (!(this._id.equals(temp._id))) 
                    return false;
            }
            else if (temp._id != null)
                return false;
            if (this._modifiable != null) {
                if (temp._modifiable == null) return false;
                else if (!(this._modifiable.equals(temp._modifiable))) 
                    return false;
            }
            else if (temp._modifiable != null)
                return false;
            if (this._group != null) {
                if (temp._group == null) return false;
                else if (!(this._group.equals(temp._group))) 
                    return false;
            }
            else if (temp._group != null)
                return false;
            if (this._type != null) {
                if (temp._type == null) return false;
                else if (!(this._type.equals(temp._type))) 
                    return false;
            }
            else if (temp._type != null)
                return false;
            if (this._label != null) {
                if (temp._label == null) return false;
                else if (!(this._label.equals(temp._label))) 
                    return false;
            }
            else if (temp._label != null)
                return false;
            if (this._description != null) {
                if (temp._description == null) return false;
                else if (!(this._description.equals(temp._description))) 
                    return false;
            }
            else if (temp._description != null)
                return false;
            if (this._status != null) {
                if (temp._status == null) return false;
                else if (!(this._status.equals(temp._status))) 
                    return false;
            }
            else if (temp._status != null)
                return false;
            if (this._annotationElementList != null) {
                if (temp._annotationElementList == null) return false;
                else if (!(this._annotationElementList.equals(temp._annotationElementList))) 
                    return false;
            }
            else if (temp._annotationElementList != null)
                return false;
            if (this._scoreList != null) {
                if (temp._scoreList == null) return false;
                else if (!(this._scoreList.equals(temp._scoreList))) 
                    return false;
            }
            else if (temp._scoreList != null)
                return false;
            if (this._linkList != null) {
                if (temp._linkList == null) return false;
                else if (!(this._linkList.equals(temp._linkList))) 
                    return false;
            }
            else if (temp._linkList != null)
                return false;
            if (this._propertyList != null) {
                if (temp._propertyList == null) return false;
                else if (!(this._propertyList.equals(temp._propertyList))) 
                    return false;
            }
            else if (temp._propertyList != null)
                return false;
            return true;
        }
        return false;
    }

    /**
     * Method getAnnotationElement.
     * 
     * @param index
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     * @return the value of the
     * uk.ac.vamsas.objects.core.AnnotationElement at the given inde
     */
    public uk.ac.vamsas.objects.core.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 (uk.ac.vamsas.objects.core.AnnotationElement) _annotationElementList.get(index);
    }

    /**
     * Method getAnnotationElement.Returns the contents of the
     * collection in an Array.  <p>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 <i>know</i> that the Array returned is of
     * exactly the correct length.
     * 
     * @return this collection as an Array
     */
    public uk.ac.vamsas.objects.core.AnnotationElement[] getAnnotationElement(
    ) {
        uk.ac.vamsas.objects.core.AnnotationElement[] array = new uk.ac.vamsas.objects.core.AnnotationElement[0];
        return (uk.ac.vamsas.objects.core.AnnotationElement[]) this._annotationElementList.toArray(array);
    }

    /**
     * Method getAnnotationElementAsReference.Returns a reference
     * to '_annotationElementList'. No type checking is performed
     * on any modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getAnnotationElementAsReference(
    ) {
        return this._annotationElementList;
    }

    /**
     * Method getAnnotationElementCount.
     * 
     * @return the size of this collection
     */
    public int getAnnotationElementCount(
    ) {
        return this._annotationElementList.size();
    }

    /**
     * Returns the value of field 'description'. The field
     * 'description' has the following description: Human readable
     * description of the annotation
     *  
     * 
     * @return the value of field 'Description'.
     */
    public java.lang.String getDescription(
    ) {
        return this._description;
    }

    /**
     * Returns the value of field 'group'. The field 'group' has
     * the following description: Annotation with the same
     * non-empty group name are grouped
     *  together 
     * 
     * @return the value of field 'Group'.
     */
    public java.lang.String getGroup(
    ) {
        return this._group;
    }

    /**
     * Returns the value of field 'id'. The field 'id' has the
     * following description: Primary Key for vamsas object
     * referencing
     *  
     * 
     * @return the value of field 'Id'.
     */
    public java.lang.String getId(
    ) {
        return this._id;
    }

    /**
     * Returns the value of field 'label'. The field 'label' has
     * the following description: Short, meaningful name for the
     * annotation - if this
     *  is absent, then the type string should be used in its
     * place.
     *  
     * 
     * @return the value of field 'Label'.
     */
    public java.lang.String getLabel(
    ) {
        return this._label;
    }

    /**
     * Method getLink.
     * 
     * @param index
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     * @return the value of the uk.ac.vamsas.objects.core.Link at
     * the given index
     */
    public uk.ac.vamsas.objects.core.Link getLink(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._linkList.size()) {
            throw new IndexOutOfBoundsException("getLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.Link) _linkList.get(index);
    }

    /**
     * Method getLink.Returns the contents of the collection in an
     * Array.  <p>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 <i>know</i>
     * that the Array returned is of exactly the correct length.
     * 
     * @return this collection as an Array
     */
    public uk.ac.vamsas.objects.core.Link[] getLink(
    ) {
        uk.ac.vamsas.objects.core.Link[] array = new uk.ac.vamsas.objects.core.Link[0];
        return (uk.ac.vamsas.objects.core.Link[]) this._linkList.toArray(array);
    }

    /**
     * Method getLinkAsReference.Returns a reference to
     * '_linkList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getLinkAsReference(
    ) {
        return this._linkList;
    }

    /**
     * Method getLinkCount.
     * 
     * @return the size of this collection
     */
    public int getLinkCount(
    ) {
        return this._linkList.size();
    }

    /**
     * Returns the value of field 'modifiable'.
     * 
     * @return the value of field 'Modifiable'.
     */
    public java.lang.String getModifiable(
    ) {
        return this._modifiable;
    }

    /**
     * Method getProperty.
     * 
     * @param index
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     * @return the value of the uk.ac.vamsas.objects.core.Property
     * at the given index
     */
    public uk.ac.vamsas.objects.core.Property getProperty(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._propertyList.size()) {
            throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
    }

    /**
     * Method getProperty.Returns the contents of the collection in
     * an Array.  <p>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 <i>know</i>
     * that the Array returned is of exactly the correct length.
     * 
     * @return this collection as an Array
     */
    public uk.ac.vamsas.objects.core.Property[] getProperty(
    ) {
        uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
        return (uk.ac.vamsas.objects.core.Property[]) this._propertyList.toArray(array);
    }

    /**
     * Method getPropertyAsReference.Returns a reference to
     * '_propertyList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getPropertyAsReference(
    ) {
        return this._propertyList;
    }

    /**
     * Method getPropertyCount.
     * 
     * @return the size of this collection
     */
    public int getPropertyCount(
    ) {
        return this._propertyList.size();
    }

    /**
     * Method getScore.
     * 
     * @param index
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     * @return the value of the uk.ac.vamsas.objects.core.Score at
     * the given index
     */
    public uk.ac.vamsas.objects.core.Score getScore(
            final int index)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._scoreList.size()) {
            throw new IndexOutOfBoundsException("getScore: Index value '" + index + "' not in range [0.." + (this._scoreList.size() - 1) + "]");
        }
        
        return (uk.ac.vamsas.objects.core.Score) _scoreList.get(index);
    }

    /**
     * Method getScore.Returns the contents of the collection in an
     * Array.  <p>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 <i>know</i>
     * that the Array returned is of exactly the correct length.
     * 
     * @return this collection as an Array
     */
    public uk.ac.vamsas.objects.core.Score[] getScore(
    ) {
        uk.ac.vamsas.objects.core.Score[] array = new uk.ac.vamsas.objects.core.Score[0];
        return (uk.ac.vamsas.objects.core.Score[]) this._scoreList.toArray(array);
    }

    /**
     * Method getScoreAsReference.Returns a reference to
     * '_scoreList'. No type checking is performed on any
     * modifications to the Vector.
     * 
     * @return a reference to the Vector backing this class
     */
    public java.util.Vector getScoreAsReference(
    ) {
        return this._scoreList;
    }

    /**
     * Method getScoreCount.
     * 
     * @return the size of this collection
     */
    public int getScoreCount(
    ) {
        return this._scoreList.size();
    }

    /**
     * Returns the value of field 'status'. The field 'status' has
     * the following description: TODO: specify this - we have
     * considered taking the GO
     *  evidence codes as a model for assessing a measure of
     * quality to an
     *  annotation. 
     * 
     * @return the value of field 'Status'.
     */
    public java.lang.String getStatus(
    ) {
        return this._status;
    }

    /**
     * Returns the value of field 'type'. The field 'type' has the
     * following description: A Das Feature has both a type and a
     * Type ID. We go the
     *  route of requiring the type string to be taken from a
     * controlled
     *  vocabulary if an application expects others to make sense
     * of it. The
     *  type may qualified - so uniprot:CHAIN is a valid type name,
     * and
     *  considered distinct from someotherDB:CHAIN 
     * 
     * @return the value of field 'Type'.
     */
    public java.lang.String getType(
    ) {
        return this._type;
    }

    /**
     * Overrides the java.lang.Object.hashCode method.
     * <p>
     * The following steps came from <b>Effective Java Programming
     * Language Guide</b> by Joshua Bloch, Chapter 3
     * 
     * @return a hash code value for the object.
     */
    public int hashCode(
    ) {
        int result = super.hashCode();
        
        long tmp;
        if (_id != null) {
           result = 37 * result + _id.hashCode();
        }
        if (_modifiable != null) {
           result = 37 * result + _modifiable.hashCode();
        }
        if (_group != null) {
           result = 37 * result + _group.hashCode();
        }
        if (_type != null) {
           result = 37 * result + _type.hashCode();
        }
        if (_label != null) {
           result = 37 * result + _label.hashCode();
        }
        if (_description != null) {
           result = 37 * result + _description.hashCode();
        }
        if (_status != null) {
           result = 37 * result + _status.hashCode();
        }
        if (_annotationElementList != null) {
           result = 37 * result + _annotationElementList.hashCode();
        }
        if (_scoreList != null) {
           result = 37 * result + _scoreList.hashCode();
        }
        if (_linkList != null) {
           result = 37 * result + _linkList.hashCode();
        }
        if (_propertyList != null) {
           result = 37 * result + _propertyList.hashCode();
        }
        
        return result;
    }

    /**
     * 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();
    }

    /**
     */
    public void removeAllLink(
    ) {
        this._linkList.clear();
    }

    /**
     */
    public void removeAllProperty(
    ) {
        this._propertyList.clear();
    }

    /**
     */
    public void removeAllScore(
    ) {
        this._scoreList.clear();
    }

    /**
     * Method removeAnnotationElement.
     * 
     * @param vAnnotationElement
     * @return true if the object was removed from the collection.
     */
    public boolean removeAnnotationElement(
            final uk.ac.vamsas.objects.core.AnnotationElement vAnnotationElement) {
        boolean removed = _annotationElementList.remove(vAnnotationElement);
        return removed;
    }

    /**
     * Method removeAnnotationElementAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.AnnotationElement removeAnnotationElementAt(
            final int index) {
        java.lang.Object obj = this._annotationElementList.remove(index);
        return (uk.ac.vamsas.objects.core.AnnotationElement) obj;
    }

    /**
     * Method removeLink.
     * 
     * @param vLink
     * @return true if the object was removed from the collection.
     */
    public boolean removeLink(
            final uk.ac.vamsas.objects.core.Link vLink) {
        boolean removed = _linkList.remove(vLink);
        return removed;
    }

    /**
     * Method removeLinkAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.Link removeLinkAt(
            final int index) {
        java.lang.Object obj = this._linkList.remove(index);
        return (uk.ac.vamsas.objects.core.Link) obj;
    }

    /**
     * Method removeProperty.
     * 
     * @param vProperty
     * @return true if the object was removed from the collection.
     */
    public boolean removeProperty(
            final uk.ac.vamsas.objects.core.Property vProperty) {
        boolean removed = _propertyList.remove(vProperty);
        return removed;
    }

    /**
     * Method removePropertyAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.Property removePropertyAt(
            final int index) {
        java.lang.Object obj = this._propertyList.remove(index);
        return (uk.ac.vamsas.objects.core.Property) obj;
    }

    /**
     * Method removeScore.
     * 
     * @param vScore
     * @return true if the object was removed from the collection.
     */
    public boolean removeScore(
            final uk.ac.vamsas.objects.core.Score vScore) {
        boolean removed = _scoreList.remove(vScore);
        return removed;
    }

    /**
     * Method removeScoreAt.
     * 
     * @param index
     * @return the element removed from the collection
     */
    public uk.ac.vamsas.objects.core.Score removeScoreAt(
            final int index) {
        java.lang.Object obj = this._scoreList.remove(index);
        return (uk.ac.vamsas.objects.core.Score) 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 uk.ac.vamsas.objects.core.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 uk.ac.vamsas.objects.core.AnnotationElement[] vAnnotationElementArray) {
        //-- copy array
        _annotationElementList.clear();
        
        for (int i = 0; i < vAnnotationElementArray.length; i++) {
                this._annotationElementList.add(vAnnotationElementArray[i]);
        }
    }

    /**
     * Sets the value of '_annotationElementList' by copying the
     * given Vector. All elements will be checked for type safety.
     * 
     * @param vAnnotationElementList the Vector to copy.
     */
    public void setAnnotationElement(
            final java.util.Vector vAnnotationElementList) {
        // copy vector
        this._annotationElementList.clear();
        
        this._annotationElementList.addAll(vAnnotationElementList);
    }

    /**
     * Sets the value of '_annotationElementList' by setting it to
     * the given Vector. No type checking is performed.
     * @deprecated
     * 
     * @param annotationElementVector the Vector to set.
     */
    public void setAnnotationElementAsReference(
            final java.util.Vector annotationElementVector) {
        this._annotationElementList = annotationElementVector;
    }

    /**
     * Sets the value of field 'description'. The field
     * 'description' has the following description: Human readable
     * description of the annotation
     *  
     * 
     * @param description the value of field 'description'.
     */
    public void setDescription(
            final java.lang.String description) {
        this._description = description;
    }

    /**
     * Sets the value of field 'group'. The field 'group' has the
     * following description: Annotation with the same non-empty
     * group name are grouped
     *  together 
     * 
     * @param group the value of field 'group'.
     */
    public void setGroup(
            final java.lang.String group) {
        this._group = group;
    }

    /**
     * Sets the value of field 'id'. The field 'id' has the
     * following description: Primary Key for vamsas object
     * referencing
     *  
     * 
     * @param id the value of field 'id'.
     */
    public void setId(
            final java.lang.String id) {
        this._id = id;
    }

    /**
     * Sets the value of field 'label'. The field 'label' has the
     * following description: Short, meaningful name for the
     * annotation - if this
     *  is absent, then the type string should be used in its
     * place.
     *  
     * 
     * @param label the value of field 'label'.
     */
    public void setLabel(
            final java.lang.String label) {
        this._label = label;
    }

    /**
     * 
     * 
     * @param index
     * @param vLink
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setLink(
            final int index,
            final uk.ac.vamsas.objects.core.Link vLink)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._linkList.size()) {
            throw new IndexOutOfBoundsException("setLink: Index value '" + index + "' not in range [0.." + (this._linkList.size() - 1) + "]");
        }
        
        this._linkList.set(index, vLink);
    }

    /**
     * 
     * 
     * @param vLinkArray
     */
    public void setLink(
            final uk.ac.vamsas.objects.core.Link[] vLinkArray) {
        //-- copy array
        _linkList.clear();
        
        for (int i = 0; i < vLinkArray.length; i++) {
                this._linkList.add(vLinkArray[i]);
        }
    }

    /**
     * Sets the value of '_linkList' by copying the given Vector.
     * All elements will be checked for type safety.
     * 
     * @param vLinkList the Vector to copy.
     */
    public void setLink(
            final java.util.Vector vLinkList) {
        // copy vector
        this._linkList.clear();
        
        this._linkList.addAll(vLinkList);
    }

    /**
     * Sets the value of '_linkList' by setting it to the given
     * Vector. No type checking is performed.
     * @deprecated
     * 
     * @param linkVector the Vector to set.
     */
    public void setLinkAsReference(
            final java.util.Vector linkVector) {
        this._linkList = linkVector;
    }

    /**
     * Sets the value of field 'modifiable'.
     * 
     * @param modifiable the value of field 'modifiable'.
     */
    public void setModifiable(
            final java.lang.String modifiable) {
        this._modifiable = modifiable;
    }

    /**
     * 
     * 
     * @param index
     * @param vProperty
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setProperty(
            final int index,
            final uk.ac.vamsas.objects.core.Property vProperty)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._propertyList.size()) {
            throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
        }
        
        this._propertyList.set(index, vProperty);
    }

    /**
     * 
     * 
     * @param vPropertyArray
     */
    public void setProperty(
            final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
        //-- copy array
        _propertyList.clear();
        
        for (int i = 0; i < vPropertyArray.length; i++) {
                this._propertyList.add(vPropertyArray[i]);
        }
    }

    /**
     * Sets the value of '_propertyList' by copying the given
     * Vector. All elements will be checked for type safety.
     * 
     * @param vPropertyList the Vector to copy.
     */
    public void setProperty(
            final java.util.Vector vPropertyList) {
        // copy vector
        this._propertyList.clear();
        
        this._propertyList.addAll(vPropertyList);
    }

    /**
     * Sets the value of '_propertyList' by setting it to the given
     * Vector. No type checking is performed.
     * @deprecated
     * 
     * @param propertyVector the Vector to set.
     */
    public void setPropertyAsReference(
            final java.util.Vector propertyVector) {
        this._propertyList = propertyVector;
    }

    /**
     * 
     * 
     * @param index
     * @param vScore
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void setScore(
            final int index,
            final uk.ac.vamsas.objects.core.Score vScore)
    throws java.lang.IndexOutOfBoundsException {
        // check bounds for index
        if (index < 0 || index >= this._scoreList.size()) {
            throw new IndexOutOfBoundsException("setScore: Index value '" + index + "' not in range [0.." + (this._scoreList.size() - 1) + "]");
        }
        
        this._scoreList.set(index, vScore);
    }

    /**
     * 
     * 
     * @param vScoreArray
     */
    public void setScore(
            final uk.ac.vamsas.objects.core.Score[] vScoreArray) {
        //-- copy array
        _scoreList.clear();
        
        for (int i = 0; i < vScoreArray.length; i++) {
                this._scoreList.add(vScoreArray[i]);
        }
    }

    /**
     * Sets the value of '_scoreList' by copying the given Vector.
     * All elements will be checked for type safety.
     * 
     * @param vScoreList the Vector to copy.
     */
    public void setScore(
            final java.util.Vector vScoreList) {
        // copy vector
        this._scoreList.clear();
        
        this._scoreList.addAll(vScoreList);
    }

    /**
     * Sets the value of '_scoreList' by setting it to the given
     * Vector. No type checking is performed.
     * @deprecated
     * 
     * @param scoreVector the Vector to set.
     */
    public void setScoreAsReference(
            final java.util.Vector scoreVector) {
        this._scoreList = scoreVector;
    }

    /**
     * Sets the value of field 'status'. The field 'status' has the
     * following description: TODO: specify this - we have
     * considered taking the GO
     *  evidence codes as a model for assessing a measure of
     * quality to an
     *  annotation. 
     * 
     * @param status the value of field 'status'.
     */
    public void setStatus(
            final java.lang.String status) {
        this._status = status;
    }

    /**
     * Sets the value of field 'type'. The field 'type' has the
     * following description: A Das Feature has both a type and a
     * Type ID. We go the
     *  route of requiring the type string to be taken from a
     * controlled
     *  vocabulary if an application expects others to make sense
     * of it. The
     *  type may qualified - so uniprot:CHAIN is a valid type name,
     * and
     *  considered distinct from someotherDB:CHAIN 
     * 
     * @param type the value of field 'type'.
     */
    public void setType(
            final java.lang.String type) {
        this._type = type;
    }

    /**
     * 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 uk.ac.vamsas.objects.core.RangeType
     */
    public static uk.ac.vamsas.objects.core.RangeType unmarshal(
            final java.io.Reader reader)
    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
        return (uk.ac.vamsas.objects.core.RangeType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.RangeAnnotation.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);
    }

}