/*
 * 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;

/**
 * Store a list of database references
 *  for this sequence record - with optional mapping
 *  from database sequence to the given sequence record 
 * 
 * @version $Revision$ $Date$
 */
public class DbRef extends uk.ac.vamsas.client.Vobject 
implements java.io.Serializable
{


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

    /**
     * TODO Database Naming
     *  Convention: either start using LSID (so
     *  change type to URI) or leave this as an
     *  uncontrolled/unspecified string ID
     *  
     */
    private java.lang.String _source;

    /**
     * Version must be specified -
     *  
     */
    private java.lang.String _version;

    /**
     * TODO: make some specification
     *  of the database field from which this
     *  accessionId is taken from - should that be a
     *  special property of the dbRef object ?
     *  
     */
    private java.lang.String _accessionId;

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

    /**
     * the local mapType maps from the parent
     *  sequence coordinate frame to the reference
     *  frame defined by the dbRef element.
     *  The mapped mapType is the mapped range defined
     *  on the dbRef element's reference frame.
     *  Conventionally, the unit attribute defaults to 1, or
     *  will be inferred from the local sequence's
     *  dictionary type and any dictionary type associated
     *  with the database being mapped to. 
     *  However, it may be used to avoid ambiguity.
     *  
     */
    private java.util.Vector _mapList;

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

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


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

    public DbRef() {
        super();
        this._mapList = new java.util.Vector();
        this._linkList = new java.util.Vector();
        this._propertyList = new java.util.Vector();
    }


      //-----------/
     //- Methods -/
    //-----------/

    /**
     * 
     * 
     * @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 vMap
     * @throws java.lang.IndexOutOfBoundsException if the index
     * given is outside the bounds of the collection
     */
    public void addMap(
            final uk.ac.vamsas.objects.core.Map vMap)
    throws java.lang.IndexOutOfBoundsException {
        this._mapList.addElement(vMap);
    }

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

    /**
     * 
     * 
     * @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);
    }

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

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

    /**
     * Method enumerateProperty.
     * 
     * @return an Enumeration over all
     * uk.ac.vamsas.objects.core.Property elements
     */
    public java.util.Enumeration enumerateProperty(
    ) {
        return this._propertyList.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 DbRef) {
        
            DbRef temp = (DbRef)obj;
            boolean thcycle;
            boolean tmcycle;
            if (this._source != null) {
                if (temp._source == null) return false;
                if (this._source != temp._source) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._source);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._source);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._source); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._source); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._source.equals(temp._source)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._source);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._source);
                    }
                }
            } else if (temp._source != null)
                return false;
            if (this._version != null) {
                if (temp._version == null) return false;
                if (this._version != temp._version) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._version);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._version);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._version); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._version); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._version.equals(temp._version)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
                    }
                }
            } else if (temp._version != null)
                return false;
            if (this._accessionId != null) {
                if (temp._accessionId == null) return false;
                if (this._accessionId != temp._accessionId) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._accessionId);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._accessionId);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._accessionId.equals(temp._accessionId)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._accessionId);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._accessionId);
                    }
                }
            } else if (temp._accessionId != null)
                return false;
            if (this._id != null) {
                if (temp._id == null) return false;
                if (this._id != temp._id) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._id.equals(temp._id)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
                    }
                }
            } else if (temp._id != null)
                return false;
            if (this._mapList != null) {
                if (temp._mapList == null) return false;
                if (this._mapList != temp._mapList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._mapList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._mapList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._mapList.equals(temp._mapList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._mapList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._mapList);
                    }
                }
            } else if (temp._mapList != null)
                return false;
            if (this._linkList != null) {
                if (temp._linkList == null) return false;
                if (this._linkList != temp._linkList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._linkList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._linkList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._linkList.equals(temp._linkList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._linkList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._linkList);
                    }
                }
            } else if (temp._linkList != null)
                return false;
            if (this._propertyList != null) {
                if (temp._propertyList == null) return false;
                if (this._propertyList != temp._propertyList) {
                    thcycle=org.castor.util.CycleBreaker.startingToCycle(this._propertyList);
                    tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._propertyList);
                    if (thcycle!=tmcycle) {
                        if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); };
                        if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); };
                        return false;
                    }
                    if (!thcycle) {
                        if (!this._propertyList.equals(temp._propertyList)) {
                            org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
                            org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
                            return false;
                        }
                        org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
                        org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
                    }
                }
            } else if (temp._propertyList != null)
                return false;
            return true;
        }
        return false;
    }

    /**
     * Returns the value of field 'accessionId'. The field
     * 'accessionId' has the following description: TODO: make some
     * specification
     *  of the database field from which this
     *  accessionId is taken from - should that be a
     *  special property of the dbRef object ?
     *  
     * 
     * @return the value of field 'AccessionId'.
     */
    public java.lang.String getAccessionId(
    ) {
        return this._accessionId;
    }

    /**
     * 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;
    }

    /**
     * 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();
    }

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

    /**
     * Method getMap.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.Map[] getMap(
    ) {
        uk.ac.vamsas.objects.core.Map[] array = new uk.ac.vamsas.objects.core.Map[0];
        return (uk.ac.vamsas.objects.core.Map[]) this._mapList.toArray(array);
    }

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

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

    /**
     * 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();
    }

    /**
     * Returns the value of field 'source'. The field 'source' has
     * the following description: TODO Database Naming
     *  Convention: either start using LSID (so
     *  change type to URI) or leave this as an
     *  uncontrolled/unspecified string ID
     *  
     * 
     * @return the value of field 'Source'.
     */
    public java.lang.String getSource(
    ) {
        return this._source;
    }

    /**
     * Returns the value of field 'version'. The field 'version'
     * has the following description: Version must be specified -
     *  
     * 
     * @return the value of field 'Version'.
     */
    public java.lang.String getVersion(
    ) {
        return this._version;
    }

    /**
     * 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 (_source != null
            && !org.castor.util.CycleBreaker.startingToCycle(_source)) {
           result = 37 * result + _source.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_source);
        }
        if (_version != null
            && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
           result = 37 * result + _version.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_version);
        }
        if (_accessionId != null
            && !org.castor.util.CycleBreaker.startingToCycle(_accessionId)) {
           result = 37 * result + _accessionId.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_accessionId);
        }
        if (_id != null
            && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
           result = 37 * result + _id.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_id);
        }
        if (_mapList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_mapList)) {
           result = 37 * result + _mapList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_mapList);
        }
        if (_linkList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_linkList)) {
           result = 37 * result + _linkList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_linkList);
        }
        if (_propertyList != null
            && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
           result = 37 * result + _propertyList.hashCode();
           org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
        }
        
        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 removeAllLink(
    ) {
        this._linkList.clear();
    }

    /**
     */
    public void removeAllMap(
    ) {
        this._mapList.clear();
    }

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

    /**
     * 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 removeMap.
     * 
     * @param vMap
     * @return true if the object was removed from the collection.
     */
    public boolean removeMap(
            final uk.ac.vamsas.objects.core.Map vMap) {
        boolean removed = _mapList.remove(vMap);
        return removed;
    }

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

    /**
     * Sets the value of field 'accessionId'. The field
     * 'accessionId' has the following description: TODO: make some
     * specification
     *  of the database field from which this
     *  accessionId is taken from - should that be a
     *  special property of the dbRef object ?
     *  
     * 
     * @param accessionId the value of field 'accessionId'.
     */
    public void setAccessionId(
            final java.lang.String accessionId) {
        this._accessionId = accessionId;
    }

    /**
     * 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;
    }

    /**
     * 
     * 
     * @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;
    }

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

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

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

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

    /**
     * 
     * 
     * @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;
    }

    /**
     * Sets the value of field 'source'. The field 'source' has the
     * following description: TODO Database Naming
     *  Convention: either start using LSID (so
     *  change type to URI) or leave this as an
     *  uncontrolled/unspecified string ID
     *  
     * 
     * @param source the value of field 'source'.
     */
    public void setSource(
            final java.lang.String source) {
        this._source = source;
    }

    /**
     * Sets the value of field 'version'. The field 'version' has
     * the following description: Version must be specified -
     *  
     * 
     * @param version the value of field 'version'.
     */
    public void setVersion(
            final java.lang.String version) {
        this._version = version;
    }

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

}